Lactobacillus ruminis strains cluster according to their mammalian gut source

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dc.contributor.author O'Donnell, Michelle M.
dc.contributor.author Harris, Hugh Michael B.
dc.contributor.author Lynch, Denise B.
dc.contributor.author Ross, R. Paul
dc.contributor.author O'Toole, Paul W.
dc.date.accessioned 2016-01-19T13:04:59Z
dc.date.available 2016-01-19T13:04:59Z
dc.date.issued 2015-04-01
dc.identifier.citation O’ DONNELL, M. M., HARRIS, H. M. B., LYNCH, D. B., ROSS, R. P. & O’TOOLE, P. W. 2015. Lactobacillus ruminis strains cluster according to their mammalian gut source. BMC Microbiology, 15:80, 1-20. http://dx.doi.org/10.1186/s12866-015-0403-y en
dc.identifier.volume 15 en
dc.identifier.startpage 1 en
dc.identifier.endpage 20 en
dc.identifier.issn 1471-2180
dc.identifier.uri http://hdl.handle.net/10468/2194
dc.identifier.doi 10.1186/s12866-015-0403-y
dc.description.abstract BACKGROUND: Lactobacillus ruminis is a motile Lactobacillus that is autochthonous to the human gut, and which may also be isolated from other mammals. Detailed characterization of L. ruminis has previously been restricted to strains of human and bovine origin. We therefore sought to expand our bio-bank of strains to identify and characterise isolates of porcine and equine origin by comparative genomics. RESULTS: We isolated five strains from the faeces of horses and two strains from pigs, and compared their motility, biochemistry and genetic relatedness to six human isolates and three bovine isolates including the type strain 27780T. Multilocus sequence typing analysis based on concatenated sequence data for six individual loci separated the 16 L. ruminis strains into three clades concordant with human, bovine or porcine, and equine sources. Sequencing the genomes of four additional strains of human, bovine, equine and porcine origin revealed a high level of genome synteny, independent of the source animal. Analysis of carbohydrate utilization, stress survival and technological robustness in a combined panel of sixteen L. ruminis isolates identified strains with optimal survival characteristics suitable for future investigation as candidate probiotics. Under laboratory conditions, six human isolates of L. ruminis tested were aflagellate and non-motile, whereas all 10 strains of bovine, equine and porcine origin were motile. Interestingly the equine and porcine strains were hyper-flagellated compared to bovine isolates, and this hyper-flagellate phenotype correlated with the ability to swarm on solid medium containing up to 1.8% agar. Analysis by RNA sequencing and qRT-PCR identified genes for the biosynthesis of flagella, genes for carbohydrate metabolism and genes of unknown function that were differentially expressed in swarming cells of an equine isolate of L. ruminis. CONCLUSIONS: We suggest that Lactobacillus ruminis isolates have potential to be used in the functional food industry. We have also identified a MLST scheme able to distinguish between strains of L. ruminis of different origin. Genes for non-digestible oligosaccharide metabolism were identified with a putative role in swarming behaviour. en
dc.description.sponsorship Science Foundation Ireland (Principal Investigator Award (07/IN.1/B1780)) en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher Biomed Central Ltd. en
dc.rights © 2015 O' Donnell et al.; licensee BioMed Central 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. en
dc.rights.uri http://creativecommons.org/licenses/by/4.0/ en
dc.subject Lactobacillus ruminis en
dc.subject Lactobacillus en
dc.subject Motility en
dc.subject Prebiotics en
dc.subject RNA-seq en
dc.subject Potential probiotic properties en
dc.subject Lactic-acid bacteria en
dc.subject Microflora en
dc.subject Antibiotic biosynthesis en
dc.subject Bacterial strain en
dc.subject Bacterium identification en
dc.subject Bacterial flagellum en
dc.subject Bacterial genome en
dc.subject Population structure en
dc.subject Bacterium isolate en
dc.subject Bovinae en
dc.subject Carbohydrate metabolism en
dc.subject Multilocus sequence typing en
dc.subject Reverse transcription polymerase chain reaction en
dc.subject RNA sequence en
dc.subject Cladistics en
dc.subject Gene cluster en
dc.subject Gene identification en
dc.subject Gene locus en
dc.subject Gene sequence en
dc.subject Horse en
dc.subject Human en
dc.subject Swine en
dc.subject Equidae en
dc.subject Mammalia en
dc.subject Mastigophora (flagellates) en
dc.subject Suidae en
dc.title Lactobacillus ruminis strains cluster according to their mammalian gut source en
dc.type Article (peer-reviewed) en
dc.internal.authorcontactother Paul W. O'Toole, Microbiology, University College Cork, Cork, Ireland. +353-21-490-3000 Email: pwotoole@ucc.ie en
dc.internal.availability Full text available en
dc.description.version Published Version en
dc.contributor.funder Science Foundation Ireland en
dc.description.status Peer reviewed en
dc.identifier.journaltitle BMC Microbiology en
dc.internal.copyrightchecked Open Access articles licensed via CC-BY 4.0 with UCC affiliated authors. Uploaded Jan 2016. en
dc.internal.IRISemailaddress pwotoole@ucc.ie en
dc.identifier.articleid 80


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© 2015 O' Donnell et al.; licensee BioMed Central 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Except where otherwise noted, this item's license is described as © 2015 O' Donnell et al.; licensee BioMed Central 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
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