Abstract
BackgroundLactobacillus 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.ResultsWe 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.ConclusionsWe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-015-0403-y) contains supplementary material, which is available to authorized users.
Highlights
Lactobacillus ruminis is a motile Lactobacillus that is autochthonous to the human gut, and which may be isolated from other mammals
But not all, bacterial flagellin proteins are recognised by toll-like receptor 5 (TLR5) [36] and we showed that the L. ruminis flagellin protein induced IL-8 secretion in several cell lines [19]
In a previous study we established the carbohydrate fermentation profile for L. ruminis [23]. This profile was exploited here to screen the candidate L. ruminis isolates from the stocked Lactobacillus strains of porcine and equine origin
Summary
Lactobacillus ruminis is a motile Lactobacillus that is autochthonous to the human gut, and which may be isolated from other mammals. Detailed characterization of L. ruminis has previously been restricted to strains of human and bovine origin. We sought to expand our bio-bank of strains to identify and characterise isolates of porcine and equine origin by comparative genomics. In an attempt to rationalize why L. ruminis might be variably present in different species and in different animals of the same species in different studies, we previously characterised the fermentation properties of human and bovine L. ruminis isolates [23]. Comparison of the fermentation profiles and genome sequences of ATCC 25644 (human isolate) and ATCC 27782 (bovine isolate) identified the enzymes and pathways that L. ruminis. The prebiotic fructooligosaccharide (FOS) was fermented by all of the human isolates tested, but the bovine isolate ATCC 27782 failed to ferment this carbohydrate, which was attributed to the absence of beta-fructofuranosidase [23,24]
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