Faecal microbiota characterisation of horses using 16 rdna barcoded pyrosequencing, and carriage rate of clostridium difficile at hospital admission

Abstract

BackgroundThe equine faecal microbiota is very complex and remains largely unknown, while interspecies interactions have an important contribution to animal health. Clostridium difficile has been identified as an important cause of diarrhoea in horses. This study provides further information on the nature of the bacterial communities present in horses developing an episode of diarrhoea. The prevalence of C. difficile in hospitalised horses at the time of admission is also reported.ResultsBacterial diversity of the gut microbiota in diarrhoea is lower than that in non-diarrhoeic horses in terms of species richness (p-value <0.002) and in population evenness (p-value: 0.02). Statistical differences for Actinobacillus, Porphyromonas, RC9 group, Roseburia and Ruminococcaceae were revealed. Fusobacteria was found in horses with diarrhoea but not in any of the horses with non-diarrheic faeces. In contrast, Akkermansia was among the three predominant taxa in all of the horses studied. The overall prevalence of C. difficile in the total samples of hospitalised horses at admission was 3.7 % (5/134), with five different PCR-ribotypes identified, including PCR-ribotype 014. Two colonised horses displayed a decreased bacterial species richness compared to the remaining subjects studied, which shared the same Bacteroides genus. However, none of the positive animals had diarrhoea at the moment of sampling.ConclusionsThe abundance of some taxa in the faecal microbiota of diarrhoeic horses can be a result of microbiome dysbiosis, and therefore a cause of intestinal disease, or some of these taxa may act as equine enteric pathogens. Clostridium difficile colonisation seems to be transient in all of the horses studied, without overgrowth to trigger infection. A large proportion of the sequences were unclassified, showing the complexity of horses’ faecal microbiota.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-015-0514-5) contains supplementary material, which is available to authorized users.

Clostridium difficile infection: Early history, diagnosis and molecular strain typing methods

“…It has been recently introduced to investigate the intestinal microbiota of healthy patients and patients suffering CDI. In the last year, most of the studies reported bacteria at the phylum and class level, but higher taxonomic resolution may reveal more differences in the population structure [206]. Preliminary results have shown that one of the taxa found in high proportions in patients with CDI is Proteobacteria, while Bacteroidetes proportions are lower in infected patients [207].…”

Unraveling microbial ecology of industrial-scale Kombucha fermentations by metabarcoding and culture-based methods

“…Sequence read processing for 16S and 26S was used as previously described using MOTHUR software package v1.35 (Schloss et al 2009), Pyronoise algorithm and UCHIME algorithm (Edgar et al 2011) for alignment and clustering, denoising and chimera detection, respectively (Rodriguez et al 2015;Degrune et al 2016). Amplicon reference alignment and taxonomical assignation were based upon the SILVA database (v1.15) of full-length SSU (16S) and LSU (26S) rDNA sequences (Quast et al 2012).…”

Use of a metagenetic approach to monitor the bacterial microbiota of “Tomme d'Orchies” cheese during the ripening process

“…Sequence reads processing were used as previously described by Rodriguez et al (2015) using respectively MOTHUR software package v1.35, Pyronoise algorithm and UCHIME algorithm for alignment and clustering, denoising and chimera detection. The clustering distance for operational taxonomic unit (OTU) is 0.03.…”