SAMEA112151385 ERS14261285 uncultured Clostridia bacterium This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR6760072 of study ERP123933. EBI Generic Generic.1.0 ERC000047 2022-11-21 2022-11-21 SAMEA112151385 EMG EMG 2022-11-21T20:19:13Z 2022-11-21T20:19:13Z public ERR6760072_bin.67_metawrap_v1.3_MAG Many fragments with little to no review of assembly other than reporting of standard assembly statistics metaSPAdes v3.15.3 MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. metawrap v1.3 mouse digestive system EMG broker account, EMBL-EBI 2018-01-01 95.16 CheckM 0.03 feces USA not provided not provided metagenome-assembled genome mouse gut metagenome digestive tube mouse gut metagenome Polycystic ovary syndrome (PCOS) impacts ~10% of reproductive-aged women worldwide. In addition to infertility, women with PCOS suffer from metabolic dysregulation which increases their risk of developing type 2 diabetes, cardiovascular disease and non-alcoholic fatty liver disease. Studies have shown differences in the gut microbiome of women with PCOS compared to women without the disorder, a pattern replicated in mouse models. Recently, using a letrozole-induced mouse model of PCOS, we demonstrated that cohousing was protective against development of both metabolic and reproductive phenotypes and showed via 16S amplicon sequencing that this protection correlated with time-dependent shifts in gut bacteria. Here, we applied untargeted metabolomics and shotgun metagenomics approaches to further analyze the longitudinal samples from the cohousing experiment. Analysis of beta diversity with the three ‘omics datasets found that untargeted metabolites had the strongest correlation to both disease and cohoused states and that shifts in metabolite diversity were detected prior to shifts in bacterial diversity. In addition, log2-fold analyses found numerous metabolite features, particularly bile acids (BA), to be highly differentiated between placebo (P) and letrozole (LET), as well as cohoused LET versus LET. Moreover, combination of BA and metagenomic features resulted in the best overall random forest classification accuracy, with BAs contributing the most to the classification accuracy. Our results indicate that changes in gut metabolites, particularly BAs, are associated with a PCOS-like phenotype in the LET mouse model as well as the protective effect of cohousing. Our results also suggest that transfer of metabolites via coprophagy occurs rapidly and may precipitate changes in bacterial diversity. This study joins a growing body of research highlighting changes in primary and secondary bile acids that may provide a link between host metabolism and gut microbes relevant to the pathology of PCOS. SAMEA7302550 ERR6760072_bin.67_metawrap_v1.3_MAG Illumina NovaSeq 6000 The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__;f__;g__;s__ multi-marker approach