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Comparative Genomics Analysis of from Different Niches.
Wang, Shuo Yang, Bo Ross, R Paul Stanton, Catherine Zhao, Jianxin Zhang, Hao Chen, Wei
Wang, Shuo
Yang, Bo
Ross, R Paul
Stanton, Catherine
Zhao, Jianxin
Zhang, Hao
Chen, Wei
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Date
08/01/2020
Date Submitted
Keywords
CRISPR/Cas
Lactobacillus ruminis
bacteriocins
carbohydrate utilization
phylogenetic relationship
prophage
Lactobacillus ruminis
bacteriocins
carbohydrate utilization
phylogenetic relationship
prophage
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genes-11-00070.pdf
Adobe PDF, 6.24 MB
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Abstract
Lactobacillus ruminis is a commensal motile lactic acid bacterium living in the intestinal tract of humans and animals. Although a few genomes of L. ruminis were published, most of them were animal derived. To explore the genetic diversity and potential niche-specific adaptation changes of L. ruminis, in the current work, draft genomes of 81 L. ruminis strains isolated from human, bovine, piglet, and other animals were sequenced, and comparative genomic analysis was performed. The genome size and GC content of L. ruminis on average were 2.16 Mb and 43.65%, respectively. Both the origin and the sampling distance of these strains had a great influence on the phylogenetic relationship. For carbohydrate utilization, the human-derived L. ruminis strains had a higher consistency in the utilization of carbon source compared to the animal-derived strains. L. ruminis mainly increased the competitiveness of niches by producing class II bacteriocins. The type of clustered regularly interspaced short palindromic repeats /CRISPR-associated (CRISPR/Cas) system presented in L. ruminis was mainly subtype IIA. The diversity of CRISPR/Cas locus depended on the high denaturation of spacer number and sequence, although cas1 protein was relatively conservative. The genetic differences in those newly sequenced L. ruminis strains highlighted the gene gains and losses attributed to niche adaptations.
Language
en
Citation
ISSN
eISSN
2073-4425
ISBN
DOI
10.3390/genes11010070
PMID
31936280