Aim:  To examine the effect of concentrate and yeast additive on the number of cellulolytic bacteria in the rumen of sheep. Methods and Results:  Fibrobacter succinogenes, Ruminococcus albus and Ruminococcus flavefaciens were quantified using real‐time PCR (targeting 16S rDNA) in parallel to cellulolytic flora enumeration with cultural techniques. Whatever the conditions tested, R. flavefaciens was slightly more abundant than F. succinogenes, with both species outnumbering R. albus. Before feeding, the shift from hay to hay plus concentrate diet had no effect on rumen pH and on the number of the three specie; while after feeding, the concentrate‐supplemented diet induced a decrease (−1 log) of the number of the three species concomitant with the rumen acidification. Overall, the presence of the live yeast resulted in a significant increase (two‐ to fourfold) of the Ruminococci. Conclusion:  The use of real‐time PCR allowed us to show changes in the number of cellulolytic bacterial species in vivo in response to diet shift and additives that could not be as easily evidenced by classical microbial methods. Significance and Impact of the Study:  This study contributes to the understanding of the negative impact of readily fermentable carbohydrates on rumen cellulolysis and the beneficial effect of yeast on rumen fermentation.

Ruminants have a unique ability to derive energy from the degradation of plant polysaccharides through the activity of the rumen microbiota. Although this process is well studied in vitro, knowledge gaps remain regarding the relative contribution of the microbiota members and enzymes in vivo. The present study used RNA-sequencing to reveal both the expression of genes encoding carbohydrate-active enzymes (CAZymes) by the rumen microbiota of a lactating dairy cow and the microorganisms forming the fiber-degrading community. Functional analysis identified 12,237 CAZymes, accounting for 1% of the transcripts. The CAZyme profile was dominated by families GH94 (cellobiose-phosphorylase), GH13 (amylase), GH43 and GH10 (hemicellulases), GH9 and GH48 (cellulases), PL11 (pectinase) as well as GH2 and GH3 (oligosaccharidases). Our data support the pivotal role of the most characterized fibrolytic bacteria (Prevotella, Ruminocccus and Fibrobacter), and highlight a substantial, although most probably underestimated, contribution of fungi and ciliate protozoa to polysaccharide degradation. Particularly these results may motivate further exploration of the role and the functions of protozoa in the rumen. Moreover, an important part of the fibrolytic bacterial community remains to be characterized since one third of the CAZyme transcripts originated from distantly related strains. These findings are used to highlight limitations of current metatranscriptomics approaches to understand the functional rumen microbial community and opportunities to circumvent them.

Protozoa are commensal eukaryotes in the rumen of herbivores. Protozoa are large producers of hydrogen, which is utilized by methanogenic archaea to produce methane, a greenhouse gas. The removal of protozoa from the rumen (defaunation) decreases methanogenesis, but also negatively affects fiber digestion, which is the main function of the rumen. The aim of this study was to examine the effect of long-term defaunation on the structure of the microbiota and particularly methanogenic archaea and fibrolytic bacteria to better understand the microbial mechanisms responsible for the decrease in methanogenesis and fibrolysis. The trial was conducted in 5 adult sheep subjected successively to long-term defaunation (2 yr), refaunation (12 wk), and short-term defaunation (10 wk). Methanogens were enumerated by quantitative PCR targeting the rrs (16S ribosomal RNA subunit) and mcrA (methyl coenzyme-M reductase) genes. The rrs gene was used to quantify the 3 major culturable rumen cellulolytic bacterial species (i.e., Fibrobacter succinogenes, Ruminococcus albus, and Ruminococcus flavefaciens) and total bacteria. Bacterial and methanogen diversity was also examined by PCR-DGGE (PCR-denaturing gradient gel electrophoresis) analysis targeting the rrs and mcrA genes, respectively. Total rumen bacterial density estimated as rrs copies per gram of DM of rumen content increased in response to long- and short-term defaunation (+1 log, P < 0.001), but without noticeable shifts in diversity. Defaunation increased the rrs copies per gram of DM of rumen content of R. albus and R. flavefaciens (+2 log, P < 0 0.001), but did not affect that of F. succinogenes. Despite a 20% reduction in methane emission in the 2 defaunated periods, the mcrA and rrs copies of methanogens per gram of DM of rumen content increased (+1 log, P < 0.001) in the absence of protozoa, whereas the diversity of the dominant methanogenic community was not modified. This study shows no major difference between long- and short-term defaunation in abundance and diversity of bacteria and archaea. It also provides evidence that monitoring the abundance and diversity of methanogens is not sufficient to comprehend the microbial mechanisms leading to a reduction in methane emissions by ruminants. This study also reports for the first time in sheep a selective effect of defaunation on the abundance of cellulolytic bacterial species.

We investigated the effects of increasing extruded linseed supply in diets based on hay (H; experiment 1) or corn silage (CS; experiment 2) on enteric methane (CH4) emission, rumen microbial and fermentation parameters, and rumen and total-tract digestibility. In each experiment, 4 lactating Holstein cows fitted with cannulas at the rumen and proximal duodenum were used in a 4×4 Latin square design (28-d periods). Cows were fed ad libitum a diet [50:50 and 60:40 forage:concentrate on a dry matter (DM) basis for experiments 1 and 2, respectively] without supplementation (H0, CS0) or supplemented with extruded linseed at 5% (H5, CS5), 10% (H10, CS10), and 15% (H15, CS15) of dietary DM (i.e., 1.8, 3.6 and 5.4% total fatty acids added, respectively). All measurements were carried out during the last 8 d of each period. Linseed supply linearly decreased daily CH4 emission in cows fed H diets (from 486 to 289g/d for H0 to H15, on average) and CS diets (from 354 to 207g/d for CS0 to CS15, on average). The average decrease in CH4 per kilogram of DM intake was, respectively, -7, -15, and -38% for H5, H10, H15 compared with the H0 diet, and -4, -8, and -34% for CS5, CS10, and CS15 compared with the CS0 diet. The same dose-response effect was observed on CH4 emission in percent of gross energy intake, per kilogram of nutrient digested, and per kilogram of 4% fat- and 3.3% protein-corrected milk (FPCM) in both experiments. Changes in the composition of rumen volatile fatty acids in response to increasing linseed supply resulted in a moderate or marked linear decrease in acetate:propionate ratio for H or CS diets, respectively. The depressive effect of linseed on total protozoa concentration was linear for H diets (-15 to -40%, on average, for H5 to H15 compared with H0) and quadratic for CS diets (-17 to -83%, on average, for CS5 to CS15 compared with CS0). Concentration of methanogens was similar among H or CS diets. The energetic benefits from the decreased CH4 emission with linseed supply in diets based on hay or corn silage did not improve digestibility or milk yield. Milk efficiency (kg of FPCM/kg of DM intake) was improved with linseed supply up to H10 in H diets and was unchanged in CS diets. Lower CH4 enteric emission from dairy cows fed linseed helps limit the environmental footprint of ruminant livestock.

BackgroundA complex community of microorganisms is responsible for efficient plant cell wall digestion by many herbivores, notably the ruminants. Understanding the different fibrolytic mechanisms utilized by these bacteria has been of great interest in agricultural and technological fields, reinforced more recently by current efforts to convert cellulosic biomass to biofuels.Methodology/Principal FindingsHere, we have used a bioinformatics-based approach to explore the cellulosome-related components of six genomes from two of the primary fiber-degrading bacteria in the rumen: Ruminococcus flavefaciens (strains FD-1, 007c and 17) and Ruminococcus albus (strains 7, 8 and SY3). The genomes of two of these strains are reported for the first time herein. The data reveal that the three R. flavefaciens strains encode for an elaborate reservoir of cohesin- and dockerin-containing proteins, whereas the three R. albus strains are cohesin-deficient and encode mainly dockerins and a unique family of cell-anchoring carbohydrate-binding modules (family 37).Conclusions/SignificanceOur comparative genome-wide analysis pinpoints rare and novel strain-specific protein architectures and provides an exhaustive profile of their numerous lignocellulose-degrading enzymes. This work provides blueprints of the divergent cellulolytic systems in these two prominent fibrolytic rumen bacterial species, each of which reflects a distinct mechanistic model for efficient degradation of cellulosic biomass.