Diet changes and microbiome testing

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This topic contains 3 replies, has 4 voices, and was last updated by  William Zile 6 months, 3 weeks ago.

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    Joe N

    So earlier this year I had sent in a sample for having my gut biome sequenced. At the time, due to the food sensitivities I had developed (lactose, wheat [specifically wheat triggered allergic responses prior to me having to eliminate other grains], gluten), I was eating low-carb with a moderate-to-high fat/protein intake (I’ve been playing around with going keto and also with intermittent fasting, but wasn’t tracking anything specifically at the time, just trying to find relief). The initial program I went through is a non-profit focused on research around sequencing and understanding the human microbiome (American Gut Project, It took a long time to get results, and when they came, it provided a large amount of data, however, no real interpretation (as they are not giving medical advice). However, that gave me a starting point to look at, and they provided a comparison to others on a few different metrics (average sample, same gender, same age, similar diet, Michael Pollan). What was interesting was that my gut was composed of about 80% baceteria from the phylum firmicutes, which was not similar to any of the other averages, generally firmicutes makes up 50% or less. The research that Ive done so far has not really provided me any useful information, and the more I learn, the less I know (and the more I realize how little we all know about how our guts really operate). I’ve found another site that works with doctors to have the tests prescribed so that they are covered through your insurance ( They send 6 kits, so that samples can be collected at a regular basis. I have not received my kits yet, but will update once I do.

    I’m just coming down from a major flare-up, during which I decided to go full no-carb and have been leaning towards eliminating my diet step by step down towards bare beef, until I find relief. As of the beginning of September (about 5 days ago) I cut out corn and potatoes (my main sources of carbs) and have noticed a major fog lift already. Once I receive the kits, I will log my diet for a week before sending off the first sample. And based on whatever information I can find through internet research, I’ll continue to eliminate foods weekly and send samples, or send samples monthly…just need more information.

    I’m curious if anyone out there who has gone full carnivore has had their biome sequenced and if they’d be willing to share their results? As Mikhaila stated on Rogan’s podcast, there really are not any population studies out there, and so we’re all going off anecdotal evidence. However the more anecdotes we can put together, the more information we have to go off of. It seems clear to me through my experience and from the shared anecdotes of others, that depression and anxiety are common comorbidities with our gut disorders, and it has already been proven that the gut is the only body system that sends signals to the brain to produce neurotransmitters, turn off receptors, or otherwise take action that can cause the mental health aspects that we experience.


    Jacki Parnell

    Hi, I was just going to post on this issue, as I have had my biome tested and now worry about going low carb, because I ate a very healthy diet but there just are some worrying things that have come up from my results and I wanted to know if anyone is tracking their biome (expensive I know) as they go ‘meat only’ or meat and greens or low carb in general. Mine has shown while mostly good, it confirms what I thought from my physical experience that I have a gut biome that promotes inflammation… I. need to reduce protein, saturated fat and increase certain types of non digestible starches found in leeks, artichoke and a few others, based on my results compared to a healthy average. So without going into any details…. just thinking that this is opposite to what the meat diet recommends, but then was it ever meant to be mainstream? how can we go low carb low saturated fat and high ‘non digestible starches’ to feed a good gut biome. I thought was eating really healthy but it seems I’m hurting my gut bacteria.. would love to know how any meat only eaters fair with their gut biome… healthy now but what about later?


    Steve Sheldon

    Hi Jacki, I would just wonder if the diet they prescribed to you reflects your specific situation or their pre-existing biases. If it were me, I’d want to rule out the latter before eating along those lines because it sounds a lot like outdated mainstream thinking with a few odd items thrown in to make it sound interesting and cutting edge.

    But I am no expert, just an older guy who has a finely tuned bullshit detector that sometimes gives false positives 😉


    William Zile

    I am a 27 year old healthy male. Besides limiting processed sugar/carbs and eating more veggies than most, I have no special diet. This is 100% just academic curiosity. I work for a clinical stage microbiome company called Seres Therapeutics and have biochemical engineering degrees, so I might have more insight than most for this topic. However, I am not in R&D at Seres, they are the people who would know the most about this topic.

    I just watched episode 1164 of The Joe Rogan Experience, where he interviewed Mikhaila. She seemed to think the inability to return to meat + greens after going meat only was due to loss of the bacteria required to metabolize the greens. She also talked about trying probiotics to restore her microbiome, saying that the probiotics seems to affect her mood and thought it could be related to leaky gut.

    At Seres, our products are essentially full microbiome (gut bacteria) replacements. One of the diseases we are targeting is ulcerative collitis, an inflammatory disease of the gut. You take antibiotics to knock down your gut bacteria by a couple log fold [think burning down a fully developed forest] and then you take our pill which provides high spore quantities of many bacterial species [think planting a diverse set of 15 foot tall trees in the ground after burning down the forest]. The bacteria engraft (are retained and grow in the gut instead of just passing through and getting pooped out) and prevent your bacteria from repopulating [15 foot tall trees block out the light for whatever weeds try to grow]. After removing the bad bacteria and bad metabolites, you stop having the immune response.

    Probiotics aren’t the solution. You need to provide like 10-15 different strains of bacteria that functionally work together to create a working microbiome (think ecosystem). If these conditions are met, they will heal that “leaky gut”.

    Most of the probiotic bacteria all provide the same “function”, meaning you’d still be missing 9-14 of the required functions to create an ecosystem. Why don’t probiotics offer a wider range of bacterial strains?
    A) You first have to isolate them from poop
    B) They are expensive to grow due to nutrient and anaerobic (no oxygen) conditions required to grow them industrially
    C) if they aren’t offered in a consortia of those 10-15 functional strains, they wouldn’t be useful

    We use metabolomics (determine the identity and concentration of metabolites in the gut) to determine the bacteria <-> human and bacteria <-> bacteria interactions. This is part of how we started to tease out the “ecosystem” I refer to above.

    There are multiple issues that could be driving this:
    1) immune response to allergens in the food (unlikely based on the sensitivity to greens after meat only diet)
    2) immune response to bacteria
    3) immune response to metabolites from bacteria digesting the food

    The simplest experiment I can think of would be to give an individual on a meat only diet our drug (antibiotic followed by bacteria) and have them keep eating a meat only diet.
    – If that triggers an immune response, it could be either 2) or 3).
    – For 2), I would want to either try a different bacterial consortia, to see if the immune response was to a specific bacteria.
    – For 3), I would want to apply a metabolomics approach to see what compounds could be causing he allergy.
    – If it didn’t trigger an immune response, you could probably rule out 2). I would then introduce different foods, apply metabolomics and see if I could identify the compound causing the immune response.

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