The complete genome sequences of the two novel probiotics were isolated from the human gut microbiota: Pediococcus acidilactici WNYM01 and Pediococcus acidilactici WNYM02, vitamin B9, and B2-producers

Abstract

Background We previously isolated the two strains Pediococcus acidilactici (P. acidilactici) WNYM01 and P. acidilactici WNYM02 from human gut microbiota as producers of vitamin B2 and B9 and they were identified by a molecular method based on sequencing of 16S rRNA gene. Their probiotic properties were confirmed in vitro and in vivo in rat colitis model. Objective This study aimed to sequence the complete genome of these two valuable probiotic strains. It will provide comprehensive data about them for further applications in research and health applications. Materials and methods The genomic DNA from P. acidilactici WNYM01 and P. acidilactici WNYM02 were extracted using AxyPrep bacterial genomic DNA miniprep kit. The Illumina NexteraTM tagmentation protocol was used to prepare libraries and then they were sequenced using the MiSeq with an Illumina v3 cassette (Illumina, USA). The genome sequences were constructed from 3.2 million paired-end reads ranging in size from 80 to 250 base pairs. The DNA sequence contigs were aligned using whole-genome alignment within CLC Genomics and annotation was done by RAST tool. Results and conclusion The genome sequence of P. acidilactici WNYM01 includes 2,002,062 bases while P. acidilactici WNYM02 includes 1,999,478 bases and they submitted to the NCBI database. The folate and riboflavin genes were detected within the two genomes and the differentiation between them has been recorded. Whole-genome alignments were used to detect functional differences related to their potential use as probiotics. The genomic sequences of these two strains will give extensive data on these interesting strains for future research uses.