Miseq 16s rrna

Draft genomes for Streptomyces were generated as described before [27 (link)]. The Streptomyces phylogenetic tree was generated by FastTree version 2.2.0 [65 (link)] from 49 concatenated core genes that were aligned then trimmed using GBLOCKS version 1.0.4 [66 (link), 67 (link)]. The phylogenetic tree for yeast species was built manually based on known taxonomic information and existing phylogenies [17 , 35 (link), 68 (link)]. DNA from the mixed microbial consortia was extracted from biomass pellets using the QIAGEN DNeasy^® PowerSoil^® Pro kit (QIAGEN, Inc., Germantown, MD, USA), according to manufacturer’s instructions. DNA was submitted to the University of Wisconsin Biotechnology Center (UWBC; https://www.biotech.wisc.edu/) for paired-end, 2 × 300 bp Illumina MiSeq 16S rRNA gene amplicon sequencing using primers targeting the V3–V4 region of the 16S rRNA gene [69 (link)]. Raw 16S rRNA gene amplicon sequences were processed through QIIME v1.9.1 [70 (link)], according to previously published methods [71 (link)], with the following modifications. Representative taxonomic groups from the Additional file 4: Table S6 were processed through the summarize_taxa.py script, which summarizes OTUs by each taxonomic level (phylum through genus).

Raw sequences were processed using QIIME following the protocol for 454 pyrosequencing data or Illumina MiSeq 16S rRNA gene amplicon sequencing data, according to previously published methods (Fortney et al., 2016 (link), 2018 (link)).

All faecal samples were collected and stored at −20°C until analysis. Each sample (250 mg) was weighed into a sterile microtube and DNA extracted using the MO-BIO PowerSoil^® DNA Isolation Kit (catalogue no. 12888; MO-BIO Laboratories). Illumina MiSeq 16S rRNA gene sequencing was performed as described in a previous study⁽¹⁶ (link)⁾.