Related posts:

• Probiotics Fundamentals: Part 1 Specific Strains
• Probiotics Fundamentals: Part 2 DOA on Shelf
• Probiotics Fundamentals: Part 3 Are they working?

In the first post of this series, Probiotics Fundamentals: Part 1 Specific Strains I cited strains that are available retail that has been researched. The logical starting point is to search for your needs, read the studies and then rank the probiotics in prefer order for doing a personal trial. You want to do one probiotic at a time with rotation and described in the prior post (see prior post).

To searching for strain specific studies of probiotics available retail. Click here.

No Study found or issue not listed

The next step is to look at the conditions that I have abstracted/extracted studies for, listed at “U.S. Nat. Lib. Medical Conditions Studies with Microbiome Shifts“. We are shifting from strain to species level. This gives several paths, let us examine Autism. There are

Based on Publish Studies of Species

Clicking on [Can You Help Improve Suggestions] will take you to a page. At the bottom you will see “Treatment Substances” which lists things that have helped in studies. Scan it for probiotic names, for example: 

A synbiotic formulation of Lactobacillus reuteri and inulin alleviates ASD-like behaviors in a mouse model: the mediating role of the gut-brain axis. Food & function (Food Funct ) Vol: 15 Issue: 1 Pages: 387-400 Pub: 2024 Jan 2 ePub: 2024 Jan 2 Authors Wang C,Chen W,Jiang Y,Xiao X,Zou Q,Liang J,Zhao Y,Wang Q,Yuan T,Guo R,Liu X,Liu Z

Which suggests L. Reuteri with inulin may help. The source is linked. Make sure you read them.

Based on Deficiencies of Probiotic Bacteria

Clicking on 🦠 Taxons will take you to a page showing all of the bacteria shifts reported for the condition.

Look for Lactobacillus, Bifidobacterium,etc  with  ⬇️

These species are found at lower levels, suggesting their metabolites are also reduced. Supplementing with them as single-strain probiotics is logical. Stay at the species level (e.g., Bifidobacterium longum) rather than higher classifications such as the genus Bifidobacterium. In general, avoid probiotic mixtures, as they may include strains that are counter-indicated (e.g., Bifidobacterium catenulatum, Bifidobacterium breve) or strains for which we lack sufficient information.

Based on Modelled correction of Bacteria

Clicking on 🥣 Candidates, will send the huge bacteria list above through a fuzzy logic expert system to compute suggestions with weights given for each one.

Note that this also lists ones to avoid.

Disagreements!

We can see that levels of Lactobacillus plantarum are low, but the model is telling us to avoid Lactobacillus plantarum. So what’s going on here?

The issue comes from the fact that the model/studies is based on multiple subgroups of people with Autism (or other conditions). The data might be accurate within each subgroup, but when you merge them together, you can end up with contradictions. So it’s not really a problem with the approach—it’s a problem with the data mix.

The best rule of thumb is to start with the things that show up as agreements across the data. For example: Bifidobacterium longum and Limosilactobacillus reuteri. Once you’ve tried probiotics that have clear agreements, then you can carefully experiment with the ones where there’s disagreement and see how your body responds.

The next level up in Probiotic Suggestions

It is pretty simple, get a microbiome test. My preferred tests are:

• Biomesight for 16s (economic, low resolution)
• Thorne for shotgun (more expensive but much higher detail)

You want to ideally get a test that reports on all of the common probiotic bacteria. Many common tests do not report many of these. For example: Diagnostic Solution GI-Map reports only

• Bifidobacterium [genus] and no species
• Lactobacillus [genus] and no species

On the other hand both of the above tests report species.

When you select a test, you should check Microbiome Prescription to see what the detection rate is. For example for Bifidobacterium longum, we see how often this is detected in samples.

• For the shotgun tests (Xenogene and Thorne) we see 96% and 100% of the time, if it show low, you can have confidence in taking some
• For SequentiaBiotech we see it is seen 25% of the time. If you have none reported we are left being uncertain if you actually have none or is the none because of the test’s methodology
  • See this post for more on these issues: The taxonomy nightmare before Christmas…

Another example is L.Reuteri where the shotgun tests find in in over 50% of samples, while some 16s finds in only 2% of samples.

Bottom Line

We’re piecing things together from lots of scattered knowledge, and there’s no single standard method—either for testing microbiomes in labs or for the studies themselves. Nothing here is clear-cut; everything’s kind of fuzzy, sometimes super fuzzy. In this post, the focus was on picking probiotics for a condition using literature (an “a priori” approach). Basically, it means trusting the data at face value, even though we know it isn’t rock-solid.

Some additional readings:

• Navigating microbiome variability: implications for research, diagnostics, and direct-to-consumer testing [2025]
• The standardisation of the approach to metagenomic human gut analysis: from sample collection to microbiome profiling [2022]
• Standardization of laboratory practices for the study of the human gut microbiome [2022]

I also foreshadowed the next post: Using a detailed microbiome test to select probiotics based on the whole microbiome.

I believe it is the consumer interest to share this email thread and to promote discussion of this issue.

Blacklisting is the action of suggesting something to be avoided or distrusted.

Request

[Customer name withheld] has forwarded me the PDF and some CSV files associated. She wishes to see what the recommendations from a fuzzy logic expert system that uses over 7.4 million facts based on data from the US National Library of Medicine will suggest.

 I know that the following data is very much available and possible to provide. Other firms like Biomesight.com, Thorne, Vitract and Precision Biome has no trouble providing it:

For all taxonomical layers (From Clade to strains [when available]) just 3 numbers are sufficient.

• NCBI Taxon Number, 
• Percentage Amount, 
• Percentile Ranking across a reference set of healthy individuals

Additional data is welcome, but not required:

1. Names
2. Your reference ranges 
3. etc

Percentiles should be actual percentiles and NOT percentiles estimated using mean and standard deviation. Most bacteria has a SKEW exceeding 20. Using the mean and average requires a SKEW of zero.

Your customer would greatly appreciate a speed return of an appropriate file. With that file in hand, we will add your lab to our list of over 50 labs that our free site supports. (See https://microbiomeprescription.com/Upload/Index ).

If you are unable to provide such, please tell us so we may black list your site as not supportable to spare other consumers a waste of money.

Response

Hi Ken, Thank you for your detailed email and for sharing your perspective on the data formats and metrics you require. We’d like to clarify that Microba uses the Genome Taxonomy Database (GTDB) for microbial classification. GTDB and NCBI classify genomes differently, our species consist of multiple genomes which may have different NCBI classifications, species level classifications cannot always be mapped to each other through name matching alone. Due to this, providing a microbiome profile in NCBI taxonomy is not practical nor would it be a correct representation of the actual microbiome profile. Once GTDB is formally supported within your workflow, please reach out and we can discuss options for providing the data your service requires. We appreciate your understanding and encourage you to support the more accurate, resolved, and phylogenetically consistent GTDB taxonomy. Kind regards, The Microba Team

Reply To Response

Many thanks for your reply. Our purpose is to provide clinical suggestions for review by medical professionals to people suffering from a wide variety of conditions using hallucination-free AI.

A simple example may be seen here. DepressionExample.

Unfortunately, Genome Taxonomy Database(GTDB) appears to be a research tool and IMHO seems very inappropriate and misleading to sell to consumers. GTD was first proposed in academic papers in August 2018. We were active in the microbiome before that and the de facto standard in the industry as then, and still is today, the NCBI. The leading consumer microbiome testing company back then was uBiome which provided NCBI identifiers. In the 7 years since first release, we have seen what appears to be some 226 revisions given the release of   10-RS226, dated April 16, 2025.

Checking the US National Library of Medicine, there appears to be less than 200 studies done using GTDB that are of likely clinical use. With NCBI, we found over 20,000 suitable studies. Regardless, no study done prior to 2020, likely 2022, can, in a legal sense, be safely used for clinical purposes. 

I am aware of many tools to convert GTDB to NCBI, a few are:

• TaxonKit: Command-line toolkit that supports creating NCBI-style taxdump files from GTDB and also reformatting and mapping taxonomies.
• gtdb_to_taxdump: Python tool to convert GTDB taxonomy files into NCBI taxdump format, usable by downstream tools like Kraken2.
• GTDB-Tk: Assigns genomes to GTDB taxonomy but includes metadata fields mapping to NCBI taxonomy, enabling conversion between formats.
• NCBI-GTDB Map: Direct tool for mapping GTDB taxonomy to NCBI taxonomy, supporting both directions and handling rank prefixes.
• gtdb-taxdump: A specialized toolkit for generating stable, trackable NCBI taxdump files from GTDB releases with reproducible taxon IDs.
• NCBI-taxonomist: Python command-line utility that retrieves, handles, and allows mapping of taxonomic information, supporting cross-database operations.

I am aware that Aussies can have an attitude, especially since NCBI is American. Intransient on this issue is not beneficial to your customers; people with challenging health issues unless you are willing to provide a GTDB based, 

hallucination-free AI that is equivalent or better than what NCBI can provide. Until such time, I would advocate that you stop making misleading sales to consumers.

Given your response, I feel that I have no option back to blacklist you for clinical use.

Related posts:

• Probiotics Fundamentals: Part 1 Specific Strains
• Probiotics Fundamentals: Part 2 DOA on Shelf

From years of using different probiotics, I have developed some simple rules of thumbs on the use of probiotics. These rules have worked very well with probiotics from my favorite source: Maple Life Science™. Their probiotics show both manufacture date and expiry date. Typically they arrive within a month of the manufacture date direct from the manufacturer. IMHO, high probability from being alive at arrival.

Do one Species at a time

Maple Life Science™ probiotics are usually single species with just FOS as an additive. My usual preference is taking probiotic powder dissolved in warm water at least one hour away from any meals. Bacteria in your gut has to enter somewhere — and that location is the mouth. You may want to also alter your mouth microbiome so it is less likely to repopulate your gut bacteria with undesirables.

My typical pattern is doing one probiotic for 2 weeks and then rotate to another. See below for the rationale.

How do I know that they are different probiotics?

I could send them off for testing, but what I have observed is this:

• They are often slightly different colors
• They tastes differently

I do not know definitively if they are as claimed, but I do see that they are different.

Are there any changes within a week?

I monitor myself after starting each probiotics. I expect at least one of the following to change:

• Smell of farts
• Number of farts
• Frequency of stools
• Characteristics of stools using the Bristol stool chart
• Changes on my smart watch monitoring
• Changes of sleep patterns
• Change of eating habits/food preferences
• Changes of mood or alertness

If there are no changes, then I label the bottle as “No effect” and put it at the back of the refrigerator shelf. To me, probiotics should change the microbiome is some observable way. The above are indicators of change. This does take some self-awareness of each.

Personal Example: My wife has Crohn’s disease. Whenever she starts to have a flare, she takes Mutaflor (E.Coli Nissle 1917) probiotics and within 1-2 hours the flare ends. Probiotics impact should be apparent in hours or a few days.

Dosages titration

When I try a new probiotic, I usually start with the standard dosage. If there are no apparent change happening in 3 days, I double the dosage (and keep doubling every 3 days for up to 14 days). In practical terms:

• Day 1: 1 capsule
• Day 4: 2 capsules
• Day 7: 4 capsules
• Day 10: 8 capulses
• Day 13: 16 capsules

The logic is simple: there may be less viable bacteria (for some reason) and thus more capsules are needed to get effective dosages to induce a change.

Probiotic Rotation

To me, the purpose of probiotics is to change the microbiome, typically, a dysbiosis. The metabolites and bacteriocins being produced by the probiotics will alter the population by either increasing metabolites that may feed (increase) other bacteria or decrease other bacteria by the bacteriocins. In other words, I view the probiotics as a course correction around a reef.

Bacteriocins Resistance

Bacteriocins are natural antibiotics. Many antibiotics are derived from bacteriocins. This means that bacteriocins resistance needs to be considered. Typically, most of the targeted bacteria has some bacteria that are resistant to some form of antibiotics. These resistors will prosper because their sibling competitors are no longer there. I have read several studies that found pulsed or rotated antibiotics were more effective than continuous antibiotics. My take away is simple: “a course of probiotics” followed by rotation. How long should the course be? I take the duration from the typical duration of prescribted antibiotics (10-14 days).

Some known bacteriocins are listed below

1. Nisin – produced by Lactococcus lactis.
2. Pediocin PA-1/AcH – produced by Pediococcus acidilactici.
3. Enterocin AS-48 – produced by Enterococcus faecalis.
4. Colicin A – produced by Escherichia coli.
5. Colicin E1 – produced by Escherichia coli.
6. Microcin J25 – produced by Escherichia coli.
7. Plantaricin E – produced by Lactobacillus plantarum.
8. Plantaricin F – produced by Lactobacillus plantarum.
9. Leucocin A – produced by Leuconostoc gelidum.
10. Helveticin I – produced by Lactobacillus helveticus.
11. Lactocin MXJ 32A – produced by Lactobacillus coryniformis.
12. Enterolysin A – produced by Enterococcus faecalis.
13. Salivaricin – produced by Lactobacillus salivarius.
14. Pyocin S2 – produced by Pseudomonas aeruginosa.
15. Microcin E492 – produced by Klebsiella pneumoniae.
16. Lactococcin G – produced by Lactococcus lactis.
17. Plantaricin JK – produced by Lactobacillus plantarum.
18. Plantaricin EF – produced by Lactobacillus plantarum.
19. Goadsporin – produced by Streptomyces sp..
20. Plantazolicin – produced by Bacillus amyloliquefaciens.

Some antibiotics obtained from bacteria:

1. Streptomycin – from Streptomyces griseus
2. Chloramphenicol – from Streptomyces venezuelae
3. Tetracycline – from Streptomyces rimosus and Streptomyces aureofaciens
4. Erythromycin – from Saccharopolyspora erythraea (formerly Streptomyces erythraeus)
5. Neomycin – from Streptomyces fradiae
6. Lincomycin – from Streptomyces lincolnensis
7. Rifamycin – from Amycolatopsis rifamycinica (previously Streptomyces rifamycinica)
8. Vancomycin – from Amycolatopsis orientalis
9. Bacitracin – from Bacillus subtilis and Bacillus licheniformis
10. Gramicidin – from Bacillus brevis
11. Polymyxin B – from Bacillus polymyxa
12. Teicoplanin – from Actinoplanes teichomyceticus
13. Fusidic acid – from Fusidium coccineum (a fungus, included due to bacterial-related antibiotic use)
14. Novobiocin – from Streptomyces niveus
15. Ristocetin – from Amycolatopsis lurida
16. Mupirocin – from Pseudomonas fluorescens
17. Tyrocidine – from Bacillus brevis
18. Clavulanic acid – from Streptomyces clavuligerus
19. Daptomycin – from Streptomyces roseosporus
20. Carbapenems (e.g., Imipenem) – from Streptomyces species and related bacteria

Bottom Line

The bottom line is simple: rotate and note changes. If there are no changes,

Related posts:

• Probiotics Fundamentals: Part 1 Specific Strains

Below you see some data information shown on a few probiotic products. Many products do not show either production date nor best by date. They are not legally required.

My preference has always favor probiotics that includes manufacturing date. Two of the products above cite a three year shelf life (assuming appropriate storage). My favorite source, Maple Life Science™, ship directly to me from their factory. Usually they arrive within one month of manufacture (occasionally, the same month!)

Some Studies of special interest

The chart below is from Study of Viability, Storage Stability, and Shelf Life of Probiotic Instant Coffee Lactiplantibacillus plantarum Subsp. plantarum Dad-13 in Vacuum and Nonvacuum Packaging at Different Storage Temperatures [2022]

From the moment that a probiotic leaves a factory, temperature control is usually non-existent. The trucks that transport them are likely not refrigerated nor are wholesale warehouse storing them. When they arrive at a health food store they are typically placed in a refrigerated cabinet for presentation to customers. In many cases, if you insist on seeing where the bottles are stored before, do not be surprise to see that it is not a refrigerated area. It is possible that the probiotics may be subject to 37C(98.6F) for months before the shop keeper places it in the refrigerated cabinet. Each number on the left scale indicate 1/10 of the number above it.

A shipment from a east coast producer to a west coast store direct, is 4-8 days. If the shipment goes to a wholesaler’s warehouse than expect a few days more. The result in summer can easily be as much as 97% of the viable bacteria that leaves the factory may be killed if it takes 15 summer days (per above chart).

From Perplexity.ai, this is clear:

The short version is that during summer in the US, the amount of viable bacteria may be 1/100 of what the probiotic had at the factory. There are stick-on labels that will change color if storage exceeds a threshold — unfortunately, no one is using that.

Microbiological Quality and Antimicrobial Resistance of Commercial Probiotic Products for Food-Producing Animals [2024] reports no viable Lactobacillus was found in some products 

In terms of probiotics sold by microbiome testing companies, the only one that I know of that “ships direct from probiotic manufacturer” is PrecisionBiome.Eu that has established a relationship with a German probiotic producer. Their client base is the EU, so transit time from “vat to customer” is short.

Absence of Regulations Problem

There are recommendations such as Best Practices Voluntary Guidelines for Probiotics[2017] provides some guidance (ignored by most producers). Producers can make claims of shelf life (best before) of 10 years without consequences. With no manufacture date, no one knows when it was made. Calls to their customer lines will usually give questionable answers. The probiotic industry have many active lobbyists to inhibit anything that may effect profits.

Figure Pointing for Probiotics being DAO

If you buy a probiotic and found it is effectively DAO and contact the manufacturer. The manufacturer will claim no responsibility once it left their premise. It is the responsibility of the trucking companies and wholesaler storage. Those folks will then point at the retail store mishandling things.

This harsh reality is why I try to buy direct from the manufacturer (no Amazon, no health food stores).

Bottom Line

“I didn’t get any benefit from probiotics, I got them refrigerated from my trusted health food store“ is a frequent complaint that I hear. IMHO, they do not work because they have been well cooked! Our habit is order our year supply of probiotics from Maple Life Science™ in the fall and winter. The colder it is outside, the better it is.

My “rules of thumbs” on taking probiotics will be the next topic.

Other post in this theme:

• Probiotics Fundamentals: Part 2 DOA on Shelf

What is the difference between a Species and a Strain? To understand this, view Species as “dogs” and strains as specific types. Is picking a Chihuahua as a police dog a good choice, or a St. Bernard suitable for someone with disability living in a one room apartment?

The chart below shows different aspects of different strains for Lactobacillus Reuteri. When you buy a probiotic names “Lactobacillus Reuteri”, it is unlikely which species if was obtained from is specified on the bottle. If it was not from a human, it is very unlikely that it will reproduce or take root in your body.

Probiotic manufacturers and packagers are focused on making money. They will ask for the cheapest source for a probiotic that they expect to be able to sell for the greatest profit. Human source is not a factor, cheapness is!

I have known people that are histamine sensitive that are fine with one brand of Lactobacillus Reuteri but get sick from another brand…. Looking at the chart below, the answer is obvious: One has a histamine producer and one does not.

From prediction to function using evolutionary genomics: human-specific ecotypes of Lactobacillusreuteri have diverse probiotic functions[2014].

Researched but not for sale

This morning I was asked about Bacteroides fragilis BF839 which is cited in several studies on the US National Library of Medicine. Most of the studies are from 2024 or 2025. At present, it is not for sale anywhere and I do not expect it to be for five(5) years at least because of approval processes. Given the authors’ location, I expect it will be first available in China.

Researched and Stain is for sale 🙂

Several years ago I set up a free page listing those available (somewhere in the world). I also automated a weekly automatic scan of the US National Library of Medicine for any new studies using these strains. The page is kept up to date.

Occasionally, someone emails me about a new strain that has one or more studies associated. I add those to the list. If you find one that I missed, please email me!

The page allows searching across the studies abstracts for key words. For example, if you are interested in Autism, just enter that and click search. The page will then show the retail brands with links to the studies.

The intent of the page is discourage random trial of probiotics which has no effect (except on bank accounts).

List of Strains with name of product or seller

At present we are at 156 different strains. These are listed below.

• Akkermansia muciniphila WB-STR-0001: Pendukum Glucose Control
• Aspergillus oryzae NK: strong wakamoto w
• Bacillus clausii MCC 0538: Biome Ultra
• Bacillus clausii N/R: Enterogermina
• Bacillus clausii O/C: Enterogermina
• Bacillus clausii SC-109: MegaSporebiotic
• Bacillus clausii SIN: Enterogermina
• Bacillus clausii T: Enterogermina
• Bacillus coagulans ATCC 5856: Nature’s Sunshine Bacillus Coagulans,
• Bacillus coagulans DSM 17654: Biome Ultra
• Bacillus coagulans GBI-30: Schiff® Digestive Advantage® Daily Probiotic
• Bacillus coagulans SC-208: MegaSporebiotic
• Bacillus coagulans SC208: Eded 3 in 1
• Bacillus Coagulans SNZ1969: Jetson FIT
• Bacillus coagulans Unique IS-2: Optibac Probiotics Adult Gummies Probiotics
• Bacillus indicus HU36: MegaSporebiotic
• Bacillus licheniformis DSM5749: PrecisionBiome
• Bacillus mesentericus (subtilis) TO-A: AOR, Probiotic 3
• Bacillus subtilis ATCC SD 7280: Biome Ultra
• Bacillus subtilis BG01-4TM: VERNX
• Bacillus subtilis DE111 : Probiotic w/ DE111
• Bacillus subtilis DSM17299: PrecisionBiome
• Bacillus Subtilis HU58: MegaSporebiotic
• Bacillus Subtilis MB40: Country Farms Super Flora Probiotics
• Bacteroides xylanisolvens DSM 23964: AVI-1 (pending on market)
• Bifidobacterium adolescentis IVS-1: Synbiotic Health ISV-1
• Bifidobacterium adolescentis PRL2019: Gabapral
• Bifidobacterium animalis ssp. lactis 420: UltraFlora® Control
• Bifidobacterium animalis ssp. lactis CUL-34 (NCIMB 30153): Genestra Brands – HMF Neuro Powder
• Bifidobacterium animalis subsp lactis HN019: Optibac Every Day Max
• Bifidobacterium animalis subsp. lactis CECT 8145: Culturelle Healthy Metabolism + Weight Management Supplement
• Bifidobacterium bifidum BB-06: Custom Probiotics
• Bifidobacterium bifidum CUL-20 (NCIMB 30172) : Genestra Brands – HMF Neuro Powder
• Bifidobacterium bifidum G9-1 (BBG9-1): Phillips’® Colon Health
• Bifidobacterium bifidum HA-132: Human Probiotics
• Bifidobacterium bifidum MIMBb75 (SYN-HI-001): IRRITABLE COLON PRO KIJIMEA
• Bifidobacterium bifidum W23: Ecologic® Barrier for Metabolic Health
• Bifidobacterium breve HA-129: Human Probiotics
• Bifidobacterium Breve LMG 11613: Bioflora (Mexico)
• Bifidobacterium breve M-16V: Optibac Probiotics Professional
• Bifidobacterium breve PRL2020: PharmExtracta / Brevicillin Stick
• Bifidobacterium lactis BB-12: Nestlé
• Bifidobacterium lactis Bi-07: UltraFlora® Balance
• Bifidobacterium lactis Bl-04: Optibac Probiotics Every Day MAX Probiotics
• Bifidobacterium lactis BL-4: Custom Probiotics
• Bifidobacterium lactis W51: Ecologic® Barrier for Metabolic Health
• Bifidobacterium lactis W52: Ecologic® Barrier for Metabolic Health
• Bifidobacterium longum 1714: Zenflore®
• Bifidobacterium longum 35624: Align
• Bifidobacterium longum BB536: Probiotic Pro Bb536
• Bifidobacterium longum BL-05: Custom Probiotics
• Bifidobacterium longum ES1: PharmExtracta / Gliadines buccal stickpacks
• Bifidobacterium longum MM-2: Phillips’® Colon Health
• Bifidobacterium longum R0175: Calm Biotic®
• Bifidobacterium longum ssp. infantis R0033: Human Probiotics
• Bifidobacterium longum ssp. longum HA-135: Human Probiotics
• Bifidobacterium longum subsp. infantis Bi-26: Custom Probiotics
• Bifidobacterium longum subsp. infantis NLS: Life Start 2
• Bifidobacterium longum Subspecies infantis Strain EVC001: Evivo® Infant Probiotic Powder
• Bifidobacterium longum W108: Ecologic® Relief
• Bifidobacterium longum W11: PharmExtracta / Bowell
• Clostridium Butyricum MIYAIRI: Miyarisan
• Clostridium butyricum TO-A: AOR, Probiotic 3
• Clostridium butyricum WB-STR-0006 : Pendukum Glucose Control
• Enterococcus faecalis T-110: AOR, Probiotic 3
• Enterococcus faecium L3: PharmExtracta / INatal Sachets
• Enterococcus faecium SBS 1: Shin Biofermin S
• Enterococcus faecium SF 68: Bioflorin
• Enterococcus faecium W54: Ecologic® AAD
• Escherichia coli , Laves strain 1931: Colibiogen
• Eubacterium hallii WB-STR-0008: Pendukum Glucose Control
• Hafnia alvei HA4597: SymbioLife ® Satylia
• Heat Killed Lactobacillus plantarum L-137: Swanson Immunobiotic Immuno-LP20
• Lacticaseibacillus paracasei subsp. paracasei CNCM I-1518: DanActive
• Lacticaseibacillus rhamnosus HN001: Optibac Probiotics Babies & Children Probiotics
• Lactobacillus acidophillus CUL-21 (NCIMB 30156): Genestra Brands – HMF Neuro Powder
• Lactobacillus acidophilus ATCC 4356: resB® Lung Support
• Lactobacillus acidophilus CL1285: Bio-K+
• Lactobacillus acidophilus CUL-60 (NCIMB 30157): Genestra Brands – HMF Neuro Powder
• Lactobacillus acidophilus HA-122: Human Probiotics
• Lactobacillus acidophilus LA-14: Custom Probiotics
• Lactobacillus Acidophilus LA1: Flora Pro Fem with Cranberry
• Lactobacillus acidophilus NCFM: UltraFlora® Balance
• Lactobacillus acidophilus W22: Ecologic Performance
• Lactobacillus acidophilus W37: Ecologic® Barrier for Metabolic Health
• Lactobacillus acidophilus W55: Ecologic® Allergycare
• Lactobacillus brevis W63: Ecologic® Barrier for Metabolic Health
• Lactobacillus casei LBC80R: Bio-K+
• Lactobacillus casei LC-11: Custom Probiotics
• Lactobacillus casei R0215: PharmExtracta / INatal Sachets
• Lactobacillus casei Shirota: Yakult
• Lactobacillus casei W56: Ecologic® Barrier for Metabolic Health
• Lactobacillus casei W79: Ecologic® Relief
• Lactobacillus crispatus LbV 88 (DSM 22566): AZO Complete Feminine Balance
• Lactobacillus fermentum ME-3: Reg’Activ Essential ME-3
• Lactobacillus gasseri KS-13: Phillips’® Colon Health
• Lactobacillus gasseri LbV 150N (DSM 22583): AZO Complete Feminine Balance
• Lactobacillus Gasseri LMG 266: Bioflora (Mexico)
• Lactobacillus gasseri SBT2055: gasseri SP strain capsule
• LACTOBACILLUS HELVETICUS L10: LACTOBACILLUS HELVETICUS LAFTI® L10
• Lactobacillus helveticus R0052: Calm Biotic®
• Lactobacillus jensenii LbV 116 (DSM 22567): AZO Complete Feminine Balance
• Lactobacillus Kefiri LKF01 (DSM 32079) LKEF : Kefibios
• Lactobacillus paracasei (case)i 431: For daily immunity
• Lactobacillus paracasei 8700:2: UltraFlora® Cold Support
• Lactobacillus paracasei F-19: Optibac Probiotics For Women Probiotics
• Lactobacillus paracasei Lpc-37: Custom Probiotics
• Lactobacillus paracasei W20: Ecologic® AAD
• Lactobacillus plantarum 299v: Jarrow Formulas Ideal Bowel Support
• Lactobacillus plantarum DR7: SymbioLact ® Pro Sleep
• Lactobacillus plantarum HEAL9: UltraFlora® Cold Support
• Lactobacillus plantarum Lp-115: Custom Probiotics
• lactobacillus plantarum LP45: Natealth
• lactobacillus plantarum ps128: Neurobiotique PS128
• Lactobacillus plantarum W1: Winclove Senior
• Lactobacillus plantarum W21: Ecologic Travel
• Lactobacillus plantarum W62: Ecologic® AAD
• Lactobacillus reuteri ATCC PTA 5289: BioGaia® ProDentis
• Lactobacillus reuteri DSM 17938: BioGaia®
• Lactobacillus reuteri RC-14: RepHresh™ Pro-B™ Probiotic
• Lactobacillus rhamnosus CLR2: Bio-K+
• Lactobacillus rhamnosus GG: Culturelle®
• Lactobacillus rhamnosus GR-1: RepHresh™ Pro-B™ Probiotic
• Lactobacillus rhamnosus HA-111: Human Probiotics
• Lactobacillus rhamnosus LbV96 (DSM 22560): AZO Complete Feminine Balance
• Lactobacillus rhamnosus Lcr35: Provacare®
• Lactobacillus rhamnosus Lr-32: Custom Probiotics
• Lactobacillus rhamnosus LR1: Flora Pro Fem with Cranberry
• Lactobacillus rhamnosus R0011: Flora Pregnancy Care Probiotic
• Lactobacillus rhamnosus W71: Ecologic® AAD
• Lactobacillus Sakei pro-Bio-65: Kimchi Power
• Lactobacillus salivarius HA-118: Human Probiotics
• Lactobacillus Salivarius Ls-33: Custom Probiotics
• Lactobacillus salivarius UCC118: UltraFlora® Integrity
• Lactobacillus salivarius W24: Ecologic® Barrier for Metabolic Health
• Lactocaseibacillus rhamnosus ATCC 53103: resB® Lung Support
• Lactococcus lactis JCM5805 (L. lactis plasma): IMMUNOFLORA
• Lactococcus lactis LL-23: Custom Probiotics
• Lactococcus lactis W19: Ecologic® Barrier for Metabolic Health
• Lactococcus lactis W58: Ecologic® Barrier for Metabolic Health
• Lactoplantibacillus plantarum ATCC BAA-793: resB® Lung Support
• Limosilactobacillus reuteri SD5865: Natures-Way-Primadophilus-Reuteri-Pearls
• Mutaflor (Escherichia coli strain Nissle 1917): Mutaflor (Canada, Australia, Findland, Germany)
• Oxalobacter formigenes DSM 4420: TrueMeds
• Pediococcus Acidilactici NRRL B-50517: Imagilin Nutri-5051
• Prescript Assist(multi species): Prescript Assist (dispute on formula change)
• Propionibacterium freudenreichii shermanii : Optim Propionibacter
• Saccharomyces boulardii (Klaire Labs): Klaire Labs Saccharomyces boulardii
• Saccharomyces boulardii CNCM I-745: Florastor®
• Saccharomyces Boulardii THT 500101: Bioflora (Mexico)
• Saccharomyces cerevisiae boulardii CNCM I-1079: Pure Encapsulations
• Streptococcus salivarius K12: BLIS ThroatHealth Oral Probiotics
• Streptococcus thermophilus ST-21: Custom Probiotics
• Symbioflor 1: German Apotheke by Paul’s Mart
• Symbioflor 2: German Apotheke by Paul’s Mart
• VSL3 / Visbiome / De Simone Formulation: Alfasigma USA, Inc.

Safest Product for Correct Identification

These strains are usually under legal protection and thus the manufacturer has a vested (financial) interest to make sure that “what is advertised is delivered”.

Why is this important, just look at some of the literature

• Microbiological Quality and Antimicrobial Resistance of Commercial Probiotic Products for Food-Producing Animals [2024]
  • 64.4% were incorrectly labeled in either number of viable cells or bacterial species
  • 51.6% exhibited resistance to at least one antimicrobial agent
  • 26.8% had a lower number of viable cells than their label claims, No viable Lactobacillus was found in some products 
  • 57.8% comprised other species rather than those claimed on the contents

Your first choice should be the probiotics strains that are most likely to be as advertised and has been studied for the symptom of condition that you are interested in.

Mast Cell Activation Syndrome (MCAS) has been a frustrating condition to deal with. It is likely that the microbiome is a factor but finding bacteria patterns has had poor results. Recently I did a post One Consistent Pattern Across Different Vendors Results where the agreement from different lab tests on the bacteria involved simply had not agreement (see this page to illustrate). Using  estimates on compounds and enzymes using KEGG: Kyoto Encyclopedia of Genes and Genomes went two ways:

• enzymes associations was worse than bacteria
• compound produced was far better than bacteria, 31x better

I decided to drill into these associations restricted it to associations seen in ALL of uBiome, Biomesight and Ombre dataset. The goal is to do a manual walkthrough of using this data to identify issues and potential solutions.

Logic Flow

1. Obtain a large collection of microbiome samples process through different labs (in our case 3)
2. Estimate the net amount of compound produce from each sample
3. Using the symptom annotation, determine which compound are significant using chi²
4. Identify the compounds that are significant for all three labs (concurrent)
5. Remove the compounds that only occur in a few labs. Assume they are probable noise
6. Take a shotgun sample from an individual and compute the compounds
7. Identify where we have compound matching 5 (same direction)
8. Ignore/discard compound that are not produced/substrate by the bacteria in sample
9. Create a list by reversing taxa->Compound to compound->Taxa that are present in sample
10. Pass the bacteria list with desired shift(increase/decrease) to the Fuzzy Logic Expert System to generate suggestions
11. List the suggestions

[Step 4 Above] The compounds identified are below with ALL OF THEM BEING LOW:

KEGG Identifier	Name (linked to KEGG site)
C04030	(2,3-Dihydroxybenzoyl)adenylate
C04236	(2S)-2-Isopropyl-3-oxosuccinate
C20844	(2Z,4S,5R)-2-Amino-4,5,6-trihydroxyhex-2-enoate
C01186	(3S,5S)-3,5-Diaminohexanoate
C20845	(4S,5R)-4,5,6-Trihydroxy-2-iminohexanoate
C22385	(L-Cysteinyl)adenylate
C01143	(R)-5-Diphosphomevalonate
C00810	(R)-Acetoin
C01769	(S)-Acetoin
C11826	[GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-g-D-Glu-L-Lys-D-Ala-D-Ala)]n-diphosphoundecaprenol
C01281	[L-Glutamate:ammonia ligase (ADP-forming)]
C21879	1-(5-O-Phospho-beta-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium-3-carbonyl adenylate
C01159	2,3-Bisphospho-D-glycerate
C17234	2-Aminobut-2-enoate
C02631	2-Isopropylmaleate
C05848	4-Hydroxy-3-polyprenylbenzoate
C21877	5-Carboxy-1-(5-O-phospho-beta-D-ribofuranosyl)pyridin-1-ium-3-carbonyl adenylate
C22267	5-Methylaminomethyl-2-(Se-phospho)selenouridine34 in tRNA
C22266	5-Methylaminomethyl-2-(S-geranyl)thiouridine34 in tRNA
C01299	Adenylyl-[L-glutamate:ammonia ligase (ADP-forming)]
C05414	all-trans-Phytofluene
C05430	all-trans-zeta-Carotene
C19875	alpha-Kdo-(2->8)-alpha-Kdo-(2->4)-alpha-Kdo-(2->6)-lipid IVA
C01563	Carbamate
C20969	Carboxyphosphate
C00417	cis-Aconitate
C19724	Cobyrinate c-monamide
C02218	Dehydroalanine
C15853	Dehydrospermidine
C06040	Diglucosyldiacylglycerol
C11930	dTDP-2,6-dideoxy-D-glycero-hex-2-enos-4-ulose
C05359	e- (electron)
C05730	Glutathionylspermidine
C22173	Harderoheme III
C02985	L-Fucose 1-phosphate
C16238	Lipoyl-AMP
C19611	Manganese(3+)
C15854	N-(4-Aminobutylidene)-[eIF5A-precursor]-lysine
C03406	N-(L-Arginino)succinate
C21009	N4-Aminopropylspermidine
C03794	N6-(1,2-Dicarboxyethyl)-AMP
C18060	N-Acetyl-alpha-D-galactosamine 1-phosphate
C05379	Oxalosuccinate
C01241	Phosphatidyl-N-methylethanolamine
C00404	Polyphosphate
C15527	Precorrin 1
C03427	Prephytoene diphosphate
C21177	Prokaryotic ubiquitin-like protein
C21878	Pyridinium-3-carboxy-5-thiocarboxylic acid mononucleotide
C03541	THF-polyglutamate
C19080	tRNA with a 3′ CC end
C22409	UDP-3-O-[(3R)-3-hydroxyacyl]-alpha-D-glucosamine

The numbers could be low due to either:

• Not enough being produced
• More being consumed than being produced
• Severe skewness combined with low occurance

Bacteria produces and consumes the above metabolites/compounds.

We are able to compute the impact of probiotics on the above, these are listed under Probiotics modeled on Compounds on this link. None makes it better, in fact all are predicted to make things worse. Checking PubMed (while some probiotics may help), the number of studies are surprisingly sparse. Sparse studies for something like this suggests that there may be a large number of unpublished studies showing no effect or a negative effect. These unfavorable studies are very rarely published, especially when funded by someone owning the patent of the probiotic being tested.

Trying this approach on a Shotgun Sample of someone with MCAS [Step 5]

There are 52 compounds identified above. I have a Thorne sample. 42 of the compounds were less than 1%ile, 6 were over 50%ile. The pattern was obtained using this trio of 16s-labs (ubiome, biomesight and ombre) and the pattern appears to hold true for a sample from a shotgun analysis. We have 80% agreement when randomness would suggest < 2% agreement.

Looking at the details, we see that most of the 42 had no bacteria producing these compounds. This suggests that we are dealing with sparse data and possible false identification. Restricting to those reported as > 0%ile with over 200 samples we ended up with just 11 compounds.

Compound	Samples
cis-Aconitate	3860
N-(L-Arginino)succinate	5806
Oxalosuccinate	3613
4-Hydroxy-3-polyprenylbenzoate	6042
UDP-3-O-[(3R)-3-hydroxyacyl]-alpha-D-glucosamine	5407
N6-(1,2-Dicarboxyethyl)-AMP	6216
N-Acetyl-alpha-D-galactosamine 1-phosphate	6118
Prokaryotic ubiquitin-like protein	5072
(R)-5-Diphosphomevalonate	5996
2,3-Bisphospho-D-glycerate	6115
(L-Cysteinyl)adenylate	5028

[Step 7 Above] Returning to our Shotgun sample above, we found the following are low.

• cis-Aconitate with 3868 producers and 3869 consumers, some found not enough. Increase producers, reduce consumers
• Oxalosuccinate with 3747 producers and 3747 consumers
• N-Acetyl-alpha-D-galactosamine 1-phosphate with 282 producers and 291 consumers, too many consumers
• (L-Cysteinyl)adenylate with 120 producers and 120 consumers

Working backwards from these 4, we end up with 3,953 taxa on our first pass. For many of these bacteria there were none reported hence the challenge of encouraging bacteria that are not there!!!

Working from what is there! [Step 9/10]

Using cis-Aconitate and N-Acetyl-alpha-D-galactosamine 1-phosphate , we want to reduce consumers and increase producers. The result is that we want to:

• Increase these bacteria (most significant is at top)
  • Corynebacterium diphtheriae
  • Streptococcus anginosus
  • Rhodopseudomonas palustris
  • Ralstonia solanacearum
  • Pseudomonas oryzihabitans
  • Sorangium cellulosum
  • Pseudomonas putida
• Decrease these bacteria ((most significant is at bottom)
  • Cupriavidus necator
  • Cupriavidus basilensis
  • Thermaerobacter sp. FW80

Note we are talking species here. KEGG is actually at the strain level and we extrapolated to species. Passing this data to the fuzzy logic expert system we get as suggestions [Step 11]:

• henopodium quinoa {Quinoa}
• hydromorphone – an addictive pain killer
• proton-pump inhibitors (prescription)
• synthetic disaccharide derivative of lactose {Lactulose}
• Moringa Oleifera {Moringa}
• Limosilactobacillus fermentum {L. fermentum}
• Heyndrickxia coagulans {B. coagulans}
• Latilactobacillus sakei {Lactobacillus sakei}

Bottom line, it is possible to get suggestions. The route is not direct. The suggestions above are typically viewed as safe (except the one crossed out), and thus I will pass it along to the person whose sample I used. At the end of multiple steps, we ended up with four (4) compounds that mapped to some 10 bacteria to shift. Those bacteria resulted in just 7 suggestions. We are travelling well outside of the mapped world.

From Perplexity AI

To increase or decrease the abundance of the listed bacteria, specific strategies should be considered, but many target species are not commonly sought for probiotic modulation due to their environmental, pathogenic, or niche-specific nature. Below, approaches to influence each are summarized when evidence is available.

Increase These Bacteria

• Corynebacterium diphtheriae: There is no safe or recommended method to purposely increase C. diphtheriae, as it is a human pathogen responsible for diphtheria, a serious disease. Laboratory studies using animal models suggest that general Actinobacteria (the phylum to which Corynebacterium belongs) can be modulated using certain yeast probiotics or lactic acid bacteria in animal models, but these findings are not intended or safe for human manipulation targeting pathogenic species. Increasing this bacterium is not medically advised.
• Streptococcus anginosus: This member of the Streptococcus anginosus group is a commensal found mainly in the mouth, throat, and gut but is also opportunistically pathogenic. There is currently no evidence-based supplement or intervention to selectively increase S. anginosus in humans; it can be affected by local tissue conditions, diet, and the existing microbiome, but any intervention to increase such bacteria outside of medical settings is not recommended.
• Rhodopseudomonas palustris: This bacterium is environmental and photosynthetic, rarely present in the human body. In agricultural or industrial settings, it is cultured using media containing carbon (like molasses), nitrogen (like corn steep liquor), and trace minerals, kept at slightly acidic to neutral pH and moderate temperatures (around 37°C). There is no role for increasing this bacteria in humans; it is used as a soil and water probiotic for plants.
• Ralstonia solanacearum, Pseudomonas oryzihabitans, Sorangium cellulosum, Pseudomonas putida: These are mainly environmental, soil, or water-dwelling microbes. There is no supplement or dietary approach to increase these in the human gut or on human mucosa, and such actions are not studied for human health.

Decrease These Bacteria

• Cupriavidus necator: This environmental bacterium can be suppressed in biotechnological fermentations by nutrient limitation (especially removing nitrogen or phosphorus), but there is no guidance for targeting this in the human body, as it is not a usual component of the human microbiome. In environmental settings, its growth is limited by removing accessible carbon, nitrogen, or phosphate sources.
• Cupriavidus basilensis: Similar to C. necator, mainly handled in environmental and fermentation settings; standard medical interventions if infection occurs would use specific antibiotics based on sensitivity.
• Thermaerobacter sp. FW80: This is a thermophilic (heat-loving) environmental bacterium not typically present in or relevant to humans. Methods to decrease it would involve lowering environmental temperatures, not relevant to dietary or supplement choices.

Practical Notes

• Most of the bacteria on your list are not normal human microbiome residents and manipulating them carries significant health risks or is not practically or ethically possible.
• For environmental and plant-associated bacteria (such as R. palustris, P. putida, Ralstonia, etc.), enrichment is done in laboratory or agricultural settings with nutrient and temperature controls but is not safe or meaningful for humans.
• For bacteria that are pathogens or opportunists (C. diphtheriae, S. anginosus), intentional enrichment is never recommended.
• For reducing rare environmental or opportunistic bacteria in humans, general good hygiene and avoiding immunosuppression help, while in clinical cases, antibiotics may be used based on sensitivity.

In my prior post, Patterns of Microbiome Distributions Across Different Vendors, we saw that the distribution patterns were not consistent. With annotated samples from several different vendors, it was logical to see if there was consistency of bacteria identified across vendors for specific symptoms. This question was directed to me by Chidozie Ojobor, Ph.D.   The results can be viewed on my Special Studies page.

• Definitions:
  • Singleton: only found in one of the labs
  • Pair: two labs reported the same
  • Triplet: all three labs reported the same

Given the difference of sample sizes and thus significance levels, some lack of consensus is expected.

• uBiome: 790
• Thryve: 1542
• Biomesight: 4604

Over P < 0.001 data, we had the following

• Looking at bacteria to symptom agreement
  • 19558 singleton relationships
  • 1914 pair relationships
  • 94 triplet relationship. or 0.436%
• Looking at enzymes to symptom agreement
  • 74159 singleton relationships
  • 1629 pair relationships
  • 3 triplet relationship or 0.004%
• Looking at compound to symptom agreement
  • 69147 singleton relationships
  • 9364 pair relationships
  • 6189 triplet relationships or 7.3%

Of special interest is when we went to P < 0.0001 for compound to symptom , we got significantly better results for compounds

• 5952 singleton
• 45439 pair relationships
• 8153 triplet relationships or 13.7%

Bottom Line

While I am doing a naive estimate for compounds using KEGG data, the results support the model:

It is not the bacteria that causes the symptoms, it is the net amount of compounds produced by the bacteria that causes the symptoms. Surplus or deficiency of compounds can come from a vast array of different collections of bacteria. The bacteria may just be noise!!

This shifts any model to generate suggestions for a symptom to one further and significant indirection.

All of the date used is available as CSV files at Citizen Science Data Share.

This week I had some discussion with several CEOs of various microbiome testing companies and the question came up:

Can we take the percentile threshold from the Kaltoft-Møldrup(KM) Range computation and apply it to other tests?

If this is likely true, then we reduce the impact of the Blue “Whale in the Room”

Fortunately, I have the data to reasonably answer that (for the common good) and show charts from some of the 60+ providers that have had samples uploaded. Most people in this area are very siloed into one lab, one way and cannot see the forest, only the leaf that they are on.

Lactobacillus

Biomesight

Ubiome

Ombre

PrecisionBiome

Vitract

Thorne

Bifidobacterium Longum

Biomesight

Ubiome

Ombre

Not sufficient data (3 samples had it)

PrecisionBiome

Vitract

Not sufficient data (3 samples had it)

Thorne

Faecalibacterium prausnitzii

Biomesight

Ubiome

Ombre

PrecisionBiome

Vitract

Thorne

Bottom Line

The first item of note: Two labs will typically (99% odds!!) report no Bifidobacterium Longum! In both cases, they do report it, but rarely detect any. Some medical practitioners (not knowing better about the test) will advocate this strongly as a probiotic with no safe evidence support that. This returns us to Scott’s quotation cited above, the blue whale!

While conceptually, the ability to transfer percentile ranges between labs is very appealing, it appears to be unsafe. Looking at the lower bounds for Faecalibacterium prausnitzii we see the following suggested (eye balling – make your own estimates):

• Biomesight: 18%ile
• uBiome: 30%ile
• Ombre: 12%ile
• PrecisionBiome: 30%ile
• Vitract: 12%ile
• Thorne: 20%ile

To me, this settles the issues. The KM percentile estimates for ranges cannot be transfered across labs. They are lab specific (and unlike the naive mean and standard deviation approach that ignores the high skews) require significant sample size.

Most contemporary AI models has a quiet unspoken assumption: data is a near normal distribution or Bayesian. This translate into assuming the data distribution has a statistical SKEWNESS of near zero(0). Often these models improve when the data is transformed to reduced skewness (often a log function is used). If a model improves with data normalization, it is skew sensitive.

A skew near zero is true for a very small percentage of taxa as shown by this table based on shotgun analysis of 1000 healthy individuals. This issue often has huge impacts for reference range computation.

NCBI Taxon	name	rank	skewness
291645	Bacteroides nordii	species	29.799
2759	Eukaryota	superkingdom	29.558
333367	Enterocloster asparagiformis	species	29.538
518636	[Clostridium] asparagiforme DSM 15981	strain	29.538
117743	Flavobacteriia	class	29.525
200644	Flavobacteriales	order	29.525
712633	Streptococcus sp. oral taxon 431	species	28.849
2759692	Streptococcus sp. Marseille-Q3533	species	28.405
712623	Streptococcus sp. oral taxon 061	species	28.334
2972784	Streptococcus sp. Marseille-Q6470	species	28.229
1386	Bacillus	genus	28.215
2005473	Muribaculaceae	family	28.206
68892	Streptococcus infantis	species	27.604
1736	Eubacterium limosum	species	27.486
2714358	Pusillibacter faecalis	species	27.285
2892397	Pusillibacter	genus	27.285
4751	Fungi	kingdom	26.227
347253	Streptococcus salivarius JIM8777	strain	26.222
2690837	Eggerthella guodeyinii	species	26.159
2762318	Weeksellaceae	family	25.877
1839799	Streptococcus sp. FDAARGOS_192	species	25.823
4890	Ascomycota	phylum	25.785
468	Moraxellaceae	family	25.736
2887326	Moraxellales	order	25.736
72274	Pseudomonadales	order	25.621
2682456	Veillonella nakazawae	species	25.587
135621	Pseudomonadaceae	family	25.569
469	Acinetobacter	genus	25.496
1547	Thomasclavelia ramosa	species	25.361
191303	Turicibacter	genus	25.108
2810281	Turicibacteraceae	family	25.108
387661	Parabacteroides johnsonii	species	25.06
2529408	Schaalia	genus	24.99
1918540	Muribaculum	genus	24.929
1683	Bifidobacterium angulatum	species	24.806
4892	Saccharomycetales	order	24.79
4891	Saccharomycetes	class	24.79
1852377	Actinomyces pacaensis	species	24.588
197614	Streptococcus pasteurianus	species	24.543
1297617	Intestinimonas butyriciproducens	species	24.533
1392389	Intestinimonas	genus	24.533
28127	Hoylesella buccalis	species	24.515
2610896	Streptococcus sp. LPB0220	species	24.27
1689	Bifidobacterium dentium	species	24.136
1871022	Parolsenella massiliensis	species	24.122
286	Pseudomonas	genus	23.772
2974257	Hoylesella	genus	23.703
2735723	Turicibacter bilis	species	23.682
1679	Bifidobacterium longum subsp. longum	subspecies	23.208
1944646	Phoenicibacter congonensis	species	23.137
1981050	Phoenicibacter	genus	23.137
1329	Streptococcus canis	species	22.882
1316408	Streptococcus sp. HSISM1	species	22.835
726	Haemophilus haemolyticus	species	22.752
1505	Paraclostridium sordellii	species	22.63
1849828	Paeniclostridium	genus	22.63
1981510	Monoglobus pectinilyticus	species	22.567
2039302	Monoglobus	genus	22.567
2834348	Caproicibacterium	genus	22.417
186804	Peptostreptococcaceae	family	22.213
49546	Flavobacteriaceae	family	22.14
186817	Bacillaceae	family	22.035
45634	Streptococcus cristatus	species	21.74
1712675	Turicibacter sp. H121	species	21.688
838	Prevotella	genus	21.625
86332	Mogibacterium pumilum	species	21.611
1903409	Erwiniaceae	family	21.56
2606626	Sodaliphilus pleomorphus	species	21.511
2815786	Sodaliphilus	genus	21.511
1903414	Morganellaceae	family	21.495
32067	Leptotrichia	genus	21.272
1129771	Leptotrichiaceae	family	21.258
135625	Pasteurellales	order	21.187
712	Pasteurellaceae	family	21.187
1433513	Streptococcus gwangjuense	species	21.148
1812935	Enterobacter roggenkampii	species	21.039
2842531	Solibaculum	genus	20.918
2780922	Solibaculum mannosilyticum	species	20.918
2944914	Allocoprobacillus halotolerans	species	20.909
3059504	Allocoprobacillus	genus	20.909
76860	Streptococcus constellatus	species	20.905
889201	Streptococcus cristatus ATCC 51100	strain	20.893
206351	Neisseriales	order	20.791
199	Campylobacter concisus	species	20.784
195	Campylobacter coli	species	20.759
724	Haemophilus	genus	20.749
481	Neisseriaceae	family	20.706
43675	Rothia mucilaginosa	species	20.655
482	Neisseria	genus	20.599
2598453	Streptococcus sp. 116-D4	species	20.541
548	Klebsiella aerogenes	species	20.51
39950	Dialister pneumosintes	species	20.383
59201	Salmonella enterica subsp. enterica	subspecies	20.349
133925	Olsenella	genus	20.343
729	Haemophilus parainfluenzae	species	20.246
518635	Bifidobacterium angulatum DSM 20098 = JCM 7096	strain	20.207
2948573	Peptoniphilus sp. SAHP1	species	20.133
1328	Streptococcus anginosus	species	20.096
2767842	Lactiplantibacillus	genus	20.094
1268	Micrococcaceae	family	19.951
32207	Rothia	genus	19.951
3018741	Cellulosilyticaceae	family	19.949
698776	Cellulosilyticum	genus	19.949
85006	Micrococcales	order	19.899
2530390	Muribaculum gordoncarteri	species	19.888
2049	Actinomycetaceae	family	19.868
2037	Actinomycetales	order	19.868
53335	Pantoea	genus	19.864
72294	Campylobacteraceae	family	19.835
194	Campylobacter	genus	19.835
84642	Aeromonadaceae	family	19.819
28037	Streptococcus mitis	species	19.786
642	Aeromonas	genus	19.782
862965	Haemophilus parainfluenzae T3T1	strain	19.769
158	Treponema denticola	species	19.679
162289	Peptoniphilus	genus	19.612
446660	Adlercreutzia equolifaciens	species	19.516
33958	Lactobacillaceae	family	19.511
28211	Alphaproteobacteria	class	19.479
204441	Rhodospirillales	order	19.456
165779	Anaerococcus	genus	19.293
433	Acetobacteraceae	family	19.269
543314	Eubacteriales Family XIII. Incertae Sedis	family	19.231
1434011	Komagataeibacter	genus	19.071
65958	Komagataeibacter oboediens	species	19.071
1485	Clostridium	genus	18.944
938288	Fenollaria massiliensis	species	18.89
1686313	Fenollaria	genus	18.89
154288	Turicibacter sanguinis	species	18.829
135614	Lysobacterales	order	18.784
1578	Lactobacillus	genus	18.769
29547	Campylobacterota	phylum	18.752
3031852	Epsilonproteobacteria	class	18.752
213849	Campylobacterales	order	18.749
1686	Bifidobacterium catenulatum	species	18.656
2942994	Buchavirus	genus	18.627
573	Klebsiella pneumoniae	species	18.592
1776384	Emergencia timonensis	species	18.586
1926556	Emergencia	genus	18.586
1639133	Citrobacter portucalensis	species	18.58
1648923	Bacillus paralicheniformis	species	18.559
136	Spirochaetales	order	18.546
2845253	Treponemataceae	family	18.545
157	Treponema	genus	18.545
506	Alcaligenaceae	family	18.54
674529	Bacteroides faecis	species	18.517
556259	Bacteroides sp. D2	species	18.427
31979	Clostridiaceae	family	18.413
365659	Streptococcus mitis B6	strain	18.407
1266	Sarcina	genus	18.393
2726954	Sarcina sp. JB2	species	18.393
1522	[Clostridium] innocuum	species	18.363
150055	Streptococcus lutetiensis	species	18.303
1352	Enterococcus faecium	species	18.288
556499	Propionibacterium acidifaciens	species	18.151
78448	Bifidobacterium pullorum	species	18.142
78344	Bifidobacterium pullorum subsp. gallinarum	subspecies	18.142
1903412	Hafniaceae	family	18.071
1796646	Muribaculum intestinale	species	18.017
2864143	Adlercreutzia equolifaciens subsp. equolifaciens	subspecies	17.965
1384484	Adlercreutzia equolifaciens DSM 19450	strain	17.965
292800	Flavonifractor plautii	species	17.91
946234	Flavonifractor	genus	17.91
32033	Lysobacteraceae	family	17.893
394340	Adlercreutzia equolifaciens subsp. celatus	subspecies	17.87
1649459	Hungatella	genus	17.797
154046	Hungatella hathewayi	species	17.79
2144175	Megasphaera stantonii	species	17.749
39778	Veillonella dispar	species	17.73
2682455	Veillonella sp. S12025-13	species	17.715
1502	Clostridium perfringens	species	17.684
544	Citrobacter	genus	17.656
735	Haemophilus parahaemolyticus	species	17.649
257758	Streptococcus pseudopneumoniae	species	17.644
208962	Escherichia albertii	species	17.64
1054460	Streptococcus pseudopneumoniae IS7493	strain	17.619
1903411	Yersiniaceae	family	17.596
680646	Rothia mucilaginosa DY-18	strain	17.513
546	Citrobacter freundii	species	17.495
2766537	Caproicibacterium amylolyticum	species	17.401
629	Yersinia	genus	17.393
1114965	Streptococcus parasanguinis FW213	strain	17.387
40323	Stenotrophomonas	genus	17.334
2819619	Streptococcus toyakuensis	species	17.312
1590	Lactiplantibacillus plantarum	species	17.249
1318	Streptococcus parasanguinis	species	17.246
1343	Streptococcus vestibularis	species	17.105
328812	Parabacteroides goldsteinii	species	17.067
204455	Rhodobacterales	order	17.018
1257	Peptostreptococcus	genus	16.978
1385942	Bifidobacterium breve 689b	strain	16.943
760570	Streptococcus parasanguinis ATCC 15912	strain	16.903
1463165	Klebsiella quasipneumoniae	species	16.89
747	Pasteurella multocida	species	16.833
203691	Spirochaetota	phylum	16.832
203692	Spirochaetia	class	16.832
2005386	Arabiibacter	genus	16.719
1870985	Arabiibacter massiliensis	species	16.719
28901	Salmonella enterica	species	16.716
105841	Anaerostipes caccae	species	16.663
61645	Enterobacter asburiae	species	16.658
1234680	Streptococcus rubneri	species	16.63
827	Campylobacter ureolyticus	species	16.573
85023	Microbacteriaceae	family	16.569
31989	Paracoccaceae	family	16.523
1260	Finegoldia magna	species	16.507
150022	Finegoldia	genus	16.507
54005	Peptoniphilus harei	species	16.453
1303	Streptococcus oralis	species	16.443
1918385	Acutalibacter	genus	16.383
1796620	Acutalibacter muris	species	16.383
2877527	Blautia parvula	species	16.379
1313	Streptococcus pneumoniae	species	16.378
487173	Dialister succinatiphilus	species	16.179
90964	Staphylococcaceae	family	16.134
1847725	Lawsonella	genus	16.112
1528099	Lawsonella clevelandensis	species	16.112
2805586	Lawsonellaceae	family	16.112
438033	Ruminococcus gauvreauii	species	16.111
1385	Bacillales	order	16.095
1314	Streptococcus pyogenes	species	16.081
590	Salmonella	genus	16.055
203490	Fusobacteriia	class	16.054
32066	Fusobacteriota	phylum	16.054
203491	Fusobacteriales	order	16.054
2743582	Peptacetobacter	genus	16.025
89152	Peptacetobacter hiranonis	species	16.025
447020	Adlercreutzia	genus	15.996
28126	Segatella buccae	species	15.942
583	Proteus	genus	15.938
137591	Weissella cibaria	species	15.924
1279	Staphylococcus	genus	15.923
1491	Clostridium botulinum	species	15.889
1357	Lactococcus	genus	15.888
135624	Aeromonadales	order	15.838
1358	Lactococcus lactis	species	15.828
739	Aggregatibacter segnis	species	15.766
862962	Bacteroides fragilis 638R	strain	15.764
2058152	Klebsiella grimontii	species	15.755
203492	Fusobacteriaceae	family	15.747
44008	Enterococcus cecorum	species	15.738
613	Serratia	genus	15.733
848	Fusobacterium	genus	15.669
221027	Treponema putidum	species	15.655
59732	Chryseobacterium	genus	15.65
626932	Alistipes indistinctus	species	15.619
564	Escherichia fergusonii	species	15.553
712122	Actinomyces sp. oral taxon 414	species	15.55
158787	Bifidobacterium scardovii	species	15.539
1150461	Bifidobacterium scardovii JCM 12489 = DSM 13734	strain	15.539
742737	Hungatella hathewayi WAL-18680	strain	15.511
766764	Debaryomycetaceae	family	15.464
839	Xylanibacter ruminicola	species	15.445
2806443	Turicibacter sp. TJ11	species	15.413
1762	Mycobacteriaceae	family	15.41
858619	Corynebacterium variabile DSM 44702	strain	15.399
1727	Corynebacterium variabile	species	15.399
727	Haemophilus influenzae	species	15.393
538949	uncultured Alistipes sp.	species	15.379
1902136	Streptococcus sp. NPS 308	species	15.327
1470540	Jeotgalibaca	genus	15.236
376805	Phocaeicola salanitronis	species	15.193
667015	Phocaeicola salanitronis DSM 18170	strain	15.193
544448	Mycoplasmatota	phylum	15.185
37734	Enterococcus casseliflavus	species	15.155
3025755	Thomasclavelia	genus	15.148
265	Paracoccus	genus	15.116
1737405	Tissierellales	order	15.088
33037	Anaerococcus vaginalis	species	15.071
1570339	Peptoniphilaceae	family	15.069
2763022	Bacteroides sp. M10	species	14.944
582	Morganella morganii	species	14.935
581	Morganella	genus	14.935
160674	Raoultella	genus	14.922
547	Enterobacter	genus	14.904
499174	Clostridioides difficile QCD-23m63	strain	14.886
2749267	Amedibacterium	genus	14.848
2583452	Amedibacterium intestinale	species	14.848
287	Pseudomonas aeruginosa	species	14.848
2585117	Alistipes onderdonkii subsp. vulgaris	subspecies	14.823
76859	Fusobacterium animalis	species	14.814
28038	Latilactobacillus curvatus	species	14.798
2816960	Lactococcus cremoris subsp. cremoris	subspecies	14.767
33959	Lactobacillus johnsonii	species	14.762
568	Hafnia	genus	14.713
46867	Clostridium chauvoei	species	14.685
837	Porphyromonas gingivalis	species	14.682
908937	Prevotella dentalis DSM 3688	strain	14.674
52227	Prevotella dentalis	species	14.674
1104322	Lactococcus cremoris subsp. cremoris A76	strain	14.606
2810280	Coprobacillaceae	family	14.602
571	Klebsiella oxytoca	species	14.567
1903410	Pectobacteriaceae	family	14.528
712150	Aggregatibacter sp. oral taxon 513	species	14.524
2497860	Cellulosilyticum sp. WCF-2	species	14.522
538	Eikenella	genus	14.517
2966552	Thermocaproicibacter melissae	species	14.504
3048127	Thermocaproicibacter	genus	14.504
579	Kluyvera	genus	14.489
76892	Caulobacteraceae	family	14.485
204458	Caulobacterales	order	14.485
85009	Propionibacteriales	order	14.472
31957	Propionibacteriaceae	family	14.471
1335	Streptococcus equinus	species	14.462
745	Pasteurella	genus	14.445
4893	Saccharomycetaceae	family	14.398
97138	Clostridium sp. MD294	species	14.388
1868794	Jeotgalibaca arthritidis	species	14.37
1504	Clostridium septicum	species	14.357
4930	Saccharomyces	genus	14.354
158847	Megamonas hypermegale	species	14.331
205913	Bifidobacterium longum DJO10A	strain	14.315
72407	Klebsiella pneumoniae subsp. pneumoniae	subspecies	14.283
423211	Streptococcus suis GZ1	strain	14.272
584	Proteus mirabilis	species	14.269
31969	Mollicutes	class	14.254
1499973	Escherichia marmotae	species	14.215
999416	Parabacteroides distasonis CL03T12C09	strain	14.203
84162	Cryptobacterium	genus	14.188
469378	Cryptobacterium curtum DSM 15641	strain	14.188
84163	Cryptobacterium curtum	species	14.188
95818	Candidatus Saccharibacteria	phylum	14.17
208479	Enterocloster bolteae	species	14.165
1229621	Anaerostipes rhamnosivorans	species	14.158
1322	Blautia hansenii	species	14.125
537007	Blautia hansenii DSM 20583	strain	14.125
981540	Streptococcus pasteurianus ATCC 43144	strain	14.114
1805478	Olsenella timonensis	species	14.114
28128	Prevotella corporis	species	14.058
135623	Vibrionales	order	14.053
641	Vibrionaceae	family	14.053
475	Moraxella	genus	14.035
410072	Coprococcus comes	species	14.022
1805431	Enterococcus saigonensis	species	14.018
53442	Eubacterium callanderi	species	14.007
762982	Paraprevotella xylaniphila YIT 11841	strain	13.99
454155	Paraprevotella xylaniphila	species	13.99
411459	Blautia obeum ATCC 29174	strain	13.974
186827	Aerococcaceae	family	13.966
1508657	Ruminiclostridium	genus	13.926
122277	Pectobacterium	genus	13.907
2942991	Cohcovirus	genus	13.901
5475	Candida	genus	13.862
208224	Enterobacter kobei	species	13.837
171551	Porphyromonadaceae	family	13.802
2093857	Dysosmobacter welbionis	species	13.801
2591381	Dysosmobacter	genus	13.801
836	Porphyromonas	genus	13.794
76857	Fusobacterium polymorphum	species	13.755
1891914	Streptococcus oralis subsp. oralis	subspecies	13.751
1134687	Klebsiella michiganensis	species	13.734
237	Flavobacterium	genus	13.709
1912216	Cutibacterium	genus	13.686
1287640	Anaerococcus obesiensis	species	13.685
539	Eikenella corrodens	species	13.674
305719	Segatella baroniae	species	13.643
46255	Weissella	genus	13.628
34062	Moraxella osloensis	species	13.621
1776379	Leyella lascolaii	species	13.605
1122992	Hoylesella timonensis 4401737 = DSM 22865 = JCM 15640	strain	13.593
386414	Hoylesella timonensis	species	13.593
1582879	Ezakiella	genus	13.574
2715212	Bacteroides faecium	species	13.561
206389	Rhodocyclales	order	13.559
1529	Clostridium cadaveris	species	13.535
553973	[Clostridium] hylemonae DSM 15053	strain	13.532
1217282	Parabacteroides faecis	species	13.519
315405	Streptococcus gallolyticus	species	13.508
41275	Brevundimonas	genus	13.484
80865	Delftia	genus	13.454
39777	Veillonella atypica	species	13.436
2942965	Steigviridae	family	13.434
1282	Staphylococcus epidermidis	species	13.421
2942980	Kehishuvirus	genus	13.411
2719313	Enterocloster	genus	13.394
879243	Porphyromonas asaccharolytica DSM 20707	strain	13.371
28123	Porphyromonas asaccharolytica	species	13.371
2576376	Streptococcus sp. 1643	species	13.366
1305	Streptococcus sanguinis	species	13.345
2692118	Winkia	genus	13.338
33007	Winkia neuii	species	13.338
2650157	Bacteroides zhangwenhongii	species	13.304
28133	Prevotella nigrescens	species	13.268
46507	Ezakiella coagulans	species	13.26
2899133	Candidatus Nanosynbacter sp. HMT-352	species	13.255
1283	Staphylococcus haemolyticus	species	13.245
662	Vibrio	genus	13.232
4932	Saccharomyces cerevisiae	species	13.218
1490	Paraclostridium bifermentans	species	13.198
1849822	Paraclostridium	genus	13.198
1309	Streptococcus mutans	species	13.179
2026240	Klebsiella quasivariicola	species	13.176
51288	Kluyvera ascorbata	species	13.172
742725	Alistipes indistinctus YIT 12060	strain	13.169
1918454	Flintibacter	genus	13.156
2610895	Flintibacter sp. KGMB00164	species	13.156
5476	Candida albicans	species	13.141
3036302	Mobiluncus massiliensis	species	13.091
33043	Coprococcus eutactus	species	13.038
33208	Metazoa	kingdom	13.029
7711	Chordata	phylum	13.029
9443	Primates	order	13.029
9604	Hominidae	family	13.029
9605	Homo	genus	13.029
9606	Homo sapiens	species	13.029
40674	Mammalia	class	13.029
28025	Bifidobacterium animalis	species	13.025
561	Escherichia	genus	13.014
2584944	Sutterella faecalis	species	13.012
575	Raoultella planticola	species	12.997
2779518	Blautia liquoris	species	12.994
2050	Mobiluncus	genus	12.966
1385939	Bifidobacterium breve JCM 7017	strain	12.917
1330545	Lelliottia	genus	12.91
204457	Sphingomonadales	order	12.863
2093818	Candidatus Saccharimonadia	class	12.854
2093822	Candidatus Nanosynbacteraceae	family	12.853
2093823	Candidatus Nanosynbacter	genus	12.853
2093819	Candidatus Nanosynbacterales	order	12.853
526525	Erysipelotrichales	order	12.849
526524	Erysipelotrichia	class	12.849
1622	Ligilactobacillus murinus	species	12.847
1737404	Tissierellia	class	12.831
33945	Enterococcus avium	species	12.735
28130	Prevotella disiens	species	12.698
2763669	Qiania dongpingensis	species	12.681
2944195	Qiania	genus	12.681
89153	[Clostridium] hylemonae	species	12.679
400634	Lysinibacillus	genus	12.654
712310	Haemophilus sp. oral taxon 036	species	12.645
322095	Porphyromonas somerae	species	12.621
28449	Neisseria subflava	species	12.616
423477	Veillonella rogosae	species	12.607
158836	Enterobacter hormaechei	species	12.604
178339	Pauljensenia hongkongensis	species	12.598
2740557	Pauljensenia	genus	12.598
131110	Schaalia radingae	species	12.587
2772059	uncultured phage cr50_1	no rank	12.573
2955711	Cohcovirus hiberniae	species	12.573
29466	Veillonella parvula	species	12.556
1359	Lactococcus cremoris	species	12.521
824	Campylobacter gracilis	species	12.501
137838	Clostridium neonatale	species	12.417
1046629	Streptococcus salivarius 57.I	strain	12.394
565040	Bifidobacterium longum subsp. infantis 157F	strain	12.379
1647	Erysipelothrix	genus	12.37
43769	Corynebacterium propinquum	species	12.369
1016	Capnocytophaga	genus	12.337
238749	Diaphorobacter	genus	12.321
248744	Marvinbryantia	genus	12.311
168384	Marvinbryantia formatexigens	species	12.311
478749	Marvinbryantia formatexigens DSM 14469	strain	12.311
1747	Cutibacterium acnes	species	12.273
1531	Enterocloster clostridioformis	species	12.266
411490	Anaerostipes caccae L1-92	strain	12.256
615	Serratia marcescens	species	12.245
1492	Clostridium butyricum	species	12.244
905	Acidaminococcus fermentans	species	12.231
591001	Acidaminococcus fermentans DSM 20731	strain	12.231
2702	Gardnerella vaginalis	species	12.225
1200793	Streptococcus salivarius K12	strain	12.194
2701	Gardnerella	genus	12.194
2901164	Stutzerimonas	genus	12.188
1348	Streptococcus parauberis	species	12.187
1796635	Longicatena caecimuris	species	12.186
1918536	Longicatena	genus	12.186
61646	Lelliottia amnigena	species	12.182
137732	Granulicatella elegans	species	12.177
1769710	Sellimonas	genus	12.175
1653434	Sellimonas intestinalis	species	12.175
2948688	Delmidovirus	genus	12.147
3029088	Dethiosulfovibrionaceae	family	12.147
81852	Enterococcaceae	family	12.113
2093824	Candidatus Nanosynbacter lyticus	species	12.113
1350	Enterococcus	genus	12.107
40324	Stenotrophomonas maltophilia	species	12.079
40520	Blautia obeum	species	12.06
638847	Pyramidobacter	genus	12.04
638849	Pyramidobacter piscolens	species	12.04
1334	Streptococcus dysgalactiae	species	12.023
1316254	Veillonella parvula HSIVP1	strain	12.021
2905967	Candidatus Minimicrobia	genus	11.998
2841264	Candidatus Minimicrobia vallesae	species	11.998
1643824	Atopobiaceae	family	11.997
1912897	Blautia argi	species	11.99
82115	Rhizobiaceae	family	11.981
657309	Bacteroides xylanisolvens XB1A	strain	11.961
2942966	Suoliviridae	family	11.948
645	Aeromonas salmonicida	species	11.931
1750	Arachnia propionica	species	11.924
1871025	Ndongobacter massiliensis	species	11.9
1930845	Ndongobacter	genus	11.9
2734150	Toutatisvirus toutatis	species	11.891
2733138	Toutatisvirus	genus	11.891
2070187	Faecalibacterium phage FP_Toutatis	no rank	11.891
1351	Enterococcus faecalis	species	11.885
1598	Limosilactobacillus reuteri	species	11.871
1653	Corynebacteriaceae	family	11.858
1716	Corynebacterium	genus	11.858
713	Actinobacillus	genus	11.836
2027293	Escherichia coli O8:H8	serotype	11.82
1613	Limosilactobacillus fermentum	species	11.785
1035817	Bifidobacterium longum subsp. longum KACC 91563	strain	11.762
85025	Nocardiaceae	family	11.735
2650158	Bacteroides luhongzhouii	species	11.726
1308	Streptococcus thermophilus	species	11.694
2772085	crAssphage cr6_1	RUCEZ877	11.691
419005	Prevotella amnii	species	11.667
2742598	Limosilactobacillus	genus	11.652
1177574	Prevotella jejuni	species	11.643
388919	Streptococcus sanguinis SK36	strain	11.551
41297	Sphingomonadaceae	family	11.516
53345	Enterococcus durans	species	11.511
1077464	Streptococcus oralis subsp. tigurinus	subspecies	11.495
850	Fusobacterium mortiferum	species	11.478
469616	Fusobacterium mortiferum ATCC 9817	strain	11.478
626940	Phascolarctobacterium succinatutens	species	11.459
657308	Gordonibacter pamelaeae 7-10-1-b	strain	11.445
471189	Gordonibacter pamelaeae	species	11.445
84566	Sphingobacteriaceae	family	11.41
200666	Sphingobacteriales	order	11.41
117747	Sphingobacteriia	class	11.41
416916	Aggregatibacter	genus	11.408
428126	Thomasclavelia spiroformis DSM 1552	strain	11.407
29348	Thomasclavelia spiroformis	species	11.407
3047432	Maliibacteriaceae	family	11.388
3047433	Maliibacterium	genus	11.388
2086585	Maliibacterium massiliense	species	11.388
99822	Streptococcus dysgalactiae subsp. dysgalactiae	subspecies	11.363
47678	Bacteroides caccae	species	11.339
2767893	Lentilactobacillus	genus	11.314
1396	Bacillus cereus	species	11.311
1155388	Clostridium sp. C1	species	11.281
12916	Acidovorax	genus	11.279
2847299	Bacteroides sp. DH3716P	species	11.274
1364	Lactococcus piscium	species	11.272
28135	Segatella oris	species	11.258
1292	Staphylococcus warneri	species	11.248
1827	Rhodococcus	genus	11.244
2767885	Latilactobacillus	genus	11.24
186818	Planococcaceae	family	11.231
630	Yersinia enterocolitica	species	11.224
1624	Ligilactobacillus salivarius	species	11.219
48736	Ralstonia	genus	11.206
2692113	Gleimia	genus	11.191
883062	Bifidobacterium bifidum S17	strain	11.176
186532	Ceduovirus	genus	11.163
28453	Sphingobacterium	genus	11.159
222	Achromobacter	genus	11.156
927666	Streptococcus oralis Uo5	strain	11.111
1433288	Streptococcus thermophilus MTH17CL396	strain	11.106
32257	Kingella	genus	11.101
1074494	Streptococcus salivarius M18	strain	11.053
876	Desulfovibrio desulfuricans	species	11.052
1363	Lactococcus garvieae	species	11.044
85007	Mycobacteriales	order	11.021
830	Butyrivibrio	genus	11.009
118882	Brucellaceae	family	11.004
66228	Gleimia europaea	species	11.003
45851	Butyrivibrio crossotus	species	10.992
1501662	Streptococcus parasuis	species	10.988
570	Klebsiella	genus	10.959
2801844	Arachnia	genus	10.94
990721	Christensenella	genus	10.924
990719	Christensenellaceae	family	10.924
626937	Christensenella minuta	species	10.924
544580	Actinomyces oris	species	10.885
1156431	Streptococcus ilei	species	10.879
712362	Leptotrichia sp. oral taxon 221	species	10.863
1643822	Eggerthellales	order	10.854
1643826	Eggerthellaceae	family	10.854
2763062	Roseburia rectibacter	species	10.835
1161942	Ruminococcus champanellensis	species	10.82
234	Brucella	genus	10.812
1623	Ligilactobacillus ruminis	species	10.81
1259973	Klebsiella electrica	species	10.807
2709390	Bacteroides sp. ZJ-18	species	10.755
712411	Olsenella sp. oral taxon 807	species	10.754
190721	Ralstonia insidiosa	species	10.752
1353	Enterococcus gallinarum	species	10.719
82135	Fannyhessea vaginae	species	10.717
2767327	Fannyhessea	genus	10.717
29430	Acinetobacter haemolyticus	species	10.716
413496	Cronobacter	genus	10.703
2047	Rothia dentocariosa	species	10.7
1599	Latilactobacillus sakei	species	10.697
1654	Actinomyces	genus	10.683
697329	Ruminococcus albus 7 = DSM 20455	strain	10.675
1264	Ruminococcus albus	species	10.675
732	Aggregatibacter aphrophilus	species	10.667
29491	Aeromonas salmonicida subsp. salmonicida	subspecies	10.665
182773	Clostridium isatidis	species	10.633
1348911	Coprobacter	genus	10.63
2092	Mycoplasmataceae	family	10.607
2085	Mycoplasmatales	order	10.607
2005519	Barnesiellaceae	family	10.606
1099853	Coprobacter fastidiosus	species	10.603
407	Methylobacterium	genus	10.597
1379	Gemella haemolysans	species	10.597
33034	Anaerococcus prevotii	species	10.573
525919	Anaerococcus prevotii DSM 20548	strain	10.573
29465	Veillonella	genus	10.559
2820817	Aggregatibacter sp. 2125159857	species	10.549
5794	Apicomplexa	phylum	10.54
1301	Streptococcus	genus	10.522
2767886	Levilactobacillus	genus	10.5
1675036	Megasphaera hexanoica	species	10.495
2893057	Shouchella	genus	10.479
54291	Raoultella ornithinolytica	species	10.475
1796652	Turicimonas muris	species	10.474
1918598	Turicimonas	genus	10.474
862970	Streptococcus anginosus C1051	strain	10.473
1032069	Campylobacter ureolyticus RIGS 9880	strain	10.462
1300	Streptococcaceae	family	10.457
2848145	Escherichia coli O170:H18	no rank	10.428
577	Raoultella terrigena	species	10.426
1280412	Conoidasida	class	10.425
75739	Eucoccidiorida	order	10.425
861906	Escherichia coli O44:H18	serotype	10.423
216592	Escherichia coli 042	strain	10.423
114527	Mogibacterium diversum	species	10.421
360104	Campylobacter concisus 13826	strain	10.418
5809	Sarcocystidae	family	10.407
255248	Leuconostoc garlicum	species	10.401
29389	Streptococcus alactolyticus	species	10.398
1580	Levilactobacillus brevis	species	10.396
244366	Klebsiella variicola	species	10.395
5811	Toxoplasma gondii	species	10.388
5810	Toxoplasma	genus	10.388
1633	Limosilactobacillus vaginalis	species	10.373
2942990	Canhaevirus	genus	10.354
2488810	Ruminiclostridium herbifermentans	species	10.349
1506577	Tyzzerella	genus	10.34
36835	[Clostridium] colinum	species	10.34
704125	Clostridium gelidum	species	10.339
502	Kingella denitrificans	species	10.328
1637	Listeria	genus	10.318
28216	Betaproteobacteria	class	10.312
80840	Burkholderiales	order	10.305
2603836	Escherichia coli O10:H32	serotype	10.3
702459	Bifidobacterium bifidum PRL2010	strain	10.286
58231	Treponema medium	species	10.286
2866570	Aggregatibacter sp. Marseille-P9115	species	10.278
1252	Leuconostoc carnosum	species	10.273
1243	Leuconostoc	genus	10.267
28129	Prevotella denticola	species	10.241
2382163	Streptococcus koreensis	species	10.22
2572088	Candidatus Nanosynbacter featherlites	species	10.208
160453	Enterococcus gilvus	species	10.204
635	Edwardsiella	genus	10.185
1759399	Streptococcus sp. A12	species	10.178
2848144	Escherichia coli O158:H23	no rank	10.177
133448	Citrobacter youngae	species	10.175
2082587	Parolsenella	genus	10.175
617123	Lachnoanaerobaculum umeaense	species	10.152
119045	Methylobacteriaceae	family	10.152
76517	Campylobacter hominis	species	10.142
684066	Streptococcus lactarius	species	10.132
2778655	Escherichia coli O167:H26	serotype	10.108
831	Butyrivibrio fibrisolvens	species	10.099
2929492	Faecalibacterium sp. I3-3-33	species	10.095
702439	Prevotella nigrescens F0103	strain	10.082
1520	Clostridium beijerinckii	species	10.078
995019	Sutterellaceae	family	10.075
1563222	Citrobacter pasteurii	species	10.071
1433289	Streptococcus thermophilus M17PTZA496	strain	10.059
1632	Limosilactobacillus oris	species	10.049
47770	Lactobacillus crispatus	species	10.036
2020965	Bifidobacterium imperatoris	species	10.034
569	Hafnia alvei	species	10.024
906	Megasphaera	genus	10.023
33039	[Ruminococcus] torques	species	10.02
657313	[Ruminococcus] torques L2-14	strain	10.02
1304	Streptococcus salivarius	species	10.01
1667327	Klebsiella quasipneumoniae subsp. quasipneumoniae	subspecies	10.001
869209	Treponema succinifaciens DSM 2489	strain	9.9992
167	Treponema succinifaciens	species	9.9992
1253	Pediococcus	genus	9.9913
1246	Leuconostoc lactis	species	9.9872
299766	Enterobacter hormaechei subsp. steigerwaltii	subspecies	9.984
1415775	Clostridium baratii str. Sullivan	strain	9.9732
2133944	Pseudoprevotella muciniphila	species	9.9676
2884814	Pseudoprevotella	genus	9.9676
201	Campylobacter lari	species	9.9633
1354	Enterococcus hirae	species	9.9626
100886	Catenibacterium mitsuokai	species	9.9443
507	Alcaligenes	genus	9.9429
45972	Staphylococcus pasteuri	species	9.9336
1280	Staphylococcus aureus	species	9.915
1453988	Campylobacter lari RM16712	strain	9.9141
35703	Citrobacter amalonaticus	species	9.9078
1340	Streptococcus porcinus	species	9.9071
40544	Sutterella	genus	9.8886
244127	Anaerotruncus	genus	9.8579
169435	Anaerotruncus colihominis	species	9.8579
985008	Aggregatibacter aphrophilus ATCC 33389	strain	9.849
297352	Lactococcus piscium MKFS47	strain	9.8328
80864	Comamonadaceae	family	9.8266
2585119	Alistipes dispar	species	9.8242
86331	Mogibacterium	genus	9.8192
713030	Selenomonas sp. oral taxon 136	species	9.812
483	Neisseria cinerea	species	9.7938
604330	Parafannyhessea umbonata	species	9.7778
2847312	Parafannyhessea	genus	9.7778
2929493	Faecalibacterium sp. I3-3-89	species	9.7764
585397	Escherichia coli ED1a	strain	9.7746
40545	Sutterella wadsworthensis	species	9.774
1244	Leuconostoc gelidum	species	9.763
29375	Lacrimispora xylanolytica	species	9.7548
2005520	Dysgonomonadaceae	family	9.7493
2767890	Paucilactobacillus	genus	9.7489
1587	Lactobacillus helveticus	species	9.7475
33035	Blautia producta	species	9.7472
2955579	Canhaevirus hiberniae	species	9.7076
2772066	uncultured phage cr10_1	no rank	9.7076
649776	Synergistales	order	9.6987
649775	Synergistia	class	9.6987
508458	Synergistota	phylum	9.6987
2107999	Lactobacillus paragasseri	species	9.6854
1458253	Streptococcus oralis subsp. dentisani	subspecies	9.6652
470	Acinetobacter baumannii	species	9.6416
644652	Gordonibacter	genus	9.6373
2546350	Citrobacter arsenatis	species	9.6244
28132	Prevotella melaninogenica	species	9.6058
1870884	Clostridioides	genus	9.5655
539813	Enterobacter mori	species	9.5614
1446746	Escherichia coli O6:H16	serotype	9.5527
1903434	Atlantibacter	genus	9.5526
131111	Schaalia turicensis	species	9.5432
631220	Desulfovibrio sp. G11	species	9.5416
2027919	Enterobacter cloacae complex sp.	species	9.5295
2772067	uncultured phage cr11_1	no rank	9.5276
2955741	Delmidovirus splanchnicus	species	9.5276
3022127	Lancefieldella sp. Marseille-Q7238	species	9.5229
546367	Hafnia paralvei	species	9.5145
2767887	Ligilactobacillus	genus	9.5127
970	Selenomonas	genus	9.4953
1069494	Trueperella	genus	9.4832
155493	Gallibacterium	genus	9.4761
32008	Burkholderia	genus	9.476
1290	Staphylococcus hominis	species	9.467
1685	Bifidobacterium breve	species	9.4339
1326	Streptococcus acidominimus	species	9.4198
1300227	Bifidobacterium longum subsp. longum GT15	strain	9.4145
2003188	Parolsenella catena	species	9.4127
907	Megasphaera elsdenii	species	9.3998
505341	Gallibacterium salpingitidis	species	9.398
565	Atlantibacter hermannii	species	9.3863
1305849	Enterococcus faecium Aus0085	strain	9.3746
1232659	Haemophilus influenzae 2019	strain	9.3629
331111	Escherichia coli O139:H28 str. E24377A	strain	9.357
1603259	Escherichia coli O139:H28	serotype	9.357
1871021	Lachnoclostridium phocaeense	species	9.3261
1661	Trueperella pyogenes	species	9.2778
2109686	Butyricicoccus sp. GAM44	species	9.2646
580596	Butyricicoccus	genus	9.2646
67827	Citrobacter werkmanii	species	9.2591
525282	Finegoldia magna ATCC 53516	strain	9.2375
2598457	Streptococcus sp. KS 6	species	9.2263
1335613	Gordonibacter urolithinfaciens	species	9.2162
301301	Roseburia hominis	species	9.2112
249188	Haemophilus pittmaniae	species	9.2072
712538	Selenomonas sp. oral taxon 478	species	9.1851
2841037	Eubacterium sp. c-25	species	9.1726
547043	Bifidobacterium pseudocatenulatum DSM 20438 = JCM 1200 = LMG 10505	strain	9.161
2811390	Sporofaciens	genus	9.1239
2681861	Sporofaciens musculi	species	9.1239
32003	Nitrosomonadales	order	9.1194
1310	Streptococcus sobrinus	species	9.1181
1302	Streptococcus gordonii	species	9.0986
71452	Enterococcus raffinosus	species	9.0831
1743	Propionibacterium	genus	9.0806
13687	Sphingomonas	genus	9.0761
1245	Leuconostoc mesenteroides	species	9.0668
2051	Mobiluncus curtisii	species	9.0624
28144	Salmonella enterica subsp. enterica serovar Derby	no rank	9.0361
1655	Actinomyces naeslundii	species	9.0272
83655	Leclercia adecarboxylata	species	9.0215
447792	Phytobacter	genus	9.0141
1375	Aerococcus	genus	9.0125
69218	Enterobacter cancerogenus	species	9.0021
33905	Bifidobacterium thermophilum	species	9.0007
2937909	Desulfitobacteriaceae	family	8.9984
47714	Lacticaseibacillus paracasei subsp. paracasei	subspecies	8.9954
1682	Bifidobacterium longum subsp. infantis	subspecies	8.975
162	Treponema phagedenis	species	8.9692
85011	Kitasatosporales	order	8.9615
2062	Streptomycetaceae	family	8.9615
1338	Streptococcus intermedius	species	8.9432
190146	Actinotignum urinale	species	8.9392
2490633	Streptococcus periodonticum	species	8.9175
1311	Streptococcus agalactiae	species	8.9139
28119	Bacteroides zoogleoformans	species	8.8714
1470347	Alistipes ihumii	species	8.8466
1211813	Alistipes ihumii AP11	strain	8.8466
866777	Bifidobacterium breve ACS-071-V-Sch8b	strain	8.8371
67824	Citrobacter farmeri	species	8.8369
1642646	Petrimonas mucosa	species	8.8241
307628	Petrimonas	genus	8.8241
47670	Lautropia	genus	8.823
47671	Lautropia mirabilis	species	8.823
2041044	Eubacterium maltosivorans	species	8.8028
2913614	Prevotella communis	species	8.8008
1589	Lactiplantibacillus pentosus	species	8.7922
248315	Veillonella rodentium	species	8.7846
33033	Parvimonas micra	species	8.7761
543311	Parvimonas	genus	8.7761
115778	Leuconostoc gasicomitatum	species	8.7657
488	Neisseria mucosa	species	8.7539
1883	Streptomyces	genus	8.7351
2919589	Vaginimicrobium	genus	8.7251
1871034	Vaginimicrobium propionicum	species	8.7251
1561	Clostridium baratii	species	8.7189
1583	Weissella confusa	species	8.7086
2479767	Blautia sp. SC05B48	species	8.6993
87541	Aerococcus christensenii	species	8.6984
328813	Alistipes onderdonkii	species	8.6973
1547448	Arachnia rubra	species	8.6843
2663009	Fusobacterium pseudoperiodonticum	species	8.6832
38304	Corynebacterium tuberculostearicum	species	8.6822
1852381	Duodenibacillus massiliensis	species	8.671
1980697	Duodenibacillus	genus	8.671
2787628	Treponema peruense	species	8.6617
1296540	Paucilactobacillus nenjiangensis	species	8.6465
890402	Bifidobacterium longum subsp. longum BBMN68	strain	8.6424
181487	Schaalia cardiffensis	species	8.6333
888050	Schaalia cardiffensis F0333	strain	8.6333
1970189	Marinilabiliales	order	8.605
2714353	Vescimonas fastidiosa	species	8.585
1496	Clostridioides difficile	species	8.5787
2742601	Limosilactobacillus portuensis	species	8.5672
1597	Lacticaseibacillus paracasei	species	8.5651
1330547	Kosakonia	genus	8.5484
363265	Leyella stercorea	species	8.543
1122981	Prevotella corporis DSM 18810 = JCM 8529	strain	8.5289
214856	Alistipes finegoldii	species	8.5266
1255	Pediococcus pentosaceus	species	8.5236
470146	Coprococcus comes ATCC 27758	strain	8.508
2974265	Leyella	genus	8.5057
868129	Prevotella bivia DSM 20514	strain	8.4966
186820	Listeriaceae	family	8.4905
90371	Salmonella enterica subsp. enterica serovar Typhimurium	no rank	8.4744
679935	Alistipes finegoldii DSM 17242	strain	8.4679
2086584	Massilistercora timonensis	species	8.4675
2717089	Massilistercora	genus	8.4675
2773707	Escherichia coli O19:H7	no rank	8.4458
2763104	Escherichia coli O150:H6	serotype	8.4447
2803850	Mammaliicoccus	genus	8.4413
873513	Segatella buccae ATCC 33574	strain	8.4355
186826	Lactobacillales	order	8.4177
490	Neisseria sicca	species	8.4171
1048332	Streptococcus salivarius CCHSS3	strain	8.4076
1288121	Alistipes senegalensis	species	8.3998
196081	Scardovia	genus	8.3914
78259	Scardovia inopinata	species	8.3914
1150468	Scardovia inopinata JCM 12537	strain	8.3914
1796616	Blautia pseudococcoides	species	8.3643
730	[Haemophilus] ducreyi	species	8.3473
706438	Actinomyces sp. oral taxon 171	species	8.3329
706439	Actinomyces sp. oral taxon 171 str. F0337	strain	8.3329
69965	Macrococcus	genus	8.309
85020	Dermabacteraceae	family	8.2955
91061	Bacilli	class	8.2911
37637	Corynebacterium pseudodiphtheriticum	species	8.2794
147802	Lactobacillus iners	species	8.2667
632	Yersinia pestis	species	8.2177
2714355	Vescimonas coprocola	species	8.2067
2494234	Sutterella megalosphaeroides	species	8.1807
113107	Streptococcus australis	species	8.1803
411903	Collinsella aerofaciens ATCC 25986	strain	8.1347
722911	Bifidobacterium longum subsp. longum F8	strain	8.1118
57493	Kocuria	genus	8.1073
1436725	Streptococcus thermophilus TH1477	strain	8.101
1926677	Raoultibacter	genus	8.1003
1907662	Raoultibacter timonensis	species	8.1003
379	Rhizobium	genus	8.095
203275	Tannerella forsythia 92A2	strain	8.0864
28134	Hoylesella oralis	species	8.0598
1643686	Brachyspirales	order	8.0537
29521	Brachyspira	genus	8.0537
143786	Brachyspiraceae	family	8.0537
1336	Streptococcus equi	species	8.0488
1843490	Sporomusaceae	family	8.0442
997873	Bacteroides caccae CL03T12C61	strain	8.0427
693979	Bacteroides helcogenes P 36-108	strain	8.0376
290053	Bacteroides helcogenes	species	8.0376
1155385	Proteiniclasticum	genus	8.0255
3036945	Proteiniclasticum sp. QWL-01	species	8.0255
33040	Streptococcus milleri	species	8.0219
2815775	Berryella	genus	7.9936
823	Parabacteroides distasonis	species	7.9932
2478954	Catenibacterium sp. co_0103	species	7.9864
157687	Leptotrichia wadei	species	7.9769
119060	Burkholderiaceae	family	7.973
29391	Gemella morbillorum	species	7.9635
2060094	Aminipila	genus	7.9504
34105	Streptobacillus moniliformis	species	7.9161
34104	Streptobacillus	genus	7.9161
1046624	Lactococcus lactis subsp. lactis IO-1	strain	7.8953
2169621	Limdunavirus	genus	7.8846
2870563	Methanobrevibacter sp. TLL-48-HuF1	species	7.8845
861	Fusobacterium ulcerans	species	7.88
1931217	Bifidobacterium longum subsp. suillum	subspecies	7.8691
83231	Xylanibacter brevis	species	7.8565
299767	Enterobacter ludwigii	species	7.847
135858	Catenibacterium	genus	7.83
856	Fusobacterium varium	species	7.798
40041	Streptococcus equi subsp. zooepidemicus	subspecies	7.7883
1623305	Skunavirus	genus	7.7779
74426	Collinsella aerofaciens	species	7.7776
356	Hyphomicrobiales	order	7.7774
1584	Lactobacillus delbrueckii	species	7.7761
102106	Collinsella	genus	7.7633
84107	Coriobacteriaceae	family	7.7624
2666138	Caproicibacterium lactatifermentans	species	7.7593
2815358	Leclercia pneumoniae	species	7.7471
1905344	Ruthenibacterium	genus	7.746
1550024	Ruthenibacterium lactatiformans	species	7.746
33011	Cutibacterium granulosum	species	7.744
94869	Clostridium gasigenes	species	7.7341
1330546	Pluralibacter	genus	7.7283
283	Comamonas	genus	7.7169
2785531	Bacteroides sp. HF-162	species	7.7131
84999	Coriobacteriales	order	7.7122
941322	Escherichia coli O25b:H4-ST131	no rank	7.7036
1504576	Pseudocitrobacter	genus	7.7031
2891570	Pseudocitrobacter corydidari	species	7.7031
61592	Corynebacterium durum	species	7.7013
338	Xanthomonas	genus	7.6781
186814	Thermoanaerobacteraceae	family	7.6745
762210	Bifidobacterium saguini	species	7.6737
1360	Lactococcus lactis subsp. lactis	subspecies	7.6651
515620	[Eubacterium] eligens ATCC 27750	strain	7.6619
1623304	Moineauvirus	genus	7.6609
671267	Phocaeicola sartorii	species	7.6568
1150460	Bifidobacterium catenulatum subsp. kashiwanohense JCM 15439 = DSM 21854	strain	7.6556
106589	Cupriavidus	genus	7.6486
2696063	Anaerocolumna sedimenticola	species	7.646
881260	Enterobacter bugandensis	species	7.6448
375288	Parabacteroides	genus	7.6353
2005525	Tannerellaceae	family	7.6349
204	Campylobacter showae	species	7.6239
1531429	Berryella intestinalis	species	7.6229
2731643	Autographiviridae	family	7.5822
1681	Bifidobacterium bifidum	species	7.5668
195950	Tannerella	genus	7.561
253239	Ethanoligenens harbinense	species	7.5595
253238	Ethanoligenens	genus	7.5595
186828	Carnobacteriaceae	family	7.5478
445974	Thomasclavelia ramosa DSM 1402	strain	7.5476
28026	Bifidobacterium pseudocatenulatum	species	7.5419
930406	Escherichia coli O157:H16	strain	7.5377
2854732	Escherichia coli O78:H4	serotype	7.5209
2748	Carnobacterium divergens	species	7.5192
79603	Denitrobacterium	genus	7.5137
79604	Denitrobacterium detoxificans	species	7.5137
83654	Leclercia	genus	7.5007
2994078	Caproicibacterium sp. BJN0003	species	7.4953
57706	Citrobacter braakii	species	7.4818
72293	Helicobacteraceae	family	7.4558
1505652	Terrisporobacter	genus	7.449
2813371	Terrisporobacter hibernicus	species	7.449
209	Helicobacter	genus	7.4295
1408428	Bilophila wadsworthia ATCC 49260	strain	7.4156
1385940	Bifidobacterium breve JCM 7019	strain	7.4014
371601	Bacteroides xylanisolvens	species	7.3943
546269	Filifactor alocis ATCC 35896	strain	7.3853
143361	Filifactor alocis	species	7.3853
44259	Filifactor	genus	7.3853
43768	Corynebacterium matruchotii	species	7.3703
1296	Mammaliicoccus sciuri	species	7.3674
225991	Comamonas aquatica	species	7.3652
2304687	Petroclostridium	genus	7.3651
2068655	Novisyntrophococcus fermenticellae	species	7.3633
2888809	Novisyntrophococcus	genus	7.3633
28131	Prevotella intermedia	species	7.3572
1118202	Cruoricaptor ignavus	species	7.3522
1433995	Cruoricaptor	genus	7.3522
649777	Synergistaceae	family	7.352
1197717	Cloacibacillus porcorum	species	7.3467
508459	Cloacibacillus	genus	7.3467
33968	Leuconostoc pseudomesenteroides	species	7.3374
904	Acidaminococcus	genus	7.3273
5204	Basidiomycota	phylum	7.3243
47715	Lacticaseibacillus rhamnosus	species	7.324
329854	Bacteroides intestinalis	species	7.318
2507160	Aminipila luticellarii	species	7.3171
28111	Bacteroides eggerthii	species	7.3138
2044467	Escherichia sp. E4742	species	7.3061
2747	Carnobacterium	genus	7.3044
1296536	Enterobacter hormaechei subsp. xiangfangensis	subspecies	7.3022
165695	Sphingobium	genus	7.2626
246787	Bacteroides cellulosilyticus	species	7.251
46124	Granulicatella adiacens	species	7.2148
244320	Escherichia coli O55:H7	no rank	7.2102
186807	Peptococcaceae	family	7.1915
3016343	Peptoniphilus equinus	species	7.1807
1852374	Ezakiella massiliensis	species	7.1398
33010	Cutibacterium avidum	species	7.1351
871541	Actinomyces oris K20	strain	7.1305
563008	Segatella oris C735	strain	7.1223
1269	Micrococcus	genus	7.1209
2942964	Intestiviridae	family	7.1129
28112	Tannerella forsythia	species	7.104
864564	Parascardovia denticolens DSM 10105 = JCM 12538	strain	7.0854
196082	Parascardovia	genus	7.0854
78258	Parascardovia denticolens	species	7.0854
909929	Selenomonadales	order	7.0844
129337	Geobacillus	genus	7.0763
545	Citrobacter koseri	species	7.0745
1680	Bifidobacterium adolescentis	species	7.0698
1579	Lactobacillus acidophilus	species	7.0498
712116	Actinomyces sp. oral taxon 169	species	7.0411
1843491	Selenomonadaceae	family	7.0396
501783	Cloacibacterium	genus	7.0337
1298	Deinococcus	genus	7.0322
118964	Deinococcales	order	7.0322
183710	Deinococcaceae	family	7.0322
502558	Eggerthella sp. YY7918	species	7.0314
1281486	Lactococcus formosensis	species	7.0247
1069534	Ligilactobacillus ruminis ATCC 27782	strain	7.0092
1659	Actinomyces israelii	species	7.0028
33682	Euglenozoa	phylum	6.9992
2704949	Trypanosomatida	order	6.9992
5654	Trypanosomatidae	family	6.9992
5653	Kinetoplastea	class	6.9992
435591	Parabacteroides distasonis ATCC 8503	strain	6.98
68933	Thermales	order	6.964
188786	Thermaceae	family	6.964
521095	Lancefieldella parvula DSM 20469	strain	6.9621
1382	Lancefieldella parvula	species	6.9621
172042	Rothia aeria	species	6.9552
5658	Leishmania	genus	6.9546
1596	Lactobacillus gasseri	species	6.9527
1501	Clostridium pasteurianum	species	6.9374
29385	Staphylococcus saprophyticus	species	6.925
718252	Faecalibacterium prausnitzii L2-6	strain	6.9208
1064535	Megasphaera elsdenii DSM 20460	strain	6.9198
2772089	uncultured phage cr115_1	no rank	6.9105
2955498	Birpovirus hiberniae	species	6.9105
84998	Coriobacteriia	class	6.9096
151276	Bacteroides coprosuis	species	6.905
679937	Bacteroides coprosuis DSM 18011	strain	6.905
61647	Pluralibacter gergoviae	species	6.9039
633147	Olsenella uli DSM 7084	strain	6.8991
133926	Olsenella uli	species	6.8991
2778656	Escherichia coli O20:H12	no rank	6.8893
622	Shigella dysenteriae	species	6.8791
712710	Tannerella serpentiformis	species	6.873
147206	Collinsella stercoris	species	6.8677
28035	Staphylococcus lugdunensis	species	6.8665
2751	Carnobacterium maltaromaticum	species	6.865
97478	Limosilactobacillus mucosae	species	6.8606
2848143	Escherichia coli O85:H1	no rank	6.8604
2823317	Phascolarctobacterium sp. Marseille-Q4147	species	6.8584
34037	Rahnella	genus	6.8453
1297793	Lacrimispora sphenoides JCM 1415	strain	6.845
29370	Lacrimispora sphenoides	species	6.845
2507162	Caproiciproducens sp. NJN-50	species	6.8446
1738645	Caproiciproducens	genus	6.8446
634176	Aggregatibacter aphrophilus NJ8700	strain	6.8286
69710	Treponema vincentii	species	6.8193
1380	Atopobium	genus	6.8137
712157	Atopobium sp. oral taxon 416	species	6.8137
496	Neisseria macacae	species	6.7759
84112	Eggerthella lenta	species	6.7669
2678885	Faecalibacillus	genus	6.7549
1982626	Faecalibacillus intestinalis	species	6.7549
2564099	Ruminococcus bovis	species	6.7505
69966	Macrococcoides caseolyticum	species	6.7491
33038	Mediterraneibacter gnavus	species	6.7395
2759736	Lacticaseibacillus	genus	6.7368
1307	Streptococcus suis	species	6.7281
31977	Veillonellaceae	family	6.7226
1843489	Veillonellales	order	6.7226
102684	Streptococcus infantarius	species	6.7157
46123	Abiotrophia	genus	6.7149
46125	Abiotrophia defectiva	species	6.7149
10239	Viruses	superkingdom	6.7143
2731360	Heunggongvirae	kingdom	6.7048
2731618	Uroviricota	phylum	6.7048
2731619	Caudoviricetes	class	6.7048
84111	Eggerthella	genus	6.7039
1866885	Mycolicibacterium	genus	6.7014
2789425	Actinomyces sp. HMT 175	species	6.6931
1297	Deinococcota	phylum	6.6774
188787	Deinococci	class	6.6774
187327	Acidaminococcus intestini	species	6.6718
2569097	Anaerobutyricum	genus	6.6708
39488	Anaerobutyricum hallii	species	6.6708
712624	Streptococcus sp. oral taxon 064	species	6.6649
2767353	Lancefieldella	genus	6.6614
649757	Anaerostipes hadrus ATCC 29173 = JCM 17467	strain	6.6558
2767881	Fructilactobacillus	genus	6.6508
1978007	Crassvirales	order	6.6435
75984	Mannheimia	genus	6.643
1694	Bifidobacterium pseudolongum	species	6.6391
1161918	Brachyspira pilosicoli WesB	strain	6.6058
2070	Pseudonocardiaceae	family	6.6023
85010	Pseudonocardiales	order	6.6023
586	Providencia	genus	6.574
577309	Paraprevotella	genus	6.5725
28113	Bacteroides heparinolyticus	species	6.5688
2955997	Jahgtovirus intestinihominis	species	6.5634
2772061	uncultured phage cr107_1	no rank	6.5634
1447716	Bifidobacterium catenulatum PV20-2	strain	6.5632
28125	Prevotella bivia	species	6.5578
117563	Granulicatella	genus	6.5547
2364787	Alistipes megaguti	species	6.5427
357	Agrobacterium	genus	6.5327
409322	Treponema pedis	species	6.5216
550	Enterobacter cloacae	species	6.5156
69823	Selenomonas sputigena	species	6.5146
479437	Eggerthella lenta DSM 2243	strain	6.5079
29388	Staphylococcus capitis	species	6.4974
225992	Comamonas kerstersii	species	6.4867
1002367	Leyella stercorea DSM 18206	strain	6.4853
76123	Hoylesella enoeca	species	6.4814
295405	Bacteroides fragilis YCH46	strain	6.4692
2995122	Leptogranulimonas	genus	6.469
2894156	Leptogranulimonas caecicola	species	6.469
2608867	Escherichia ruysiae	species	6.4602
282402	Prevotella multiformis	species	6.4572
454154	Paraprevotella clara	species	6.4555
387090	Phocaeicola coprophilus	species	6.4459
1232428	Megasphaera massiliensis	species	6.4433
2948767	Jahgtovirus	genus	6.4375
862967	Streptococcus intermedius B196	strain	6.4322
679191	Prevotella amnii CRIS 21A-A	strain	6.4208
28141	Cronobacter sakazakii	species	6.4014
77635	Bifidobacterium subtile	species	6.3808
2035811	Pseudodesulfovibrio	genus	6.3616
200795	Chloroflexota	phylum	6.3564
29347	[Clostridium] scindens	species	6.3545
166486	Roseburia intestinalis	species	6.3404
361101	Streptococcus pseudoporcinus	species	6.3338
2707299	Adlercreutzia hattorii	species	6.3315
39948	Dialister	genus	6.3261
536231	Roseburia intestinalis L1-82	strain	6.3257
2691580	Prevotella sp. Rep29	species	6.3242
52584	Brachyspira pilosicoli	species	6.2966
2946830	Birpovirus	genus	6.276
186822	Paenibacillaceae	family	6.2575
1216932	Clostridium bornimense	species	6.249
83334	Escherichia coli O157:H7	serotype	6.2455
44249	Paenibacillus	genus	6.2446
33964	Leuconostoc citreum	species	6.2316
1458465	Megasphaera elsdenii 14-14	strain	6.2267
384636	Lacrimispora xylanisolvens	species	6.2198
1051631	Streptococcus phage YMC-2011	species	6.2196
270	Thermus	genus	6.1948
2093856	Butyricimonas faecalis	species	6.1941
2679910	Intestinibaculum	genus	6.1884
2487118	Intestinibaculum porci	species	6.1884
84135	Gemella sanguinis	species	6.1868
85019	Brevibacteriaceae	family	6.1839
1696	Brevibacterium	genus	6.1839
2718	Cardiobacterium hominis	species	6.1641
1231072	Clostridium tetani 12124569	strain	6.1618
2892396	Vescimonas	genus	6.1578
52773	Schaalia meyeri	species	6.1559
2081702	Actinomyces sp. oral taxon 897	species	6.1547
818	Bacteroides thetaiotaomicron	species	6.1537
1625	Fructilactobacillus sanfranciscensis	species	6.1495
420247	Methanobrevibacter smithii ATCC 35061	strain	6.1307
2929491	Faecalibacterium sp. HTF-F	species	6.1091
68295	Thermoanaerobacterales	order	6.1008
291644	Bacteroides salyersiae	species	6.0944
1507512	Romboutsia hominis	species	6.0655
515622	Butyrivibrio proteoclasticus B316	strain	6.0578
43305	Butyrivibrio proteoclasticus	species	6.0578
69277	Phyllobacteriaceae	family	6.0402
2767879	Companilactobacillus	genus	6.0245
161879	Corynebacterium kroppenstedtii	species	6.0242
1042156	Clostridium sp. SY8519	species	6.0184
2841528	Eubacterium sp. MSJ-33	species	6.0089
1506553	Lachnoclostridium	genus	6.0082
1660	Schaalia odontolytica	species	6.0077
216816	Bifidobacterium longum	species	6.0001
1573534	Faecalitalea	genus	5.9918
717960	Faecalitalea cylindroides T2-87	strain	5.9918
39483	Faecalitalea cylindroides	species	5.9918
59310	Streptococcus macedonicus	species	5.9885
33967	Leuconostoc mesenteroides subsp. mesenteroides	subspecies	5.9866
5042	Eurotiales	order	5.977
147545	Eurotiomycetes	class	5.977
714	Aggregatibacter actinomycetemcomitans	species	5.9456
301297	Dehalococcoidia	class	5.9432
1378	Gemella	genus	5.9309
243164	Dehalococcoides mccartyi 195	strain	5.9267
61434	Dehalococcoides	genus	5.9031
1202464	Dehalococcoidaceae	family	5.9031
1202465	Dehalococcoidales	order	5.9031
61435	Dehalococcoides mccartyi	species	5.881
31983	Helcococcus	genus	5.8788
40091	Helcococcus kunzii	species	5.8788
3029087	Aminobacteriaceae	family	5.855
651822	Fretibacterium fastidiosum	species	5.855
1434006	Fretibacterium	genus	5.855
2316020	Mediterraneibacter	genus	5.8469
1366	Lactococcus raffinolactis	species	5.8243
762948	Rothia dentocariosa ATCC 17931	strain	5.8122
470565	Prevotella histicola	species	5.8068
2737	Vagococcus	genus	5.8051
2733199	Oengusvirus	genus	5.8011
2734262	Oengusvirus oengus	species	5.8011
2070188	Faecalibacterium phage FP_oengus	no rank	5.8011
128827	Erysipelotrichaceae	family	5.7976
862966	Streptococcus intermedius C270	strain	5.7869
119602	Streptococcus dysgalactiae subsp. equisimilis	subspecies	5.7807
84108	Slackia	genus	5.7723
84110	Slackia heliotrinireducens	species	5.7723
469617	Fusobacterium ulcerans ATCC 49185	strain	5.7705
624	Shigella sonnei	species	5.7682
1501226	Romboutsia	genus	5.7627
1449093	Lactococcus cremoris subsp. cremoris IBB477	strain	5.7419
158846	Megamonas	genus	5.7268
44742	Desulfovibrio fairfieldensis	species	5.7252
768503	Cytophagia	class	5.7247
768507	Cytophagales	order	5.7247
997879	Bacteroides fragilis CL03T12C07	strain	5.7183
2489014	Klebsiella variicola subsp. tropica	subspecies	5.6997
187101	Sneathia vaginalis	species	5.6958
168808	Sneathia	genus	5.6958
2724150	Romboutsia sp. CE17	species	5.6846
197	Campylobacter jejuni	species	5.6711
551	Erwinia	genus	5.6707
437897	Megamonas funiformis	species	5.6624
2806552	Bulleidia sp. zg-1006	species	5.6621
118747	Bulleidia	genus	5.6621
1744	Propionibacterium freudenreichii	species	5.6534
1601	Ligilactobacillus agilis	species	5.6514
2764325	[Eubacterium] hominis	species	5.6479
89966	Hymenobacter	genus	5.6449
1131492	Aspergillaceae	family	5.6363
1852373	Murdochiella vaginalis	species	5.6353
1161127	Murdochiella	genus	5.6353
186329	Acholeplasmatales	order	5.6347
2146	Acholeplasmataceae	family	5.6347
868	Cardiobacteriaceae	family	5.6326
135615	Cardiobacteriales	order	5.6316
589437	Prevotella scopos	species	5.6177
1236518	Prevotella scopos JCM 17725	strain	5.6177
77095	Segatella bryantii	species	5.5925
2717	Cardiobacterium	genus	5.5818
1160721	Ruminococcus bicirculans (ex Wegman et al. 2014)	species	5.5818
859	Fusobacterium necrophorum	species	5.575
2025876	Parabacteroides sp. CT06	species	5.5687
1585	Lactobacillus delbrueckii subsp. bulgaricus	subspecies	5.5675
40214	Acinetobacter johnsonii	species	5.5605
1115758	Romboutsia ilealis	species	5.5565
751585	Coprococcus sp. ART55/1	species	5.5551
2709410	Chordicoccus furentiruminis	species	5.5376
3031933	Chordicoccus	genus	5.5376
495	Neisseria elongata	species	5.5305
623	Shigella flexneri	species	5.5099
851	Fusobacterium nucleatum	species	5.5022
1853232	Hymenobacteraceae	family	5.4842
433286	Anaerocolumna cellulosilytica	species	5.4546
549	Pantoea agglomerans	species	5.4521
971	Selenomonas ruminantium	species	5.4355
114197	Selenomonas ruminantium subsp. lactilytica	subspecies	5.4355
927704	Selenomonas ruminantium subsp. lactilytica TAM6421	strain	5.4355
46503	Parabacteroides merdae	species	5.4332
2763670	Wujia chipingensis	species	5.4314
2944152	Wujia	genus	5.4314
2490855	Lachnoanaerobaculum gingivalis	species	5.3855
2528203	Bacteroides sp. A1C1	species	5.3817
2582419	Dialister hominis	species	5.3716
2662363	Alistipes sp. dk3624	species	5.3691
1703250	Citrobacter sp. CRE-46	species	5.3544
302911	Bifidobacterium animalis subsp. lactis	subspecies	5.3507
41294	Nitrobacteraceae	family	5.3501
1871109	Neisseria sp. RH3002v2g	species	5.3386
66219	Lachnoclostridium phytofermentans	species	5.3383
357809	Lachnoclostridium phytofermentans ISDg	strain	5.3383
40215	Acinetobacter junii	species	5.3372
2161821	Dialister massiliensis	species	5.3275
46205	Pseudobutyrivibrio	genus	5.3271
185007	Pseudobutyrivibrio xylanivorans	species	5.3271
1183380	Campylobacter coli RM5611	strain	5.3228
1249	Weissella paramesenteroides	species	5.3221
484	Neisseria flavescens	species	5.3157
2585118	Alistipes communis	species	5.2944
649756	Anaerostipes hadrus	species	5.2889
1649	Kurthia	genus	5.2799
2732414	Petitvirales	order	5.2753
2732412	Phixviricota	phylum	5.2753
2732091	Sangervirae	kingdom	5.2753
2732413	Malgrandaviricetes	class	5.2753
10841	Microviridae	family	5.2753
841	Roseburia	genus	5.2685
1843210	Anaerocolumna	genus	5.2599
817	Bacteroides fragilis	species	5.2242
294702	Proteiniphilum	genus	5.2238
847	Oxalobacter formigenes	species	5.2219
479831	Clostridioides difficile QCD-63q42	strain	5.1847
29393	Dolosigranulum	genus	5.1813
29394	Dolosigranulum pigrum	species	5.1813
1513	Clostridium tetani	species	5.1794
79880	Shouchella clausii	species	5.1644
143387	Fusobacterium necrophorum subsp. funduliforme	subspecies	5.1549
872	Desulfovibrio	genus	5.1511
135622	Alteromonadales	order	5.1463
2733190	Lughvirus	genus	5.1334
2734248	Lughvirus lugh	species	5.1334
2070184	Faecalibacterium phage FP_Lugh	no rank	5.1334
207244	Anaerostipes	genus	5.1222
374	Bradyrhizobium	genus	5.044
2942993	Blohavirus	genus	5.0409
901	Desulfovibrio piger	species	5.0326
712361	Leptotrichia sp. oral taxon 218	species	5.0265
2708053	Romboutsia sp. 13368	species	5.0245
1263	Ruminococcus	genus	5.0125
2956053	Kehishuvirus primarius	species	5.0117
2301731	Bacteroides phage crAss001	no rank	5.0117
884684	Mageeibacillus indolicus	species	4.9975
699246	Mageeibacillus indolicus UPII9-5	strain	4.9975
1637257	Mageeibacillus	genus	4.9975
1647988	Akkermansiaceae	family	4.9733
239934	Akkermansia	genus	4.9733
48461	Verrucomicrobiales	order	4.9731
203494	Verrucomicrobiia	class	4.9731
74201	Verrucomicrobiota	phylum	4.973
2709317	Bacteroides phage crAss002	no rank	4.9597
2955998	Jahgtovirus secundus	species	4.9597
2913621	Prevotella sp. E9-3	species	4.9552
941323	Escherichia coli VR50	strain	4.9255
562	Escherichia coli	species	4.923
568816	Acidaminococcus intestini RyC-MR95	strain	4.9002
411470	Mediterraneibacter gnavus ATCC 29149	strain	4.8944
28890	Euryarchaeota	phylum	4.8866
2734096	Brigitvirus brigit	species	4.8861
2070181	Faecalibacterium phage FP_Brigit	no rank	4.8861
2733097	Brigitvirus	genus	4.8861
1653174	Actinotignum	genus	4.8813
239935	Akkermansia muciniphila	species	4.8803
2157	Archaea	superkingdom	4.8576
1583098	Fusobacterium hwasookii	species	4.8541
2789424	Actinomyces sp. HMT897	species	4.8316
38284	Corynebacterium accolens	species	4.8257
85015	Nocardioidaceae	family	4.8191
1796613	Bacteroides caecimuris	species	4.8184
2576755	Caproicibacter	genus	4.8161
2576756	Caproicibacter fermentans	species	4.8161
630129	Bifidobacterium catenulatum subsp. kashiwanohense	subspecies	4.8136
589436	Prevotella fusca	species	4.8083
1236517	Prevotella fusca JCM 17724	strain	4.8083
936351	Bifidobacterium breve S27	strain	4.8057
2845437	Skunavirus P656	species	4.7933
2662298	Lactococcus phage P656	no rank	4.7933
2874051	Escherichia coli O99:H6	serotype	4.7887
208223	Kosakonia cowanii	species	4.7698
204037	Dickeya	genus	4.7678
2792859	Bacteroides humanifaecis	species	4.7329
84030	Lacrimispora saccharolytica	species	4.7099
2719231	Lacrimispora	genus	4.6978
1655645	Parabacteroides phage YZ-2015b	species	4.6918
657314	Blautia obeum A2-162	strain	4.6831
1117	Cyanobacteriota	phylum	4.68
1051074	Streptococcus thermophilus JIM 8232	strain	4.6739
2773705	Escherichia coli O18ac:H14	no rank	4.6698
2751153	Coprobacter secundus subsp. similis	subspecies	4.6668
1501392	Coprobacter secundus	species	4.6668
3031451	Desulfobulbia	class	4.6547
3024411	Desulfobulbales	order	4.6547
33882	Microbacterium	genus	4.6498
459786	Oscillibacter	genus	4.5986
2763056	Oscillibacter hominis	species	4.5986
411486	Clostridium sp. M62/1	species	4.5983
185008	Butyrivibrio hungatei	species	4.5971
997877	Phocaeicola dorei CL03T12C01	strain	4.5875
33042	Coprococcus	genus	4.5745
1727145	Anaerocolumna chitinilytica	species	4.5703
3028117	Cyanophyceae	class	4.5658
28116	Bacteroides ovatus	species	4.5602
1122979	Prevotella amnii DSM 23384 = JCM 14753	strain	4.5417
203682	Planctomycetota	phylum	4.5364
411474	Coprococcus eutactus ATCC 27759	strain	4.5352
2944198	Wansuia	genus	4.5336
2763667	Wansuia hejianensis	species	4.5336
28137	Prevotella veroralis	species	4.53
267890	Shewanellaceae	family	4.5142
42817	Corynebacterium argentoratense	species	4.5132
1348662	Corynebacterium argentoratense DSM 44202	strain	4.5132
2173	Methanobrevibacter smithii	species	4.5082
2159	Methanobacteriaceae	family	4.5036
183925	Methanobacteria	class	4.5035
2158	Methanobacteriales	order	4.5035
22	Shewanella	genus	4.4975
75682	Oxalobacteraceae	family	4.4902
2944193	Simiaoa	genus	4.4833
2763672	Simiaoa sunii	species	4.4833
718255	Roseburia intestinalis XB6B4	strain	4.4785
2837504	Heyndrickxia	genus	4.4783
61648	Kluyvera intermedia	species	4.4707
239759	Alistipes	genus	4.4593
171550	Rikenellaceae	family	4.4593
909932	Negativicutes	class	4.4521
213121	Desulfobulbaceae	family	4.4201
226186	Bacteroides thetaiotaomicron VPI-5482	strain	4.4156
2172	Methanobrevibacter	genus	4.415
2779519	Thermophilibacter immobilis	species	4.3952
2847307	Thermophilibacter	genus	4.3952
1822464	Paraburkholderia	genus	4.3847
236753	Fastidiosipila sanguinis	species	4.3749
236752	Fastidiosipila	genus	4.3749
1656	Actinomyces viscosus	species	4.3346
846	Oxalobacter	genus	4.3282
46228	[Ruminococcus] lactaris	species	4.3105
471875	[Ruminococcus] lactaris ATCC 29176	strain	4.3105
2070186	Faecalibacterium phage FP_Taranis	no rank	4.3072
2733134	Taranisvirus	genus	4.3072
2734146	Taranisvirus taranis	species	4.3072
1729679	Faecalibaculum	genus	4.274
1702221	Faecalibaculum rodentium	species	4.274
46506	Bacteroides stercoris	species	4.2581
620	Shigella	genus	4.2577
39486	Dorea formicigenerans	species	4.2514
2583584	Streptococcus sp. NCTC 11567	species	4.248
2316	Methanosphaera	genus	4.2035
657315	Roseburia intestinalis M50/1	strain	4.2022
2108523	Lawsonibacter asaccharolyticus	species	4.1622
2172004	Lawsonibacter	genus	4.1622
1385938	Bifidobacterium breve 12L	strain	4.1593
310298	Phocaeicola coprocola	species	4.142
470145	Phocaeicola coprocola DSM 17136	strain	4.142
328814	Alistipes shahii	species	4.1124
717959	Alistipes shahii WAL 8301	strain	4.1124
2070182	Faecalibacterium phage FP_Epona	no rank	4.1016
2734105	Eponavirus epona	species	4.1016
2733103	Eponavirus	genus	4.1016
397864	Barnesiella	genus	4.0951
397865	Barnesiella viscericola	species	4.0951
880074	Barnesiella viscericola DSM 18177	strain	4.0951
2317	Methanosphaera stadtmanae	species	4.091
39496	Eubacterium ventriosum	species	4.0826
2899121	Tannockella kyphosi	species	4.0805
2943184	Tannockella	genus	4.0805
1398	Heyndrickxia coagulans	species	4.0793
2866573	Cardiobacterium sp. Marseille-Q4385	species	4.0783
196	Campylobacter fetus	species	4.07
997890	Bacteroides uniformis CL03T12C37	strain	4.0546
116085	Coprococcus catus	species	4.032
2929490	Faecalibacterium sp. I2-3-92	species	4.02
39485	Lachnospira eligens	species	4.0161
28050	Lachnospira	genus	4.0161
393921	Porphyromonas crevioricanis	species	4.0144
37923	Rothia kristinae	species	4.0086
572511	Blautia	genus	3.9996
155615	Fusobacterium vincentii	species	3.979
32020	Campylobacter fetus subsp. venerealis	subspecies	3.9746
418240	Blautia wexlerae	species	3.9542
1121115	Blautia wexlerae DSM 19850	strain	3.9542
2948680	Diorhovirus	genus	3.9512
2929494	Faecalibacterium sp. I4-1-79	species	3.918
138851	Treponema parvum	species	3.8965
2929488	Faecalibacterium sp. IP-1-18	species	3.8962
657322	Faecalibacterium prausnitzii SL3/3	strain	3.8736
1164882	Lachnoanaerobaculum	genus	3.8719
88431	Dorea longicatena	species	3.8655
2489010	Klebsiella africana	species	3.8568
1870984	Anaerococcus mediterraneensis	species	3.856
853	Faecalibacterium prausnitzii	species	3.8524
449673	Bacteroides stercoris ATCC 43183	strain	3.8297
1643513	Treponema sp. OMZ 857	species	3.7909
2603322	Vallitaleaceae	family	3.764
357276	Phocaeicola dorei	species	3.7613
2946593	Oxalobacter aliiformigenes	species	3.7341
34084	Riemerella	genus	3.7314
2518495	Duncaniella	genus	3.7118
203	Campylobacter rectus	species	3.6624
2029659	Lactococcus phage 16802	no rank	3.6177
2845153	Skunavirus sv16802	species	3.6177
28124	Porphyromonas endodontalis	species	3.6127
2755405	Bacteroides sp. CACC 737	species	3.6041
2772080	uncultured phage cr53_1	no rank	3.6009
2955510	Blohavirus americanus	species	3.6009
44283	Pasteurella multocida subsp. multocida	subspecies	3.5988
543	Enterobacteriaceae	family	3.5941
1730	Eubacterium	genus	3.5859
186806	Eubacteriaceae	family	3.5857
91347	Enterobacterales	order	3.5611
85004	Bifidobacteriales	order	3.5348
31953	Bifidobacteriaceae	family	3.5348
1678	Bifidobacterium	genus	3.5344
189330	Dorea	genus	3.5324
1760	Actinomycetes	class	3.5314
1236	Gammaproteobacteria	class	3.4912
35832	Bilophila	genus	3.4836
35833	Bilophila wadsworthia	species	3.4836
1224	Pseudomonadota	phylum	3.4676
3024823	Anaeromicropila	genus	3.4646
2785025	Anaeromicropila herbilytica	species	3.4646
2845434	Skunavirus P4565	species	3.4294
2662297	Lactococcus phage P4565	no rank	3.4294
228603	Hoylesella shahii	species	3.4198
2981344	Xiamenia	genus	3.4192
2682776	Xiamenia xianingshaonis	species	3.4192
28256	Halomonadaceae	family	3.4033
575614	Prevotella sp. oral taxon 299 str. F0039	strain	3.3998
652716	Prevotella sp. oral taxon 299	species	3.3998
574697	Butyricimonas	genus	3.3966
420952	Paraburkholderia bryophila	species	3.358
28264	Arcanobacterium haemolyticum	species	3.3414
544645	Butyricimonas virosa	species	3.3361
2162637	Bacteroides sp. PHL 2737	species	3.3095
1534	Clostridium kluyveri	species	3.3081
2763068	Streptococcus sp. NSJ-72	species	3.2893
201174	Actinomycetota	phylum	3.2891
13076	Globicatella sanguinis	species	3.2685
13075	Globicatella	genus	3.2685
186823	Alicyclobacillaceae	family	3.2346
2518971	Duncaniella dubosii	species	3.2306
183963	Halobacteria	class	3.2226
1737424	Blautia massiliensis (ex Durand et al. 2017)	species	3.1839
717605	Thermobacillus composti KWC4	strain	3.1738
377615	Thermobacillus composti	species	3.1738
76632	Thermobacillus	genus	3.1738
292632	Subdoligranulum	genus	3.1698
214851	Subdoligranulum variabile	species	3.1698
33024	Phascolarctobacterium	genus	3.1137
135619	Oceanospirillales	order	3.0941
165179	Segatella copri	species	3.006
2974251	Segatella	genus	3.006
194924	Desulfovibrionaceae	family	3.0022
213115	Desulfovibrionales	order	3.0017
3031449	Desulfovibrionia	class	3.0017
200940	Thermodesulfobacteriota	phylum	2.999
28263	Arcanobacterium	genus	2.9903
2375	Sporomusa	genus	2.9612
411483	Faecalibacterium duncaniae	species	2.96
171552	Prevotellaceae	family	2.9365
394503	Ruminiclostridium cellulolyticum H10	strain	2.9305
1521	Ruminiclostridium cellulolyticum	species	2.9305
33926	Candidatus Phytoplasma	genus	2.9252
1843488	Acidaminococcales	order	2.9156
909930	Acidaminococcaceae	family	2.9156
1853229	Chitinophagales	order	2.9063
563835	Chitinophagaceae	family	2.9063
1853228	Chitinophagia	class	2.9063
3031651	Desulfuromonadia	class	2.9025
33025	Phascolarctobacterium faecium	species	2.8972
2377	Sporomusa termitida	species	2.8942
3039116	Anaerocolumna sp. AGMB13025	species	2.8324
3031668	Geobacterales	order	2.8267
213422	Geobacteraceae	family	2.8267
621	Shigella boydii	species	2.8033
537011	Segatella copri DSM 18205	strain	2.7553
1538075	Malasseziomycetes	class	2.7053
742845	Malasseziaceae	family	2.7053
55193	Malassezia	genus	2.7053
162474	Malasseziales	order	2.7053
2734634	Berryella wangjianweii	species	2.6998
76775	Malassezia restricta	species	2.6771
2929495	Faecalibacterium sp. I4-3-84	species	2.6632
109328	Leptotrichia trevisanii	species	2.6442
359110	Pseudomonas extremaustralis	species	2.6212
2929489	Faecalibacterium sp. IP-3-29	species	2.6134
213118	Desulfobacterales	order	2.566
3024418	Desulfobacteria	class	2.566
28118	Odoribacter splanchnicus	species	2.5061
283168	Odoribacter	genus	2.5061
820	Bacteroides uniformis	species	2.4089
709991	Odoribacter splanchnicus DSM 20712	strain	2.3887
2913616	Prevotella sp. E13-17	species	2.3359
28446	Anaerotignum propionicum	species	2.3254
2039240	Anaerotignum	genus	2.3254
991789	Anaerotignum propionicum DSM 1682	strain	2.3254
1853231	Odoribacteraceae	family	2.276
821	Phocaeicola vulgatus	species	2.1936
2725997	Escherichia sp. SCLE84	species	2.1911
611	Salmonella enterica subsp. enterica serovar Heidelberg	no rank	2.1785
2818505	Myxococcota	phylum	2.0115
1124936	Salmonella enterica subsp. enterica serovar Heidelberg str. 41578	strain	1.9976
216851	Faecalibacterium	genus	1.9532
909656	Phocaeicola	genus	1.7058
592316	Pantoea sp. At-9b	species	1.6002
216572	Oscillospiraceae	family	1.5468
186803	Lachnospiraceae	family	1.5367
1239	Bacillota	phylum	0.9549
816	Bacteroides	genus	0.9515
186801	Clostridia	class	0.9074
186802	Eubacteriales	order	0.9074
815	Bacteroidaceae	family	0.2148
171549	Bacteroidales	order	-0.482
200643	Bacteroidia	class	-0.482
976	Bacteroidota	phylum	-0.498

As a FYI, my preferred transformation reduces skew to zero for everyone above. Life is good.