Miseq 2 150 bp platform

Pseudomonas sp. isolate 9.1 (DSM 105530; Ravi et al. [19 (link)]) and P. putida KT2440 (DSM 6125) were cultivated in liquid LB medium (Sambrook and Russell [55 ]; see “Culture media and conditions,” below), and genomic DNA from strain 9.1 was extracted using the Invitrogen PureLink genomic DNA minikit (Thermo Scientific, Carlsbad, CA, USA) and eluted with Invitrogen UltraPure DNase/RNase-free distilled water (Thermo Fisher Scientific, Waltham, MA, USA). Genomic DNA from P. putida KT2440 was purified using the GeneJET genomic DNA purification kit from Thermo Fisher Scientific Baltics (Vilnius, Lithuania). Paired-end whole-genome sequencing was performed using an Illumina MiSeq (2 × 150 bp) platform at GATC Biotech AG (Cologne, Germany). The raw data from the sequencer consisted of 6,829,359 paired reads with an average read length of 151 bp and 58% GC content (Table 1). Read quality was assessed with FastQC (v0.11.5; Andrews [56 ]).

DNA was extracted from fecal, ileal, and cecal samples using the Mobio 96-well extraction kit following the manufacturer’s instructions. For amplicon library generation, the V4 region of the 16S rRNA gene was amplified with gene-specific primers, as described^{38 (link)}. The reverse amplification primers contained a 12-base pair Golay barcode for multiplexed sequencing runs that support pooling up to 864 samples. Amplicons were prepared in triplicate, pooled, and quantified. The 254 bp V4 region was sequenced using the Ilumina MiSeq 2 × 150 bp platform. OTUs were picked using GreenGenes 13_8 for reference, using the open reference picking strategy.