Fig. 3

A library of bacterial strains isolated from the fecal-derived chemostat community is representative of the donor’s microbiota. Bacterial strains from the fecal-derived chemostat community of NS0 or NS1 study participants were isolated by axenic culture using a variety of media formulations. Eighty unique bacterial strains were archived, constituting a library of the NS0 donor, and 118 unique bacterial strains were archived, constituting a library of NS1 donor. a, b, c, d Alluvial plots show relative abundances of bacterial ASVs identified in the fecal sample (left columns), fecal-derived chemostat community at stability (right columns), and the respective bacterial isolate library (idealized equal proportions of ASVs shown for comparison, middle columns) from NS0 (a, b) and NS1 (c, d) individuals. Lines connecting the columns indicate identical ASV across samples. a, c ASVs were stratified by the presence or absence in each sample, indicated by color. The relative abundance of ASVs from the fecal sample found in the isolate library is indicated in brackets adjacent to the left fecal sample bar. b, d Colors represent the nine predominant phyla. ASVs are ordered by prevalence categories. e Prevalence distribution of all CHILD cohort infants at 12 months of age (n = 842 samples) bacterial species (red) or species matched to bacterial isolates from NS0 and NS1 libraries (blue) displaying extensive similarity in representation of bacteria between the two data sets across both common and rare prevalence species