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Time For Better Microbiome Research

The microbiome needs no introduction – it has been several years since you could pick up a biomedical research journal and not run into an article on possible connections of human gut bacteria and disease. There were thousands of such papers last year alone. But it’s a very hard field to work in. You can establish correlations between certain gut profiles and some diseases, but causality is another matter. Do the bacteria cause or exacerbate the disease, or does the disease give you an altered gut bacteria profile? Or neither? There’s no particular reason that they should be connected at all (which is an option that our human brains are not always ready to consider, frankly). It’s worth remembering that we don’t even really have a baseline: there is no agreement on what a healthy human gut microbiome looks like, how that might vary depending on diet and environment, how many such microbial states might be considered healthy, and how much deviation from these would be considered acceptable.

Attempts to answer these questions can involve human microbiota-associated (HMA) mice, which are gnotobiotic (germ-free) animals that have had human microbiota transplanted into them. That sounds like a pretty useful experiment, although it has to be said that gnotobiotic rodents are not only expensive but a bit weird (and certainly not normal). It would seem like the sudden-microbiome-from-a-standing-start experience that they get is not exactly like what goes on in a human gut – you hope, anyway – but one could also hope that looking at differences and disease states could be useful.

But this new paper casts doubt. The authors have found 38 such studies in the literature over the last few years, and 36 of them apparently report a transfer of disease phenotype. That, they say, is a little too useful: it is implausible that so many of these experiments should work. (The two exceptions, by the way, were on possible microbiome effect in colorectal cancer). The paper suggests that a combination of loose experimental design (not enough donors, small n on the mice, etc.), lack of rigor on determining the disease state in both the humans and animals, and flat-out wishful thinking have skewed the literature. A whole range of diseases, many known to be multifactorial, should not be able to simply transfer into mice with the human bacteria with a 95% success rate. A big factor, which is also a silent one, is publication bias. The studies that show an effect get published, the studies that don’t go into the drawer (or its electronic equivalent).

At this point you’d be hard-pressed to find a prominent human disease that hasn’t had some connection made to the microbiome. Does this indicate its extraordinary importance, or is this a sign of people getting ahead of the evidence? The only way to be sure about this is to run more rigorous experiments – put these hypotheses to stricter tests and see if they survive. That’s not the say that the whole field is hype, because it certainly isn’t. But we need to get the hype out of it in order to work on the real stuff. This new paper has a number of specific recommendations for improving the quality of HMA mouse studies, and it’s hard to argue that we wouldn’t be better off if people followed them.

These include (a) compare donor samples from individuals with a specific disease to samples from donors without it, and try to determine the microbiome alterations associated with pathology, (b) use enough donors to account for biological variation, keeping effect size in mind, (c) avoid “pseudoreplication – that is, use the number of donors as the N for statistics, rather than the number of animals you transferred their samples into, (d) use more rigorous animal handling techniques to prevent the spread of microbes between animals, (e) don’t pool donor samples, because you’re eliminating important differences between individuals, (f) run confirmatory assays to make sure that the microbial transplants were actually successful, and do this with a time course because some of these things may take a while to get established, and (g) be honest about the power of your experiments and their ability to explain causality.

Long-term, we’re going to need complex experiments to really nail down causality and mechanism, but we can’t even get those off the ground (not and have them mean anything) unless the foundations are more solid than they are now. Basically, the authors are saying that it’s time for this field to grow up, for there to be fewer statistically thin publications that claim connections to human diseases that are poorly modeled in mice to start with. Case in point. There’s real science to be done in this field, and it could lead to some real advances in medical treatment, but we’re not going to get there with the sort of stuff that’s cluttering up the literature now.


21 comments on “Time For Better Microbiome Research”

  1. Some Dude says:

    In other words: Microbiome studies are full of shit.

    1. John Wayne says:


  2. Lane Simonian says:

    There are many unanswered questions in this field. One being how or if do products of beneficial gut bacteria (gluthathione, for instance) or harmful bacteria (microglia) make it to the central nervous system.

    Certainly the gut is not the only pathway to neurological diseases. One may be at increased risk of neurological disease by ingesting food laden with pesticides but one could also be at increased risk of neurological disease by breathing in air pollutants. And the same compounds that may help with a “leaky” gut may also independently help with a “leaky” brain (what is good for the gut is good for the brain).

    Taking that all into account here are two recent studies on the effects of probiotics/synbiotics on cognitive function:

    And just for cultural heritage and family memory reasons, I will add this story:

  3. Jb says:

    My buddy is a bariatric surgeon. According to him, at least, it isn’t unheard of for someone to develop raging alcoholism or to start to have problems with gambling after having gut surgery that removes a significant portion of their bowels. People who’ve never had any previous problems with these issues go into surgery and then come out having strange compulsive behaviors that they didn’t previously that you’d have never guessed might be linked to gut surgery. There very well could be a gut-brain axis, but even though we can’t ID a plausible molecular mechanism of action to satisfy our over reliance on reductionism in science it doesn’t mean that there isn’t one. At what point does observation trump a need for mechanism?

    Ancient eygptians only needed to observe that when you put honey on a wound that it prevented infection. They didn’t need to know a biological mechanism for why it was useful. It just was.

    1. Alia says:

      Coming from the field of psychology (yeah, yeah, not a real science, I know), there is another possible mechanism. If some of the people who undergo bariatric surgery suffer from compulsive eating disorders and following surgery are unable to fulfil their unmet need by overeating (because it hurts, for example), they might go on to another compulsion that gives them temporary relief. Because while compulsions might be different, be it eating, alcohol, gambling or shopping, the underlying psychological mechanism is the same – you feel stress/anxiety and you need to do something, anything to relieve it.

      1. johnnyboy says:

        Not a psychologist, but this explanation sounds a hell of a lot more likely than any microbiome shift.

        1. Ray says:

          The phenomenon seems to be more common with medical procedures involving changes in microbiota, though, at least as far as I can tell.

          I think it’s important to note that the implication isn’t that there is some specific alcoholism or gambling inducing factor that changes, but rather a more subtle shift in some other factor that leads to a change in mood which results in compulsive behavior that may manifest as an alcohol or gambling addiction.

    2. matt says:

      I’ll put a different just-so story out here. Perhaps some of his patients were significantly depressed going into the surgery because they had not been able to manage their weight, and because society in general dumps on people who don’t control themselves according to norms.

      After the surgery, instead of wanting to die all the time, they suddenly found themselves rising out of depression, trying to manage the will to live and catch up on life, and ran off into the ditch on the other side of the road. If you’ve ever found yourself fishtailing on bald tires on a wet, curvy road with ditches on both sides, you’ll know the feeling.

      I know this doesn’t fit all or most bariatric surgery patients, but then most do not suddenly display an affinity for drinking or gambling.

      As a side note, I understand there’s a new film on Oliver Sacks, whose wonderful, sympathetic, and humane musings on patients continue to inspire.

  4. bhip says:

    I find it likely that there are important physiological interactions btwn us & or neighbors in our gut (we are poo-filled donuts after all) & we will eventually sort it out given time.
    Overstating the impact of latest shiny object/technology/observation is hardly a new phenomenon (Hello, GPCR dimers! What’s up, nano-whatever! I’ve been thing of you, AI….) & will continue as long as it is rewarded with grant $, VC investments, etc

  5. Thoryke says:

    Although microbiome research relating to human health may have its problems, it is not the only arena where researchers are exploring relationships among microbial populations. It would be useful to avoid saying “the” microbiome as if the only one that matters is inside human guts [or other body regions; microbial ecologies in the mouth are different from those on the skin surface, etc…]

  6. fecal transplant says:

    but microbiome is the next big thinggg. can anyone make gluetan degraders??

  7. zero says:

    When encountering a swampy morass of confusing factoids with no strong patterns (let alone a cohesive roadmap), the next step is not to boldly leap ahead with confidence. It is to observe.

    Instead of spending a bunch of money on a few thousand poorly designed studies, let’s spend some time taking samples from the general population. Build a database of gut microbiome characteristics which we can then use to guide hypotheses which will hopefully lead to better-designed studies.

    There are too many basic questions in the field that are unanswerable with our current knowledge. Right now the primary outputs of this research appear to be quack therapies and unreproducible papers, and that’s not helpful to anyone.

    1. zero: The NIH Human Microbiome Project is doing qhat you describe. From their website (linked in my name):

      The HMP has characterized the microbial communities found at several different sites on the human body: nasal passages, oral cavity, skin, gastrointestinal tract, and urogenital tract. The project has examined the role of these microbes in human health and disease. The 5 stated aims of the project included:

      – Development of a reference set of 3,000 isolate microbial genome sequences
      – Initial 16S & mWGS metagenomic studies to generate an estimate of the complexity of the microbial community at each body site, providing initial answers to the questions of whether there is a “core” microbiome at each site
      – Demonstration projects to determine the relationship between disease and changes in the human microbiome
      – Development of new tools and technologies for computational analysis, establishment of a data analysis and coordinating center (DACC), and resource repositories
      – Examination of the ethical, legal and social implications (ELSI) to be considered in the study and application of the metagenomic analysis of the human microbiota

  8. One thing about microbiome studies is that when you “transplant the microbiome” you also have a good opportunity to transfer plain old diseases caused by microbes — microbes that don’t primarily live in the gut but have enough of a presence there to cause infection: hepatitis A, for instance. So these studies can be positive, and can be positive because of microbe transfer, but without having anything to do with “the microbiome” in the sense of the ecosystem of gut bacteria.

    1. matt says:

      Ah, in agreement with this, I’ll insert a shout-out to Vincent Racaniello and the Virology Blog here, about polio and how the Sabin attenuated polio vaccine (OPV) could mutate in the gut and become neurovirulent again, and how viral genomic analysis of the sewer system in a country could indicate polio replicating and circulating in guts even without extant full-blown cases of the disease. Link in the handle to one of his discussions on the topic.

      1. Anonymous says:

        There is another fecal transplant reference, above, but I’ll reply to matt, here, with this NPR news article: “Be Careful Of Fecal Transplants, Warns FDA, After Patient Death. June 14, 2019. Two people got very sick, and one died, during a trial of an experimental procedure known as fecal transplant, according to a statement issued Thursday from the Food and Drug Administration. As a result, the agency is suspending several clinical trials investigating the procedure until safety standards can be assured. …” Link in my handle.

        1. Some Other Dude says:

          Or as Some Dude would say, “eat s%$^ and die”

        2. Radioactive Man says:

          Fecal transplantation seems very primitive. Wouldn’t it make more sense to use a cocktail of cultured “good” bacteria of exactly known composition? Is there a reason this isn’t done?

  9. Allchemistry says:

    In microbiome research it is common practice to use fecal samples as a proxy for the gut microbiome. It has to be seen whether this is indeed the case. Until that murky detail has been settled, I would strongly plea to talk of ‘fecome’ (‘fake’-‘ome’) instead of ‘gut microbiome’.

  10. Zemyla says:

    “The studies that show an effect get published, the studies that don’t go into the drawer (or its electronic equivalent).”

    Isn’t there supposed to be a journal of negative results for this sort of thing?

  11. Lane Simonian says:

    Another interesting aspect of gut-brain research: polyphenols can contribute to a healthy microbiome and a healthy microbiome can increase the bioavailability of polyphenols.

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