Synthetic community used to colonize germ-free C57BL/6 females, sequences collected from F1 offspring
Bacteria from frozen culture stocks were introduced as a synthetic community (AC) into 6 week old female and male gnotobiotic C57BL/6 mice. Mice were housed by sex for 4 weeks prior to establishment of mating trios. Mothers were allowed to carry pregnancies to term and F1 progeny were weaned at 21 days of age. F1 offspring were sexed and maintained in sex seperated cages until the time of sacrifice at 8 weeks of age.  Cells were therefore maintained over the course of the experiment within mice until sampling occurred. Immediately after collection, samples were subjected to flash-freezing in ethanol chilled with dry ice and stored at -80 C until total community DNA extractions could be performed. DNA was extracted from intestinal samples using mechanical disruption (bead-beating with 0.1 mm zirconium beads) in phenol:chloroform:IAA in the same manner as described by McNulty et al. in a previous publication (PMID: 22030749).Organisms used:  Bacteroides_caccae_ATCC_43185, Bacteroides_ovatus_ATCC_8483, Bacteroides_thetaiotaomicron_VPI-5482,  Collinsella_aerofaciens_ATCC_25986, Eubacterium_rectale_ATCC_33656, Escherichia_coli_MS_200-1. community composition was determined by amplicon sequencing of the variable 4 (V4) region of the 16S rRNA gene (Kozich et al., 2013) using the Illumina MiSeq platform (San Diego, CA). Sequences were analyzed in mothur (Schloss et al., 2009) following recommended procedures (Kozich et al., 2013). Sequences were clustered into 97% operational taxonomic units (OTUs) using OptiClust (Westcott and Schloss, 2017) and classified to a custom database containing the species used in this study: Bacteroides caccae (AAVM02000001), Bacteroides ovatus (AAXF02000018), Bacteroides thetaiotaomicron (AE015928), Collinsella aerofaciens (AAVN02000007), Eubacterium rectale (L34627), and a number of Escherichia coli MS strains as the strain used (MS 200-1) was not available (ADTK01000014, ADTL01000003, ADTP01000052, ADTR01000016, ADTX01000014, ADUA01000035, ADUG01000003, ADWQ01000120, ADWR01000036, ADWS01000032, ADWT01000015, ADWU01000043, ADWV01000069).