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American Gut results: feedback?

Discussion in 'Gastrointestinal and Urinary' started by aquariusgirl, Jun 17, 2016.

  1. aquariusgirl

    aquariusgirl Senior Member

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    Hi, I just got the results of my first American Gut analysis back. results as follows. Comments welcome.

    Most enriched microbes:
    clostridium 7x normal ; Finegoldia 17x average; Prevotella x9 average; Collinsella x 8.
    Rare taxa :
    Varibaculum, Neisseria; Campylobacter
    Most abundant microbes:
    Prevotella;Ruminococcaceae; Lachnospiraceae;
    Bacteroides
     
    Last edited: Jun 17, 2016
  2. aquariusgirl

    aquariusgirl Senior Member

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  3. alicec

    alicec Senior Member

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    Let us know the % of the main phyla - viz Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria - plus any minor phyla reported. This gives a very broad overview of the balance of the gut.

    From the results you do report, probably the most notable is the considerable overgrowth of Finegoldia.

    I have observed in my regular gut tests that sometimes there will be a large overgrowth of something (say around 10x) that has completely disappeared by the next test. Nothing has changed as far as I am aware so I have no idea what lies behind these sudden overgrowths. It seems though that they don't necessarily last.

    So the overgrowths you see in this test could be different in a subsequent test.

    In the case of Finegoldia ( a member of Clostridiales Family XI in the Firmicutes phylum), however, it has some properties that might be causing you problems.

    It is a normal member of the gut, usually in moderate abundance. It is also one of a group of organisms that have been termed GPAC, gram positive anaerobic cocci, that are sometimes isolated from infections.

    So Finegoldia is an opportunistic pathogen. This doesn't mean you have an infection - you would undoubtedly know about it if you did - but lots of this bacterium in your gut increases the risk of it moving outside the gut and causing trouble.

    More immediately relevant is that Finegoldia is asacchrolytic. It ferments amino acids, not sugars. Several products of amino acid fermentation are potentially problematic, most notably ammonia. Increased production of this in your gut could have considerable metabolic consequences.

    There are so many different Clostridium species with very different properties that it is hard to know what to make of the increased incidence. uBiome provides at least a partial species breakdown and I imagine American Gut might also. It could be useful to know if any overgrown species have been identified.

    Prevotella (a member of the Bacteroidetes phylum) is a normal gut constituent, often in very high abundance, particularly in people eating high carbohydrate, esp high grain, diets.

    Very elevated levels are associated with adverse health conditions and inflammatory conditions. It too is an opportunistic pathogen, especially in the oral cavity.

    Collinsella (a member of the Actinobacteria phylum) is a normal gut constituent of lowish abundance, which is a major lactate utiliser in the gut (a good thing). It has various beneficial properties but overabundance is associated with symptomatic atherosclerosis and dyslipidaemia. This doesn't mean that you will have these conditions, rather it suggests that over expression over time might have significant impact on host lipid metabolic pathways.

    All your most abundant microbes are normally in high abundance. Of the rare taxa, campylobacter is a notable pathogen but also a normal low level gut constituent.

    What to do about the overgrowths. Well first I'd be having another test soon to see if it is a consistent pattern. If it is consistent, then you have some difficult choices.

    The immediate instinct to take antibiotics to kill off the overgrowths can lead to more problems, promoting the growth of something else which might be worse. On the other hand, a short course of rifaximin, accompanied by plenty of probiotics could be helpful. In this respect you would need to consider the susceptibility of Finegoldia - it is one of the most antibiotic resistant of all the GPACs.

    Regardless of whether you go the antibiotic track or not, I'd be looking to diet and prebiotics.
     
    voner and Sushi like this.
  4. Daffodil

    Daffodil Senior Member

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    didnt dr demeirleir show that many CFS patients have provotella overgrowth?

    was this DNA testing?
     
  5. Sushi

    Sushi Senior Member Albuquerque

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    I don't think prevotella in particular but that most had problems in the microbiome.
     
  6. Daffodil

    Daffodil Senior Member

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  7. Sushi

    Sushi Senior Member Albuquerque

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    Oh, I see something he wrote in 2009 is footnoted in that paper.
     
  8. alicec

    alicec Senior Member

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    That reference is about increased D-lactate formation by Enterococcus and Streptococcus. Actually I didn't pick up any reference to Prevotella in the cited paper but could have missed it - I just skimmed it.

    What I would say about the paper is that its information on the composition of the gut flora is greatly distorted by the technology used to study it. It uses culture-based techniques, albeit ones developed by Henry Butt at Bioscreen Australia to try to preserve anaerobes in stool samples. It succeeds only partially, so is a bit better than the usual culture tests, but it still misses the vast majority of anaerobes.

    There might be some value in the general mechanisms canvassed in the paper but it doesn't illuminate what is really going on in the gut.

    The 2009 paper of KDM with Henry Butt used that old-fashioned technology.

    It is telling I think that KDM has since moved on to DNA based techniques.
     
  9. Sushi

    Sushi Senior Member Albuquerque

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    Yes, he now uses DNA tests.
     

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