Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific.

Aim: To determine whether Megasphaera elsdenii YE34 (lactic acid degrader) and Butyrivibrio fibrisolvens YE44 (alternative starch utilizer to Streptococcus bovis) establish viable populations in the rumen of beef cattle rapidly changed from a forage-based to a grain-based diet. Methods and Results: Five steers were inoculated with the two bacterial strains (YE34 and YE44) and five served as uninoculated controls. With the exception of one animal in the control group, which developed acidosis, all steers rapidly adapted to the grain-based diet without signs of acidosis (pH decline and accumulation of lactic acid). Bacterial populations of S. bovis, B. fibrisolvens and M. elsdenii were enumerated using real-time Taq nuclease assays. Populations of S. bovis remained constant (except in the acidotic animal) at ca 10 7 cell equivalents (CE) ml )1 throughout the study. Megasphaera elsdenii YE34, was not detectable in animals without grain in the diet, but immediately established in inoculated animals, at 10 6 CE ml )1 , and increased 100-fold in the first 4 days following inoculation. Butyrivibrio fibrisolvens, initially present at 10 8 CE ml )1 , declined rapidly with the introduction of grain into the diet and was not detectable 8 days after grain introduction. Conclusion: Megasphaera elsdenii rapidly establishes a lactic acid-utilizing bacterial population in the rumen of grain-fed cattle 7-10 days earlier than in uninoculated cattle. Significance and Impact of the Study: The study has demonstrated that rumen bacterial populations, and in particular the establishment of bacteria inoculated into the rumen for probiotic use, can be monitored by real-time PCR.

The ecology of the uncultured, but large and morphologically conspicuous, rumen bacterium Oscillospira spp. was studied. Oscillospira-specific 16S rRNA gene sequences were detected in North American domestic cattle, sheep from Australia and Japan, and Norwegian reindeer. Phylogenetic analysis of the sequences obtained allowed definition of three operational taxonomic units within the Oscillospira clade. Consistent with this genetic diversity, we observed atypical smaller morphotypes by using an Oscillospira-specific fluorescence in situ hybridization probe. Despite the visual disappearance of typical large Oscillospira morphotypes, the presence of Oscillospira spp. was still detected by Oscillospira-specific PCR in the rumen of cattle and sheep. These observations suggest the broad presence of Oscillospira species in various rumen ecosystems with the level, and most likely the morphological form, dependent on diet. An ecological analysis based on enumeration of the morphologically conspicuous, large-septate form confirms that the highest counts are associated with the feeding of fresh forage diets to cattle and sheep and in two different subspecies of reindeer investigated.Morphologically unique, large bacteria of the genus Oscillospira, which have not been grown in pure culture yet, can be routinely detected microscopically in the rumen contents of cattle and sheep (11,18). A number of Oscillospira spp. are responsive to the advent of green pastures and fluctuate seasonally (13, 17) (see also Table 1). The only species of Oscillospira described in Bergey's Manual of Systematic Bacteriology (8) is Oscillospira guilliermondii, and this entry refers to the original morphological description by Chatton and Perard in 1913. Warner (34) proposed that at least two strains or species be included in the Oscillospira group based on cell diameter and the tendency to form spores as the main characteristic differences. This implies that there are different morphological forms or species related to different diets or in different gut ecosystems.Detection and identification of microbial populations are the most basic prerequisites for microbial ecology studies. Over the last decade, several molecular techniques have been developed that when applied to the rumen microbiota have revealed enormous microbial diversity not recognized previously because of limitations and biases inherent in the cultivation approach (24,(30)(31)(32)37). The cultivation-independent approach provides technology for detection and monitoring of microorganisms such as Oscillospira, for which growth requirements are unknown and undetermined. The only requirement for the development of molecular detection techniques is the availability of a marker molecule. Fortunately, several 16S rRNA gene sequences have recently been retrieved from this large bacterium isolated by flow cytometric sorting (39), and this enabled the design of various molecular probes for detection and monitoring. We designed and validate here PCR and PCR-denaturing gradient gel electroph...

Summary Ruminococcus bromii is a dominant member of the human colonic microbiota that plays a ‘keystone’ role in degrading dietary resistant starch. Recent evidence from one strain has uncovered a unique cell surface ‘amylosome’ complex that organizes starch‐degrading enzymes. New genome analysis presented here reveals further features of this complex and shows remarkable conservation of amylosome components between human colonic strains from three different continents and a R. bromii strain from the rumen of Australian cattle. These R. bromii strains encode a narrow spectrum of carbohydrate active enzymes (CAZymes) that reflect extreme specialization in starch utilization. Starch hydrolysis products are taken up mainly as oligosaccharides, with only one strain able to grow on glucose. The human strains, but not the rumen strain, also possess transporters that allow growth on galactose and fructose. R. bromii strains possess a full complement of sporulation and spore germination genes and we demonstrate the ability to form spores that survive exposure to air. Spore formation is likely to be a critical factor in the ecology of this nutritionally highly specialized bacterium, which was previously regarded as ‘non‐sporing’, helping to explain its widespread occurrence in the gut microbiota through the ability to transmit between hosts.