Bacterial DNA was extracted from ca. 50 mg of fecal samples and 30–50 mg of cecal content using the Repeated Bead Beating (RBB) method for automated DNA purification.92 (link) 200 µL of the clarified supernatant collected from the two bead beating rounds was used for DNA extraction with the Ambion Magmax™ −96 DNA Multi-Sample Kit (4413022, Thermo Fisher Scientific, USA) using the KingFisher™ Flex automated purification system (Thermo Fisher Scientific, USA). DNA was quantified using Quant-iT™ Pico Green dsDNA Assay (Invitrogen, San Diego, CA, USA). Library preparation and Illumina MiSeq sequencing of the hypervariable V3-V4 regions of the 16S rRNA gene were performed as previously described.93 (link)Sequences were processed using QIIME2 v.2020.11 pipeline.94 (link) Demultiplexed 250-bp paired-end sequences were denoised using DADA2 to obtain an amplicon sequence variant (ASV) table.95 (link) Singletons (ASV present <2 times) and ASVs present in less than 10% of the samples were discarded. Taxonomic classification was performed using a pre-trained naive Bayes classifier implemented in QIIME2 against the SILVA 132 reference database.96 (link) Taxa that could not be identified at genus-level are referred to as the highest taxonomic rank identified. Samples meeting quality criteria (107 out of 108) had a mean sequencing depth of 11952 reads.