Veillonella probiotics appear to be available in a mixture (ULTRA-VEILLONELLA) however, I have reservations about the seller (site is new – 2022, no species information, no safety or other studies (legally required in the USA), no information about the company, etc. in other words has an unpleasant smell)
Note that Lactobacillus is far down this list.
CLICK ON THE BACTERIA BELOW TO SEE WHAT INCREASES OR DECREASES EACH
With this being the Thanksgiving Weekend, I had time to work on my backlog. One of the items was special studies. I have done the following changes:
Executed the analysis for both uBiome and Thryve/Ombre samples. So more samples will have the option of using special studies.
Implemented Consensus/Monte Carlo between the bacteria, casting the species (which are not reported consistently between labs) to their genus. These are shown on the [Key Bacteria] link below.
Last, I have added per Peripheral neuropathy to the symptom list.
REMEMBER TO ANNOTATED YOU SAMPLES WITH YOUR SYMPTOMS
This is what Special Studies use.
Common Bacteria across labs is now available for each. https://microbiomeprescription.com/Library/CitizenScience
Example: for Chronic Fatigue Syndrome
The page below shows a distinct pattern for ME/CFS with Bifidobacterium being the greatest significance. For this bacteria, my first suggestion is simple: Human milk oligosaccharides (HMOs) and Bifidobacerium infantis probiotics.
“The results reflect the metabolic abilities of the respective bifidobacteria. B. bifidum used secretory glycosidases to degrade HMOs, whereas B. longum subsp. infantis assimilated all HMOs by incorporating them in their intact forms.” [2011]
It is interesting to note that Lactobacillus does not appear as significant.
Bottom Line
Special Studies are still a “work-in-progress”. Using them “as is” have not produced superior results to those from the standard triplet (Outside Lab Range, Box-Plot-Whiskers, Kaltoft-Møldrup) — see this post for an example. How do I determine which is better? For ME/CFS, we should have the top suggested items being cross validated with clinical studies. Feel free to explore the results.
I will continue working on getting superior results from special studies — stay tune!
I go this email from someone who just moved to Spain from the U.S. She has being using Microbiome Prescription to try improving her ME/CFS. She had the testing done by Ombre Labs, and then transfer the data to BiomeSight. This allows her to keep consistent analysis on her journey of recovery.
I’m doing pretty well with bacillus coagulans and pretty bad with some other recommendations so I’m looking for some extra clarity. When I hit a great herbal antibiotic and a great probiotic life gets so much better, but oftentimes it’s harder than that. Sometimes I don’t get enough herbal antibiotic recommendations. Some of the probiotics I may need, like e-coli or bifidus, cannot sustain me the way coagulans does -keeping my local infections at bay. So I try to combine them or if it’s not clear if they are compatible, I tend to not take them, which is a shame. So I’m considering prescription medicine to see if I can get a bit more help.
I’m also figuring out where to buy supplements etc. Life is really an adventure!
Comparison Between Samples And Lab Interpretations
For those not familiar with the issue of Lab Interpretation of the identical data see The taxonomy nightmare before Christmas…[2019]. Ombre typically reports on 25-30% more bacteria types than BiomeSight. The quality improved, but the number of bacteria identified are very similar. I give observations below:
Ombre
Lab
Results
BiomeSight
Lab
Results
Criteria
6-Jul
19-Aug
10-Oct
6-Jul
19-Aug
10-Oct
Lab Read Quality
2.1
5.4
7.1
2.1
5.4
7.1
Bacteria Reported By Lab
365
628
625
280
497
490
Bacteria Over 99%ile
5
6
0
2
7
1
Bacteria Over 95%ile
27
24
1
19
31
11
Bacteria Over 90%ile
49
51
1
37
58
24
Bacteria Under 10%ile
18
60
485
45
62
224
Bacteria Under 5%ile
10
28
411
28
30
175
Bacteria Under 1%ile
1
7
317
1
13
135
Lab: Thryve
Rarely Seen 1%
0
9
1
0
4
2
Rarely Seen 5%
8
40
27
4
18
17
Pathogens
19
28
25
15
26
16
Outside Range from Medivere
16
16
5
4
4
4
Outside Range from Metagenomics
7
7
19
17
17
16
Outside Range from MyBioma
14
14
8
7
7
7
Outside Range from Nirvana/CosmosId
23
23
8
9
9
7
Outside Range from XenoGene
33
33
25
22
22
19
Outside Lab Range (+/- 1.96SD)
10
14
42
28
28
22
Outside Box-Plot-Whiskers
64
61
12
6
13
7
Outside Kaltoft-Møldrup
112
182
31
70
84
64
Condition Est. Over 99%ile
0
0
542
70
113
175
Condition Est. Over 95%ile
0
0
0
0
1
0
Condition Est. Over 90%ile
2
2
10
0
4
0
Enzymes Over 99%ile
13
15
17
0
6
0
Enzymes Over 95%ile
69
82
0
0
10
0
Enzymes Over 90%ile
155
411
0
22
32
0
Enzymes Under 10%ile
55
138
2
45
51
21
Enzymes Under 5%ile
22
67
1593
308
219
212
Enzymes Under 1%ile
5
2
1320
187
132
146
Compounds Over 99%ile
104
126
641
12
47
67
Compounds Over 95%ile
385
397
4
30
7
19
Compounds Over 90%ile
533
548
60
112
76
138
Compounds Under 10%ile
183
248
103
342
313
323
Compounds Under 5%ile
109
127
359
180
125
224
Compounds Under 1%ile
16
17
303
37
64
73
Compounds Under 1%ile
17
21
224
17
21
40
Comparison Table
The following are apparent, between the last two samples, the reader was trying to follow the suggestions.
The number of high bacteria (> 90%ile, > 95%ile, > 99%ile) show significant decline
Rarely Seen bacteria show significant decline
The number of low bacteria (< 10%ile, < 5%ile, < 1%ile) show significant increases – suggesting more diversity
The Outside Range is a little mixed, with either both labs showing a decline, OR one showing a decline and one an increase. None showed increase on both.
High Enzymes show decline. Low Enzymes had inconsistent results.
Compounds and Conditions had inconsistent results
Enzymes, Compounds and Conditions are best effort estimates (and experimental) and be taken with a grain of salt (50 mg). By conventional thinking, the microbiome has improved (less extreme high levels), less pathogenic bacteria types.
Going Forward
Consensus approach (also known as Monte Carlo Simulation) remains the safest choice. To simplify the analysis, I will use the standard triplet (Outside Lab Range, Box-Plot-Whiskers, Kaltoft-Møldrup) on both latest samples processed through Ombre and Biomesight data processing. Given the report that some did not work subjectively, I decided to proceed down the most restrictive approach. I used the new quick suggestions (best choice for someone with brain fog).
Probiotics
The #1 and #2 choices are lactobacillus paracasei and bacillus subtilis. Kegg choices are Escherichia coli, Bacillus subtilis (with Biomesight numbers being much less than Ombres).
Thryve
Biomesight
Microbiome Modifier
Suggestions
Clinical Dosage
Est Confidence
Suggestions
Est Confidence
bacillus subtilis
Take
10 BCFU/day
340.4
Take
223.6
bacillus lichenformis
Take
279.1
Take
20.9
enterococcus faecium
Take
1 BCFU/day
13.2
Take
8
bifidobacterium longum
Take
10 BCFU/day
516.2
Take
182.5
lactobacillus paracasei
Take
40 BCFU/day
58.7
Take
397.5
pediococcus acidilactici
Take
157.7
Take
215.4
Items with Agreement
For other items, there were a surprisingly few in agreement.
Microbiome Modifier
Suggestions
Clinical Dosage
Est Confidence
Suggestions
Clinical Dosage
Est Confidence
galactooligosaccharides (GOS)
Take
10 gm/day
15
Take
10 gm/day
139.1
Calcium
Take
500 mg/day
129.2
Take
500 mg/day
36.2
Magnesium
Take
500 mg/day
189.7
Take
500 mg/day
119.2
D-Ribose
Take
10 gm/day
80.6
Take
10 gm/day
23.6
Glycine
Take
15 gm/day
409.2
Take
15 gm/day
258.5
Omega-3 fatty acids
Take
4 gm/day
166.8
Take
4 gm/day
289.4
Using the Consensus across Multiple Samples
This gives a lot more information, but at the cost of more complexities.
The approach is similar to the above, except for suggestions we change to Every thing. I have extracted the items > 100 that are 5 or 6 Take Count with 0 or 1 Avoid Count to the table below in decreasing order
Cacao (426) — not an item on the quick suggestions
“A study by Fallon et al found that some of the PTLDS patients in their trial experienced moderate short-term cognitive improvement from ceftriaxone treatment” [2008]
“Ceftriaxone has excellent penetration of the blood-brain barrier and is one of the most effective drugs for Lyme disease. Ceftriaxone is typically given once a day intravenously, typically in 45 minutes.” [Columbia-Lyme.Org]
See this 2015 post, Rifaximin and CFS , for CFS/ME that have used this
So every item at the top of the list (from over a possible choice of 3000 different prescription drugs), are cross-validated against the literature with the exception of proton-pump-inhibitor. This person can show their medical professional that the microbiome model suggests it and clinical studies confirm that they are reasonable.
I favor Dr. Cecile Jadin protocol of rotating antibiotics typically a course (7-10 days), then a break of 1-2 weeks, and then proceed to the next one.
Feedback from Reader
I love Dr. AI [Artificial Intelligence], which other doctor asks you to eat as much 100% chocolate I can??? And I tolerate it, luckily. And there are so many yummy brands in Spain, I don’t remember having that much choice when I left!
Thanks for all the info, very helpful, very encouraging to see progress “on paper”, and to have clear things to share with my new doctor. I’m confident I’ll find a microbiome helper here in Barcelona.
The greatest challenge in treating ME/CFS is that there is no clear test to see if something is helping. Using repeated microbiome samples with systematic trials of suggestions, provides objective evidence — even when the subjective evidence is not pronounced. ME/CFS patients have a real challenge on doing subjective evaluation — they often cannot recall how they were two weeks ago!
Postscript – and Reminder
I am not a licensed medical professional and there are strict laws where I live about “appearing to practice medicine”. I am safe when it is “academic models” and I keep to the language of science, especially statistics. I am not safe when the explanations have possible overtones of advising a patient instead of presenting data to be evaluated by a medical professional before implementing.
I cannot tell people what they should take or not take. I can inform people items that have better odds of improving their microbiome as a results on numeric calculations. I am a trained experienced statistician with appropriate degrees and professional memberships. All suggestions should be reviewed by your medical professional before starting.
The answers above describe my logic and thinking and is not intended to give advice to this person or any one. Always review with your knowledgeable medical professional.
A reader asked to look at the data from an experiment she did.
I have provided two biomesight results from biomesight (BS) to microbiome prescription (MP). The sample consuming kefir daily was sent first (both to BS and MP). The second sample was after stopping kefir consumption between the two samples.
This was not the ideal sequence, getting a sample before doing Kefir and one after would be the typical approach. This approach should indicate what is lost by stopping. There was 3 weeks washout time before samples.
Analysis
The stopped Kefir sample is higher quality, so the expectation would be for the numbers to be higher. This is not the case. Stopping resulted in more extreme ranges for bacteria(1.5x more), less types of bacteria, dramatic drop in the count of bacteria out of range (93% decrease in Outside Lab Range). There was a significant in compounds being produced by the microbiome that were more extreme (8x increase) and enzymes also (3.6x increase).
Criteria
On Kefir
Stopped Kefir
Lab Read Quality
3.9
5.3
Bacteria Reported By Lab
470
404
Bacteria Over 99%ile
11
0
Bacteria Over 95%ile
30
5
Bacteria Over 90%ile
43
19
Bacteria Under 10%ile
10
74
Bacteria Under 5%ile
1
39
Bacteria Under 1%ile
0
7
Lab: BiomeSight
Rarely Seen 1%
2
2
Rarely Seen 5%
12
14
Pathogens
29
22
Outside Range from JasonH
4
4
Outside Range from Medivere
14
14
Outside Range from Metagenomics
7
7
Outside Range from MyBioma
5
5
Outside Range from Nirvana/CosmosId
19
19
Outside Range from XenoGene
21
21
Outside Lab Range (+/- 1.96SD)
18
1
Outside Box-Plot-Whiskers
73
29
Outside Kaltoft-Møldrup
81
74
Condition Est. Over 99%ile
0
0
Condition Est. Over 95%ile
0
0
Condition Est. Over 90%ile
1
1
Enzymes Over 99%ile
1
0
Enzymes Over 95%ile
3
2
Enzymes Over 90%ile
24
41
Enzymes Under 10%ile
79
240
Enzymes Under 5%ile
26
158
Enzymes Under 1%ile
1
47
Compounds Over 99%ile
0
2
Compounds Over 95%ile
4
113
Compounds Over 90%ile
29
453
Compounds Under 10%ile
44
163
Compounds Under 5%ile
18
61
Compounds Under 1%ile
2
8
As often happens, there is a Yin/Yang with some indicators improving and other worst. My general impression is that this microbiome does better on Kefir.
Bacteria Specifics
I then went to compare specific bacteria shifts that had special interest or large shifts
In terms of the literature, I could only find Bacteroides and Phocaeicola, which are both reported to increase (agrees). Different Kefirs will have different impact because each has different bacteria in it. “The kefir granules are a consortium of bacteria and yeasts embedded in a exopolysaccharide matrix. ” [2022]
The following list illustrates why I tend not to recommend Kefir — too many possible bacteria, some good and some bad. It’s probiotic roulette! If you buy commercial Kefir, have some fun — email the producer and ask which strains are in it, and the last full shotgun lab report verifying it.
There are two border walls that can be important to health, we will used these terms:
increased intestinal permeability or IIP (often called Leaky Gut, but note: “Leaky gut syndrome is a hypothetical condition that’s not currently recognized as a medical diagnosis.”[src])
blood–brain barrier permeability or BBBP
The first is an indicator of the availability of bacteria, fungi, chemicals, etc. to move from the intestines into the body/blood. The second is the ability of bacteria, fungi, chemicals, etc. to enter the brain. Both are important — the latter with neurological conditions (for example brain fog, autism, etc).
Zonulin is a protein modulator of intercellular tight junctions. It has been shown to induce a significant and reversible increase in gastroduodenal and small intestinal permeability and is involved in tolerance/immune response balance. The hybridization of wheat to dramatically increase gluten (gliadin) content and its overconsumption, multiple times a day, every day, in the typical diet, chronically disrupts this tolerance/immune response balance.
Zonulin is a member of the MASP (mannose‐binding lectin‐associated serine protease) family of proteins, and elevated serum zonulin levels have been reported in a number of neurological conditions such as multiple sclerosis 7 and Alzheimer’s disease. 8
The molecular weight impacts the ability to cross the barrier ” An increase of the surface area of a drug from 52 A2 (e.g., a drug with a MW of 200 Da) to 105 A2 (e.g., a drug with a MW of 450 Da) dramatically decrease its BBB permeation [Blood-brain barrier permeation: molecular parameters governing passive diffusion].”
When dealing with neurological issues when there is a choice of several different substances, I have looked up the molecular weight and advocated for the lower molecular weight choice. For illustration,
Acetylcysteine (N-acetylcysteine) has a weight of 163.19
It is an easy way to do quick evaluation— for example, I would expect Resveratrol to have a greater effect on brain function than Curcumin, with Aspirin having a still greater potential effect.
Bottom Line
The purpose of this post is frame questions that may be relevant to you — and not provide general answers.
A reader reminded me of A short ME/CFS/MCS remission with microbiome samples [2019], which used uBiome. The toolset has changed a lot since those days, so I thought it would be a good learning activity to look at the samples with the new tools.
The person had a short remission from ME/CFS after:
The table below shows about the same number of bacteria identified but with an increase in the number of bacteria at extreme values. Condition Est. had a dramatic drop which would agree with the remission. We also see a dramatic drop in extreme Enzymes and Compounds.
In my humble opinion, it suggests that reducing extremes of enzymes and compounds is a desired objective goal.
Short term remission causes are often difficult to identify the cause. In this patient, the evidence appears to be for a model of Amoxicillin and Clavulanate being effective against existing lactic acid producing species (i.e. Lactobacillus). It takes time for the lactic acid to clear the body. On the flip side, the lactobacillus would start regrowing and producing lactic acid (thus ending the remission).
For the subset of people with ME/CFS that improves on antibiotics and then regress; it is likely because the antibiotic suppress (but does not eliminate) lactic acid bacteria which then regrows…
Quick question—I noticed, for my BiomeSight-via-Ombre sample, that I’m not getting Vitamins, Minerals and similar suggestions. I used to get them on this sample. This only happens when I set the “Everything” option.
Anything I might be doing wrong? I’m generating the suggestions with the KM, Box Plot whisper, and Standard Lab Ranges. Avoiding Special Studies per your recent advice.
Hi I’m a 15 year CFS sufferer with severe GI / neuro problems. I got my second Thryve results recently. They look really quite normal to me and it says I have significant diversity. Is there any help / analysis you could provide to help me narrow down if there’s something actionable? I’m not sure how much capacity you have for that, but it doesn’t hurt to ask.
And unfortunately have been sick for longer. Got sick at age 25 with an infection (low grade fever for months), lost 30 pounds, had vision problems, headaches, fatigue and so on. I was able to work four years in this state but eventually I had much worsening neuro and vision symptoms and was unable to work. I developed POTS a couple years later and at times was using a walker to get to the bathroom and was bedbound. I’ve had some episodes of vision loss that are very strokelike in that they debilitated me cognitively and visually for long afterwards (the vision loss itself resolves after some minutes or hours).
I want to emphasize the visual and cognitive impairment are totally debilitating. I can barely read anything or reliably focus my eyes on anything, and I went from a previously extremely high functioning person to feeling drugged, barely here 24/7. I have severe eye pain all the time.
So I’ve been sick for really my whole adult life, to varying degrees. Primary debilitation is visual and cognitive but I have severe physical fatigue, POTS, am 30 pounds underweight, have been diagnosed with gastroparesis years back I just can’t keep the pounds on. Also it is notable food makes me feel TERRIBLE. Right away I can feel stupid and drugged from it, but also 2-5 hours later is when I ache everywhere and get tired and non-functional. The 2-5 hours I’m presuming is from some dysbiosis but right away is a little more puzzling.
I clearly have such bad digestion that it is not hard to imagine it is perpetuating my brain / eye / POTS symptoms. I’ve tried everything under the sun, mainstream and holistic and nothing that is supposed to help the gut helps. I think fasting gives me some relief but is not practical for someone so underweight.
My first thryve was on January 13, 2020.
My most recent thryve (now ombre) was October 2, 2022.
In between the two times I’ve cycled through several gut protocols, such as taking s boulardii, soil probiotics, bifidobacteria, sourkraut, and polyphenols. Other times I tried a more killing oriented protocol with oregano oil, berberine, and once based on a stool test a prescription antifungal (sporonox). I eat a very restricted diet and seem to react to pretty much every food, but I have cycled through different foods in the last couple years. I’ve tried prebiotics like PHGG and lactulose recently and are finding at least in the short term I am losing weight and have worse neuro symptoms.
My digestion and overall symptoms have not really changed between the two times. ombre says I have a quite high microbial diversity score which is surprising because I have a massive history of antibiotics.
The request
First Look at the sample
Comparing the samples, I see a much lower quality report (2.5) in 2020. It was interesting to see
Bacteria Over numbers drop despite more bacteria is latest sample
Bacteria Under numbers grew — which may be due to a better quality of sample (more bacteria)
Two of my usual measures showed improvement (despite more bacteria) — Outside Lab Range, Outside Box-Plot-Whiskers while the last one showed an increase which was a smaller percentage than the increase of bacteria reported.
My impression is that objectively he appears better than in 2020.
Criteria
Jan-20
Sep-22
Lab Read Quality
2.5
8.5
Bacteria Reported By Lab
442
656
Bacteria Over 99%ile
10
2
Bacteria Over 95%ile
45
10
Bacteria Over 90%ile
88
23
Bacteria Under 10%ile
54
154
Bacteria Under 5%ile
21
94
Bacteria Under 1%ile
6
19
Lab: Thryve
Rarely Seen 1%
5
7
Rarely Seen 5%
28
37
Pathogens
32
32
Outside Range from JasonH
6
6
Outside Range from Medivere
16
16
Outside Range from Metagenomics
10
10
Outside Range from MyBioma
13
13
Outside Range from Nirvana/CosmosId
18
18
Outside Range from XenoGene
9
9
Outside Lab Range (+/- 1.96SD)
27
5
Outside Box-Plot-Whiskers
124
51
Outside Kaltoft-Møldrup
183
239
Condition Est. Over 99%ile
0
0
Condition Est. Over 95%ile
1
0
Condition Est. Over 90%ile
4
0
Enzymes Over 99%ile
12
190
Enzymes Over 95%ile
208
516
Enzymes Over 90%ile
457
585
Enzymes Under 10%ile
59
265
Enzymes Under 5%ile
20
154
Enzymes Under 1%ile
2
20
Compounds Over 99%ile
73
24
Compounds Over 95%ile
264
101
Compounds Over 90%ile
368
172
Compounds Under 10%ile
297
265
Compounds Under 5%ile
225
223
Compounds Under 1%ile
62
165
In terms of bacteria distribution (not “diversity”). we see an abundance of domineering bacteria (90-99) in the earlier sample which flipped to proliferation of weak bacteria (0-9). Have tons of small amounts of bacteria at low levels should result in a good diversity. The over-representation of these nominal bacteria is a concern to me.
His attempts to change was successful. Ideally we can help more change in the desired direction.
Approach
Using PubMed data, nothing stands out and we have a very short list. This simply means that there is not a good match to the conditions reported there. In terms of Dr. Jason Hawrelak Recommendations we are at 89%ile, so generally good. The main items missing the goals by his criteria are: Faecalibacterium prausnitzii, Lactobacillus, Bifidobacerium and Akkermansia.
Given no strong pattern to match against, I will build a consensus fromLab Range, Box-Plot-Whiskers, Kaltoft-Møldrup and Dr. Jason Hawrelak Recommendations
Consensus – similar to a pattern common with ME/CFS patients
Cross validation to the literature on the above (i.e. seeing if any has been documented to help ME/CFS). Since neurological issues were called out (and I had just done another sample with this recommendation, a few more for Hesperidin)
So all of the top suggestions appear to have documented benefits for various subsets of ME/CFS. I use the term subsets because, while similar in some symptoms, there may be a lot of differences.
Looking at this list, we see that he should consider using some of the probiotics he cited in his history: bacillus subtilis, bacillus clausii, bifidobacterium (animalis)lactis, bifidobacterium breve bifidobacterium infantis. We also have 3 lactobacillus which seems to often appear with ME/CFS samples: lactobacillus casei, lactobacillus gasseri and lactobacillus salivarius.
In terms of prebiotics, only chitosan was a positive. Selenium shows up as a strong recommended supplement. See the above download for more details.
Very atypically, KEGG probiotics reports very low recommendation values with E.Coli NOT being on the top of the list. I would keep to the above probiotics and ignore the KEGG list because of the low values.
Going over to the last, experimental, modelled food suggestions, Barley was the sole take. In terms of the consensus report, it’s a toss up with different variation being good to take or to avoid. Checking oats by itself, it’s a significant negative so I would exclude the last item below and suggests barley be considered.
Bottom Line
The top suggestions can all be verified in medical literature as helping ME/CFS and the suggestions are based on this individual’s microbiome — hence patient (and not study group) specific. Hopefully he will try them and in 3-4 months do another sample so we can evaluate the change (for better or worse — I want to learn, not be right).
Because of the weight issue, I would suggest trying Pendulum, the akkermansia probiotic. I noticed that it resulted in weight loss for me and recall that is also reported in the literature.
I am not a licensed medical professional and there are strict laws where I live about “appearing to practice medicine”. I am safe when it is “academic models” and I keep to the language of science, especially statistics. I am not safe when the explanations have possible overtones of advising a patient instead of presenting data to be evaluated by a medical professional before implementing.
I cannot tell people what they should take or not take. I can inform people items that appears to have better odds of improving their microbiome as a results on numeric calculations. I am a trained experienced statistician with appropriate degrees and professional memberships. All suggestions should be reviewed by your medical professional before starting.
I use modelling and various mathematical technique to estimate forecasts when there is no hard data available.
The information below comes from Integrated analysis of gut microbiome and host immune responses in COVID-19 [2022]. While the data comes from COVID patients, there is a good chance that it may apply to other conditions. The items below are for the strongest p-values (most likely). My intent is to add all items with a value with a p Value of 0.05 or less as an experimental page, before creating the page I hope people will find similar studies that can be combined with this data. Please add as comments.
Gut_microbes
Blood_clinical_features
Correlation
Pvalue
Coprococcus_comes
CD8_counts
0.73173549
1.95E-06
Coprococcus_comes
CD3_counts
0.714258257
4.41E-06
Coprococcus_comes
Lymphocytes_counts
0.649787455
5.71E-05
Coprococcus_comes
CD45_counts
0.647009338
6.29E-05
Roseburia_intestinalis
CD8_counts
0.63669604
8.94E-05
Roseburia_intestinalis
CD3_counts
0.619860729
0.00015457
Roseburia_intestinalis
CD45_counts
0.611747625
0.000199038
Streptococcus_oralis
Eosinophil_counts
0.603056198
0.000258997
Gut_microbes
Organ_damage_related_factors
Correlation
Pvalue
Akkermansia_muciniphila
Creatine_kinase_isoenzymes
0.889522704
1.00E-11
Bacteroides_cellulosilyticus
Creatine_kinase_isoenzymes
0.88177523
2.63E-11
Streptococcus_oralis
Gamma_glutamyltransferase
0.788443186
8.39E-08
Akkermansia_muciniphila
Aspartate_Transaminase
0.784368908
1.08E-07
Bacteroides_cellulosilyticus
Aspartate_Transaminase
0.766075518
3.22E-07
Gut_microbes
Cytokines
Correlation
Pvalue
Ruminococcus_gnavus
IL17
0.513431966
0.002652723
Klebsiella_pneumoniae
IFNG
0.484801301
0.004922183
Klebsiella_pneumoniae
IL10
0.431582818
0.01364772
Lachnospira_eligens
IL2
0.393008018
0.026072229
Gut_microbes
Coagulation_factors
Correlation
Pvalue
Enterococcus_durans
APTT
0.358216937
0.044101648
Enterococcus_faecium
APTT
0.357152676
0.044780215
APTT is activated partial thromboplastin time, the time to form blood clots
I started Microbiome Prescription site using data uploads from ubiome, a firm that was founded by a crowdfunding campaign, went to venture capitalists, and went unethical due to pressure from venture capitalists and died. I received over 800 samples processed by ubiome.
Readers started to request the microbiome reports to be processed on the Microbiome Prescription site and I started adding them according to constraints of the reports available. BiomeSight.com, a UK firm, has been the most cooperative. We worked together to allow automatic transfers directly from their web site to the Microbiome Prescription site by using a API.
Xenogene | Metagenómica y Biología Molecular Reports were shared to me. I found that I could do an accurate extract from one of the reports they made available to users. The result was that they became the most comprehensive report as see by the statistics below
There were few uploads because of their higher costs. The report that I used is shown below.
They Changed Their Report
Recently I have had two people trying to upload their reports. The report was different than the above. I asked them to contact Xenogene to get the above; they were not successful. I examined their reports (they were several years apart), and found two different formats, as shown below:
While both give the same information, the structure of the page was different. The report do not give the hierarchy, for example, Eubacteriaceae was found in neither report. I looked for Blautia and could find species and strains — but no total, so you cannot apply Dr Jason Hawrelak criteria.
Summing up all of the species and strains under Blautia does not give a correct total, in some cases the Blautia total will be 2x higher. Why, because many strains and species has not received names and / or “fingerprints”.
Example of the synthesis to higher levels… Issues at the species level and below can be identified
Bottom line: I no longer recommend this lab
Despite these issues, I have updated the import to support both of the above PDF formats and synthesize all of the missing layers of the bacteria hierarchy. The new import should be on line by November 13th.
WARNING: the genus level and above may often be low because of the total synthesis.
I did extract their recommended ranges and added it as an option:
Citizen Science Action
I would suggest emailing them and asking them if they make a CSV file available of the results (including the bacteria NCBI taxon number), if so, can you get a sample. If you do not get a positive results, do a return email asking you to be informed if they change and indicating that you are going to use Ombre or Biomesight instead…… The risk of loosing customers can often change business practice.
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