Comparative genomics analysis of Lactobacillus ruminis from different niches
dc.contributor.author | Wang, Shuo | |
dc.contributor.author | Yang, Bo | |
dc.contributor.author | Ross, R. Paul | |
dc.contributor.author | Stanton, Catherine | |
dc.contributor.author | Zhao, Jianxin | |
dc.contributor.author | Zhang, Hao | |
dc.contributor.author | Chen, Wei | |
dc.contributor.funder | National Natural Science Foundation of China | en |
dc.contributor.funder | National First-Class Discipline Program of Food Science and Technology | en |
dc.contributor.funder | Collaborative Innovationcenter of Food Safety and Quality Control in Jiangsu Province | en |
dc.date.accessioned | 2023-03-03T10:14:51Z | |
dc.date.available | 2023-03-03T10:14:51Z | |
dc.date.issued | 2020-01 | |
dc.date.updated | 2023-03-03T09:52:57Z | |
dc.description.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. | en |
dc.description.sponsorship | National Natural Science Foundation of China (Nos. 31771953, 31820103010); National First-Class Discipline Program of Food Science and Technology (JUFSTR20180102) | en |
dc.description.status | Peer reviewed | en |
dc.description.version | Published Version | en |
dc.format.mimetype | application/pdf | en |
dc.identifier.articleid | 70 | en |
dc.identifier.citation | Wang, 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/genes11010070 | en |
dc.identifier.doi | 10.3390/genes11010070 | en |
dc.identifier.endpage | 17 | en |
dc.identifier.issn | 2073-4425 | |
dc.identifier.issued | 1 | en |
dc.identifier.journaltitle | Genes | en |
dc.identifier.startpage | 1 | en |
dc.identifier.uri | https://hdl.handle.net/10468/14275 | |
dc.identifier.volume | 11 | en |
dc.language.iso | en | en |
dc.publisher | MDPI | en |
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.uri | https://creativecommons.org/licenses/by/4.0/ | en |
dc.subject | Bacteriocins | en |
dc.subject | Carbohydrate utilization | en |
dc.subject | CRISPR/Cas | en |
dc.subject | Lactobacillus ruminis | en |
dc.subject | Phylogenetic relationship | en |
dc.subject | Prophage | en |
dc.title | Comparative genomics analysis of Lactobacillus ruminis from different niches | en |
dc.type | Article (peer-reviewed) | en |
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