Comparative genomic analyses of Lactobacillus rhamnosus isolated from Chinese subjects

Abstract

Lactobacillus rhamnosus has been found in many niches, including human intestine, vagina, mouth and dairy products. To intensively investigate the genomic diversity of this species, draft genomes of 70 L. rhamnosus strains isolated from different Chinese subjects were sequenced and further investigated. The pan-genome of L. rhamnosus was open. And gene-trait matching (GTM) was done to explore the carbohydrate utilization ability and antibiotic resistance, and to establish a pattern of gene existence/absence and growth/absence. There were no significant correlations between genetic diversity of the strains and the age or region of the donors. The current results extend the understanding of L. rhamnosus, which could be used as a reference for subsequent research as well as mining and application of the species.

Introduction

Lactobacillus is the most diverse genus of lactic acid bacteria (LAB), and is usually found in fermented foods, feeds, oral and gastrointestinal tracts (Barrons & Tassone, 2008). Lactobacillus in the gut have an important role, for example, immunity regulation, cholesterol control, and gastrointestinal function improvement, on the intestinal micro-ecological balance and health of hosts (Damodharan et al., 2016; Reuman et al., 1986). In addition, Lactobacillus have an important role in food production and processing, such as fermented dairy products (Todorov, 2010).

L. rhamnosus is a Gram-positive bacterium that exists in a variety of niches, such as the human intestine and vagina (Pascual et al., 2008). L. rhamnosus GG is one of the best commercialized strain among L. rhamnosus. It has a strong resistance to gastrointestinal digestion and potential probiotic characteristics. Previous studies on L. rhamnosus focused on its functional benefits including various diarrhea treatments, immunity improvement, and respiratory infections prevention (Barbieri et al., 2017; Evans et al., 2016). Phenotype studies were carried out, such as acid tolerance, bile salt tolerance, carbohydrate utilization and adherence to epithelial cells (Ceapa et al., 2016, 2015; Succi et al., 2005; Tripathi et al., 2013).

To explore the metabolism, evolution and speciation, high-throughput methods (e.g., site sequence typing (MLST) and OmniLog (Biolog) phenotyping (Di Cagno et al., 2010) have been used to analyze genotype and phenotype (Bao et al., 2016). Comparative genomic analysis is a common tool in bioinformatics (Kant et al., 2011) that is able to identify the association between strains and their origins as well as to evaluate the gene distribution of specific species (Kelleher et al., 2017). It is significant for strain characteristics such as combining phenotypic profiles with strain-specific genetic diversity allows the assignment of unknown functions to specific genetic loci and to determine interactions with the hosts (Siezen et al., 2010). It also provides a new approach to effectively assess the diversity of strains. Genetic diversity of several species among the Lactobacillus genus had been carried out, such as L. plantarum (Duar et al., 2017; Martino et al., 2016), L. casei (Broadbent, 2012), L. reuteri (Zheng et al., 2015) and L. salivarius (Raftis et al., 2011). Current research on the L. rhamnosus genome was primarily concerned with the use of carbohydrates. Ceapa et al. (2015; 2016) predicted that L. rhamnosus had a number of carbohydrate transport and utilization genes, combined with phenotypic analysis, with which the adhesion-related functional genes were predicted. To investigate the genomic diversity of L. rhamnosus, Douillard et al. (2013b) sequenced and compared the genome and phenotype validation of 100 L. rhamnosus strains from different niches.

To further learn about the genetic diversity of L. rhamnosus from Chinese subjects, 70 L. rhamnosus strains were isolated, draft-genome sequenced and analyzed with comparative genomics approaches as well as gene-trait matching analysis for both carbohydrate utilization and antibiotic resistance based on the genotype-phenotype combination.