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[…] All isolates were determined to be L. johnsonii by 16S rRNA analysis, and all grew in and acidified MRS at indistinguishable rates. Thus, one isolate was chosen, designated LB1, and used for further experiments., L. johnsonii strains LB1 and NCK88, a well-studied L. johnsonii isolate, were each inoculated from frozen glycerol stocks into sterile MRS and incubated anaerobically at 37°C overnight. Cells were precipitated by centrifugation and genomic DNA was extracted using Promega’s Wizard DNA kit. Whole genome sequencing was performed by the Penn State Genomics Core Facility using an Illumina MiSeq instrument with 300 bp paired end reads. Sequencing data was assembled de novo with DNASTAR’s SeqMan NGen (DNASTAR Inc.), and contigs were mapped against the reference L. johnsonii NCC533 genome with progressiveMauve [,]. Genomes were compared with WebACT and dotplots of translated open reading frames were generated with PROmer in Galaxy [–]. Sequence data is available under BioProject ID PRJNA315676., BSH sequences from each strain in our Lactobacillus collection with publically available genomes were identified using NCBI’s Gene database. BSH genes from the fully sequenced and annotated strain L. johnsonii NCC533 [] were used to identify BSH genes from L. johnsonii LB1 and L. johnsonii NCK88 contigs using BLASTp. All putative translated open reading frames were also screened to ensure no additional BSH genes were present in either LB1 or NCK88. Sequences were translated and aligned by ClustalW with MEGA6 []. Maximum Likelihood phylog […]

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