Backstory

My son is born in 2009 and diagnosed with autism in 2011. When he was 3 months old he has lot of reflux and unable to digest milk always used to throw up and we ended up using antibiotics because of mucus forming issues and at 10 months he had few words.

• And at 18 months he got diagnosis’s of autism and was completely Non-Verbal.
• After removing gluten and dairy from his diet at age 3.5 he started saying words
• he also got diagnosed with Lyme and coinfections like bartonella and Babesia .
• Now he is 11 years still having lot of issues like his weight is just 55 Lbs  he has focus issues and lot/severe OCDs and tantrums and lot of rigidity and not conversational yet ,cognitive issues cannot understand abstract concepts and has lot of echolilia and  no social skills and gets head pain all of a sudden which might be PANS will last for few minutes and will be fine again.
• And he has lot of Gut issues like  failure to thrive even though his diet his healthy he does not gain weight at all and he has leaky gut and always have constipation issues  and poor digestion issues and picky eating and he complaints some times that his stomach hurts and some times his stomach gets very tight like gas forming. And he has brain and Gut inflammation.
• Very recently from couple of months  he started having Acid Reflux issues after eating he will be spitting for an hour as if something is coming back from his stomach. 
  • We also noticed that when ever he eats chicken and eggs he is more constipated. We did the GI work up and everything came up normal except one thing that he does not have enzymes to digest lactose and also we make sure he is not constipated and his bowls are moving everyday with some laxative.

We have two samples for this person, while we will use the last one for suggestions, a comparison may be spark insights.

Basic Analysis

Looking at the two samples, we see that things are very different than with the ME/CFS person in this post. Instead of over representation in rare bacteria, there is over representation in common bacteria (i.e. the bacteria that most people have).

	Earlier	Sample	Latest	Sample
Percentile	Genus	Species	Genus	Species
0 – 9	10	1	7	7
10 – 19	10	9	9	12
20 – 29	6	9	8	13
30 – 39	10	18	7	10
40 – 49	12	9	6	12
50 – 59	12	15	9	18
60 – 69	10	7	8	12
70 – 79	10	16	10	16
80 – 89	25	39	22	38
90 – 99	103	149	40	64
Std Dev	29.31	44.00	10.65	17.61

• Looking at “Potential Medical Conditions Detected” for both samples we see a very long list of candidate conditions for both samples
• For “Bacteria deemed Unhealthy”, again we have some long lists
• For “Dr. Jason Hawrelak Recommendations”, we have the earlier sample at 75%ile and the latest sample at 98.8%ile, i.e. “no issues”
• AI Computer Probiotics.
  • Earlier sample: L. Bulgaricus Probiotic Powder, miyarisan (jp) / miyarisan, PIANETA FARMA/KefiBios were top suggestions by with a low weight (1.0)
  • Later sample: Prescript-Assist®/SBO Probiotic as only suggest and with almost no weight (0.07)
• AI Computed supplements at 10% level: Neither sample had any.

There is the appearance of improvement between the sample. This may be solely due to the changes due to age (18 months between samples), or moving further away from microbiome disruptive events of the past.

Going Forward

We need to go with some caution because the child microbiome is different than an adult’s and most of the data we are using are from adults.

I am going to build the consensus in a slightly different way than usual:

•  Use JasonH (15 Criteria) – 6 bacteria picked
•  Standard Lab Ranges (+/- 2 Std Dev) – 17 bacteria picked
•  Box Plot Whisker – 59 bacteria picked
•  Kaltoft-Moltrup Normal Ranges – 92 bacteria picked
•  Percentile in top or bottom  10 % – 160 bacteria picked
• Canned Autism using U.S. Nation Library of Medicine Data – 8 bacteria picked
• Using Experimental Page using Official Diagnosis Autism only – 9 bacteria picked

Looking at Consensus Items

I scanned the top items and picked items that I suspect will be acceptable, easy to obtain and reasonable cost:

Take / Add to regime

• Herbs (may be added to food, tea or as capsules)
  • neem
  • syzygium aromaticum (clove)
  • thyme (thymol, thyme oil)
  • Ajwain (trachyspermum ammi)
  • ashwagandha (withania somnifera)
  • olea europaea (olive leaf)
• Probiotics (better choices are hard to obtain in the US at reasonable costs)
  • Lactobacillus salivarius
• Diet Style
  • Vegetarians
  • tea
  • rice
  • mastic gum (prebiotic)
  • saccharin
  • stevia
• Vitamins
  • vitamin b3 (niacin)
  • Cyanocobalamin (Vitamin B-12)
  • pyridoxine hydrochloride (vitamin B6)
  • retinoic acid,(Vitamin A derivative)
  • thiamine hydrochloride (vitamin B1)

There were some interesting AVOIDS (very different than ME/CFS people)

Avoid / Remove or Reduce use of

• magnesium (and foods rich in it, like walnuts)
• selenium
• zinc
• Conjugated Linoleic Acid (CLA)
• quercetin
• resveratrol (grape seed/polyphenols/red wine)
• oregano (origanum vulgare, oil) |
• noni
• Ginseng
• ginko
• inulin (prebiotic), jerusalem artichoke (prebiotic), chicory (prebiotic)
• Most probiotics!
• raffinose(sugar beet), lactulose

Seeing lactulose as a very strong to be avoid agrees so much with no tolerance for milk. I checked the antibiotics positive/negative benefit and was actually surprise to see on the positive impact many of the antibiotics used for ME/CFS and Lyme: fluoroquinolone (antibiotic)s, tetracycline (antibiotic)s, minocycline (antibiotic)s with the best one being vancomycin (antibiotic). This was interesting because “Vancomycin is used to treat colitis (inflammation of the intestine caused by certain bacteria) that may occur after antibiotic treatment.”[MedlinePlus]

Questions And Answers

1. Do you mean your current recommendations is not to use any probiotics or use only Lactobacillus salivarius strain of probiotics ?
   1. Only a very small number of probiotics appear to have a positive impact, less than 18. The other 39 came out with a negative effect. You need to read the labels carefully.
2. I also for the earlier sample you mentioned the PDF use of prescript assist soil based probiotic and also lactobacillus bulgaricus (probiotics) and lactobacillus kefiri . I have not used these so now do you think using them might be helpful based on the analysis 
   1. Those are on the recommended list, so YES
3. And based on your analysis what is most pathogenic bacteria that I need to address from the sample which is problematic such that I research and see how to reduce it?
   1. Unlike most people, this child has a huge amount of Lactobacillus bacteria, he has 98% more than anyone else in the database. Clicking on the link above (and those below) are the worst offenders where his levels are higher than 95% of peoples
   2. [Ruminococcus] gnavus, Actinomyces, Bacillus, Dorea, Erysipelatoclostridium ramosum, Shigella (especially Shigella dysenteriae),Streptococcus pyogenes, Streptococcus sanguinis
   3. In the video, I will show how you can find suggestions EXPLICIT for these.
4. What key strains of good bacteria do you think is missing for weight gain or in general ?
   1. Every good strain becomes bad if there are too many of them, for example Lactobacillus above. The microbiome should be viewed as “Yin/Yang” and not good and bad. I really do not have a clean answer for that question.
5. Which Lactobacillus strains does he have has 95% which I need to avoid further is it Lactobacillus Reutri and Lactobacillus Johnson and Lactobacillus planetarium are those the ones which I need to avoid completely to give or any other list?
   1. ALL Lactobacillus are similar with only small changes between them. They are a family. As with human families, they cross support each other. You want to lower all of the Lactobacillus, ideally have no lactobacillus probiotics.
6. Currently I started using sauerkraut , thinking he needs more Lactobacillus strains and I read sauerkraut has lot of different good strains. Would it be still okay to use it?
   1. He DOES NOT need more Lactobacillus strains — he needs a lot less!
   2. In my humble opinion NO. Two main reasons:
      1. You have no idea of which bacteria are in. Commercial versions usually do not list the
         species. On the few that do, it is very questionable if the label is correct.
         ” the species of lactic acid bacteria present in sauerkraut fermentations are more diverse than previously reported and include Leuconostoc citreum, Leuconostoc argentinum, Lactobacillus paraplantarum, Lactobacillus coryniformis, and Weissella sp.” [2007]
         For Weissella, he is at 90%ile — too high. He does not need more
7. Do I need to do anything to reduce Lactobacillus strains that are high?
   1. There is no studies that target explicit strains.
   2. melatonin supplement, B-vitamins reduce it too.
   3. A word of caution here. Are you going to target just one item of concern in several dozens by focusing on this item (with the potential cost of many other things becoming worst); or work from suggestions that are targeted to improve the microbiome as a whole?

In response to question #3, I did a hand picked of all of those over 95%ile on the Health Summary with the results shown below

A short list of Suggestions

To be discussed with family MD before starting

• Antibiotics
  • A course of vancomycin (antibiotic) to start
  • 3 weeks after this course is finished one of (piperacillin-tazobactam or gentamicin)
• Supplements (add one a week for 3 weeks than take 2 weeks off)
  • A baby aspirin once a day — watch especially for any improvement in brain activity
    • He may have a sub-clinical (mild) form of Antiphospholipid syndrome (thick blood) triggered by the microbiome shifts – I am reflecting my own experience here.
  • Vitamins B-3, B-6, B-12
  • N-Acetyl Cysteine (NAC),
• Diet
  • low carbohydrate diet with either (high-saturated fat diet/high beef diet or vegetarians)
    • Avoid magnesium rich foods
    • Use sunflower oil
    • rice
    • cruciferous vegetables (broccoli cabbage)
  • Ample use of the following herbs in cooking, as tea (or as capsules)
    • neem
    • syzygium aromaticum (clove)
    • Sumac(Rhus coriaria)
    • thyme (thymol, thyme oil)
    • Ajwain (trachyspermum ammi)
    • ashwagandha (withania somnifera)
• Probiotics
  • bacillus laterosporus (probiotic) would be the best choice — but finding that may be a challenge
  • REMEMBER he is very high in Lactobacillus and Bifidobacterium — what is in most probiotics…
• Fruit/ Juices
  • cherry
  • lemon
  • blackcurrant
  • strawberry
  • papaya
• Misc
  • melatonin supplement

Items to AVOID (You may wish to read the full list

• sesame cake/meal
• almonds/ almond skins, walnuts
• barley,oat whole grain,bran, wheat, quinoa
• pea (fiber, protein), bean
• fish oil
• apple
• pomegranate
• Kiwifruit
• Goji (berry,juice)
• dates
• corn
• plantain bananas
• Cacao

One of the easiest modern ways to do it, is to download this data as a CSV and save on your smart phone when shopping.

REMINDER: The items indicate odds/confidence in shifting the microbiome is the intended direction. It is NOT how effective it is. Each item in the take likely improves your odds of improving when taken; keep taking items the avoid list — continuing likely increase the odds of not changing.

Short bio: 35yr Male have had ME/CFS for about 7 years, see A review of a ME/CFS Microbiome for prior review plus backstory. This was my review for “A – Thryve:2021-11-21 self” below.

This person has had done three samples, so we will both look at the latest sample and across samples.

• A – Thryve:2021-11-21 self
• B – Thryve:2022-03-15 self (he used the microbiome prescription site himself to get next course adjustment)
• C – Thryve:2022-05-16 self (this review)

The key questions focus on objective improvement and subjective improvement.

General Health Issues

The evenness of Genus and Species across percentile is shown below

	A	A	B	B	C	C
Percentile	Genus	Species	Genus	Species	Genus	Species
0 – 9	11	16	6	9	11	15
19-Oct	12	30	15	30	19	27
20 – 29	19	31	20	24	12	31
30 – 39	18	35	23	45	16	33
40 – 49	16	24	20	37	18	30
50 – 59	21	31	25	45	21	33
60 – 69	18	20	17	30	14	22
70 – 79	16	23	11	28	16	23
80 – 89	5	14	16	24	13	21
90 – 99	3	14	13	20	5	14
Total	139	238	166	292	145	249
Std.Dev.	6.05	7.71	5.72	11.10	4.60	7.02

My reading is that at the Genus level, the microbiome is stablizing. An ideal microbiome would have a Standard Deviation of 0.0 (i.e. the appropriate percentage is in each class). We see for Genus move from 6.0 -> 5.7 -> 4.6. Species have a far greater degree of randomness because may species are not identified, most genus are identified.

Potential Medical Conditions Detected

The count has been similar: A:3 B:6 C:2 with the one items in common being Allergies.

Unhealth Bacteria

The counts were similar between all samples: A:18, B:20, C:21

Dr. Jason Hawrelak Recommendations

We had significant improvement between the first two samples and a slight loss going to the third: A: 56.5%(5) B:95.5% (8) C: 89% (7)

AI Computed Probiotics

AI Suggested Supplements

Using the default 10% level, we found samples A and B only suggested one supplement. C suggested 2 (L-Histidine and manganese). I looked up the item from A and B and saw that it had continued to improve. 🙂

Supplements	A	B	C
beta-alanine	7.3	9.2	17.3

Has there been positive change?

My reading of the above objective numbers is yes in several vectors. There was nothing show a clear negative change. Somethings stayed put — that is fine, it is small steps. As the picture below illustrates, it is not a direct line/tunnel through the mountain ranges of dysbiosis, we have to work our way across passes and valleys.

The “I don’t feel better” quicksand

I have too often seen — especially with people suffering from Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) — patients giving up on a course of action because they reached a point where they may state “I don’t feel better from doing this, so I am changing…”. For these people, this is often caused by several factors:

• They do not remember how they were actually 2 weeks or 2 months ago…
• Their MD have no objective tests to show progress
• They expect significant constant change constantly (they are frustrated waiting for improvement)

Using the microbiome and repeated testing, they can get objective measurement of changes instead of relying on subjective measurement being done under the influence of brain fog with memory problems.

In this person case, we do see objective improvement of the dysbiosis. What about subjective?

“You’re welcome to mention I have noticed improved sleep and lower anxiety despite my good and bad bacteria shifting around “

From the reader

Moving Forward

As reviewed above, we have no KEGG suggested probiotics, but do have these supplements suggested:

• L-Histidine – Percentile: 2.7
• manganese – Percentile: 3.7
• NADH – Percentile: 15.6 (this has been studied for ME/CFS
  • Effect of Dietary Coenzyme Q10 Plus NADH Supplementation on Fatigue Perception and Health-Related Quality of Life in Individuals with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: A Prospective, Randomized, Double-Blind, Placebo-Controlled Trial, 2021
  • Effect of coenzyme Q10 plus nicotinamide adenine dinucleotide supplementation on maximum heart rate after exercise testing in chronic fatigue syndrome – A randomized, controlled, double-blind trial 2015
  • Does oral coenzyme Q10 plus NADH supplementation improve fatigue and biochemical parameters in chronic fatigue syndrome? [2014]
  • Comparison of oral nicotinamide adenine dinucleotide (NADH) versus conventional therapy for chronic fatigue syndrome [2004]
  • Is NADH effective in the treatment of chronic fatigue syndrome? [2000]
  • [Nicotinamide adenine dinucleotide (NADH) in patients with chronic fatigue syndrome] [2010]
  • Therapeutic effects of oral NADH on the symptoms of patients with chronic fatigue syndrome [1999]
  • Chronic lactic acidosis in an adult. A new syndrome associated with an altered redox state of certain NAD-NADH coupled reactions [1970] – this paper was pre ME/CFS existing, but lactic acidosis has been establish as frequently happening with ME/CFS subsequently.

On a personal note, I used NADH during my 1999-2000 relapse (1st time diagnosis). I eventually switched to 400 mg of flushing niacin twice a day (after MD checked my liver function see facts) and have continue to do so (with liver being tested every year).

Getting suggestions based on US National Library of Medicine Studies

As is my pro forma approach, I did each of the following (with number of bacteria picked after):

•  Use JasonH (15 Criteria) – 8
•  Use Medivere (54 Criteria) – 8
•  Use Metagenomics (59 Criteria) – 8
•  Use Nirvana/CosmosId (36 Criteria) – 8
•  Use XenoGene (22 Criteria) – 8
•  Standard Lab Ranges (+/- 2 Std Dev) – 2 (Too High:   Bacteroides clarus, Roseburia hominis)
•  Box Plot Whisker – 39
•  Kaltoft-Moltrup Normal Ranges – 85
•  Percentile in top or bottom 10% 69

The new layout of the consensus page is shown below

My suggestion for 3 probiotics to rotate thru are:

• bifidobacterium animalis lactis (probiotics) – the cheapest source (per BCFU) is Custom Probiotics
• Akkermansia muciniphila (probiotic) – the only source is Pendulum
• Any bacillus only probiotic containing bacillus coagulans (probiotics) and Bacillus clausii (Probiotics)
  • Many possible products, search this page

For more information on probiotics see the bottom section of this recent review.

For supplements, there are only 3 easily accessed items that are positive, everything else is negative impact!!: Ferric citrate (iron supplement), magnesium (commonly used for ME/CFS) and vitamin k2

For other things, see the video or the suggestions on your microbiome.

Bottom Line

You are making objective progress. A word of caution, if some of the items that you are currently taking on the avoid list, slowly remove them by reducing amount and watching for potential adverse effect. Some of the positive objective changes may be due to them (there is a risk of a feedback loop: if you are taking them, they are not needed BUT it you stop taking them, your microbiome may devolve to a state needing them).

Last – Using Symptoms

This is EXPERIMENTAL. It is a thought experiment and I am still learning it’s behavior. For some symptoms it may reduce awesome results, for others it may improve one set of symptoms at a cost of other symptoms getting worst. I picked two of the more unusual symptoms that he had:

• Comorbid: Methylation issues (MTHFR)
• Immune: Chronic Sinusitis

This resulted in this list being selected with a very strong Filter (first time I have seen this)

Rank	Name	Your value	Percentile
class	Flavobacteriia	21	7
order	Chromatiales	21	9.4
order	Flavobacteriales	21	7
order	Marinilabiliales	21	13.5
phylum	Tenericutes	42	9.5
species	Bifidobacterium bohemicum	21	11.8
species	Eubacterium ramulus	8720	95.5
species	Prevotella disiens	946	84.1

With the top suggestions for this small subset being:

Modifier	Confidence
daesiho-tang	0.982
chicory (prebiotic)	0.955
inulin (prebiotic)	0.955
jerusalem artichoke (prebiotic)	0.955  📏
resveratrol (grape seed/polyphenols/red wine)	0.955  📏
glycyrrhizic acid (licorice)	0.509  📏

I would suggest using it to increase the priority of some items that are positive suggestions in the consensus list, I would not go with using this set of suggestions alone.

Questions from Reader

• Ferric Citrate ,  haven’t been able to find this type? Have you seen it anywhere? Also how would one figure out the dose for gut bacteria shifting?
  • I am an ex-science teacher and thus know it more common name, Iron Citrate. Swanson and others sells it.
• Bacillus- taking terraflora , think I’m up to 6 caps. I saw in a study I need to get to 20 !! …I also have prescript on hand BUT that has a lot of other SBO strains. Would you stuck to TERRAflora for now?  
  • I would keep the Prescript Assist on the shelf, and keep to Terraflora, I would keep increasing the dosage every second day until the bottle was finished. I would look around for ones with similar probiotics for the next cycle, for example Youtheory, Spore Probiotic, 6 Billion CFU, 60 Vegetarian Capsules – for two reasons:
    • Cheaper per BCFU (and also higher BCFU per dosage)
    • Different strains often helps because they produce slightly different products
• Miyarisan , I thought I saw this in my results somewhere , maybe it was far down the list…would you save or finish if you had my results?
  • It is on the list, I would finish it before starting the next cycle of probiotics (REMEMBER: we want to be rotating the probiotics – not take them continuously)
    

• Akkermansia – I have 2 bottle of this stuff actually from pendulum . I read you and your wife has taken it. How much did you take or I know it’s a new product but if you’ve seen a study with dosing please let me know. 
  • The one existing study used 10 BCFU/day, and the bottle reads 0.4 gm. Lacking more information, I would just keep to the bottle recommended dosage.
• NADH- I have the flush stuff and cq10? Do you think that combo works or does it have to be Nadh?
  • Personally, I found flush niacin had greater impact and still look forward to my morning flush to get the mind working (it improves oxygen delivery because it’s a vascular dilator). Assuming you can tolerate the flush.

ALWAYS REVIEW WITH YOUR MEDICAL PROFESSIONAL FIRST

This person has limited experience with the microbiome, so the video provides an enriched commentary on this blog post.

Person’s Back Story

• August 30th, 2016 I was in the post office and I got vey light headed and almost fainted. I was never the same. I was very dizzy and extremely lethargic. A brain MRI found a pituitary adenoma which MDs and neurosurgeons said had nothing to do with my symptoms.
• Symptoms were getting worse; head pressure, head tightness, extremely sensitive to sound, sensitive to light, low body temp and resting heart rate of 112. I went on a 25 day course of doxycycline to treat what some thought could have been Lyme disease.
  • This destroyed my already compromised gut. I had my gallbladder out in 2006, h pylori in 2007 and have since had stomach issues.
  • All kinds of additional testing and they could find nothing.
  • Every doctor recommended anti depressants which I refused.
• November of 2016, I started ozone injections directly into the vein.
• I was put on hundreds of supplements for Leaky gut.
• Feb 2017, Neurologist found the brain SPECT scan was not normal. Poor blood flow to certain parts of the brain due to systemic inflammation.
  • I had changed my diet and eliminated gluten entirely.
  • Started coffee enemas a week prior to having these tests done
• New medical professional after reading my labs, she believed 100% I had celiac.
  • I had eliminated all gluten and was also sugar, dairy, soy, grain and nightshade free.
• Started hyperbaric oxygen therapy and completed 45 dives in a hard chamber. I purchased a chamber for home use in August and received in October. I was doing daily dives until I got a sinus infection and got fluid in my ears do I have not dove in weeks.
• I’m scared because I have done so much for my health I don’t understand how I have a fatty liver.
• I am 5’2″ 114 lbs and eat and live so healthy.
• I have a whole house filtration system
• Purchased an infrared sauna in December and use that a couple of times a week. 
• Diagnosed with SIBO in Feb 2018 after breath test at gastroenterologist. 
• I kept going to doctors and they were telling me nothing was wrong.
• I had my gallbladder out in 2006, umbilical hernia in 2007 and h pylori in 2007 treated with triple antibiotic therapy.

And this is the very edited version, lots of specialists (many of whom have written books or have articles published on peer-review journals).

My Blinkered View

I am not a medical professional, I am a data scientist, statistician and software developer (see my Linked In for details). I am also very high function ASD — which gives me the ability to handle massive amounts of data with unbroken focus. The limits of my expertise is with building tools and designing artificial intelligence systems for the microbiome.

I work off the hypothesis that many symptoms and their severity are the results of microbiome dysfunction.

Looking a Potential Medical Conditions — there are definitely major issues, there are mountains of concerning shifts.

And on the normal side of the house, bacteria deemed unhealthy and Jason Hawrelak suggestions appear normal. In other words, it is not your usual case of gut dysbiosis. Rare bacteria are over represented as shown below. This will create some challenges, because modification of rare bacteria has very little information.

Looking at the Antibiotics page, we see that her poor response to the antibiotics she was given is reflected in the numbers computed from her microbiome.

Moving forward

Given the high number of unusual bacteria, my prefer start is at the DNA level, i.e. using KEGG data to see if there are deficiencies that can be moderated.

• RETAIL Probiotics is very similar to many people with dysfunction (so much that I keep double checking the computation). I listed the species after so you can better understand what you want in the probiotics)
  • miyarisan (jp) / miyarisan – 907 (clostridium butyricum)
  • enviromedica terraflora sbo probiotic -812 (bacillus clausii,bacillus coagulans, bacillus megaterium, bacillus pumilus, bacillus subtilis)
  • CustomProbiotics.com / L. Plantarum Probiotic Powder -727 (lactobacillus plantarum)
  • perfect pass / perfect pass probiotic bacillus spore (bacillus clausii, bacillus coagulans, bacillus subtilis)
  • Sun Wave Pharma/Bio Sun Instant – 683 (bacillus coagulans, bacillus mesentericus, clostridium butyricum, enterococcus faecalis
  • symbiopharm / symbioflor 1 -681(enterococcus faecalis)
  • CustomProbiotics.com / L. Casei Probiotic Powder – 666 (lactobacillus casei)

• Supplements – this is a much longer list than I usually see. Magnesium and Molybdenum are the my first choice from this list since they are involved in a lot of biological processes.
  • Amylase (Enzyme) – Percentile: 5.7
  • beta-alanine – Percentile: 1.5
  • L-Cysteine – Percentile: 10.4
  • L-glutamine – Percentile: 5.9
  • L-Lysine – Percentile: 3.6
  • L-Proline – Percentile: 5.7
  • L-Threonine – Percentile: 6.5
  • magnesium – Percentile: 1
  • Molybdenum – Percentile: 5
  • NADH – Percentile: 2.8
  • Phytase (Enzyme) – Percentile: 12.7

I will move on to the usual process of generating consensus suggestions. Given the unusualness of this sample, I do not know what to expect. It could be outside of our existing database (the above suggestions was based on DNA and thus we have almost complete coverage).

The top 5 selected 9 bacteria; Standard Lab Ranges came in with a very low (and surprising) 5 bacteria;  Box Plot Whiskers Ranges had lower than usually seen, just 36; Kaltoft-Moltrup Ranges came in with a normal looking 137 bacteria, Filter by 10 percentile came in with a massive 332 bacteria!! Given what we saw above, these unusual atypical results are not surprising.

Looking thru the top consensus suggests, I see

• bacillus subtilis (probiotics)
• bacillus coagulans (probiotics)
• pediococcus acidilactic (probiotic)
• clostridium butyricum (probiotics)
• walnuts – a food very high in magnesium
• Cacao
• avocado peel
• brown rice
• grape polyphenols
• Holy Basil

On the highest avoid list

• Slippery Elm
• glycyrrhizic acid (licorice)
• high red meat diet
• saccharin
• stevia
• l-glutamine – counter indicated to the DNA suggestions above, so I would omit it

There are 568 different items (I downloaded the file and open in Excel). With the exception of l-glutamine, all of the DNA based suggestions were either positive or not found (i.e. no clinical studies using them).

For diet planning, it may be good to write out your weekly supplements, food (including herbs used) and check each against the Excel spreadsheet and make minor changes as appropriate.

Trying the new Experimental Symptom Filtering

This person entered their symptoms, so it is available. If you are not familiar with this process, see this post.

• Symptoms Picked
  • Immune Manifestations: Hair loss
  • Comorbid: Small intestinal bacterial overgrowth (SIBO)
  • Comorbid: High Anxiety
  • Comorbid: Hypothyroidism
  • Neurological-Audio: Tinnitus (ringing in ear)

When I went to the bacteria list, I was impressed by the number of bacteria listed with Weak Association

Rank	Name	Your value	Percentile
clade	Bacteroidetes/Chlorobi group	664840	79.8
clade	FCB group	664840	78.5
class	Bacteroidia	660490	80.3
class	Holophagae	40	61.6
class	Negativicutes	260	0.7
class	Verrucomicrobiae	60	11.9
family	Akkermansiaceae	60	15.9
family	Bacillales Family X. Incertae Sedis	200	28.7
family	Bacteroidaceae	598650	87.7
family	Ectothiorhodospiraceae	10	2.7
family	Holophagaceae	40	62.1
family	Rhodanobacteraceae	10	3
family	Rhodothermaceae	80	30.7
family	Selenomonadaceae	100	25.7
family	Syntrophomonadaceae	10	2.1
family	Veillonellaceae	260	9.3
family	Xanthomonadaceae	20	13.4

Rank	Name	Your value	Percentile
genus	Acetivibrio	150	30.6
genus	Acetobacterium	110	32.3
genus	Akkermansia	60	15.8
genus	Alkaliphilus	80	23
genus	Anaerotruncus	170	20.6
genus	Bacteroides	598650	98.9
genus	Bifidobacterium	440	26.3
genus	Caloramator	30	7.8
genus	Coprobacillus	150	30.6
genus	Coprococcus	3960	28.2
genus	Geothrix	40	62.8
genus	Megasphaera	10	0.7
genus	Peptococcus	200	40
genus	Phocaeicola	310709	96.3
genus	Rothia	10	3.3
genus	Slackia	30	10.6
genus	Thermicanus	20	5.5
genus	Veillonella	20	2

With Expected Association (more restricted criteria to be included, we had a reduced list. (Nothing showed up for Strong)

Rank	Name	Your value	Percentile
family	Rhodanobacteraceae	10	3
family	Selenomonadaceae	100	25.7
family	Verrucomicrobiaceae	60	24.6
genus	Alkaliphilus	80	23
norank	Bacillales incertae sedis	20	4.1
species	Butyrivibrio proteoclasticus	10	3.3

The list of suggestions to take was short (we have limited or no data we have on many of these bacteria).

Modifier	Confidence	Citations
berberine	1	📚
cranberry (flour, polyphenols)	1	📚
fasting	1	📚
quercetin,resveratrol	1	📚
choline deficiency	0.51	📚
PreforPro	0.51	📚
arabinoxylan oligosaccharides (prebiotic)	0.5	📚
bacillus licheniformis,(probiotics)	0.5	📚
barley	0.5  📏	📚
fibre-rich macrobiotic ma-pi 2 diet	0.5	📚
fish oil	0.5	📚
fructo-oligosaccharides (prebiotic)	0.5  📏	📚
cranberry bean flour	0.5	📚

I went back to Weak Association, and the list was very similar.

A trip to the wilderness…

There is a manual “back door” to suggestions when there is no direct clinical study. Clicking on the bacteria listed above takes you to the information page. Note that there is an Interactions with Other Bacteria link.

Clicking on this link, goes to a page showing the estimates for these interaction. On that page, there is a quiet link that we will now use.

For this one, we wish to increase it (in fact for all of them), only one items shows up as increasing for any of them:

• choline deficiency  - i.e. reduce choline in your diet if applicable

All of them have very similar list (likely because they are in the same “bacteria fraternity” )

Bottom Line

At this point, I have covered all of the paths that I prefer to shift the microbiome closer to normal / healthy. I would suggest the person takes this information and development an action plan (diet, supplement changes). As always, it should be reviewed by a medical professional familiar with the patient. After 2-3 months, a new microbiome should be done. I will gladly do a follow up to see how well things work or did not work.
I am interested in learning, not being right!

Now to feedback from this person:

This is too much information!

To prevent people from being overwhelmed, I would suggest working from the DNA suggestions above. The other suggestions have a bias because it is based on the number of studies (and thus popularity with researchers). The DNA suggestions lack this bias, there is a little bias because the bacteria sequenced for DNA are influenced by researchers choices, but the data is reasonably comprehensive.

Probiotics: Which product, dosage, when to take, for how long?

 Q: “Enviromedica terraflora has 3 different sbo probiotics; advanced care, immune and daily. How do I know which one to get?”

A: Compare the contents to the list that it was computed from (click on enviromedica terraflora sbo probiotic to see the bacteria in it) . If all of these produces have the same amount of bacteria/probiotic, then use the one that is best pricing (i.e. BCFU/ $). The bacteria are:

1. bacillus clausii
2. bacillus coagulans
3. bacillus megaterium
4. bacillus pumilus
5. bacillus subtilis

I went to amazon to compare prices:

• Terraflora Advanced Care SBO Probiotic – $54, 1 BCFU per TWO capsules
• Terraflora Daily Care – $43, 1 BCFU per TWO capsules
• Terraflora Deep Immune SBO Probiotic – $51, 1 BCFU per TWO capsules

The daily care is what you want. The other have additional additives which may help or hurt — you need to check each one additives. We are keeping to the least complex route — so go with the Daily Care.

In general, these additives allows firms to upsell to more expensive products (far more than the price of the additives).

Dosages

There is a page with dosages for many supplements and probiotics — based on clinical studies (not what the manufacturer suggests on the bottle). The page is located here. Unfortunately, you will not find the retail product name listed, the list is by the bacteria name in the product.

bacillus clausii
bacillus coagulans – 1050 mg/day [Src]
bacillus megaterium
bacillus pumilus
bacillus subtilis – 1000 – 10,000 MCFU/day [src]

Since two capsules are 1 BCFU (aka 1000 MCFU), I would start a two capsules and every second day increase it by two capsules until you hit 10,000 MCFU (20 capsules!). If you notice changes, then either keep that dosage or step back the dosage. 10BCFU have been explicitly tested for safety [Study]

When to take?

This is a personal opinion, but just before bed time seems best. There are many many opinions out there and no well done studies. Typically there are one of two responses (depending on the person)

• Deep sleep, often with night sweats, as the bacteria interact with your immune system rebuilding itself (i.e. energy is not being directed at your activities, but the immune system) [Taking probiotics at night could make them way more effective. 2019]
• Insomnia — the effect of the probiotics is releasing chemicals causing wakefulness. If this is the case, switch to 1 hr after breakfast.

For how long?

Since probiotics do not persists, often their effect on “bad bacteria” is caused by them producing antibiotic compounds (most of our commercial antibiotics were discovered in bacteria). There are several studies that found that rotating antibiotics is far more effective than keeping to the same one. We should do the same with probiotics. A rule of thumb that I use is simple (and helps with monthly budget), is to do one month or one bottle (which ever comes first) and then move on to a different probiotic. For Terraflora, it’s a 60 count, doing the suggested dosage pattern cited above, it will last just 8 days until the bottle is empty.

For Miyarisan, (🍽️ clostridium butyricum (probiotics)) we have 330 tablets in a bottle. And studies [list] range from 60mg/day to 1050 mg/day. The literature says: 270 mg of butyrate-producing bacteria (Miyairi bacteria) in 9 tablets … so start with 4 capsules and keep increasing every 2nd day. It will take 21 days to get thru a bottle.

CustomProbiotics.com / L. Plantarum Probiotic Powder . This can come as a price shock to many people ($115 for a bottle) but their bottle recommends 0.8g, that is 320 BCFU per day. So one bottle is 62 days at that dosage (suddenly the price/day is similar to the above). The maximum for reference studies is 60 BCFU/day [src], so you go with lower dosage (this is a powder, not capsules). In this case, switch after 3-4 weeks.

Question: Where does this information come from

This was a question from this reader. The short form:

• the US National Library of Medicine (link) and
  • Some 1,845,803 facts were extracted and entered into a database.
• Kyoto Encyclopedia of Genes and Genomes (link)
  • Some 8,052,707 facts were extracted and entered into a database.

This data from used to build a mathematic model of the microbiome, what happens in it and what modifies it.

A longer form can be done as a walk thru:

If you go to the ad-hoc suggestion page, there is a checkbox, “Show links to studies used for suggestions“. Checking this and then asking for suggestions results in the suggestion page showing a 📚

Clicking on this will list off the studies used to make this decision. An example below

What is very different from this versus advice from a MD is extremely simple. A MD may make a decision on typically a dozen facts that stuck in their mind, not the 10 million facts that this program, Artificial Intelligence, considers.

The downside is that a MD will not overwhelm you with information, he may prescribe just one drug or suggest something vague like “eat more fiber”. With this Artificial Intelligence, it will often identify which types of fiber should be eaten and which should be avoided. All of this is based on studies with the where did you get this suggestion from documented and linked to. If you ask a MD, you will be lucky to get a single document and could get an angry MD because asking for documentation could cause him offense.

Bottom line, you are investing in your body, similar to investing in the stock market. You are told to invest in tech stocks — so you buy some bit-coin stock…. and discover that you are worth a lot less (looking at recent history), or you start wading thru the various stocks and reading opinions for each, and likely make better choices and have a healthy collection of stocks (or body). There is no easy route for investing in either the stock market or your body (unfortunately).

Citations Found – Note: Subsidized 16s Test Kits may be available
Reversion of Gut Microbiota during the Recovery Phase in Patients with Asymptomatic or Mild COVID-19: Longitudinal Study. Microorganisms (Microorganisms ) Vol: 9 Issue 6 Pages: Pub: 2021 Jun 7 Epub: 2021 Jun 7 Authors Kim HN , Joo EJ , Lee CW , Ahn KS , Kim HL , Park DI , Park SK , Summary
The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort. Gut microbes (Gut Microbes ) Vol: 13 Issue 1 Pages: 1-15 Pub: 2021 Jan-Dec Epub: Authors Newsome RC , Gauthier J , Hernandez MC , Abraham GE , Robinson TO , Williams HB , Sloan M , Owings A , Laird H , Christian T , Pride Y , Wilson KJ , Hasan M , Parker A , Senitko M , Glover SC , Gharaibeh RZ , Jobin C , Summary
Gut Microbiota May Not Be Fully Restored in Recovered COVID-19 Patients After 3-Month Recovery. Frontiers in nutrition (Front Nutr ) Vol: 8 Issue Pages: 638825 Pub: 2021 Epub: 2021 May 13 Authors Tian Y , Sun KY , Meng TQ , Ye Z , Guo SM , Li ZM , Xiong CL , Yin Y , Li HG , Zhou LQ , Summary
Temporal association between human upper respiratory and gut bacterial microbiomes during the course of COVID-19 in adults. Communications biology (Commun Biol ) Vol: 4 Issue 1 Pages: 240 Pub: 2021 Feb 18 Epub: 2021 Feb 18 Authors Xu R , Lu R , Zhang T , Wu Q , Cai W , Han X , Wan Z , Jin X , Zhang Z , Zhang C , Summary
16S rRNA gene sequencing of rectal swab in patients affected by COVID-19. PloS one (PLoS One ) Vol: 16 Issue 2 Pages: e0247041 Pub: 2021 Epub: 2021 Feb 17 Authors Mazzarelli A , Giancola ML , Farina A , Marchioni L , Rueca M , Gruber CEM , Bartolini B , Ascoli Bartoli T , Maffongelli G , Capobianchi MR , Ippolito G , Di Caro A , Nicastri E , Pazienza V , INMI COVID-19 study group. , Summary
Alterations of the Gut Microbiota in Patients with COVID-19 or H1N1 Influenza. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America (Clin Infect Dis ) Vol: Issue Pages: Pub: 2020 Jun 4 Epub: 2020 Jun 4 Authors Gu S , Chen Y , Wu Z , Chen Y , Gao H , Lv L , Guo F , Zhang X , Luo R , Huang C , Lu H , Zheng B , Zhang J , Yan R , Zhang H , Jiang H , Xu Q , Guo J , Gong Y , Tang L , Li L , Summary
Gut Microbiota Interplay With COVID-19 Reveals Links to Host Lipid Metabolism Among Middle Eastern Populations. Frontiers in microbiology (Front Microbiol ) Vol: 12 Issue Pages: 761067 Pub: 2021 Epub: 2021 Nov 5 Authors Al Bataineh MT , Henschel A , Mousa M , Daou M , Waasia F , Kannout H , Khalili M , Kayasseh MA , Alkhajeh A , Uddin M , Alkaabi N , Tay GK , Feng SF , Yousef AF , Alsafar HS , Summary
Gut microbiota dynamics in a prospective cohort of patients with post-acute COVID-19 syndrome. Gut (Gut ) Vol: Issue Pages: Pub: 2022 Jan 26 Epub: 2022 Jan 26 Authors Liu Q , Mak JWY , Su Q , Yeoh YK , Lui GC , Ng SSS , Zhang F , Li AYL , Lu W , Hui DS , Chan PK , Chan FKL , Ng SC , Summary
Alterations in microbiota of patients with COVID-19: potential mechanisms and therapeutic interventions. Signal transduction and targeted therapy (Signal Transduct Target Ther ) Vol: 7 Issue 1 Pages: 143 Pub: 2022 Apr 29 Epub: 2022 Apr 29 Authors Wang B , Zhang L , Wang Y , Dai T , Qin Z , Zhou F , Zhang L , Summary
Alterations in Gut Microbiota of Patients With COVID-19 During Time of Hospitalization. Gastroenterology (Gastroenterology ) Vol: 159 Issue 3 Pages: 944-955.e8 Pub: 2020 Sep Epub: 2020 May 20 Authors Zuo T , Zhang F , Lui GCY , Yeoh YK , Li AYL , Zhan H , Wan Y , Chung ACK , Cheung CP , Chen N , Lai CKC , Chen Z , Tso EYK , Fung KSC , Chan V , Ling L , Joynt G , Hui DSC , Chan FKL , Chan PKS , Ng SC , Summary
Alterations in Fecal Fungal Microbiome of Patients With COVID-19 During Time of Hospitalization until Discharge. Gastroenterology (Gastroenterology ) Vol: 159 Issue 4 Pages: 1302-1310.e5 Pub: 2020 Oct Epub: 2020 Jun 26 Authors Zuo T , Zhan H , Zhang F , Liu Q , Tso EYK , Lui GCY , Chen N , Li A , Lu W , Chan FKL , Chan PKS , Ng SC , Summary
Challenges in the Management of SARS-CoV2 Infection: The Role of Oral Bacteriotherapy as Complementary Therapeutic Strategy to Avoid the Progression of COVID-19. Frontiers in medicine (Front Med (Lausanne) ) Vol: 7 Issue Pages: 389 Pub: 2020 Epub: 2020 Jul 7 Authors d`Ettorre G , Ceccarelli G , Marazzato M , Campagna G , Pinacchio C , Alessandri F , Ruberto F , Rossi G , Celani L , Scagnolari C , Mastropietro C , Trinchieri V , Recchia GE , Mauro V , Antonelli G , Pugliese F , Mastroianni CM , Summary
It Ain`t Over `Til It`s Over: SARS CoV-2 and Post-infectious Gastrointestinal Dysmotility. Digestive diseases and sciences (Dig Dis Sci ) Vol: Issue Pages: Pub: 2022 Mar 30 Epub: 2022 Mar 30 Authors Coles MJ , Masood M , Crowley MM , Hudgi A , Okereke C , Klein J , Summary
Gut Microbiota Disruption in COVID-19 or Post-COVID Illness Association with severity biomarkers: A Possible Role of Pre / Pro-biotics in manipulating microflora. Chemico-biological interactions (Chem Biol Interact ) Vol: 358 Issue Pages: 109898 Pub: 2022 May 1 Epub: 2022 Mar 21 Authors Alharbi KS , Singh Y , Hassan Almalki W , Rawat S , Afzal O , Alfawaz Altamimi AS , Kazmi I , Al-Abbasi FA , Alzarea SI , Singh SK , Bhatt S , Chellappan DK , Dua K , Gupta G , Summary
The significance of the gut microbiome in post-COVID-19 gastrointestinal symptoms. Clinical medicine (London, England) (Clin Med (Lond) ) Vol: 22 Issue 2 Pages: 189-190 Pub: 2022 Mar Epub: Authors Lampejo T , Summary
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Respiratory dysfunction three months after severe COVID-19 is associated with gut microbiota alterations. Journal of internal medicine (J Intern Med ) Vol: 291 Issue 6 Pages: 801-812 Pub: 2022 Jun Epub: 2022 Mar 17 Authors Vestad B , Ueland T , Lerum TV , Dahl TB , Holm K , Barratt-Due A , Kåsine T , Dyrhol-Riise AM , Stiksrud B , Tonby K , Hoel H , Olsen IC , Henriksen KN , Tveita A , Manotheepan R , Haugli M , Eiken R , Berg Å , Halvorsen B , Lekva T , Ranheim T , Michelsen AE , Kildal AB , Johannessen A , Thoresen L , Skudal H , Kittang BR , Olsen RB , Ystrøm CM , Skei NV , Hannula R , Aballi S , Kvåle R , Skjønsberg OH , Aukrust P , Hov JR , Trøseid M , NOR-Solidarity study group. , Summary
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This sample reminds me of an earlier sample that was similar frustratingly normal looking despite the person having significant issues. That person went with the suggestions that I could muster for 2 months and then did another sample. His symptoms improved slightly AND the microbiome because usefully abnormal. I am hoping that will be the case with this person.

In terms of mathematic models, the person’s microbiome seems to be on an infection point. The diagram below illustrates this concept with the blue line indicating recovery.

Back Story

• I’m 33 years old and I have been sick for my last 12 years.
• I suffer from:
  • Multiple chemical sensitivity,
  • Gut issues,
  • Severe insomnia,
  • Loss of collagen in joints and muscle
  • along many others.
• The 1000 doctors that I have visited in Spain never had much idea.
• The OAT test says bad methylation but i don’t know how to interpreted it or what to do, nor my doctors.
• I’ve already doing all the basics, no gluten, cow dairy, processed foods etc.
• I can’t eat much but I eat fish, meat and some very cooked tomato and cauliflower.
• I was diagnosed with Giardia but it was not treated because I did not have diarrhea or constipation.
• I feared the antibiotics causing candida issues. In other test more recent didnt show up but i think was another method of testing

Analysis

See the YouTube for more information and walk thru. Note: Giardia has a high incidence of evolving into chronic microbiome dysfunction (treated or untreated), see this post.

Using Health Analysis Page

• Health Status – 1 Healthy, 7 Unhealthy
• Jason Hawrelak – at 99%ile , no significant issues
• Potential Medical Conditions showed only hypersomnia, the opposite of what is being experienced

Looking at Unhealthy Bacteria, one caught my eye: Rickettsia (i.e. any of the spotted fevers, including Mediterranean Spotted Fever – Boutonneuse Fever). I would suggest getting tested for spotted fevers.

First Probiotics

I am finding that this is a friendly start point because we have multiple logics available to determine them (which, of course, can result in disagreement). To my surprise, nothing showed up – it appears that the collection of bacteria where outside of expected/supported species! (I spent a couple of hours verifying that if was not a coding error). Similar for using symptoms with KEGG Enzymes. This was totally unexpected and a little concerning (both in terms of this person’s microbiome as well as what the site is able to handle). Fortunately, we have the other logic that produces results

The top probiotic suggestions in my view are just two:

• mutaflor escherichia coli nissle 1917 (probiotics) (which is available in Spain 🙂 )
• lactobacillus bulgaricus (probiotics) – typically in many yogurt. NOTE: Mutaflor and this should NOT be taken at the same time, they are hostile to each other. Alternate each one week )

Consensus Report

As has become my custom, I whipped thru all of the suggestions using expert criteria.

•  Use JasonH (15 Criteria) – 5 matches
•  Use Medivere (54 Criteria) – 5 matches
•  Use Metagenomics (59 Criteria) – 5 matches
•  Use Nirvana/CosmosId (36 Criteria) – 5 matches
•  Use XenoGene (22 Criteria) – 5 matches
•  Standard Lab Ranges (+/- 2 Std Dev) – 40 matches (5%_)
•  Box Plot Whisker – 68 matches (9%)
•  Kaltoft-Moltrup Normal Ranges – 70 matches (9%)
•  Percentile in top or bottom 10%ile – 134 matches (18%)

Looking at the consensus number of suggestions for the above, the numbers were similar, suggesting that despite the differences number of bacteria selected, the suggestions were likely similar.

Takes

My personal pick of the top suggestions are below (excluding probiotics cited above):

• oolong teas, green tea
• Cranberry
• Cacao
• lard (instead of butter etc)
• herbs:
  • grape seed extract, red wine polyphenols
  • hypericin(St. John’s Wort)
  • nigella sativa seed (black cumin)
  • oplopanax horridus(Devil’s Club)
  • selenium

Avoids

The following are items that are highest concern in my opinion

• Slippery Elm,
• garlic (allium sativum)
• lauric acid(fatty acid in coconut oil,in palm kernel oil,)
• high-saturated fat diet
• probiotics to avoid:
  • bifidobacterium longum bb536 (probiotics)
  • lactobacillus reuteri (probiotics)
  • saccharomyces boulardii (probiotics)
  • lactobacillus rhamnosus gg (probiotics)
  • lactobacillus gasseri (probiotics)
  • Lactobacillus salivarius

Number of suggests from best take to worst avoid (139, 53, 40, 116, 25, 63)

The land of Supplements

We only have consensus report producing examples. There was very few items that occurred in more than 1 or 2 suggestions. The best of a poor situation were:

• selenium
• vitamin d
• zinc
• thiamine hydrochloride (vitamin B1)
• vitamin b7 biotin (supplement) (vitamin B7)

Definitely avoid the following

• Lithium
• Vitamin B (complex)
• vitamin b2(Riboflavin)
• Vitamin E
• vitamin a

In general, the rest of vitamins and minerals were too close to come to a conclusion for. In that situation, I would suggest avoiding instead of rolling dice.

Supplemental Information

The reader also provided an OATS test done by Teletest Lab Analisis(laboratory@teletest.es) in Spain (and in Spanish). Abnormal values were (with links to Spanish Wikipedia)

• α-ketoglutaric acid: low
• Indole-3-butyric acid: high
• Methylmalonic acid: low
• Quinolinic acid low
• 5-Hydroxyindoleacetic Acid: low

Post Script

I’ve been prescribed rifaximin + boulardii based on symptoms only. Ive been told is.”” Good antibiotic”” 

Feedback

We were not as lucky with saccharomyces boulardii (probiotics) which has a 1:3 ratio between take and avoid. I would suggest doing Rifaximin without the boulardii, after the course is finished — give it a try in isolation. Doing both at the same time will generate confusion over the cause of improvement or deterioration. As always, discuss with your MD before doing.

Bad methylation

This was reported from the oats test. “The OAT assesses organic acid markers which indicate methylation status through the crucial cofactors ie B12, folate B9, B6. One of the most sensitive markers for vitamin B12 deficiency is methylmalonic acid and kynurenate is a reliable marker for B6 status.” [Src]

• On safer takes are Cyanocobalamin (Vitamin B-12) and pyridoxine hydrochloride (vitamin B6), with folic acid,(supplement Vitamin B9) being a slight avoid. I would suggest that methylcobalamin, ( methyl B12) as well as methylated B6 be considered over the usual forms.

Few medical professionals are aware of the microbiome side-effects of the medications they prescribe. As a result of exchanges with a user about to be prescribed antibiotics based on a positive Lyme test, I created here 2 pages intended for you to share with your Medical Professional.

The Antibiotic Page

Drugs Page

Today I had a long Zoom call with someone that we hope to cooperate with for Long COVID. She mentioned that one species of probiotics works very well for some people with long COVID and it’s sibling do not. I explained that my working hypothesis is that a lot of interactions depends on the enzymes.

This resulted in us doing a quick lookup experiment using Microbiome Prescription databases.

• Bifidobacterium adolescentis is what worked well. I looked up what enzymes it had, 469
• Then I removed those that are also found in Bifidobacterium animalis subsp. lactis, that left 51 that was only in Bifidobacterium adolescentis
• Removed those also found in Bifidobacterium breve dropping the count to 28
• Removed those also found in Bifidobacterium longum subsp. infantis dropping the count to 17
• Removed those also found in Bifidobacterium longum dropping the count to 15
• Removed those also found in Bifidobacterium bifidum dropping the count to 13 unique enzymes not in the sibling strains.

I kept to only the probiotics that are retail available.

This hints that the reason that it works is due to the following enzymes (linked to Kyoto Encyclopedia of Genes and Genomes):

• sorbose reductase;Sou1p
• coenzyme F420 hydrogenase;8-hydroxy-5-deazaflavin-reducing hydrogenase;F420-reducing hydrogenase;coenzyme F420-dependent hydrogenase
• opine dehydrogenase;(2S)-2-{[1-(R)-carboxyethyl]amino}pentanoate dehydrogenase (NAD+, L-aminopentanoate-forming)
• homocysteine S-methyltransferase;S-adenosylmethionine homocysteine transmethylase;S-methylmethionine homocysteine transmethylase;adenosylmethionine transmethylase;methylmethionine:homocysteine methyltransferase;adenosylmethionine:homocysteine methyltransferase;homocysteine methylase;homocysteine methyltransferase;homocysteine transmethylase;L-homocysteine S-methyltransferase;S-adenosyl-L-methionine:L-homocysteine methyltransferase;S-adenosylmethionine-homocysteine transmethylase;S-adenosylmethionine:homocysteine methyltransferase
• lysyltransferase;L-lysyl-tRNA:phosphatidylglycerol 3-O-lysyltransferase
• cellobiose phosphorylase
• diacylglycerol kinase (ATP);diglyceride kinase (ambiguous);1,2-diacylglycerol kinase (phosphorylating) (ambiguous);1,2-diacylglycerol kinase (ambiguous);sn-1,2-diacylglycerol kinase (ambiguous);DG kinase (ambiguous);DGK (ambiguous);ATP:diacylglycerol phosphotransferase;arachidonoyl-specific diacylglycerol kinase;diacylglycerol:ATP kinase;ATP:1,2-diacylglycerol 3-phosphotransferase;diacylglycerol kinase (ATP dependent)
• beta-glucoside kinase;beta-D-glucoside kinase (phosphorylating)
• sulfur carrier protein ThiS adenylyltransferase;thiF (gene name)
• allantoinase
• 5-oxoprolinase (ATP-hydrolysing);pyroglutamase (ATP-hydrolysing);oxoprolinase;pyroglutamase;5-oxoprolinase;pyroglutamate hydrolase;pyroglutamic hydrolase;L-pyroglutamate hydrolase;5-oxo-L-prolinase;pyroglutamase
• glutamate decarboxylase;L-glutamic acid decarboxylase;L-glutamic decarboxylase;cysteic acid decarboxylase;L-glutamate alpha-decarboxylase;aspartate 1-decarboxylase;aspartic alpha-decarboxylase;L-aspartate-alpha-decarboxylase;gamma-glutamate decarboxylase;L-glutamate 1-carboxy-lyase
• sirohydrochlorin cobaltochelatase;CbiK;CbiX;CbiXS;anaerobic cobalt chelatase;cobaltochelatase [ambiguous];sirohydrochlorin cobalt-lyase

In theory, the 13 items above may be excellent candidates for novel pharmaceuticals to be trialed for treating long COVID.

This same approach may be done with other conditions and probiotics. By trials identify which probiotics have the most impact, use the same approach to identify possible enzymes causing the difference, then do a clinical trial.

This blog is using reports from NirvanaBiome for three members of a family. NirvanaBiome use CosmosID for processing.

In this analysis we have people from the same family, implies DNA and inherited microbiome are similar.

• A 10 y.o. son who has ASD/ADHD.
  • Eats various meats, dairy, grains, some beans, and a limited variety of vegetables and fruit. 
• A 7 y.o. daughter who has been battling constipation for a little over a year now and had some sort of traveler’s diarrhea back in 2017 from which her GI system never seemed to fully recover IMO.
  • She’s a very picky and self-limited eater.  Refuses to eat any meat, but she does consume dairy in the form of yogurt and cheese and ice cream.  Most of her diet is some form of processed carb, and the only fruits and vegetables she consumes are in the form of vegetable powders – potato starch based vegetable chips, granola bars with vegetable powder in them, fruit and vegetable powder added to pancakes, etc.  She will eat fruit pouches that contain peach, apricot and banana, and she will sometimes eat fresh broccoli, cauliflower, some hummus and red lentil pasta..  She will drink a whey protein drink , and mother adds pea protein powder to things like pancakes as well. 
• The mother diet is similar to the son’s diet

Analysis

Before getting to suggestions, I want to use the available information to understand better the three microbiome, especially since two are children. Children have a different microbiome than adults. Caution has to be taken with any data of children — we do not know what “normal” is because studies are rarely age specific.

• Aging progression of human gut microbiota [2019]
• The microbiome: An emerging key player in aging and longevity [2020]
• Unique gut microbiome patterns linked to healthy aging, increased longevity [2021]
• “We show that disease-microbiome associations display specific age-centric trends.” [2020]

I first look at clustering of bacteria, looking at bacteria in common to all three using percentiles. The number of bacteria that had readings very close to each other was shockingly high, far more than I had expected.

Bacteria Name	Rank	Son	Mother	Daughter
Ruminococcus lactaris	species	92.4	93.7	93.5
Oscillibacter ruminantium	species	81.5	83.6	83.3
Alistipes indistinctus	species	79.5	76.8	80.2
Faecalibacterium	genus	25.4	27.9	29
[Bacteroides] coagulans	species	41.4	44.7	41.1
Hungatella	genus	0.2	4	4
Porphyromonadaceae	family	20.4	16.3	20.8
Adlercreutzia equolifaciens	species	95	98	92.8
Bifidobacterium catenulatum	species	95.4	99.2	93.9
Ruminococcaceae bacterium CC59_002D	strain	88.9	94.4	94.4
Aminicella	genus	90.6	85.4	91.2
Salinispirillum marinum	species	34.2	30.9	37.5
Eubacteriaceae	family	61.8	66.2	58.8
CCUG 54292	species	67.3	59.6	67.3
Eubacterium ruminantium	species	57.8	54.4	62.1
Eubacterium	genus	58.9	63.5	55.8
Burkholderiales	order	18.2	25.9	22.2
Fibrobacteria	class	18.3	26.1	22.5
Bifidobacterium pseudocatenulatum	species	87.2	93.8	86
Coprococcus catus GD/7	strain	37.5	33.3	29.2
Sutterellaceae	family	19	16.3	24.7
Clostridium sp.	species	79.4	76.7	85.2

The amount of similarity caused me to want to cross check that this pattern is actually there and not the result of randomness.

Is this “seeing things” in the data or Seeing things?

I grab three other samples from different people who used CosmosId and plotted the difference between bacteria that were share in common. The number of bacteria in common with the family is 2.3x more than a random sample. Remember that many families will be found in almost all samples.

Filtering on species, results in a more dramatic change, with 2.68x more in common. Moving down to strains, it increased further to 3.64x more in common.

The shared diet, living space and DNA clearly results in a “family microbiome” pattern. It would be interesting to do an analysis of some couples that have lived together for at least 10 years (any volunteers?)

We will be using this shared pattern for a customized analysis. It may allow us to better isolated what may be contributing to the two issues cited above (and ignore items that may be high or low compared to the general population)

Identifying Probable Age related items

The microbiome changes with age, and for a number of bacteria we see what appear to be an age based signature.

Given that two are children and one is an adult, we can use how the microbiome changes with age to explain more of the results. The mother is either significantly higher to the levels seen by the kids, or significantly lower.

Bacteria Name	Rank	Son	Mother	Daughter
Rhodocyclaceae	family	0.3	10.8⬆️	3.5
Lactobacillaceae	family	6.4	12.5⬆️	2.4
Fibrobacteres	phylum	5.1	16.3⬆️	7.5
Varibaculum cambriense	species	3.5	16.6⬆️	8.8
Clostridium clostridioforme	species	0	11.3⬆️	3.8
FCB group	clade	8.7	19.2⬆️	4.7
Bacteroidetes/Chlorobi group	clade	8.2	19.1⬆️	4.2
Bacteroidetes	phylum	7.2	18.3⬆️	2.8
Tyzzerella	genus	0.7	17.3⬆️	3
Fusobacterium	genus	3	17.1⬆️	0.5
Bacteroidetes	class	7.3	20.2⬆️	3
Bacteroidales	order	7.3	20.2⬆️	3
Faecalibacterium prausnitzii (Hauduroy et al. 1937) Duncan et al. 2002	species	22	40.1⬆️	21.1
Corynebacteriaceae	family	9.2	21.3⬆️	1.6
Caseobacter	genus	9	21.4⬆️	1.6
Christensenella	genus	69.4	90.3⬆️	68.2
Christensenellaceae	family	66.4	88.9⬆️	65.2
Fibrobacteria	class	18.3	26.1⬆️	22.5
Bacteroides rodentium	species	3.8	28.1⬆️	5.4
Bryantella formatexigens	species	5.4	28.8⬆️	0.7
unclassified Erysipelotrichaceae (miscellaneous)	no rank	28.8	5.8👇	34.6
Lachnospira	genus	3.2	30.3⬆️	1
Parabacteroides distasonis CL09T03C24	strain	70	40👇	70
Ruminococcus gnavus	species	60.8	30.7👇	60.7
Desulfovibrionaceae	family	27.5	58.1⬆️	31.9
Desulfovibrionales	order	27.3	58⬆️	31.8
Phocaeicola	genus	57.6	25.6👇	55.3
Eubacterium hallii	species	58.4	90.5⬆️	69.8
Butyrivibrio	genus	9.2	36.9⬆️	4.2
Intestinimonas	genus	26.3	6.4👇	46.5
Bilophila	genus	31	71.⬆️1	37.5

The kids have two different issues:

• ASD/ADHD
• Constipation

If there was a third normal child in the same age range, picking bacteria would likely be trivial. What we have are just the difference. We do not know if having higher or lower is the cause of the issue. What we do have are bacteria to research and the mother.

Bacteria Name	Rank	Son	Mother	Daughter
Actinobaculum	genus	84.4	29.9	4.5👇
Actinomadura	genus	36.9	26.2	0.1👇
Agathobaculum	genus	0.7	1.4	21.7⬆️
Alistipes	genus	77.4	96.9	35.6👇
Clostridioides	genus	81.3⬆️	24.4	35.6
Coprobacillus	genus	81.3⬆️	4	0.7
Discomyces	genus	4.8👇	93.9	42.5
Dorea	genus	75.3	98.9	20.1👇
Eggerthella	genus	95.8⬆️	46	21.7
Erysipelatoclostridium	genus	0.8👇	9.4	6.1
Escherichia	genus	32.5👇	70.8	61.8
Flavonifractor	genus	0.1👇	15.4	20.4
Holdemania	genus	12.1👇	17.9	21.5
Intestinibacter	genus	26.8	6	58.3⬆️
Lactobacillus	genus	20.4	29.9	11👇
Oscillibacter	genus	44.7	43.5	80.3⬆️
Pseudoflavonifractor	genus	0.3👇	47.7	40.8
Roseburia	genus	4.7	28.7	57.7⬆️
Ruminococcus	genus	3.7👇	95.4	37.9
Streptococcus	genus	83.3⬆️	69.1	2.6
Subdoligranulum	genus	37.2	47.9	74.2⬆️
Veillonella	genus	0.4👇	14.9	9.4

Looking at US Library of Medicine studies on ADHD, we have the following matches for the son:

• Alistipes (NCBI:239759 )
• Eggerthella (NCBI:84111 )
• Ruminococcus (NCBI:1263 )

Looking at Autism

• Alistipes (NCBI:239759 )
• Dorea (NCBI:189330 )
• Escherichia (NCBI:561 )
• Flavonifractor (NCBI:946234 )
• Lactobacillus (NCBI:1578 )
• Roseburia (NCBI:841 )
• Ruminococcus (NCBI:1263 )
• Veillonella (NCBI:29465 )

Nine shifts appear to match studies reported for the son.

Shifting to the daughter for constipation (using Functional constipation / chronic idiopathic constipation), we have just one

• Ruminococcus (NCBI:1263 )

It is important to remember that the studies being referred to, were done on adults usually.

I was curious about Actinomadura because of the differences. It appears to occur in about 3% of samples, hence to get a reasonable sample to get relationships from, a clinical study would need to have 30/3% = 1000 participants and use a 16s processor that detects this bacteria (many do not). Worst yet, because of this rarity, we know of nothing that impacts it.

What to do when there is no information on changing a bacteria!!!

This actually opens the door to using bacteria-to-bacteria associations. We have 111 of them!

Looking at one with the highest positive associations, Desulfofarcimen, we see some items that will increase this bacteria (and by increasing that bacteria, Actinomadura should increase): cranberry polyphenols, Goji (berry,juice), walnuts, saccharin. Using all of the 111 interactions, we found only one thing that shows up as increasing Actinomadura (and many things to decrease), choline deficiency (i.e. reduce choline in diet). Items to avoid would be:

• jatropha curcas linn. (euphorbiaceae)
• nigella sativa seed (black cumin)
• oplopanax horridus(Devil’s Club)
• hypericin(St. John’s Wort)
• kefe cumin (laser trilobum l.)
• foeniculum vulgare (Fennel)
• lactobacillus bulgaricus (probiotics)

The only likely item would be yogurt containing lactobacillus bulgaricus).

Fortunately, most of the bacteria at the genus level has some studies on them.

Symptom Prediction

This is from binary logistic regression which I have been working on but have not released. I picked the symptoms that appear viable for the reported issues. This is problematic because the regression was trained on adult data and not children — this is a mere exploration

The higher the number, the more likely, the lower the number the less likely.

SYmptomName	Son	Mother	Daughter
Neurological: Short-term memory issues	-1.8	-4.0	-2.5
Neurological: Disorientation	-5.1	-7.2	-6.6
Immune Manifestations: Constipation	0.5	-0.2	1.2
Neurological: High degree of Empathy before onset	-5.6	-45.7	-18.4
Comorbid: Small intestinal bacterial overgrowth (SIBO)	-3.4	1.1	-3.9
Asymptomatic: Live in house with person with probable microbiome dysfunction	-7.2	1.5	-11.2
Neurocognitive: Difficulty paying attention for a long period of time	0.7	0.3	-0.3
Neurocognitive: Can only focus on one thing at a time	0.0	-4.5	-3.6
Autism: Official Diagnosis	-1.8	-3.8	-2.5
Comorbid: Constipation and Explosions (not diarrohea)	0.9	– ∞	1.7
Comorbid: Constipation and Diarrohea (not explosions)	-2.4	0.3	-0.5

The son is the most probable for:

• Autism: Official Diagnosis
  • Neurological: Disorientation
• Neurocognitive: Difficulty paying attention for a long period of time (i.e. ADHD)
  • Neurological: Short-term memory issues
  • Neurocognitive: Can only focus on one thing at a time

The daughter is the most probable for:

• Immune Manifestations: Constipation
  • Comorbid: Constipation and Explosions (not diarrohea)

The mother is most probable for:

• Asymptomatic: Live in house with person with probable microbiome dysfunction
• Comorbid: Small intestinal bacterial overgrowth (SIBO)
• Comorbid: Constipation and Diarrohea (not explosions)

While we had regression-training issues, using the “in the same microbiome family” comparison approach, the prediction largely modelled the actual symptoms reported.

Suggestions

For Daughter

The daughter is the most challenging — only one match to PubMed studies that matches for constipation. I went to the sample, and made sure these two symptoms were marked. Then I went to the new feature:

• #1 is o’donnell / flora-balance containing only bacillus laterosporus or brevibacillus laterosporus
• #2 is Prescript-Assist®/SBO Probiotic
• #3 is bacillus subtilis – which is available in many products
• Others high on the list contains bacillus subtilis

Next I flip over to data from Clinical Studies, The most studied was Lactobacillus rhamnosus GG (i.e. Culturelle®), followed by my old favorite Mutaflor (Escherichia coli strain Nissle 1917) which has limited availability Mutaflor (Canada, Australia, Finland, Germany) with Symbioflor-2 being a good alternative. Remember this is based on number of studies, not effectiveness.

Last, Ruminococcus is a bit of a challenge because both high and low values are associated in the literature — given the age, I deem it not safe to pursue changes in isolation.

Looking at the heath analysis, everything looks good except for high Escherichia coli and Bacteroides fragilis. I suspect bad E.Coli is a factor for the constipation which suggests that the strong good E.Coli in Symbioflor-2 (or Mutaflor) would be beneficial. Using the various expert opinions (remember those are for adults!) we see 8,25, 76, 141 and 172 bacteria being selected.

Going over to consensus, we see the following items outstanding (and likely path of least resistance to the daughter):

• pediococcus acidilactic (probiotic)
• bacillus coagulans (probiotics)
• bifidobacterium longum (probiotics)

And the should-avoid including:

• broccoli
• low energy diet/ calorie restriction
• sorghum

Bottom Line for Daughter

I would be inclined to bacillus subtilis alternating every 2 weeks with bacillus coagulans (probiotics) and bifidobacterium longum (probiotics) as the likely easiest to get. If not sufficient progress, then order Symboflor-2 from Germany (site that ships to the world)

For Son

Doing the same pattern, adding symptoms and then doing KEGG computations for probiotics, we end up with a short list (in order): Prescript-Assist®/SBO Probiotic, enviromedica terraflora sbo probiotic, microbiome labs/ megasporebiotic, o’donnell / flora-balance — not a single lactobacillus or bifidobacterium in the list.

We have a reasonable list of bacteria identified above for Autism and ADHD, so I will run two advance suggestions with 15% selection and US Library of Medicine findings. The results were interesting – there was nothing in common with both sets of suggestions. The top items were:

• arabinoxylan oligosaccharides (prebiotic)
• soy
• inulin (prebiotic)
• lactobacillus plantarum (probiotics)
• lactobacillus rhamnosus gg (probiotics) ** this has been used in 3 studies with positive effects (Effect of probiotic supplementation on cognitive function in children and adolescents: a systematic review of randomised trials.)
• barley

Now over to the canned expert suggestions, Using the various expert opinions (remember those are for adults!) we see 7,10, 66, 121 and 225 bacteria being selected. With the following being good suggestions:

• pediococcus acidilactic (probiotic)
• inulin (prebiotic)
• lactobacillus plantarum (probiotics)
• lactobacillus reuteri (probiotics)
• soy
• Pulses
• high fiber diet

The avoid list top items were

• broccoli
• low energy diet/ calorie restriction
• l-taurine

This is very similar to the daughter and likely reflect the commonality of the microbiome.

The Mother

The meals for the kids are likely good suggestions for the entire family. There are not any active issues with the mother and the commonality of bacteria in all of the microbiome will lead to similar diet. I should mention that alcohol appears on the avoid list (not called out for the kids).

REMINDER

All of these are suggestions coming from mathematical models and not clinical experience. Suggestions should be reviewed by a knowledgeable medical professional before starting.

I am a computer scientist and a statistician. I am not licensed to practice medicine, and where I live has strict laws about ‘appearing to practice medicine’. What I can do for readers is to write a public blog (anonymous) from your data and back story as an education post on using the software and the statistics it produces. I cannot consult. The content should be reviewed by a medical professional before implementing.

This is a follow up to my blog post of Dec 30, 2021. Rosacea, Circulation and mild CFS. The person has tried the suggestions, and now we will attempt to see what the consequences are and the next set of suggestions.

Remember, the suggestions are based on mathematical modelling using clinical studies on study populations, so they may work or not work for individuals.

High Level Measures

• Bacteria Reported
  • Prior: 427
  • Latest: 591 (38% increase in taxonomy)
• Health Status
  • Prior: Healthy 1, Unhealthy 8
  • Latest: Healthy 1, Unhealthy 9
• Dr. Jason Hawrelak Recommendations
  • Prior: 99.7% (effectively excellent!)
  • Latest: 75.3%. What left ideal is below, nothing moved to ideal
    • Bacteroidia went up
    • Bacteroides went up
    • Methanobrevibacter went down
    • Roseburia went down
    • Faecalibacterium prausnitzii still not ideal but went up significantly
• Unhealthy Bacteria: here we had a definite improvement, less ones, lower value
  • Ruminococcus] gnavus dropped off list
  • Anaerotruncus colihominis decreased
  • Bacillus decreased
  • Blautia producta decreased
  • Clostridium decreased
  • Collinsella decreased
  • Corynebacterium dropped off list
  • Dorea decreased
  • Eggerthella lenta dropped off list
  • Legionella drop off list
  • Streptococcus australis decreased
  • Streptococcus vestibularis dropped off list
  • Veillonella atypica joined the list

Bacteria Selected using Expert Criteria

Method	Prior	Latest
Use JasonH (15 Criteria)	5	6
Use Medivere (54 Criteria)	5	6
Use Metagenomics (59 Criteria)	5	6
Use Nirvana/CosmosId (36 Criteria)	5	6
Use XenoGene (22 Criteria)	5	6
Standard Lab Ranges (+/- 2 Std Dev)	8	6
Box Plot Whisker	30	27
Kaltoft-Moltrup Normal Ranges	78	84
Percentile in top or bottom 10 %	63	99

My impression is that the microbiome has become more diverse, in one sense, unstable. The increase in the number of bacteria types reported (591) moved it just above the typical count for BiomeSight (578). My personal experience is that this is a good sign, the microbiome is changing, I experienced this spike is variety before my microbiome settled down into a new, healthier normal.

Symptoms Change

“This things has improved:

• Less bloated
• Seborrhoeic dermatitis is gone 
• Better stool
• Better libido“

Using the regression for all symptoms we had regressions for, we had 154 improved out of 209 items, or 74% had improvement in the prediction of symptoms.

Overall: Appears to be Improved

This person was a challenge originally because there was no dominate shifts or “smoking guns”. Being at the 99+% for Dr. Jason Hawrelak recommendations and the same items returned from other expert suggestions (many with more criteria) had no significant change. Supporting improvement: Increase in bacteria types closer to typical; significant decrease in number of Unhealthy Bacteria; improved symptoms; and last, prediction of symptoms had a major improvement.

Next Round of Suggestions

After the above sample, he actually started two more items:

• 10 days with doxycycline
• started to take rosemary “Feels pretty good taking it. ” 

Probiotics

There are many Ways of Choosing Probiotics, I will look at two below:

KEGG AI Computed Probiotics

The differences actually shocked me, a very very dramatic difference. On the current sample I see what is often on ME/CFS patients list appear at the top: miyarisan (jp) / miyarisan with also L. Plantarum Probiotic Powder. This suggests that he is moving towards/through a more typical ME/CFS microbiome. Given that he has issues but everything appeared normal or good, I take this as a good sign – we are exposing the issues.

Prior Sample

Current Sample

CustomProbiotics.com / L. Brevis Probiotic Powder 2 CustomProbiotics.com / L. Rhamnosus Probiotic Powder 2 digestive care 2 Metabolics / Lactobacillus Rhamnosus Powder 2 miyarisan (jp) / miyarisan 2 PureGG 2 spain (es) / bivos 2 spain (es) / kaleidon 2 spain (es) / ns florabiotic instant 2 spain (es) / suerobivos 2 reg’activ / immune & vitality 1.83 CustomProbiotics.com / L. Salivarius Probiotic Powder 1.67

miyarisan (jp) / miyarisan 907 enviromedica terraflora sbo probiotic 828.67 bio-botanical research / proflora4r restorative probiotic 730.25 perfect pass / perfect pass probiotic bacillus spore 730.25 CustomProbiotics.com / L. Plantarum Probiotic Powder 722.2 goodbelly drink 722.2 HLH BIOPHARMA(DE) / LACTOBACT ® LDL-CONTROL 722.2 jarrow formula / ideal bowel support® lp299v® 722.2 Metabolics / Lactobacillus Plantarum Powder 722.2 Prescript-Assist®/SBO Probiotic 694.5 Sun Wave Pharma/Bio Sun Instant 690.92

We also have the option of probiotics based on symptoms (adjusted for the microbiome). See Using Samples and Symptoms to Suggest Probiotics post. The data is shown below in decreasing weight order. The nice thing to see is the decrease in the weight of everyone. One totally disappeared (the sole enterococcus faecalis one). It is interesting to note that while above using only the microbiome and resulted in major shifts between samples, when the symptoms are combined the suggestions are very similar and actually reflect improvement of the microbiome.

Prior Sample	Latest Sample
Prescript-Assist®/SBO Probiotic (34) enviromedica terraflora sbo probiotic (4.4) symbiopharm / symbioflor 1 (3.8) klaire labs / biospora (3.7) microbiome labs/ megasporebiotic (3.6)	Prescript-Assist®/SBO Probiotic (22.6) enviromedica terraflora sbo probiotic (3.5) perfect pass / perfect pass probiotic bacillus spore (2.9) klaire labs / biospora (2.8) microbiome labs/ megasporebiotic (2.7)

Suggestions

I am going to do my current practice of relying on consensus reports because they are now quick to generate. I will be doing a consensus from:

• Standard Lab Ranges (+/- 2 Std Dev)
• Box Plot Whisker
• Kaltoft-Moltrup Normal Ranges
• Percentile in top or bottom 10 %

I will be including everything, since the reader is able to persuade his medical professional to prescribe.

Consensus Results

The following are my picks from the options presented. I provided some links to where it helped ME/CFS –i.e. the suggestions are reasonable

• On all Safest Suggestions (Take:avoid ration)
  • Cacao (21:1) — you likely want 85% chocolate or higher [2010]
  • lactobacillus casei (probiotics) (8:1) [2009]
  • polymannuronic acid (6:1) impacts restless leg syndrome
  • bacillus subtilis (probiotics) (5:1) see 2016 post
  • high fiber diet (5:1)
  • garlic (allium sativum) (5:1)
  • rosmarinus officinalis (rosemary) (3:1)
  • lauric acid(fatty acid in coconut oil,in palm kernel oil,) (7:1)
  • Only take – no negatives
    • fucoidan
    • pediococcus acidilactic (probiotic)
    • green tea
    • capsaicin (hot pepper)
    • fish oil

Items to reduce or avoid

• stevia
• xylan (prebiotic)
• high sugar diet
• sugar
• galactose (milk sugar)
• low fodmap diet
• high-saturated fat diet
• rare meat
• low fiber diet
• high processed foods diet
• vegetable/fruit juice-based diets
• nuts
• white button mushrooms
• partially hydrolysed guar gum,fructo-oligosaccharides (prebiotic)
• cranberry bean flour
• kefir
• kombucha
• Prescript Assist (Original Formula)

Remember: These are suggestions, items that improve odds.

Prescription Suggestions

This is done using advance suggestions and flipping the selections:

The top suggestions were:

• rifaximin (antibiotic)s
• piperacillin-tazobactam (antibiotic)s
• loracarbef (antibiotic)
• benzylpenicillin sodium (antibiotic)
• clindamycin (antibiotic)s
• benzathine benzylpenicillin (antibiotic)
• clarithromycin (antibiotic)s

Secondary positive suggestions are:

• lymecycline (antibiotic)
• minocycline (antibiotic)s
• doxycycline (antibiotic)s

Dangers of Filtering

The person tried using the ME/CFS filter and got very different results. This person has mild ME/CFS; the studies on the US National Library of Medicine are for ME/CFS are typically severe and matches a yard of criteria for inclusion in the study. It is often not safe to use there filters when you self-diagnosis or are mild/controlled.

Bacteria Selected using Expert Criteria

Method	Filtering By ME/CFS	Latest
Use JasonH (15 Criteria)	4	6
Use Medivere (54 Criteria)	4	6
Use Metagenomics (59 Criteria)	4	6
Use Nirvana/CosmosId (36 Criteria)	4	6
Use XenoGene (22 Criteria)	4	6
Standard Lab Ranges (+/- 2 Std Dev)	3	6
Box Plot Whisker	5	27
Kaltoft-Moltrup Normal Ranges	12	84
Percentile in top or bottom 10 %	8	99

My usual criteria has been to have at least 1-2 dozen bacteria. With the new consensus report, having a large number of bacteria seems to produce clearer results.

Bottom Line

Suggestions to be discussed with their medical probiotics

• miyarisan (jp) / miyarisan
• bacillus probiotics (enviromedica terraflora sbo probiotic contains 5 different one)
• L. Plantarum Probiotic

In terms of prescription (doing rotation with breaks between):

• rifaximin (antibiotic)s see this post.
• lymecycline (antibiotic) or minocycline (antibiotic)s There is a long history of successful tetracycline (this family of antibiotics) use with ME/CFS

Supplements to try:

• Monolaurin (lauric acid(fatty acid in coconut oil,in palm kernel oil,)
• Fish Oil – if you love herring… go to it
• High Fiber Diet

We saw improvements between the sample when this reader implemented some of the suggestions. Remember, the suggestions improves the odds, they do not guarantee nor is there any requirement or protocol to follow.

Follow up Comments from the person

Watched the video you uploaded – it was great to get a video and watch how you did for my test.
Quercetin and resveratrol seems to be something to avoid when I did it your way – so I will cut that out.

High red meat and high beef diet seems to be something to avoid (felt it myself also).Been cutting out all red meat for some days now – feels pretty good.
One thing to avoid is also “vegetable/fruit juice-based diets”. I drink like 1-1,5 liter juice a day. I will try to reduce it but it’s really hard – do not feel good eating to much meat, fat or starch. So when cutting out juice I do not get enough calories. Calories are really important to me – which I also see now on my avoid-list – “low energy diet/ calorie restriction” is on it. 
One other thing that is interesting is that potatoes is on the “Highest Adverse Risk”-list. I eat potatoes every day.

I extracted out the items that are recurring as good predictors for various symptoms. These are listed below. This is intended for those interested in research and diving deep. See AI Computed Probiotics from Symptoms for background.

See also Key Enzymes for Symptoms and Key Compounds for Symptoms. What is surprising is that “non-of-the-usual suspects” were included with the exception of spotted fever groups (i.e. Rickettsia, Lyme) and Staphylococcus aureus (see Staphylococcus aureus – the CFS maintainer?)

tax_name	tax_rank	Taxon
Protostomia	clade	33317
Calditrichia	class	1962850
Paraneoptera	cohort	33342
Alteromonadaceae	family	72275
Coxiellaceae	family	118968
Euzebyaceae	family	908622
Holophagaceae	family	574976
Ignavibacteriaceae	family	795749
Nocardiopsaceae	family	83676
Thermoanaerobacterales Family III. Incertae Sedis	family	543371
unclassified Clostridiales	family	186813
Alkalibaculum	genus	696745
Anaerobium	genus	1855714
Anaerocella	genus	1634949
Anaerococcus	genus	165779
Cellulosilyticum	genus	698776
Cryomorpha	genus	246876
Desulfomonile	genus	2357
Euzebya	genus	908623
Haliangium	genus	162027
Hungatella	genus	1649459
Lacibacterium	genus	1500420
Pectobacterium	genus	122277
Spiroplasma	genus	2132
Sporomusa	genus	2375
Terrisporobacter	genus	1505652
Trichococcus	genus	82802
Vagococcus	genus	2737
Neoptera	infraclass	33340
unclassified Chloroflexi	norank	167963
Actinomycetales	order	2037
Chlorobiales	order	191411
Euzebyales	order	908621
Hemiptera	order	7524
Ignavibacteriales	order	795748
Acetonema longum	species	2374
Anaerobranca zavarzinii	species	436000
Anaeromyxobacter dehalogenans	species	161493
Bacteroides propionicifaciens	species	392838
Bifidobacterium thermacidophilum	species	246618
Brevibacterium paucivorans	species	170994
Brochothrix thermosphacta	species	2756
Caloramator mitchellensis	species	908809
Candidatus Tammella caduceiae	species	435141
Carboxylicivirga linearis	species	1628157
Casaltella massiliensis	species	938278
Corynebacterium canis	species	679663
Desemzia incerta	species	82801
Desulfarculus baarsii	species	453230
Desulfonispora thiosulfatigenes	species	83661
Desulfovibrio idahonensis	species	575978
Desulfovibrio psychrotolerans	species	415242
Desulfurispirillum alkaliphilum	species	393030
Dolosigranulum pigrum	species	29394
Haliscomenobacter hydrossis	species	2350
Lactobacillus japonicus	species	29399
Marvinbryantia formatexigens	species	168384
Mediterraneibacter faecis	species	592978
Megasphaera hominis	species	159836
Phascolarctobacterium succinatutens	species	626940
Proteiniborus ethanoligenes	species	415015
Pseudoflavonifractor capillosus	species	106588
Pseudoramibacter alactolyticus	species	113287
Pseudoscillatoria coralii	species	693994
Skermanella aerolata	species	393310
Slackia sp. NATTS	species	647703
Spiroplasma ixodetis	species	2141
Staphylococcus aureus	species	1280
Streptomonospora alba	species	183763
Thermoactinomyces vulgaris	species	2026
Thermophagus xiamenensis	species	385682
Thermovenabulum ferriorganovorum	species	159731
Uliginosibacterium gangwonense	species	392736
Veillonella criceti	species	103891
Verrucomicrobium spinosum	species	2736
spotted fever group	species group	114277
Eukaryota	superkingdom	2759