Random thoughts on the ‘biome

If you’re healthy, no major complaints, then you probably won’t benefit from tweaking your ‘biome.  Ymmv.  But if you’re gonna do it anyway, here are some tips (mostly my opinions).





1) Listen to podcasts by some of the experts like Bryan Davis (Doc Fermento) and Grace Liu (Gut Goddess).  Jane Plain (ItsTheWooo) also has some unique views on the topic.  If there are more good ones out there, please leave them in the comments!

2) Start with small servings of fermented foods: sauerkraut, kimchi, kefir, pickles, etc.  Same goes for prebiotics (like 1/4 TEASPOON, not TABLESPOONS).  Too much can easily cause bloating, GI discomfort, gas, diarrhea: no bueno.

3) Probiotic supps alone are relatively useless; if you choose to go this route, they should be co-ingested with prebiotics and fibrous plants.  LC-friendly.



4) My personal bias when it comes to supps: it’s better to supplement a few strains combined with selective prebiotics than to use products with a ton of strains.  For example, I prefer Jarrow Bifidus over SBO bombs because the former has just a few strains we know are beneficial, whereas the latter has a lot of mystery strains.  And combine with galactooligosaccharides, garlic, leek, onion, etc., to selectively feed ’em.

5) Many Paleo-biome studies show ‘variety’ is a potentially valuable ancestral characteristic, but I’m wary supplementing a million random strains to achieve said variety… seems like a high possibility of something going wrong.  The ‘biome has been implicated in regulating brain functions, mood, immunity, stress, adiposity, etc., etc.  Do you really want to hit it with a million mystery strains?  And I imagine if something does go wrong, it could be very difficult to fix.

6) Anecdotally, people complain that the effects of certain ‘biotics on gut function crap-out after a few days.  Try a different product, and see points 3 and 4 (above).  Also, I totally wouldn’t be surprised if regulating gut function turns out to be a relatively minor role of the ‘biome (see point 5).


To summarize, I have no strong opinion about total microbe numbers or variety.  I do believe higher percentages of certain strains are healthy and the evidence supporting this is pretty strong.  For example, many healthy populations have high bifidobacteria, many sick populations have low bifido, few sick pops have high bifido, etc.   This is where my collective thinking on the topic arises.  There are other potentially healthy strains, but few with such wide-ranging support.  Maybe.


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  • Sky King

    OK, thanks!


  • Gerard Pinzone

    A while back, I saw a study mentioning propionibacterium freudenreichii, but it was difficult to find a probiotic that included it. I eventually found Securil by Nutricology on Amazon. I’ve been trying it for a while, but I don’t know if it’s any better or worse than other products.

    I’m interested in the one you linked: “Jarrow Formulas Bifidus Balance plus FOS,” but I’m concerned that the FOS in it will disagree with me. Is there another without the FOS?

    • Sky King

      Are you having a problem with your gut? If so, then trying a probiotic may help but my question is… how does one know if the type of probiotic you choose is the one needed for the type of diet you’re consuming? If on the other hand your gut is fine (not broken), then why try and fix it?

      The Kitavans have a very diversified biome because they eat quite a diversified diet of tubers/fiber. Since they’re traditional farmers, their diet consists mainly of tubers such as yams,
      sweet potatoes, taro, etc., and fruit, fish, and coconut. They don’t use dairy
      products, alcohol, coffee, or tea. Their intake of oils, margarine,
      cereals, and sugar is practically nil. Western foods, on the other hand, constitute less than 1%
      of their diet!

      So my thinking on this subject is this… the Kitavans have acquired a biome that’s needed/required for their diet, while Westerners have acquired one that’s suitable for theirs. Will adding specific probiotics “fix” the problems created by a Western diet? If it eliminates the “bad” bugs and takes up residence, then you might as well forfeit a Western diet in order to keep those “good” bugs around, otherwise… you’re defeating the purpose.

    • FOS as a prebiotic is usually used in the >20 g/d range. There’s only 200 mg in the Jarrow product… so maybe won’t disagree with you?

      There are other products with similar strains, but they also contain a ton of mystery strains…

  • Gerard Pinzone

    One more thing that Jane Plain (ItsTheWooo) mentioned once: Metformin.

    • similar MOA (in theory): abx

    • Do you mean regarding the recent metformin works through the gut microbiome paper?

  • TechnoTriticale

    More random ruminations:

    Human guts can harbor almost anything that physically fits. The spectrum of such things is already known to include bacteria, eukaryotic parasites, fungi, protozoans, viruses and yeasts. A recent paper is strongly suggestive that there might also be as-yet unknown domains of life.

    These things quite likely have material inter-dependencies with each other. This means that there may be no clean classification as “beneficial” or “pathological” for each. Relative populations and diversity probably matter.

    Any attempt to cultivate the microbiome requires routine substrate for the populations desired (prebiotic fiber, resistant starch).

    The “optimal” microbiome for any individual is probably phenotype-specific, and must be matched to diet. A recent paper suggests that microbiome can drive epigenetics, creating changes heritable over multiple generations.

    Anyone claiming today to understand all this is mistaken. If they are confidently promoting a gut-related product, “mistaken” might be too polite.

    All but one of two of the probiotics on the market include only bacteria. This is probably why FMT often succeeds where probiotics (even PB enemas) fail.

    The use of prescription antibiotics, OTC antibiotics and casual antibiotics (e.g. triclosan) is pervasive. Trends thought to be related to microbiome (ASD) are not encouraging. Extinctiosn may be serious and not trivial to fix.

    The vast majority of people today are also consuming food-like substances that are microbiome (if not gut wall) antagonists, ranging from wheat to preservatives and emulsifiers. This sort of suggests that if a probiotic works for you, routine consumption of it, or periodic courses, might be indicated until more is known about re-colonization (not to mention which species, strains and proportions to use, and how to feed them).

    We know about as much about the microbiome today as was known 150 years ago about microbes generally. Mind your results. Be skeptical of developments. Be deeply suspicious of consensus.

    • Sky King

      Well said!

  • Maybe this is leftover John Harvey Kellogg nonsense? Things can go very wrong in the gut, but I doubt this is where the magic happens.

  • Eve

    Speaking of ‘biomes (and possible ramifications of low-carb protein bars!): http://www.nature.com/nature/journal/v514/n7521/full/nature13793.html

  • Jack Kruse

    the size and diversity of the biome = the amount of light they release. Neolithic disease is associated with a sparse less diverse flora = less light. Fritz Popp showed us this long ago. Bacteria release 5000 times the light eukaryotes do. This biome is a story of light release to control optical signaling = quorum sensing controlling arm. FYI.

  • JD Shields – Microbiologist

    First of all a microbiome is defined as the genetic makeup of the microbiota in or on the human body as distinguished from the human genetic makeup.

    The microbiota is defined by microbes in specific habitat/place. A microbe is just a shorten version of microorganism.
    (see: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3426293/ )

    Bill: As far as probiotics being “relatively useless” is a statement made without knowledge of the vast subject of helpful and not so helpful microbes. Since this field of science has limited research documents up to this point in time, yet growing each day, you get a pass for that lack of knowledge. But your statement reflects the lack of active useful probiotics available to the consumer. I would see ProbioticsAmerica DOT com for effective probiotics.

    The alternative is using naturally occurring probiotics such as the ones you describe: sauerkraut, kimchi, and kefir

    Realize that those of us who are DOING the research into the microbiota have a daunting task. Since very little research has been done on the interactions of microbes in the human gut with each individual having virtually different colonies of various microbes we cannot assume how the microbiota control the human systems in the body.

    We in research observe, we document, and we continue to open up the mysteries of the microbes that we share this body with.

  • David Birsen

    Dr. Rhonda Patrick (FoundmyFitness podcast) also a thought leader in the microbiome space