I Sing The Body's Microbiome

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Ah, our body’s microbiome, the bacteria living in symbiotic harmony in our gut, that newly discovered source of wellness, its mysteries only slowly being revealed. Our microbiome is an inner ecology of Planet Us. And thought of in that context, two new small, exploratory studies, may provide lessons about change and resilience.


The current understanding of the gut microbiome is anchored by the belief that both diet and geography influence its composition. In the first study, researchers looked at the diversity of our gut flora as individuals immigrated and assimilated, changing diet and geography. The inspiration may have been the finding that immigrants to the US often develop weight gain and Western diseases - obesity, hypertension, diabetes, and coronary artery disease. While refeeding of individuals who came from food challenged areas is felt to be part of the issue, changing diet has also been implicated.

The authors collected stool samples, 24-hour food recall surveys and demographics from two distinct Thai populations, the Hmong and Karen. Individuals included those still living in Thailand as well as immigrants (1st generation) and their children (2nd generation). Thai immigrants were chosen because the study was conducted in Minnesota a central site for their immigration; women formed the predominant research population because they were more frequently the immigrants. Americans of European ancestry served as the control.

  • Microbiologic richness and diversity were greatest in current Thai residents.
  • 30% of that diversity was lost in the first generation immigrants, and the diversity continued to decline and resemble that of the control group as time in the US increased and in the 2nd generation, American born Thai children.
  • Bacteroides strains replaced Prevotella strains among immigrants, the extent of that shift again associated with length of residence in the US.
  • The loss of Prevotella was felt to be the driving force behind a decreasing functional ability of the microbiome to degrade dietary fibers indigenous to the native Thai diet. Think of it as use it or lose it.
  • Dietary shifts to a Western diet was felt to account for only about 16% of total variation.
  • Westernization of the microbiome began within nine months of arrival.


A second, "proof of concept" like study, looked at 12 healthy men treated for four days with an antibiotic cocktail meant to mimic common first-line choices for intensive care patients. [1] The outcome was the effect on the gut microbiome over a subsequent six month period, again measured by stool cultures taken at various time intervals. It is no surprise, at least to clinicians, that the antibiotics did not sterilize the gut, but it did bring about changes.

  • There was an immediate drop in the diversity and richness of the microbiologic populations, but by Day 8 diversity was returning although it never reached baseline values.
  • By Day 8, the relative abundance of about 50 species changed, some increasing and others decreasing – clearly, the ecology was different. And while some bacterial species were still absent after six months, by Day 42, the ecology had, for the most part, returned to its baseline.
  • Antibiotic resistance was only one of many virulence factors enhanced by the antibiotic exposure that lead to an early increase in pathologic bacteria. But over time the pathologic bacteria were again overrun by more symbiotic species. Virulence factors
  • Interestingly, Clostridium species which had not been seen initially were now present – this is a species that forms spores as protection in an unhealthy environment and then returns to its other form when “the coast is clear;” it is the source of antibiotic-related hospital-acquired morbidity, C. difficile diarrhea.

The forces of evolution

Within Planet US, the ecology we call the gut microbiome is subject to evolutionary pressures we deploy. It can show resilience when a one-off force, like a course of antibiotics, alters the relative hostility of their environment. It recovers but may bear a few scars. And that same population when subject to more consistent evolutionary pressures, specifically of diet, shows more long-term changes, perhaps we can characterize them as a new accommodation to the environment rather than a failed restoration.

The choices we make in our lives, exercise, diet, medication all impact the ecology we call ourselves. But the impact is more similar to evolution than an intentional design; more a subtle shift or nudge than a marked change. Our ability to identify cause and effect of our life choices are tied up in evolutionary forces, that we still struggle to understand fully.

[1] Vancomycin, Gentamicin, and Meropenem


Source: US Immigration Westernizes the Human Gut Microbiome  Cell DOI: 10.1016/j.cell.2018.10.029

Recovery of gut microbiota of healthy adults following antibiotic exposure Nature Microbiology DOI:10.1038/s41564-018-0257-9