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Comparative Genomics Analysis of Lactobacillus ruminis from Different Niches
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2020-01-08
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Wang, S.; Yang, B.; Ross, R.P.; Stanton, C.; Zhao, J.; Zhang, H.; Chen, W. Comparative Genomics Analysis of Lactobacillus ruminis from Different Niches. Genes 2020, 11, 70. https://doi.org/10.3390/genes11010070
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.