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.

The molecular diversity of rumen methanogens in sheep in Australia was investigated by using individual 16S rRNA gene libraries prepared from the rumen contents obtained from six merino sheep grazing pasture (326 clones), six sheep fed an oaten hay-based diet (275 clones), and five sheep fed a lucerne hay-based diet (132 clones). A total of 733 clones were examined, and the analysis revealed 65 phylotypes whose sequences (1,260 bp) were similar to those of cultivated methanogens belonging to the order Methanobacteriales. Pasturegrazed sheep had more methanogen diversity than sheep fed either the oaten hay or lucerne hay diet. Methanobrevibacter strains SM9, M6, and NT7 accounted for over 90% of the total number of clones identified. M6 was more prevalent in grazing sheep, and SM9, despite being found in 16 of the 17 sheep, was more prevalent in sheep fed the lucerne-based diet. Five new species were identified. Two of these species exhibited very little sequence similarity to any cultivated methanogens and were found eight times in two of the six sheep that were grazing pasture. These unique sequences appear to represent a novel group of rumen archaea that are atypical for the rumen environment.The rumen is a unique environment and is home to billions of microbes, including bacteria, methanogenic archaea, protozoa, and fungi. These different microbes form a complex community of organisms that interact with one another and play an important role in the digestion of feed and the supply of energy to the host in the form of volatile fatty acids and microbial protein. In the past decade, there has been an increasing amount of interest in the rumen methanogenic archaea. This has primarily resulted from the role of these organisms in global warming due to the production of methane by domesticated livestock.In Australia, ruminant livestock are the single largest source of agricultural greenhouse gas emissions and alone account for at least 12% of Australian's total anthropomorphic national emissions (3). In New Zealand, enteric emissions are responsible for approximately 60% of that country's total greenhouse gas emissions (27). Approximately 95.5% of the methane emitted by ruminants is produced in the rumen (3), and the associated loss of energy for the ruminant has been estimated to be between 2 and 15% of the gross energy intake (18,25,40).Methane production is influenced by feed intake and the digestibility of the dry matter in the feed that is consumed. The effects of diet on changes in the diversity and numbers of a wide range of bacterial species in the rumen are known (20,30,36,37,45), but there is little information available concerning the composition of the methanogen population and their numbers of methanogens with regard to diet. Therefore, it is necessary to understand the diversity of methanogens in the rumen.In the past, methanogens from the digestive tracts of domesticated ruminants were identified by classical microbiological techniques (46). However, because of the fastidious growth requirements of ru...

BackgroundMethanogens that populate the gastrointestinal tract of livestock ruminants contribute significantly to methane emissions from the agriculture industry. There is a great need to analyze archaeal microbiomes from a broad range of host species in order to establish causal relationships between the structure of methanogen communities and their potential for methane emission. In this report, we present an investigation of methanogenic archaeal populations in the foregut of alpacas.ResultsWe constructed individual 16S rRNA gene clone libraries from five sampled animals and recovered a total of 947 sequences which were assigned to 51 species-level OTUs. Individuals were found to each have between 21 and 27 OTUs, of which two to six OTUs were unique. As reported in other host species, Methanobrevibacter was the dominant genus in the alpaca, representing 88.3% of clones. However, the alpaca archaeal microbiome was different from other reported host species, as clones showing species-level identity to Methanobrevibacter millerae were the most abundant.ConclusionFrom our analysis, we propose a model to describe the population structure of Methanobrevibacter-related methanogens in the alpaca and in previously reported host species, which may contribute in unraveling the complexity of symbiotic archaeal communities in herbivores.

Subacute ruminal acidosis (SARA) is characterized by ruminal pH depression and microbial perturbation. The impact of SARA adaptation and recovery on rumen bacterial density and diversity was investigated following high-grain feeding. Four ruminally cannulated dairy cows were fed a hay diet, transitioned to a 65% grain diet for 3 weeks, and returned to the hay diet for 3 weeks. Rumen fluid, rumen solids, and feces were sampled during weeks 0 (hay), 1 and 3 (high grain), and 4 and 6 (hay). SARA was diagnosed during week 1, with a pH below 5.6 for 4.6±1.4 h. Bacterial density was significantly lower in the rumen solids with high grain (P=0.047). Rumen fluid clone libraries from weeks 0, 3, and 6 were assessed at the 98% level and 154 operational taxonomic units were resolved. Week 3 diversity significantly differed from week 0, and community structure differed from weeks 0 and 6 (P<0.0001). Clones belonging to the phylum Firmicutes predominated. Compared with the hay diet, the high-grain diet contained clones from Selenomonas ruminantium and Succiniclasticum ruminis, but lacked Eubacterium spp. SARA adaptation was found to significantly alter bacterial density, diversity, and community structure, warranting further investigation into the role bacteria play in SARA adaptation.

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Non-lactating dairy cattle were transitioned to a high-concentrate diet to investigate the effect of ruminal pH suppression, commonly found in dairy cattle, on the density, diversity, and community structure of rumen methanogens, as well as the density of rumen protozoa. Four ruminally cannulated cows were fed a hay diet and transitioned to a 65% grain and 35% hay diet. The cattle were maintained on an high-concentrate diet for 3 weeks before the transition back to an hay diet, which was fed for an additional 3 weeks. Rumen fluid and solids and fecal samples were obtained prior to feeding during weeks 0 (hay), 1, and 3 (high-concentrate), and 4 and 6 (hay). Subacute ruminal acidosis was induced during week 1. During week 3 of the experiment, there was a significant increase in the number of protozoa present in the rumen fluid (P=0.049) and rumen solids (P=0.004), and a significant reduction in protozoa in the rumen fluid in week 6 (P=0.003). No significant effect of diet on density of rumen methanogens was found in any samples, as determined by real-time PCR. Clone libraries were constructed for weeks 0, 3, and 6, and the methanogen diversity of week 3 was found to differ from week 6. Week 3 was also found to have a significantly altered methanogen community structure, compared to the other weeks. Twenty-two unique 16S rRNA phylotypes were identified, three of which were found only during high-concentrate feeding, three were found during both phases of hay feeding, and seven were found in all three clone libraries. The genus Methanobrevibacter comprised 99% of the clones present. The rumen fluid at weeks 0, 3, and 6 of all the animals was found to contain a type A protozoal population. Ultimately, high-concentrate feeding did not significantly affect the density of rumen methanogens, but did alter methanogen diversity and community structure, as well as protozoal density within the rumen of nonlactating dairy cattle. Therefore, it may be necessary to monitor the rumen methanogen and protozoal communities of dairy cattle susceptible to depressed pH when methane abatement strategies are being investigated.

A long-term monensin supplementation trial involving lactating dairy cattle was conducted to determine the effect of monensin on the quantity and diversity of rumen methanogens in vivo. Fourteen cows were paired on the basis of days in milk and parity and allocated to one of two treatment groups, receiving (i) a control total mixed ration (TMR) or (ii) a TMR with 24 mg of monensin premix/kg of diet dry matter. Rumen fluid was obtained using an ororuminal probe on day ؊15 (baseline) and days 20, 90, and 180 following treatment. Throughout the 6-month experiment, the quantity of rumen methanogens was not significantly affected by monensin supplementation, as measured by quantitative real-time PCR. The diversity of the rumen methanogen population was investigated using denaturing gradient gel electrophoresis (DGGE) and 16S rRNA clone gene libraries. DGGE analysis at each sampling point indicated that the molecular diversity of rumen methanogens from monensin-treated cattle was not significantly different from that of rumen methanogens from control cattle. 16S rRNA gene libraries were constructed from samples obtained from the rumen fluids of five cows, with a total of 166 clones examined. Eleven unique 16S rRNA sequences or phylotypes were identified, five of which have not been recognized previously. The majority of clones (98.2%) belonged to the genus Methanobrevibacter, with all libraries containing Methanobrevibacter strains M6 and SM9 and a novel phylotype, UG3322.2. Overall, long-term monensin supplementation was not found to significantly alter the quantity or diversity of methanogens in the rumens of lactating dairy cattle in the present study.Rumen methanogens are involved in interspecies hydrogen transfer and the production of methane gas as an end product of fermentation (28). The accumulation of hydrogen as a waste product of rumen microbe fermentation has the ability to inhibit metabolism, and so the removal of hydrogen by methanogens is important to maintain normal rumen functioning (28). Methane produced by rumen methanogens, as well as being a potent greenhouse gas, is produced at a loss, ranging from 2 to 12%, of gross energy for the animal (13). For these reasons, the inhibition of methane is an important area of research in greenhouse gas mitigation and ruminant production systems.Recent efforts have been directed at methane mitigation in the bovine rumen, and monensin treatment is one strategy that is being investigated due to the role of monensin as a carboxylic polyether ionophore capable of interfering with ion flux within prokaryotic cells through its action as an ion carrier (2). It is generally accepted that the impact of monensin on methane production is through its suppression of other rumen microorganisms that provide methanogens with substrates (2,4,31). In a recent in vivo study, the use of long-term monensin supplementation for lactating dairy cattle decreased ruminal methane production by 7% (18). Along with the information now available about the long-term success of monensin treat...

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