Comparative genomics analysis of Lactobacillus ruminis from different niches

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dc.contributor.authorWang, Shuo
dc.contributor.authorYang, Bo
dc.contributor.authorRoss, R. Paul
dc.contributor.authorStanton, Catherine
dc.contributor.authorZhao, Jianxin
dc.contributor.authorZhang, Hao
dc.contributor.authorChen, Wei
dc.contributor.funderNational Natural Science Foundation of Chinaen
dc.contributor.funderNational First-Class Discipline Program of Food Science and Technologyen
dc.contributor.funderCollaborative Innovationcenter of Food Safety and Quality Control in Jiangsu Provinceen
dc.date.accessioned2023-03-03T10:14:51Z
dc.date.available2023-03-03T10:14:51Z
dc.date.issued2020-01
dc.date.updated2023-03-03T09:52:57Z
dc.description.abstractLactobacillus 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.en
dc.description.sponsorshipNational Natural Science Foundation of China (Nos. 31771953, 31820103010); National First-Class Discipline Program of Food Science and Technology (JUFSTR20180102)en
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.articleid70en
dc.identifier.citationWang, S., Yang, B., Ross, R.P., Stanton, C., Zhao, J., Zhang, H. and Chen, W. (2020) ‘Comparative genomics analysis of lactobacillus ruminis from different niches’, Genes, 11(1), 70 (17pp). doi: 10.3390/genes11010070en
dc.identifier.doi10.3390/genes11010070en
dc.identifier.endpage17en
dc.identifier.issn2073-4425
dc.identifier.issued1en
dc.identifier.journaltitleGenesen
dc.identifier.startpage1en
dc.identifier.urihttps://hdl.handle.net/10468/14275
dc.identifier.volume11en
dc.language.isoenen
dc.publisherMDPIen
dc.rights© 2020, by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).en
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en
dc.subjectBacteriocinsen
dc.subjectCarbohydrate utilizationen
dc.subjectCRISPR/Casen
dc.subjectLactobacillus ruminisen
dc.subjectPhylogenetic relationshipen
dc.subjectProphageen
dc.titleComparative genomics analysis of Lactobacillus ruminis from different nichesen
dc.typeArticle (peer-reviewed)en
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