Microbiome testing reports discussion

I'm a proponent of the microbiome being a central factor in ME /CFS. I am starting this thread to provide a space for discussion of microbiome testing (e.g. Ubiome) reports, and possible interventions. I will be posting some of my own results soon.

 

I've done a few uBiome tests. I find them pretty interesting.
To my surprise I've found that most probiotics don't tend to stick around once you stop taking them. Not sure if this is just me or if others find the same?

 

Yes, most probiotics are transient. Have you tried some human based strains such as miyarisan or mutaflor?

 

I always suspected this but have wondered why

 

My uBiome report:

Diversity is at 91st percentile which is surprisingly good. There are some rare bacteria (in under 5% of samples):

Cruoricaptor genus 0.1%
Pelistega genus 0.2%
Alcaligenaceae family 3.2%
Pseudoclavibacter genus 4.2%


Pelistega is associated with respiratory disease in pigeons:
http://ijs.microbiologyresearch.org/content/journal/ijsem/10.1099/00207713-48-2-431

I was once hit in the face by a pigeon. I wonder if this is worth treating?


Cruoricaptor is associated with bacteraemia:
http://www.sciencedirect.com/science/article/pii/S0723202012001087

Same with Pesudoclavibacter:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3716097/


Again, I wonder if it worth trying to eradicate these rare bacteria?

 

I think that this is normal. If you look at a person's diet, within a few weeks of changing what you eat will greatly affect your microbiome. I watched a show a few years ago about gut bacteria, and they had someone who ate a lot of fruits and veggies change their diet to eating McDonald's food for two weeks, and their microbiome before and after changed significantly.

An interesting thing is that the bacteria in Yogurt are only present in the gut as long as you are consuming it, whereas there are bacteria in Kefir that will actually colonize in the gut.

 

I have heard this before, but when I searched for evidence i couldn't find any. Do you know of any?

 

I wouldn't worry about them at all.

A lot of the individual variation in the gut seems to come from the large collection of very low level constituents, most of which are a complete mystery.

It has been hypothesised that the minor phyla in the gut represent resilience; the minor constituents have the capacity to expand and fill in if disaster strikes and important constituents are wiped out. Really though we don't know what all of the many minor components do.

Even things which are known, for example, to be opportunistic pathogens, are not really a problem, especially if present at very low level. Very many higher abundance members are potentially opportunistic pathogens but are also normal gut constituents. They are only a problem if they get out of hand and this is because of other problems going on in the body.

I've had quite a few uBiome tests and I've noticed great variability in these low level constituents from test to test.

 

Here is a review of Lactobacillus in the human GIT. There appear to be very few lab species which colonise the gut - most originate from the mouth or fermented foods and are just passing through.

Here is a detailed study of the fate of Lab strains from the probiotic VSL 3 in the gut. Once the probiotic was stopped, the strains gradually disappeared. They don't colonise.

Similar results were obtained for one Lab strain from kefir. I don't know about other kefir constituents.

 

Thanks @alicec. I won't worry about them at this point. My next question would be if there would be any value in doing a FMT, when the diversity of the microbiome is already quite high (according to the uBiome report)?

 

Probably not though you don't say anything about the dominant genera in your gut. Is there a good range of known beneficial organisms? - eg Bacteroides, Faecalibacterium, Roseburia?

 

TBH I have not taken a lot of notice of this subject so far, not enough to have a considered opinion, but I am aware of general discussion.

Off hand I do not know how that is done. Does that involve antibiotics or other chemicals? Personally I would worry if taking out one strain will have collateral damage. Or are the methods developed enough to have that kind of precision?

Maybe I am still horrified by the concept. At present I have in my head something I read recently (I have no reference) that a woman took an FMT from her obese daughter, and the woman became obese after the event. An anecdote, but do we have enough evidence to be confident of avoiding unintended consequences?

 

When comparing my bacteria to the average at the genus level, I guess it doesn't look too good. Most seem way underrepresented:

Your Bacteria at the Genusrank compared to All Samples
Bacteria
Ratio
Intestinimonas: 1.39 X
Butyricimonas: 0.74 X
Intestinibacter: 0.30 X
Catenibacterium: 0.19 X
Cruoricaptor: 0.29 X
Terrisporobacter: 0.53 X
Anaerotruncus: 0.11 X
Streptococcus: 0.15 X
Enterobacter: 0.09 X
Hespellia: 0.85 X
Asaccharospora: 0.20 X
Lactobacillus: 0.06 X
Peptococcus: 0.45 X
Mobiluncus: 0.16 X
Victivallis: 0.21 X
Gelria: 1.06 X
Brevibacterium: 0.08 X
Candidatus Soleaferrea: 0.53 X
Cloacibacillus: 0.10 X
Finegoldia: 0.03 X
Actinomyces: 0.14 X
Porphyromonas: 0.03 X
Adlercreutzia: 0.17 X
Shuttleworthia: 0.25 X
Holdemania: 0.43 X
Senegalimassilia: 0.11 X
Eisenbergiella: 0.06 X
Dielma: 0.07 X
Murdochiella: 0.02 X
Turicibacter: 0.06 X
Marvinbryantia: 0.06 X
Peptoniphilus: 0.01 X
Eggerthella: 0.06 X
Anaerofilum: 0.03 X
Megasphaera: < 0.01 X
Sporobacter: 0.15 X
Pseudoclavibacter: 0.03 X
Papillibacter: 0.04 X
Gordonibacter: 0.06 X
Anaerofustis: 0.07 X
Acetanaerobacterium: 0.09 X
Lactonifactor: 0.05 X
Anaerococcus: < 0.01 X
Mogibacterium: < 0.01 X
Prevotella: < 0.01 X
Bacteroides: 1.03 X
Faecalibacterium: 0.89 X
Blautia: 0.91 X
Alistipes: 2.22 X
Paraprevotella: 2.49 X
Collinsella: 1.93 X
Subdoligranulum: 1.36 X
Megamonas: 0.70 X
Parabacteroides: 1.25 X
Akkermansia: 1.00 X
Roseburia: 0.34 X
Oscillospira: 11.12 X
Pseudobutyrivibrio: 0.76 X
Anaerostipes: 0.59 X
Phascolarctobacterium: 0.87 X
Odoribacter: 2.34 X
Fusobacterium: 0.45 X
Parasutterella: 1.05 X
Clostridium: 1.35 X
Sutterella: 0.53 X
Sarcina: 0.39 X
Erysipelatoclostridium: 1.18 X
Bilophila: 2.02 X
Enterorhabdus: 2.11 X
Lachnospira: 0.43 X
Pelistega: 0.50 X
Moryella: 0.98 X
Dorea: 0.27 X
Flavobacterium: 0.84 X
Oscillibacter: 1.07 X
Corynebacterium: 0.20 X
Barnesiella: 0.31 X
Fusicatenibacter: 0.13 X
Flavonifractor: 0.60 X

 

Not sure, but perhaps avoid obese donors?

 

I've heard or read that story somewhere too, but can't remember where.

 

I've also read of people receiving donations from overweight or obese people who have then ended up with the same weight issue. I've also read that if the donor tends to suffer from depression or anxiety, that that can also potentially be passed along to the recipient.

 

It doesn't seem to bad - many of the ones that are very underrepresented are minor species. You need to rearrange that list starting at Bacteroides as your most abundant genus. Then you will see that many of the major components are not terribly different. Some are of course, some are more abundant, a few are missing.

I've uploaded a list of genera in decreasing order of average abundance, derived from my uBiome data. They have a peculiar way of reporting things; they don't present a total average picture, just the average for the organisms in your own gut.

Because I know I am missing Prevotella and Ruminococcus which are major genera for many, I have added them to my list, but there could be others missing from my list. For example, I see you have Megamonas, which I don't. You can work out from the reported percentage abundance and the comparison with average what the abundance of this genus is on average and add it to my list. Apart from a few very low level genera, I think I recognised most things on your list as being on mine also.

So my list is not completely comprehensive, especially at the low levels where there is tremendous variation which I haven't tried to include, but it gives a fair idea of the abundance of the major gut constituents.

 

I could not find Ruminococcus in my report. Interestingly, my Prevotella is almost non-existent. This genera is frequently high in ME/CFS, according to Lassesen. I don't know if this is important.

 

Prevotella tends to be high with high carbohydrate diets, especially high grain, presumably reflecting its capacity to digest complex polysaccharides, particularly xylans which are high in grains.

The genus tends to have an inverse relationship to Bacteroides; ie one or the others tends to be dominant, not both.

Prevotella abundance correlates with inflammatory conditions and as far as I am aware, there are no correlations which suggest an important positive role.

Since I eat a lowish CHO diet with few grains I don't seem to have a great need for it and there's nothing known that suggests it is essential - so I decided I didn't care about its absence.

Ruminococcus I would like to have, especially R. bromii. It is a major starch fermentor, facilitating starch use by others and as well plays an important role in maintaining the mucosal barrier.

I had hoped that long term prebiotic use might stimulate its growth as it has with other genera, but so far no. Maybe I have lost the seeding stock.

Note if you are reading older work on the gut microbiome, the Ruminococcus genus is one which has been completely revised as a result of genetic analysis.

The genus was found to contain two groups, group 1 belonging to Clostridium cluster IV and group 2 belonging to Clostridium cluster XIV a.

Group 1 has now been classified as Ruminococcus senso stricto in the family Ruminococcaceae and includes R. bromii.

Group 2 has been reclassified as Blautia in the family Lachospiraceae and includes R. gnavus.

The two groups have significantly different properties.

 

Despite supplement lacto won't budge but bifido has. I find it interesting but don't think Ubiome is a tool at the moment for us aside from taking a look.