Genomic insights about the Lactobacillus genus

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Title: Genomic insights about the Lactobacillus genus
Author: Kant, Ravi
Contributor: University of Helsinki, Faculty of Veterinary Sciences, Department of Veterinary Biosciences
Doctoral Programme in Food Chain and Health
Thesis level: Doctoral dissertation (article-based)
Abstract: This thesis details an in silico exploration of the genetic potential of the Gram-positive genus Lactobacillus through the establishment and analysis of a pan-genome dataset. Lactobacilli are an intensively researched and studied group of bacteria, which is in part owed to their exploitation for various man-made food and industrial purposes and their advocated beneficial use as gut probiotics. Bacterial pan-genomics is an outgrowth of the comparative genomics field and by comparing the genomes from many strains of the same species the data obtained serves to catalogue the entire genetic repertoire available to a particular species. In effect, the pan-genome represents the complete assortment of putative genes in a species (or genus) of bacteria. The research presented in this thesis is comprised of three distinct studies (I, II, and III), each of which used the pan-genome approach to give a theoretical account of Lactobacillus genetics. In study I, a pan-genome was assembled at the genus level using 20 fully sequenced genomes from 14 different Lactobacillus species. Here, complete genome sequences were selected for creating a broader framework that would allow more comprehensive genomic comparisons. Varying aspects were apparent among the genome sequences used, including sizes that ranged from ~1.8 to ~3.3 Mbps and a G+C content of between ~33% and ~51%. The assembled pan-genome was sized at 14,000 protein-encoding genes, and out of which a small 383-gene Lactobacillus core genome (LCG) was derived. The genetic content of the LCG was used for reconstructing a molecular phylogeny, which then permitted a taxonomic grouping of the 20 genomes into three main clades. Additional classifications of the LCG involved identifying core group and signature group genes, as well as so-called ORFan genes that were further sorted as either LCG-specific or group-specific. In study II, a pan-genome of the Lactobacillus rhamnosus species was constructed from 13 different genomes. L. rhamnosus is a highly adaptable bacterium that thrives in a variety of hosts and environments. Presumably, there is little doubt that numerous genetic peculiarities are the source of the niche-related phenotypes that enable the inherent ecological adaptability of L. rhamnosus strains. For this, the genetic content of the assembled pan-genome was examined for those geno-phenotypic variations occurring at the cell-surface level and whether these correlate to a particular habitat preference of various L. rhamnosus strains. The L. rhamnosus pan-genome itself had an estimated size of 4,893 protein-encoding genes, which was further partitioned into the 2,095-gene core and 2,798-gene accessory genomes. Pan-genomic comparisons were benchmarked against the gut-adapted L. rhamnosus GG strain and focused primarily on seven functionally characterized surface-exposed proteins. Most notably, the operonic genes for the mucoadhesive SpaCBA pilus were part of the accessory genome and can be regarded as a genomic novelty in L. rhamnosus. Nonetheless, for those L. rhamnosus strains with a functional SpaCBA piliation trait, this would improve niche-specific fitness and presumably prolong transient (allochthonous) colonization of mucosal epithelial surfaces in the gut or elsewhere in the body. In study III, a pan-genomic appraisal was performed on the Lactobacillus ruminis species by compiling the genomes of nine different strains obtained from human, bovine, porcine, and equine digestive tracts. L. ruminis is a piliated and flagellated strict anaerobe and one of the few indigenous (autochthonous) lactobacilli in the gut. The pan-genome was utilized to pinpoint the molecular basis for the intractable colonization behavior of L. ruminis, where the focus was on those geno-phenotypes associated with cellular surface morphology and anaerobic fermentation and respiration. The size of the L. ruminis pan-genome was predicted to contain 4,301 protein-related genes, while the number of genes in the core and accessory genomes was 1,234 and 3,067, respectively. As inferred from the pan-genomic data, the presence of certain surface proteins and a substitute anaerobic energy-yielding metabolism might represent the adaptive phenotypes that help make L. ruminis a gut-autochthonic species.not available
URI: URN:ISBN:978-951-51-4333-4
Date: 2018-06-26
Rights: This publication is copyrighted. You may download, display and print it for Your own personal use. Commercial use is prohibited.

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