Comparative analysis of probiotic bacteria based on a new definition of core genome.

Maria Satti,Masanori Arita,Yasuhiro Tanizawa,Akihito Endo

doi:10.1142/s0219720018400127

Abstract

The commensal genus Bifidobacterium has probiotic properties. We prepared a public library of the gene functions of the genus Bifidobacterium for its online annotation. Orthologous gene cluster analysis showed that the pan genomes of Bifidobacterium and Lactobacillus exhibit striking similarities when mapped to the Clusters of Orthologous Group (COG) database of proteins. When the core genes in each genus were selected based on our statistical definition of "core genome", core genes were present in at least 92% of 52 Bifidobacterium and in 97% of 178 Lactobacillus genomes. Functional comparison of the core genes of the two genera revealed a significant difference in the categories "amino acid transport and metabolism" representing their difference in niche specificity. Over-represented Bifidobacterium protein families were primarily involved in host interactions, the complex compound metabolism, and in stress responses. These findings coincide with the published information and validate our bias-resilient definition of the core genome.

Highlights

The Bidobacterium wasrst isolated in 1899 by Henri Tissier from the feces of healthy breast-fed infants.[1]
We collected the complete genomes of 67 Bidobacterium, 8 lactic acid bacteria strains and Bacillus subtilis contained in the NCBI Assembly Database (Table 1)
The approximate G þ C content ranged from 53–66% (Fig. 1(b)) and the approximate number of coding sequences (CDS) from 1200–2500 (Fig. 1(c))

Summary

Introduction

The Bidobacterium wasrst isolated in 1899 by Henri Tissier from the feces of healthy breast-fed infants.[1]. Bidobacterium species have been isolated from various ecological niches In human, they are present in gastrointestinal tract (GIT) and oral cavity. They are present in gastrointestinal tract (GIT) and oral cavity They are the dominant clade of the gut microbiota of healthy breast-fed infants,[3] and commensal species are considered important for microbial modulation at birth, e.g. the immune programming of its host.[4,5] Most members of the genus are safe and nontoxic in humans. Certain species of bidobacteria are found in environmental niches such as sewage, fermented products, and anaerobic digesters.[6] Animal guts are suspected as the major source of these contaminants

Methods

Results

Conclusion