Use of stomach tubing as an alternative to rumen cannulation to study ruminal fermentation and microbiota in sheep and goats

Rumen cannulation is the reference method for collection of representative samples of rumen digesta. However, it is not always viable, which obliges to depend on less invasive techniques, such as stomach tubing. The aim of this work was to study if the differences in fermentation parameters and rumen microbial populations observed between species (sheep and goats), diets (forage and forage plus concentrate) and sampling times (pre- and post-feeding) are consistent when collecting the samples through stomach tube or rumen cannula, in an attempt to validate the use of the former as an alternative to the latter. Four sheep and four goats, fitted with ruminal cannula, were fed either forage (F diet; alfalfa hay) or forage plus concentrate (1:1; FC diet), in two 15-day periods. At the end of each period (days 14 and 15), samples of rumen digesta were taken by stomach tube and rumen cannula, before and 4 h after morning feeding, for determination of ruminal fermentation parameters (pH, and lactate, ammonia and total VFA concentrations). The three main rumen microbial groups (bacteria, protozoa and methanogenic archaea) and two fibrolytic bacteria (Ruminococcus flavefaciens andFibrobacter succinogenes) were quantified by real-time PCR and, additionally, PCR-DGGE analysis of the bacterial community on the rumen digesta samples collected post-feeding was carried out. Overall, sampling through ruminal cannula and stomach tube gave similar results regarding fermentation parameters when comparing species, diets and sampling times. Despite samples for microbiology assays contained liquid plus solid fractions when collected through rumen cannula and mostly liquid when collected through stomach tube, both techniques showed certain consistency in the effects of treatments on the rumen microbiota (e.g., both revealed no differences between species in total bacteria, archaea and R. flavefaciens concentrations, and higher protozoa numbers in goats than in sheep). However, there was also some discrepancy regarding microorganism concentrations, particularly concerning sampling times (e.g., differences between pre- and post-feeding samplings were only observed in rumen cannula samples for total bacteria and methanogenic archaea, and in stomach tube samples for R. flavefaciens concentrations). Therefore, this study supports that non-invasive stomach tubing is a feasible alternative to surgical rumen cannulation in sheep and goats to examine ruminal fermentation. Nonetheless, caution should be taken when using this technique to assess the structure and composition of the rumen microbial community.