McDonald et al., 2018. American Gut: an open platform for citizen science microbiome research. mSystems.

This is a summary of our DalMUG journal club discussion of the above paper written by [Emily Lamoureux].

Summary

The American Gut Microbiome Project branches off of the Earth Microbiome Project, with the goal of comparing the human microbiome to the environmental microbiome. The project employs citizen-scientists, meaning the general population can send in samples, allowing them to collect data from over 10,000 participants, which was made publicly available. This article summarizes some of the important health and lifestyle relationships that this data has uncovered.

The researchers selected a subset of samples corresponding to almost 4000 healthy adults. They first compared how the microbiome varies between individuals living either industrial and traditional lifestyles and found that sample diversity differs between these two groups and that variation is higher within industrial populations.

Since samples were swabbed and shipped without preservatives, bacterial blooms were characterized using culturing and mass spectrometry. They were able to confirm that sequences identified as blooms (sub OTUs) in silico corresponded to sequences that bloomed when samples were cultured.

When comparing environmental and host-associated samples, they found that while human gut microbiomes are not as phylogenetically diverse as different environments, the dispersion of samples on a PCoA plot is comparable and emphasizes the need to deepen the sample space of the human gut microbiome. Geographic location had only a weak association with sample composition. It was also observed that an individual’s microbiome changed over time, they still resembled themselves more than others.

Consumption of a diverse number of plants (>30) was correlated with having more short-chain fatty acid producer compared to those consuming low plant diversity (<10), as well as less of certain antibiotic resistance genes. Metabolomics revealed that octadecadienoic acid levels were higher in individuals consuming high plant diversity.

Finally, high-performance liquid chromatography mass spectrometry (HPLC-MS) allowed the identification of novel molecules in the gut microbiome. N-acyl amides, important in host metabolism were observed and correlated with thyroid disease. They also found evidence that both antibiotics and dietary plant diversity promote higher molecular diversity in the gut.

Points of Interest

  • Endocrine associations: HPLC-MS identified several important ties between endocrine function and the microbiome, including increased levels of a cholic acid produced through microbial dihydroxylation in persons without thyroid disease. To date there are not many specific examples of how microbial products affect human health and physiology
  • Dietary correlations: The idea that eating a higher diversity of carbohydrates and dietary fibers promotes higher microbial diversity is pretty cool and could also conversely explain why certain individuals have difficulty digesting fibers
  • There is a lot of data and no doubt lots of information that has yet to be uncovered from this cohort, but we felt that the authors concisely presented a number of thorough analyses in this article

Points of Consideration

  • Authors discuss only unweighted results apart from data in Figure 2 – Did weighted UniFrac plots show a significant difference in any other analyses apart from figure 2?
  • Metabolite blooms: Can similar methods for removal of bacterial blooms be used to remove stool metabolites that were produced during transport of the sample without preservatives?
  • Figure 5C – distribution of samples in box plots does not look as significant as the statistics show. Why is that?
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