Lactobacillus ruminis strains cluster according to their mammalian gut source

O'Donnell, Michelle M.; Harris, Hugh Michael B.; Lynch, Denise B.; Ross, R. Paul; O'Toole, Paul W.

Lactobacillus ruminis strains cluster according to their mammalian gut source

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.contributor.funder	Science Foundation Ireland	en
dc.date.accessioned	2016-01-19T13:04:59Z
dc.date.available	2016-01-19T13:04:59Z
dc.date.issued	2015-04-01
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.description.status	Peer reviewed	en
dc.description.version	Published Version	en
dc.format.mimetype	application/pdf	en
dc.identifier.articleid	80
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.doi	10.1186/s12866-015-0403-y
dc.identifier.endpage	20	en
dc.identifier.issn	1471-2180
dc.identifier.journaltitle	BMC Microbiology	en
dc.identifier.startpage	1	en
dc.identifier.uri	https://hdl.handle.net/10468/2194
dc.identifier.volume	15	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