PCR-DGGE analysis reveals a distinct diversity in the bacterial population attached to the rumen epithelium

Abstract

Bacteria attached to the rumen epithelium (or epimural community) are not well characterised and their role in rumen functioning is not totally understood. There is just one published report of a clone library from one cow that suggests that this epimural community differs from the bacteria associated with the rumen digestive contents. However, this time-consuming approach is not adapted for examining microbial population changes in groups of animals. In in vivo studies, when samples from several animals have to be analysed simultaneously, a simpler technique has to be used. In this study, a genetic fingerprinting technique, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), was used to characterise the structure of the bacterial population attached to the rumen epithelium. This community was compared with that present in the solid and liquid phases of rumen content under two contrasting diets. Rumen samples were obtained from four forage-fed and four high-concentrate-fed (80 : 20, wheat grain : hay) 5-month-old lambs. After slaughter, samples from five epithelial sites and the solid and liquid digesta phases were taken for DNA extraction and analysis. Bacterial communities were profiled by PCR-DGGE using bacterial-specific 16S rDNA primers. Analysis of the fingerprint revealed that the epithelial community differed from those of rumen content in both diets. As expected, the nature of the feed influenced the bacterial communities from the solid and liquid rumen phases but no diet effect was observed in the rumen epithelial profiles suggesting a strong host effect on this bacterial population. Additionally, no differences were observed among the five epithelial sampling sites taken from each animal. The profile of the bacterial population attached to the rumen epithelium presented a high interanimal variation, whether this difference has an influence in the function of this community remains to be determined.

Design, implementation and interpretation of in vitro batch culture experiments to assess enteric methane mitigation in ruminants—a review

“…The rumen microbiome consists of three sub-populations of microbes: those in the fluid phase, adherent to the particulate phase (further divided into loosely-and firmly-associated with the feed particles) (Cheng et al, 1993) or attached to the epithelium (Sadet et al, 2007). The latter tends to be primarily involved in the release of ammonia from urea absorbed across the rumen epithelium and, as such, has only a minor role in feed degradation, and for this reason does not need to be sampled (Mueller et al, 1984).…”

Rumen microbial (meta)genomics and its application to ruminant production

“…These methods using a non-targeted approach are able to pick up differences and similarities in the community of different microbial groups in the rumen associated with host ruminant species, diet and feed efficiency (Larue et al, 2005;Sadet et al, 2007;Guan et al, 2008 and references above; Suen et al, 2011) but they do not provide direct sequence information. In addition, the number of bands or peaks detected by these techniques is several orders of magnitude lower than the estimated diversity in the rumen (Hess et al, 2011;Kim et al, 2011).…”

Advances in microbial ecosystem concepts and their consequences for ruminant agriculture

“…Traditionally, the structure of the rumen bacterial population is considered to be the sum of three pools of microorganisms; those that are solid associated, liquid associated and tissue associated. It is clear that these populations are different from each other (LaRue et al, 2005; Cho et al, 2006;Sadet et al, 2007), and that, of these, the solid-associated microbial biomass is the largest (Craig et al, 1987) and plays the most important role in feed digestion (McAllister et al, 1994).…”