Environment dominates over host genetics when it comes to “shaping” gut microbiota

The gut microbiome has become increasingly recognized as having an extremely important role in innumerable aspects of human physiology and health. A fundamental question has been the extent to which microbiome composition is determined by host genetics. Previous studies have identified several heritable bacterial taxa (in biology, a taxon, the plural is ‘taxa’, is a group of populations of an organism, determined by taxonomists to form a unit) –– but the combined bacterial abundance accounted for by all the taxa has not yet been quantified. Other studies have found associations between host single-nucleotide polymorphisms or variants (SNPs; SNVs) and individual bacterial taxa or pathways. However, most previously reported association studies are not statistically significant after correction for multiple-testing.

A recent study identified 42 SNPs that together explained 10% of the variance of microbiome diversity. However, the statistical significance of those data have not yet been evaluated. Therefore, the extent to which the human genome shapes the microbiome composition remains unclear. In the attached article, authors studied microbial–genetic associations using a cohort of 1,046 healthy Israeli individuals with meta-genome-sequenced and 16S ribosomal RNA (rRNA) gene-sequenced gut microbiomes, the host genotypes, anthropometric (dimensions & propertions of the human body such as height and weight) and blood metabolic profiles, and dietary habits. The volunteers in this cohort were of several different ancestral origins, but the authors assumed, owing to their broadly similar lifestyles, that they share a relatively homogeneous environment (i.e. the gut microbiomes would be expected to be much more different –– if one studied a group from sub-Saharan Africa vs a group from Boulder, Colorado).

Authors show [attached] that the gut microbiome is not significantly associated with the host’s genetic ancestry, and that host genetics contribute a minor role in determining microbiome composition. In contrast, authors noted that there are significant similarities in compositions of the microbiomes of genetically unrelated individuals who share a household, and that >20% of the inter-person microbiome variability is associated with factors related to diet, drugs being taken, and anthropometric measurements. Furthermore, authors demonstrate that microbiome data significantly improve the prediction accuracy for many human phenotypes (traits, such as glucose or lipoprotein levels and obesity measurements), compared with models that use only host genetic and environmental data. These intriguing results suggest that microbiome alterations aimed at improving clinical outcomes may be studied across diverse genetic backgrounds.

Nature 8 Mar 2o18; 555: 210–215
COMMENT: I have to wonder if a basic precept is being missed, misunderstood, or not considered.
The microbiome is being addressed as an entity — maybe likened to an arm or an organ. But there is evidence I have read, indicating the microbiome can change — say, with antibiotics or medications with known toxic effects. That being the case, are we perhaps focusing on the microbiome as a static, rather than a dynamic, force? D.R.

Sorry if you got that impression. Certainly antibiotics (below it was mentioned ‘drugs being taken’) and dietary changes can alter the microbiome. The gut microbiome is definitely dynamic, not static. Also, keep in mind that distinct microbiomes exist in the nose, ear, vagina and umbilicus (belly button) –– and even on the skin and around the conjunctiva (inside & outside of eyelid).

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