The opportunistic pathogenic yeast Candida albicans was co-cultured alongside mixed faecal microbiota inocula from six different healthy human donors under anaerobic conditions. 16S rRNA gene sequencing was then carried to determine which gut microbiota taxa were most associated with inhibition of C. albicans growth in these co-cultures.

The human gut microbiota protects the host from invading pathogens and the overgrowth of indigenous opportunistic species via mechanisms such as competition for nutrients and by production of antimicrobial compounds. Here, we investigated the antagonist activity of human gut bacteria towards Candida albicans, an opportunistic fungal pathogen, which can cause severe infections and mortality in susceptible patients. Co-culture batch incubations of C. albicans in the presence of faecal microbiota from six different healthy individuals were carried out, and revealed varying levels of inhibitory activity against C. albicans. 16S rRNA gene sequence profiling, using variable regions V1-V2, of these faecal co-culture bacterial communities was used to indicate which gut microbiota taxa were most strongly correlated with antagonistic activity against C. albicans after co-culture. The dataset includes 16S rRNA gene amplicon data from the faecal inocula of the healthy donors utilised in the culture-based experiments, as well as from the samples collected after roughly one or two days of incubation, with or without the concurrent presence of C. albicans in co-culture. Two technical replicates (a and b) were sequenced per culturing condition time point. Samples were sequenced on the Illumina MiSeq platform, using 2 x 250 bp read length.