Complete Genome Sequencing and Comparative Genome Characterization of Lactobacillus johnsonii ZLJ010, a Potential Probiotic With Health-Promoting Properties.

Wei Zhang,Sixin Wang,Hui Liu,Haifeng Ji,Yamin Wang,Jing Wang,Dongyan Zhang

doi:10.3389/fgene.2019.00812

Abstract

Lactobacillus johnsonii ZLJ010 is a probiotic strain isolated from the feces of a healthy sow and has putative health-promoting properties. To determine the molecular basis underlying the probiotic potential of ZLJ010 and the genes involved in the same, complete genome sequencing and comparative genome analysis with L. johnsonii ZLJ010 were performed. The ZLJ010 genome was found to contain a single circular chromosome of 1,999,879 bp with a guanine–cytosine (GC) content of 34.91% and encoded 18 ribosomal RNA (rRNA) genes and 77 transfer RNA (tRNA) genes. From among the 1,959 protein coding sequences (CDSs), genes known to confer probiotic properties were identified, including genes related to stress adaptation, biosynthesis, metabolism, transport of amino acid, secretion, and the defense machinery. ZLJ010 lacked complete or partial biosynthetic pathways for amino acids but was predicted to compensate for this with an enhanced transport system and some unique amino acid permeases and peptidases that allow it to acquire amino acids and other precursors exogenously. The comparative genomic analysis of L. johnsonii ZLP001 and seven other available L. johnsonii strains, including L. johnsonii NCC533, FI9785, DPC6026, N6.2, BS15, UMNLJ22, and PF01, revealed 2,732 pan-genome orthologous gene clusters and 1,324 core-genome orthologous gene clusters. Phylogenomic analysis based on 1,288 single copy genes showed that ZLJ010 had a closer relationship with the BS15 from yogurt and DPC6026 from the porcine intestinal tract but was located on a relatively standalone branch. The number of clusters of unique, strain-specific genes ranged from 42 to 185. A total of 219 unique genes present in the genome of L. johnsonii ZLJ010 primarily encoded proteins that are putatively involved in replication, recombination and repair, defense mechanisms, transcription, amino acid transport and metabolism, and carbohydrate transport and metabolism. Two unique prophages were predicted in the ZLJ010 genome. The present study helps us understand the ability of L. johnsonii ZLJ010 to better adapt to the gut environment and also its probiotic functionalities.

Highlights

The gastrointestinal tract (GIT) is home to a massive and diverse collection of symbiotic microbes
A single colony of L. johnsonii ZLJ010 was inoculated in modified De Man, Rogosa, and Sharpe (MRS) broth (20 g of sucrose, 20 g of soy peptone, 20 g of beef extract, 7.5 g of yeast extract, 5 g of sodium acetate, 2 g of diammonium hydrogen citrate, 2 g of potassium dihydrogen phosphate, 0.58 g of magnesium sulfate, 0.19 g of manganese sulfate, and 1 ml of Tween 80 per liter; pH 6.8) for 18 h at 37°C under microaerophilic condition
Our results indicated that the genome sequences may differ even in the same bacterial species, and phylogenomic analysis represents a reliable and high resolved approach to distinguish closely related species

Summary

Introduction

The gastrointestinal tract (GIT) is home to a massive and diverse collection of symbiotic microbes. A total of seven publicly available complete genome sequences of L. johnsonii strains were obtained from the NCBI database (Table 1). The sequence data for L. johnsonii ZLJ010 genome has been deposited at GenBank under the accession number CP032680.

Results

Conclusion