1. Experimental design for high‐throughput characterization of synthetic human gut microbiome consortia
Experimental design for high‐throughput characterization of synthetic human gut microbiome consortia Phylogenetic tree of the 12‐member synthetic ecology spanning the major phyla in the gut microbiome including Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. Phylogenetic analysis was performed using a concatenated alignment of single‐copy marker genes obtained via PhyloSift (preprint: Darling et al, 2014). Maximum likelihood trees were generated using default options. The scale bar represents the number of substitutions per site in the alignment.Schematic of the experimental design for this study. Species were combined using an approximately 1:1 or 19:1 initial proportion based on absorbance measurements at 600 nm (OD600) into microtiter plates using liquid‐handling robotic manipulation. Approximately every 12 h, samples were collected for multiplexed 16S rRNA gene sequencing (black circles). Relative abundance was measured using multiplexed 16S rRNA gene sequencing of the V3–V4 region using dual‐indexed primers compatible with an Illumina platform (stacked bar plot, bottom right). Serial transfers were performed in approximately 24 intervals (purple bars, top) by transferring an aliquot of the communities into fresh media using a 1:20 dilution. In parallel, time‐resolved OD600 measurements of monospecies and consortia were performed.
Ophelia S Venturelli et al. Mol Syst Biol 2018;14:e8157
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