New paper out and about: An ecological perspective on human infant gut microbiome assembly

Post-doc John Guittar, Ashley, and John's co-advisor at Michigan State's Kellogg Biological Station Elena Litchman have a new publication this week in Nature Communications.

Title: Trait-based community assembly and succession of the infant gut microbiome

Abstract:

The human gut microbiome develops over early childhood and aids in food digestion and immunomodulation, but the mechanisms driving its development remain elusive. Here we use data curated from literature and online repositories to examine trait-based patterns of gut microbiome succession in 56 infants over their first three years of life. We also develop a new phylogeny-based approach of inferring trait values that can extend readily to other microbial systems and questions. Trait-based patterns suggest that infant gut succession begins with a functionally variable cohort of taxa, adept at proliferating rapidly within hosts, which gradually matures into a more functionally uniform cohort of taxa adapted to thrive in the anoxic gut and disperse between anoxic patches as oxygen-tolerant spores. Trait-based composition stabilizes after the first year, while taxonomic turnover continues unabated, suggesting functional redundancy in the traits examined. Trait-based approaches powerfully complement taxonomy-based approaches to understanding the mechanisms of microbial community assembly and succession.

In my opinion, there are two neat take-homes from this work:

1. Trait-based analysis of communities stabilize/converge BEFORE they do based on composition, *suggesting* functional redundancy

2. John developed a new tool for phylogenetic inference of traits that provides an idea of confidence of coherence of the trait within lineages. So, it can be used more precisely than a one-size-fits-all phylogenetic inference of traits, and to inform how "far back" traits should be inferred along a phylogeny. Cool, right?

Let us know what you think!