2.1. Genome Sequencing of Bacteria

L. salivarius SNK-6 was isolated from the ileum of Xinyang black-feather laying hens and grown in De Mann, Rogosa and Sharp broth, and incubated at 41 °C for 24 h under anaerobic conditions. Whole-genome sequencing of L. salivarius SNK-6 was performed on the PacBio (Pacific Biosciences, Menlo Park, CA, USA) and Illumina MiSeq (Illumina, San Diego, CA, USA) sequencing platforms. SOAPec v2.0 software was used to assemble paired-end reads de novo into high-quality sequences [16]. Clean reads were assembled using SPAdes genome assembler v3.11.1 [17]. PacBio reads were assembled using HGAP and CANU (v1.6) software to obtain scaffold sequences [18,19]. The contigs and scaffolds sequences obtained from the two platforms were assembled and the inner gaps within each scaffold were filled by pilson v1.22 software [20]. Putative coding sequences were annotated with GeneMarkS software. tRNA and rRNA were annotated by tRNAscan-SE and Barrnap (0.9-dev) (http://github.com/tseemann/barrnap (accessed on 3 March 2022)), respectively. The complete genome sequence of L. salivarius SNK-6 is available at GenBank under accession number {"type":"entrez-nucleotide-range","attrs":{"text":"CP011403-CP011405","start_term":"CP011403","end_term":"CP011405","start_term_id":"822667909","end_term_id":"822669573"}}CP011403-CP011405. The strain was deposited at the Chinese Center for Type Culture Collection, accession number CCTCC No: M2018044, Wuhan, China).