16S rRNA amplicon sequencing of a defined five-strain gut bacterial consortium

This study presents 16S rRNA gene amplicon sequencing data from a defined five-strain gut bacterial consortium composed of Bifidobacterium longum subsp. infantis, Bifidobacterium adolescentis, Roseburia intestinalis, Roseburia hominis, and Roseburia inulinivorans. The consortium was cultivated anaerobically in YCFA medium and subjected to four sequential growth cycles under different carbon substrate conditions: glucose, human milk oligosaccharides (HMOs supplemented with 2'-fucosyllactose), dietary fibers (arabinoxylan and galactomannan), and alternating substrate-switch conditions between HMOs and fibers. Cultures were diluted 100-fold into fresh medium at the start of each cycle and incubated for 14–16 hours. Samples were collected at the end of each cycle, washed, and stored prior to DNA extraction. DNA was extracted using the PureLink Microbiome DNA Purification Kit and used for 16S rRNA gene amplicon sequencing on an Illumina platform to monitor community composition dynamics across substrate conditions. This dataset captures controlled shifts in community structure in response to sequential exposure to milk-derived and plant-derived glycans in a defined microbial consortium.