An evolution-based framework for describing human gut bacteria

The human gut microbiome contains many bacterial strains of the same species (‘strain-level variants’). Describing strains in a biologically meaningful manner rather than purely taxonomic objects is an important goal but challenging due to the complexity of strain-level variation. Here, we measured patterns of co-evolution across >7,000 strains spanning the bacterial tree-of-life. Using these patterns as a prior for studying hundreds of gut commensal strains that we isolated, sequenced, and metabolically profiled revealed widespread structure beneath the phylogenetic level of species. Defining strains by their co-evolutionary signatures enabled predicting their metabolic phenotypes and engineering consortia from strain genome content alone. Our findings demonstrate a biologically relevant organization to strain-level variation and motivate a new schema for describing bacterial strains based on their evolutionary history., Materials and Methods (futher details and metadata in associated article's supplementary material) Creating a bank of commensal human gut microbiome strains Fecal samples were obtained from 28 human donors that fell within the age range of 18 to 63 with a median age of 35. Donors were selected as those with no antibiotic use in the past year, no known history of diabetes, colitis, autoimmune disease, cancer, pneumonia, dysentery, or cellulitis at time of consent. Institutions that approved protocols of fecal sample collection were Memorial Sloan Kettering (MSK) and the University of Chicago. Fresh fecal samples were immediately reduced in an anaerobic chamber upon collection and diluted and cultured on various growth media. Agar media types vary, but include any of following: Columbia Blood Agar, Brain Heart Infusion +Yeast, Brain Heart Infusion + Mucin, Brain Heart Infusion + Yeast + Acetate or N-Acetylglucosamine, reinforced Clostridial Agar, Peptone Yeast Glucose, Yeast Casitone Fatt..., , # An evolution-based framework for describing human gut bacteria

Extended Data for \"An evolution-based framework for describing human gut bacteria\".

## Description of the data and file structure

**Data: xslx file**

·     **Panel A:** Data matrix of Orthologous Gene Groups (OGGs) annotations for each of the 669 strains in the Commensal Strain Bank. First column holds the unique ID for each strain. Subsequent columns hold the data for each OGG as listed in first row. Each value denotes the number of sequences from the strains coding regions that are mapped to that OGG (see methods).

·     **Panel B:** Projections of each of 669 strains onto the principal components describing co-evolutionary variation in UniProt (see methods). First column is the strain id, subsequent columns are for each of the 7047 principal components with each value denoting the contribution of strain *i* onto principal component *k.*

·      **Panel C:** Spectral tree of all 669 strains from commensal strain b...