Shifts in the microbial community and metabolome in rumen ecological niches during antler growth

Antlers are hallmark organ of deer, exhibiting a relatively high growth rate among mammals, and requiring large amounts of nutrients to meet its development. The rumen microbiota plays key roles in nutrient metabolism. However, changes in the microbiota and metabolome in the rumen during antler growth are largely unknown. We investigated rumen microbiota (liquid, solid, ventral epithelium, and dorsal epithelium) and metabolic profiles of sika deer at the early (EG), metaphase (MG) and fast growth (FG) stages. Our data showed greater concentrations of acetate and propionate in the rumens of sika deer from the MG and FG groups than in those of the EG group. However, microbial diversity decreased during antler growth, and was negatively correlated with short-chain fatty acid (SCFA) levels. Prevotella, Ruminococcus, Schaedlerella and Stenotrophomonas were the dominant bacteria in the liquid, solid, ventral epithelium, and dorsal epithelium fractions. The proportions of Stomatobaculum, Succiniclasticum, Comamonas and Anaerotruncus increased significantly in the liquid or dorsal epithelium fractions. Untargeted metabolomics analysis revealed that the metabolites also changed significantly, revealing 237 significantly different metabolites, among which the concentrations of γ-aminobutyrate and creatine increased during antler growth. Arginine and proline metabolism and alanine, aspartate and glutamate metabolism were enhanced. The co-occurrence network results showed that the associations between the rumen microbiota and metabolites different among the three groups. Our results revealed that the different rumen ecological niches were characterized by distinct microbiota compositions, and the production of SCFAs and the metabolism of specific amino acids were significantly changed during antler growth.

Differential Effect of Dietary Fibers in Intestinal Health of Growing Pigs: Outcomes in the Gut Microbiota and Immune-Related Indexes

Although dietary fibers (DFs) have been shown to improve intestinal health in pigs, it is unclear whether this improvement varies according to the type/source of DF. In the current study, we investigated the impact of dietary supplement (15%) of pea-hull fiber (PF), oat bran (OB), and their mixture (MIX, PF, and OB each accounted for 7.5%) in the growth performance as well as intestinal barrier and immunity-related indexes in growing pigs. Twenty-four cross-bred pigs (32.42 ± 1.95 kg) were divided into four groups: CON (basal diet with no additional DF), PF, OB, and MIX. After 56 days of feeding, we found that the growth performance of PF pigs was decreased (p < 0.05) compared with pigs in other groups. Results of real-time polymerase chain reaction and Western blot showed that the improvement of immune-related indexes (e.g., interleukin 10 [IL-10]) in OB and MIX pigs mainly presented in the ileum, whereas the improvement of intestinal barrier–related indexes (e.g., MUC1 and MUC2) mainly presented in the colon. Whether in the ileum or colon, such improvement of immune function may be dependent on NOD rather than TLR-associated pathways. Amplicon sequencing results showed that PF and MIX pigs shared a similar bacterial community, such as lower abundance of ileal Clostridiaceae and colonic Streptoccocus than that of CON pigs (p < 0.05). Our results indicate that OB and MIX, rather than PF, benefit the intestinal health in growing pigs, and multiple-sourced DF may reduce the adverse effect of single-soured DF on the growth performance and gut microbiota in pigs.

Comparative Microbiome Analysis Reveals the Ecological Relationships Between Rumen Methanogens, Acetogens, and Their Hosts

Ruminant methane, which is generated by methanogens through the consumption of hydrogen and supports the normal function of the rumen ecosystem, is a major source of greenhouse gases. Reductive acetogenesis by acetogens is a possible alternative sink that can dispose of hydrogen for acetate production. However, the distribution of rumen methanogens and acetogens along with the relationships among methanogens, acetogens, and their host are poorly understood. Therefore, we investigated the rumen methanogen and acetogen communities of 97 individual animals representing 14 ruminant species within three ruminant families Cervidae (deer), Bovidae (bovid), and Moschidae (musk deer). The results showed that the Methanobrevibacter spp. and acetogens associated with Eubacteriaceae were the most widespread methanogens and acetogens, respectively. However, other methanogens and acetogens exhibited host specificity in the rumen of reindeer and Chinese muntjac deer. Acetogen and methanogen communities were not correlated in these species, and the phylosymbiosis signature between host phylogeny and the composition of both communities was lacking. The abundance of Methanobrevibacter gottschalkii was negatively correlated with the degree of papillation of the rumen wall. Finally, co-occurrence analysis showed that the variation of the predicted methane yields was characterized by the interactive patterns between methanogens, acetogens, and concentrations of rumen metabolites. Our results show that rumen methanogen and acetogen communities have low compositional interdependence and do not exhibit parallel host evolution, which suggests that the strategies for mitigating methane production should be based on a species-specific rumen microbiota analysis.

Host genetics and the rumen microbiome jointly associate with methane emissions in dairy cows

Cattle and other ruminants produce large quantities of methane (~110 million metric tonnes per annum), which is a potent greenhouse gas affecting global climate change. Methane (CH4) is a natural by-product of gastro-enteric microbial fermentation of feedstuffs in the rumen and contributes to 6% of total CH4 emissions from anthropogenic-related sources. The extent to which the host genome and rumen microbiome influence CH4 emission is not yet well known. This study confirms individual variation in CH4 production was influenced by individual host (cow) genotype, as well as the host's rumen microbiome composition. Abundance of a small proportion of bacteria and archaea taxa were influenced to a limited extent by the host's genotype and certain taxa were associated with CH4 emissions. However, the cumulative effect of all bacteria and archaea on CH4 production was 13%, the host genetics (heritability) was 21% and the two are largely independent. This study demonstrates variation in CH4 emission is likely not modulated through cow genetic effects on the rumen microbiome. Therefore, the rumen microbiome and cow genome could be targeted independently, by breeding low methane-emitting cows and in parallel, by investigating possible strategies that target changes in the rumen microbiome to reduce CH4 emissions in the cattle industry.

The Development of Microbiota and Metabolome in Small Intestine of Sika Deer (Cervus nippon) from Birth to Weaning

The dense and diverse community of microorganisms inhabiting the gastrointestinal tract of ruminant animals plays critical roles in the metabolism and absorption of nutrients, and gut associated immune function. Understanding microbial colonization in the small intestine of new born ruminants is a vital first step toward manipulating gut function through interventions during early life to produce long-term positive effects on host productivity and health. Yet the knowledge of microbiota colonization and its induced metabolites of small intestine during early life is still limited. In the present study, we examined the microbiota and metabolome in the jejunum and ileum of neonatal sika deer (Cervus nippon) from birth to weaning at days 1, 42, and 70. The microbial data showed that diversity and richness were increased with age, but a highly individual variation was observed at day 1. Principal coordinate analysis revealed significant differences in microbial community composition across three time points in the jejunum and ileum. The abundance of Halomonas spp., Lactobacillus spp., Escherichia–Shigella, and Bacteroides spp. tended to be decreased, while the proportion of Intestinibacter spp., Cellulosilyticum spp., Turicibacter spp., Clostridium sensu stricto 1 and Romboutsia spp. was significantly increased with age. For metabolome, metabolites separated from each other across the three time points in both jejunum and ileum. Moreover, the amounts of methionine, threonine, and putrescine were increased, while the amounts of myristic acid and pentadecanoic acid were decreased with age, respectively. The present study demonstrated that microbiota colonization and the metabolome becomes more developed in the small intestine with age. This may shed new light on the microbiota-metabolome-immune interaction during development.

Different Types of Dietary Fibers Trigger Specific Alterations in Composition and Predicted Functions of Colonic Bacterial Communities in BALB/c Mice

Soluble dietary fibers (SDF) are fermented more than insoluble dietary fibers (IDF), but their effect on colonic bacterial community structure and function remains unclear. Thus, bacterial community composition and function in the colon of BALB/c mice (n = 7) fed with a high level (approximately 20%) of typical SDF, oat-derived β-glucan (G), microcrystalline cellulose (M) as IDF, or their mixture (GM), were compared. Mice in group G showed a lowest average feed intake (p < 0.05) but no change on the average body weight gain (p > 0.05) compared to other groups, which may be associated with the highest concentration of colonic propionate (p < 0.05) in these mice. The bacterial α-diversity of group G was significantly lower than other groups (p < 0.01). In group G, the relative abundance of bacteria belonging to the phylum Bacteroidetes was significantly increased, whereas bacteria from the phylum Firmicutes were significantly decreased (p < 0.01). The core bacteria for different treatments showed distinct differences. Bacteroides, Dehalobacterium, and Prevotella, including known acetogens and carbohydrate fermenting organisms, were significantly increased in relative abundance in group G. In contrast, Adlercreutzia, Odoribacter, and Coprococcus were significantly more abundant in group M, whereas Oscillospira, Desulfovibrio, and Ruminoccaceae, typical hydrogenotrophs equipped with multiple carbohydrate active enzymes, were remarkably enriched in group GM (p < 0.05). The relative abundance of bacteria from the three classes of Proteobacteria, Betaproteobacteria, Gammaproteobacteria (including Enterobacteriaceae) and Deltaproteobacteria, were significantly more abundant in group G, indicating a higher ratio of conditional pathogenic bacteria in mice fed dietary β-glucan in current study. The predicted colonic microbial function showed an enrichment of “Energy metabolism” and “Carbohydrate metabolism” pathways in mice from group G and M, suggesting that the altered bacterial community in the colon of mice with the two dietary fibers probably resulted in a more efficient degradation of dietary polysaccharides. Our result suggests that the influence of dietary β-glucan (SDF) on colonic bacterial community of mice was more extensively than MCC (IDF). Co-supplementation of the two fibers may help to increase the bacterial diversity and reduce the conditional pathogens in the colon of mice.

Implications from distinct sulfate-reducing bacteria populations between cattle manure and digestate in the elucidation of H2S production during anaerobic digestion of animal slurry

Biogas produced from the anaerobic digestion of animal slurry consists mainly of methane (CH₄) and carbon dioxide (CO₂), but also includes other minor gases, such as hydrogen sulfide (H₂S). Since it can act as a potent corrosive agent and presents a health hazard even at low concentrations, H₂S is considered an undesirable by-product of anaerobic digestion. Sulfate-reducing bacteria (SRBs) have been identified as the main biological source of H₂S in a number of natural, biological, and human-made habitats, and thus represent likely candidate microorganisms responsible for the production of H₂S in anaerobic manure digesters. Phylogenetically, SRBs form a divergent group of bacteria that share a common anaerobic respiration pathway that allows them to use sulfate as a terminal electron acceptor. While the composition and activity of SRBs have been well documented in other environments, their metabolic potential remains largely uncharacterized and their populations poorly defined in anaerobic manure digesters. In this context, a combination of in vitro culture-based studies and DNA-based approaches, respectively, were used to gain further insight. Unexpectedly, only low to nondetectable levels of H₂S were produced by digestate collected from a manure biogas plant documented to have persistently high concentrations of H₂S in its biogas (2000-3000 ppm). In contrast, combining digestate with untreated manure (a substrate with comparatively lower sulfate and SRB cell densities than digestate) was found to produce elevated H₂S levels in culture. While a 16S rRNA gene-based community composition approach did not reveal likely candidate SRBs in digestate or untreated manure, the use of the dsrAB gene as a phylogenetic marker provided more insight. In digestate, the predominant SRBs were found to be uncharacterized species likely belonging to the genus Desulfosporosinus (Peptococcaceae, Clostridiales, Firmicutes), while Desulfovibrio-related SRBs (Desulfovibrionaceae, Desulfovibrionales, Proteobacteria) were the most highly represented in untreated manure. Intriguingly, the same species-level OTUs with a similar pattern of opposite relative abundance were also found in two other digesters with lower H₂S levels in their biogas. Together, our results suggest that elevated H₂S production in anaerobic digesters requires the combination of biological and nutritional factors from both untreated manure and digestate.

Aviisotricha hoazini n. gen., n. sp., the Morphology and Molecular Phylogeny of an Anaerobic Ciliate from the Crop of the Hoatzin (Opisthocomus hoazin), the Cow Among the Birds

The hoatzin is the only known avian species that has evolved a foregut fermentation system similar to that of ruminant animals. Due to the closeness of the bird's fermentation chamber, the crop, to the bird's beak it exudes an unpleasant odour; therefore, the hoatzin is called the "cow among the birds". In addition to Eubacteria and Archaea, responsible for digestion of the vegetation they consume, the bird's crop contains a holotrich ciliate, described here for the first time in detail. Cytological staining of this isotrichid-like ciliate with the Chatton-Lwoff and Protargol staining procedures, as well as SEM and TEM, justified the establishment of the new genus Aviisotricha n. gen. with its new type species Aviisotricha hoazini n. gen., n. sp.. Phylogenetic analyses of a portion of the small subunit rRNA gene supported the taxonomic placement of this new genus and species in the family Isotrichidae. Aviisotricha is compared with Balantidium, Dasytricha and Isotricha with special reference to their dorsal brushes, which show similarity to the paralabial organelle of the Entodiniomorphida. The possible phylogenetic origin of Aviisotricha is discussed and a taxonomic revision of the family Isotrichidae is given.

Changes in the rumen microbiome and metabolites reveal the effect of host genetics on hybrid crosses

The rumen microbiota plays important roles in nutrient metabolism and absorption of the host. However, it is poorly understood how host genetic variation shapes the community structure of the rumen microbiota and its metabolic phenotype. Here, we used sika deer (Cervus nippon) and elk (Cervus elaphus) to produce the following two types of hybrid offspring: sika deer ♀ × elk ♂ (SEH) and elk ♀ × sika deer ♂ (ESH). Then, we examined the rumen microbiome and metabolites in the parents and their hybrid offspring. The rumen microbiota in the hybrids differed from that in their parents, suggesting a significant effect of host genetics on the rumen microbiome that may have resulted from vertical transmission. The rumen metabolites displayed patterns similar to the structure of the rumen microbiome, with changes in the amounts of volatile fatty acids and metabolites of amino acids. The alanine, arginine, proline and phenylalanine pathways were enriched in the rumen of hybrid animals. The enriched metabolites in the above pathways were positively correlated with the bacteria Prevotella spp., Acetitomaculum spp., Quinella spp., Succinivibrio spp. and Ruminobacter spp. These results suggest that host genetics has a major impact on the rumen microbiome and metabolites in hybrid animals.

Rumen and Cecum Microbiomes in Reindeer (Rangifer tarandus tarandus) Are Changed in Response to a Lichen Diet and May Affect Enteric Methane Emissions

Reindeer (Rangifer tarandus tarandus) are large Holarctic herbivores whose heterogeneous diet has led to the development of a unique gastrointestinal microbiota, essential for the digestion of arctic flora, which may include a large proportion of lichens during winter. Lichens are rich in plant secondary metabolites, which may affect members of the gut microbial consortium, such as the methane-producing methanogenic archaea. Little is known about the effect of lichen consumption on the rumen and cecum microbiotas and how this may affect methanogenesis in reindeer. Here, we examined the effects of dietary lichens on the reindeer gut microbiota, especially methanogens. Samples from the rumen and cecum were collected from two groups of reindeer, fed either lichens (Ld: n = 4), or a standard pelleted feed (Pd: n = 3). Microbial densities (methanogens, bacteria and protozoa) were quantified using quantitative real-time PCR and methanogen and bacterial diversities were determined by 454 pyrosequencing of the 16S rRNA genes.

In general, the density of methanogens were not significantly affected (p>0.05) by the intake of lichens. Methanobrevibacter constituted the main archaeal genus (>95% of reads), with Mbr. thaueri CW as the dominant species in both groups of reindeer. Bacteria belonging to the uncharacterized Ruminococcaceae and the genus Prevotella were the dominant phylotypes in the rumen and cecum, in both diets (ranging between 16–38% total sequences). Bacteria belonging to the genus Ruminococcus (3.5% to 0.6%; p = 0.001) and uncharacterized phylotypes within the order Bacteroidales (8.4% to 1.3%; p = 0.027), were significantly decreased in the rumen of lichen-fed reindeer, but not in the cecum (p = 0.2 and p = 0.087, respectively). UniFrac-based analyses showed archaeal and bacterial libraries were significantly different between diets, in both the cecum and the rumen (vegan::Adonis: pseudo-F<0.05). Based upon previous literature, we suggest that the altered methanogen and bacterial profiles may account for expected lower methane emissions from lichen-fed reindeer.

Influence of periparturient and postpartum diets on rumen methanogen communities in three breeds of primiparous dairy cows

BACKGROUND

Enteric methane from rumen methanogens is responsible for 25.9 % of total methane emissions in the United States. Rumen methanogens also contribute to decreased animal feed efficiency. For methane mitigation strategies to be successful, it is important to establish which factors influence the rumen methanogen community and rumen volatile fatty acids (VFA). In the present study, we used next-generation sequencing to determine if dairy breed and/or days in milk (DIM) (high-fiber periparturient versus high-starch postpartum diets) affect the rumen environment and methanogen community of primiparous Holstein, Jersey, and Holstein-Jersey crossbreeds.

RESULTS

When the 16S rRNA gene sequences were processed and assigned to operational taxonomic units (OTU), a core methanogen community was identified, consisting of Methanobrevibacter (Mbr.) smithii, Mbr. thaueri, Mbr. ruminantium, and Mbr. millerae. The 16S rRNA gene sequence reads clustered at 3 DIM, but not by breed. At 3 DIM, the mean % abundance of Mbr. thaueri was lower in Jerseys (26.9 %) and higher in Holsteins (30.7 %) and Holstein-Jersey crossbreeds (30.3 %) (P < 0.001). The molar concentrations of total VFA were higher at 3 DIM than at 93, 183, and 273 DIM, whereas the molar proportions of propionate were increased at 3 and 93 DIM, relative to 183 and 273 DIM. Rumen methanogen densities, distributions of the Mbr. species, and VFA molar proportions did not differ by breed.

CONCLUSIONS

The data from the present study suggest that a core methanogen community is present among dairy breeds, through out a lactation. Furthermore, the methanogen communities were more influenced by DIM and the breed by DIM interactions than breed differences.

Microorganisms in the rumen and reticulum of buffalo (Bubalus bubalis) fed two different feeding systems

Background

The community of microorganisms in the rumen and reticulum is influenced by feeding as well as the species and geographical distribution of ruminant animals. Bacteria, methanogenic archaea and ciliate protozoa existing in the rumen and reticulum were evaluated by real-time polymerase chain reaction and light microscopy in buffalo in two feeding systems, grazing and feedlot.

Results

No significant differences were observed in the total concentrations of bacteria/mL and archaea between rumen and reticulum, and between pasture and feedlots, or interactions between variables. However, the largest density of bacteria and smallest density of archaea was observed in the rumen of grazing animals. The total ciliates protozoa community was higher in grazing buffalo than those in the feedlot on a concentrated diet. There were significant interactions between location in the gastrointestinal tract (rumen vs reticulum) and types of diets (grazing vs feedlot) in the composition of ciliates.

Conclusions

Our data showed differences in the microbial community of the rumen and reticulum between grazing and feedlot feeding systems demonstrating relevant changes in the microorganism:host relationship existing on rumen–reticulum ecosystem.

Rumen bacterial communities shift across a lactation in Holstein, Jersey and Holstein × Jersey dairy cows and correlate to rumen function, bacterial fatty acid composition and production parameters

Rumen bacteria form a dynamic, complex, symbiotic relationship with their host, degrading forages to provide volatile fatty acids (VFA) and other substrates as energy to the animal. The objectives were to characterize rumen bacteria in three genetic lines of primiparous dairy cattle, Holstein (HO, n = 7), Jersey (JE, n = 8), and HO × JE crossbreeds (CB, n = 7) across a lactation [3, 93, 183 and 273 days in milk (DIM)] and correlate these factors with VFA, bacterial cell membrane fatty acids (FA), and animal production (i.e. milk yield). This study employed Illumina MiSeq (v. 3) to investigate rumen bacterial communities and gas-liquid chromatography/mass spectroscopy to identify bacterial membrane FA. Lactation stage had a prominent effect on rumen bacterial communities, whereas genetics had a lesser effect on rumen bacteria. The FA composition of bacterial cell membranes was affected by both lactation stage and genetics. Few correlations existed between VFA and bacterial communities; however, moderate correlations occurred between milk yield, protein percentage, fat yield and rumen bacterial communities. Positive correlations were found between branched-chain FA (BCFA) in bacterial cell membranes and bacterial genera. In conclusion, bacterial communities and their FA compositions are more affected by stage of lactation than by genetics of dairy cow.

Breed and Lactation Stage Alter the Rumen Protozoal Fatty Acid Profiles and Community Structures in Primiparous Dairy Cattle

The protozoal fatty acid (FA) composition and community structure are important to dairy cattle nutrition and their products. The purpose of the study was to observe if the rumen protozoal FA profiles and protozoal community structure differed by breed and lactation stage. At 93, 183, and 273 days in milk (DIM), whole rumen digesta samples were collected from seven co-housed Holstein (H), eight Jersey (J), and seven Holstein-Jersey crossbreed (C) cows. Rumen protozoal linoleic acid was higher at 183 DIM (8.1%) and 273 DIM (8.3%) than at 93 DIM (5.7%). Oleic acid was the most abundant protozoal unsaturated FA (10.1%). Protozoal rumenic acid and protozoa of the genus Metadinium were higher in J (9.9%) than in H (0.52%) and C (0.96%). Protozoa belonging to the genus Entodinium were more abundant in H (45.2%) than in J (23.4%) and C (30.2%). In conclusion, breed and DIM affected several protozoal FAs and genera.

Content and Composition of Branched-Chain Fatty Acids in Bovine Milk Are Affected by Lactation Stage and Breed of Dairy Cow

Dairy products contain bioactive fatty acids (FA) and are a unique dietary source of an emerging class of bioactive FA, branched-chain fatty acids (BCFA). The objective of this study was to compare the content and profile of bioactive FA in milk, with emphasis on BCFA, among Holstein (HO), Jersey (JE), and first generation HO x JE crossbreeds (CB) across a lactation to better understand the impact of these factors on FA of interest to human health. Twenty-two primiparous cows (n = 7 HO, n = 7 CB, n = 8 JE) were followed across a lactation. All cows were fed a consistent total mixed ration (TMR) at a 70:30 forage to concentrate ratio. Time points were defined as 5 days in milk (DIM), 95 DIM, 185 DIM, and 275 DIM. HO and CB had a higher content of n-3 FA at 5 DIM than JE and a lower n-6:n-3 ratio. Time point had an effect on the n-6:n-3 ratio, with the lowest value observed at 5 DIM and the highest at 185 DIM. The content of vaccenic acid was highest at 5 DIM, yet rumenic acid was unaffected by time point or breed. Total odd and BCFA (OBCFA) were higher in JE than HO and CB at 185 and 275 DIM. Breed affected the content of individual BCFA. The content of iso-14:0 and iso-16:0 in milk was higher in JE than HO and CB from 95 to 275 DIM. Total OBCFA were affected by time point, with the highest content in milk at 275 DIM. In conclusion, HO and CB exhibited a higher content of several bioactive FA in milk than JE. Across a lactation the greatest content of bioactive FA in milk occurred at 5 DIM and OBCFA were highest at 275 DIM.

Intra-ruminal gas-sensing in real time: a proof-of-concept

An intra-rumen (IR) gas-sensing system incorporating commercially available gas sensors [methane (CH4), carbon dioxide (CO2) and hydrogen (H2)] and a wireless sensor network was developed to measure rumen gas concentrations of grazing animals in real-time. The IR gas-sensing devices also measure temperature and pressure near the sensors and the design isolates the electronics and battery from exposure to gases. Membranes were developed that allow the desired gases to diffuse through to the sensors while excluding corrosive hydrogen sulfide (H2S). Performance of the prototype IR devices was tested in cattle and sheep fed once a day as a proof-of-concept. Concentrations of expired gases from respiration chambers were compared with the concentrations obtained by the IR gas-sensing device within the rumen digesta. Direct measurements of rumen gas cap samples demonstrate a similar gas profile to that observed with the IR gas-sensing device with the ratio of CO2 : CH4 peaking shortly after feeding and CO2 levels nearly 2.5 times greater than those of CH4. The gas ratio then declines over time to a point when at 23 h post-feeding the concentration of CH4 exceeds that of CO2. The H2 gas concentration in the rumen varied throughout the day reaching maximum levels of 2500 ppm after feeding and declining to 250 ppm over the day. Although the IR device was able to detect H2 in the rumen throughout the entire day, expired H2 was often below the limits of detection in the respiration chamber. Current work is focussed on extending the longevity of the devices in the rumen so that replicated trials can be performed on the accuracy and precision of the measurements.

Fibrolytic Bacteria Isolated from the Rumen of North American Moose (Alces alces) and Their Use as a Probiotic in Neonatal Lambs

Fibrolytic bacteria were isolated from the rumen of North American moose (Alces alces), which eat a high-fiber diet of woody browse. It was hypothesized that fibrolytic bacteria isolated from the moose rumen could be used as probiotics to improve fiber degradation and animal production. Thirty-one isolates (Bacillus, n = 26; Paenibacillus, n = 1; and Staphylococcus, n = 4) were cultured from moose rumen digesta samples collected in Vermont. Using Sanger sequencing of the 16S rRNA gene, culturing techniques, and optical densities, isolates were identified and screened for biochemical properties important to plant carbohydrate degradation. Five isolates were selected as candidates for use as a probiotic, which was administered daily to neonate lambs for 9 weeks. It was hypothesized that regular administration of a probiotic to improve fibrolysis to neonate animals through weaning would increase the developing rumen bacterial diversity, increase animal production, and allow for long-term colonization of the probiotic species. Neither weight gain nor wool quality was improved in lambs given a probiotic, however, dietary efficiency was increased as evidenced by the reduced feed intake (and rearing costs) without a loss to weight gain. Experimental lambs had a lower acetate to propionate ratio than control lambs, which was previously shown to indicate increased dietary efficiency. Fibrolytic bacteria made up the majority of sequences, mainly Prevotella, Butyrivibrio, and Ruminococcus. While protozoal densities increased over time and were stable, methanogen densities varied greatly in the first six months of life for lambs. This is likely due to the changing diet and bacterial populations in the developing rumen.

High-throughput DNA sequencing of the moose rumen from different geographical locations reveals a core ruminal methanogenic archaeal diversity and a differential ciliate protozoal diversity

Moose rumen samples from Vermont, Alaska and Norway were investigated for methanogenic archaeal and protozoal density using real-time PCR, and diversity using high-throughput sequencing of the 16S and 18S rRNA genes. Vermont moose showed the highest protozoal and methanogen densities. Alaskan samples had the highest percentages of Methanobrevibacter smithii, followed by the Norwegian samples. One Norwegian sample contained 43 % Methanobrevibacter thaueri, whilst all other samples contained < 10 %. Vermont samples had large percentages of Methanobrevibacter ruminantium, as did two Norwegian samples. Methanosphaera stadtmanae represented one-third of sequences in three samples. Samples were heterogeneous based on gender, geographical location and weight class using analysis of molecular variance (AMOVA). Two Alaskan moose contained >70 % Polyplastron multivesiculatum and one contained >75 % Entodinium spp. Protozoa from Norwegian moose belonged predominantly (>50 %) to the genus Entodinium, especially Entodinium caudatum. Norwegian moose contained a large proportion of sequences (25–97 %) which could not be classified beyond family. Protozoa from Vermont samples were predominantly Eudiplodinium rostratum (>75 %), with up to 7 % Diploplastron affine. Four of the eight Vermont samples also contained 5–12 % Entodinium spp. Samples were heterogeneous based on AMOVA, principal coordinate analysis and UniFrac. This study gives the first insight into the methanogenic archaeal diversity in the moose rumen. The high percentage of rumen archaeal species associated with high starch diets found in Alaskan moose corresponds well to previous data suggesting that they feed on plants high in starch. Similarly, the higher percentage of species related to forage diets in Vermont moose also relates well to their higher intake of fibre.

Toward the identification of methanogenic archaeal groups as targets of methane mitigation in livestock animalsr

In herbivores, enteric methane is a by-product from the digestion of plant biomass by mutualistic gastrointestinal tract (GIT) microbial communities. Methane is a potent greenhouse gas that is not assimilated by the host and is released into the environment where it contributes to climate change. Since enteric methane is exclusively produced by methanogenic archaea, the investigation of mutualistic methanogen communities in the GIT of herbivores has been the subject of ongoing research by a number of research groups. In an effort to uncover trends that would facilitate the development of efficient methane mitigation strategies for livestock species, we have in this review summarized and compared currently available results from published studies on this subject. We also offer our perspectives on the importance of pursuing current research efforts on the sequencing of gut methanogen genomes, as well as investigating their cellular physiology and interactions with other GIT microorganisms.

The nasopharyngeal microbiota of feedlot cattle that develop bovine respiratory disease

Bovine respiratory disease is the major cause of morbidity and mortality in feedlot cattle. The objective of this study was to compare the nasopharyngeal bacterial microbiota of healthy cattle and cattle treated for BRD in a commercial feedlot setting using a high-density 16S rRNA gene microarray (Phylochip). Samples were taken from both groups of animals (n=5) at feedlot entry (day 0) and ≥60 days after placement. Cattle diagnosed with BRD had significantly less bacterial diversity and fewer OTUs in their nasopharynx at both sampling times. The predominant phyla in both groups were Proteobacteria and Firmicutes. The relative abundance of the phylum Actinobacteria was lower in cattle treated for BRD. At the family-level there was a greater relative abundance (P<0.05) of Micrococcaceae (day 0 only), Lachnospiraceae (≥60 days), Lactobacillaceae (day 0), and Bacillaceae (day 0) in healthy cattle compared to BRD-affected cattle. The community structure of the BRD-affected and healthy cattle were also significantly different from each other at both sampling times as measured using unweighted UniFrac distances. All entry samples of cattle diagnosed with BRD had 16S rRNA gene sequences representative of the BRD-associated bacteria Mannheimia haemolytica or Pasteurella multocida, although 3/5 healthy cattle were also positive for M. haemolytica at this time point. The results also indicate that the bovine nasopharyngeal microbiota is relatively unstable during the first 60 days in the feedlot.

Response of the Rumen Microbiota of Sika Deer (Cervus nippon) Fed Different Concentrations of Tannin Rich Plants

High throughput sequencing was used to examine the rumen microbiota of sika deer fed high (OLH) and low concentration (OLL) of tannin rich oak leaves. The results showed that Prevotella spp. were the most dominant bacteria. The most predominant methanogens were the members of the order Methanoplasmatales. The dominant rumen protozoa were Entodinium longinucleatum, Eudiplodinium maggii, and Epidinium caudatum, and the fungal communities were mostly represented by Piromyces spp. Moreover, the relative abundance of Pseudobutyrivibrio spp. (P=0.026), unidentified bacteria (P=0.028), and Prevotella spp. (P=0.022) was lower in the OLH group than in the OLL group. The concentration of propionate in the OLH group was greater than in the OLL group (P=0.006). Patterns of relationships showed that methanogens belonging to the order Methanoplasmatales were negatively correlated with Treponema spp., Ent. Longinucleatum, and acetate. Methanosphaera stadtmanae was positively correlated to propionate, while Methanobrevibacter ruminantium was negatively associated with Methanobrevibacter thaueri and Methanobrevibacter millerae. Tannins altered the rumen microbes and fermentation patterns. However, the response of the entire rumen microbiota and the relationship between rumen microorganisms and the fermentation parameters were not fully understood.

Examination of the rumen bacteria and methanogenic archaea of wild impalas (Aepyceros melampus melampus) from Pongola, South Africa

Although the rumen microbiome of domesticated ruminants has been evaluated, few studies have explored the rumen microbiome of wild ruminants, and no studies have identified the rumen microbiome in the impala (Aepyceros melampus melampus). In the present study, next-generation sequencing and real-time polymerase chain reaction were used to investigate the diversity and density of the bacteria and methanogenic archaea residing in the rumen of five adult male impalas, culled during the winter dry season in Pongola, South Africa. A total of 15,323 bacterial 16S rRNA gene sequences (from five impala), representing 3,892 different phylotypes, were assigned to 1,902 operational taxonomic units (OTUs). A total of 20,124 methanogen 16S rRNA gene sequence reads (from four impala), of which 5,028 were unique, were assigned to 344 OTUs. From the total sequence reads, Bacteroidetes, Proteobacteria, and Firmicutes were the most abundant bacterial phyla. While the majority of the bacterial genera found were unclassified, Prevotella and Cupriavidus were the most abundant classified genera. For methanogens, the genera Methanobrevibacter and Methanosphaera represented 94.3% and 4.0% of the classified sequences, respectively. Most notable was the identification of Methanobrevibacter thaueri-like 16S rRNA gene sequence reads in all four impala samples, representing greater than 30% of each individual's total sequences. Both data sets are accessible through NCBI's Sequence Read Archive (SRA), under study accession number SRP [048619]. The densities of bacteria (1.26 × 10(10)-3.82 × 10(10) cells/ml whole rumen contents) and methanogens (4.48 × 10(8)-7.2 × 10(9) cells/ml of whole rumen contents) from five individual impala were similar to those typically observed in domesticated ruminants.

Bacterial community composition and fermentation patterns in the rumen of sika deer (Cervus nippon) fed three different diets

Sika deer (Cervus nippon) rely on microorganisms living in the rumen to convert plant materials into chemical compounds, such as volatile fatty acids (VFAs), but how the rumen bacterial community is affected by different forages and adapt to altered diets remains poorly understood. The present study used 454-pyrosequencing of bacterial 16S ribosomal RNA (rRNA) genes to examine the relationship between rumen bacterial diversity and metabolic phenotypes using three sika deer in a 3 × 3 latin square design. Three sika deer were fed oak leaves (OL), corn stover (CS), or corn silage (CI), respectively. After a 7-day feeding period, when compared to the CS and CI groups, the OL group had a lower proportion of Prevotella spp. and a higher proportion of unclassified bacteria belonging to the families Succinivibrionaceae and Paraprevotellaceae (P<0.05). Meanwhile, the concentration of isobutyrate was significantly lower (P<0.05) in the OL group than in the CS and CI groups. There was no significant change of dominant bacterial genera in the OL group after 28 days of feeding. Conversely, total volatile fatty acids (TVFAs) showed an increase after 28 days of feeding, mainly due to the increasing of acetate, propionate, and valerate (P<0.05). The interplay between bacteria and metabolism in the OL group differed from that in the CS and CI groups, especially for the interaction of TVFAs and acetate/propionate. Overall, the current study suggested that Prevotella spp. played critical roles in the fermentation of feed in the rumen of sika deer. However, the differences in interplay patterns between rumen bacterial community composition and metabolic phenotypes were altered in the native and domesticated diets indicating the changed fermentation patterns in the rumen of sika deer.

Differences in the methanogen population exist in sika deer (Cervus nippon) fed different diets in China

Understanding the methanogen structure from sika deer (Cervus nippon) in China may be beneficial to methane mitigation. In the present preliminary study, we investigated the methanogen community in the rumen of domesticated sika deer fed either tannin-rich plants (oak leaf, OL group) or corn stalk (CS group) using 16S rRNA gene clone libraries. Overall, we obtained 197 clone sequences, revealing 146 unique phylotypes, which were assigned to 36 operational taxonomic units at the species level (98 % identity). Methanogens related to the genus Methanobrevibacter were the predominant phylotypes representing 83.9 % (OL library) and 85.9 % (CS library) of the clones. Methanobrevibacter millerae was the most abundant species in both libraries, but the proportion of M. millerae-related clones in the CS library was higher than in the OL library (69.5 and 51.4 %, respectively). Moreover, Methanobrevibacter wolinii-related clones (32.5 %) were predominant in the OL library. Methanobrevibacter smithii-related clones and Methanobrevibacter ruminantium-related clones accounted for 6.5 and 6.6 % in the CS library, respectively. However, these clones were absent from the OL library. The concentrations of butyrate and total short-chain fatty acids (SCFAs) were significantly higher in the OL group, but the concentrations of acetate, propionate, and valerate and the acetate to propionate ratio in the OL group were not significantly different between the two groups. Tannin-rich plants may have affected the distribution of genus Methanobrevibacter phylotypes at the species level and the concentration and composition of SCFAs.

Comparative metagenomic analysis of bacterial populations in three full-scale mesophilic anaerobic manure digesters

While the use of anaerobic digestion to generate methane as a source of bioenergy is increasing worldwide, our knowledge of the microbial communities that perform biomethanation is very limited. Using next-generation sequencing, bacterial population profiles were determined in three full-scale mesophilic anaerobic digesters operated on dairy farms in the state of Vermont (USA). To our knowledge, this is the first report of a metagenomic analysis on the bacterial population of anaerobic digesters using dairy manure as their main substrate. A total of 20,366 non-chimeric sequence reads, covering the V1-V2 hypervariable regions of the bacterial 16S rRNA gene, were assigned to 2,176 operational taxonomic units (OTUs) at a genetic distance cutoff value of 5 %. Based on their limited sequence identity to validly characterized species, the majority of OTUs identified in our study likely represented novel bacterial species. Using a naïve Bayesian classifier, 1,624 anaerobic digester OTUs could be assigned to 16 bacterial phyla, while 552 OTUs could not be classified and may belong to novel bacterial taxonomic groups that have yet to be described. Firmicutes, Bacteroidetes, and Chloroflexi were the most highly represented bacteria overall, with Bacteroidetes and Chloroflexi showing the least and the most variation in abundance between digesters, respectively. All digesters shared 132 OTUs, which as a "core" group represented 65.4 to 70.6 % of sequences in individual digesters. Our results show that bacterial populations from microbial communities of anaerobic manure digesters can display high levels of diversity despite sharing a common core substrate.

Diversity of methanogens in the hindgut of captive white rhinoceroses, Ceratotherium simum

BACKGROUND

The white rhinoceros is on the verge of extinction with less than 20,200 animals remaining in the wild. In order to better protect these endangered animals, it is necessary to better understand their digestive physiology and nutritional requirements. The gut microbiota is nutritionally important for herbivorous animals. However, little is known about the microbial diversity in the gastrointestinal tract (GIT) of the white rhinoceros. Methanogen diversity in the GIT may be host species-specific and, or, function-dependent. To assess methanogen diversity in the hindgut of white rhinoceroses, an archaeal 16S rRNA gene clone library was constructed from pooled PCR products obtained from the feces of seven adult animals.

RESULTS

Sequence analysis of 153 archaeal 16S rRNA sequences revealed 47 unique phylotypes, which were assigned to seven operational taxonomic units (OTUs 1 to 7). Sequences assigned to OTU-7 (64 out of 153 total sequencs - 42%) and OTU-5 (18%, 27/153) had 96.2% and 95.5% identity to Methanocorpusculum labreanum, respectively, making Methanocorpusculum labreanum the predominant phylotype in these white rhynoceroses. Sequences belonging to OTU-6 (27%, 42/153) were related (97.6%) to Methanobrevibacter smithii. Only 4% of the total sequences (6/153) were assigned to Methanosphaera stadtmanae (OTU-1). Sequences belonging to OTU-2 (4%, 6/153), OTU-3 (3%, 5/153) and OTU-4 (2%, 3/153) were distantly related (87.5 to 88,4%) to Methanomassiliicoccus luminyensis and were considered to be novel species or strains that have yet-to-be cultivated and characterized.

CONCLUSION

Phylogenetic analysis indicated that the methanogen species in the hindgut of white rhinoceroses were more similar to those in the hindgut of horses. Our findings may help develop studies on improving the digestibility of forage for sustainable management and better health of these endangered animals.

Board-invited review: Rumen microbiology: leading the way in microbial ecology

Robert Hungate, considered the father of rumen microbiology, was the first to initiate a systematic exploration of the microbial ecosystem of the rumen, but he was not alone. The techniques he developed to isolate and identify cellulose-digesting bacteria from the rumen have had a major impact not only in delineating the complex ecosystem of the rumen but also in clinical microbiology and in the exploration of a number of other anaerobic ecosystems, including the human hindgut. Rumen microbiology has pioneered our understanding of much of microbial ecology and has broadened our knowledge of ecology in general, as well as improved the ability to feed ruminants more efficiently. The discovery of anaerobic fungi as a component of the ruminal flora disproved the central dogma in microbiology that all fungi are aerobic organisms. Further novel interactions between bacterial species such as nutrient cross feeding and interspecies H2 transfer were first described in ruminal microorganisms. The complexity and diversity present in the rumen make it an ideal testing ground for microbial theories (e.g., the effects of nutrient limitation and excess) and techniques (such as 16S rRNA), which have rewarded the investigators that have used this easily accessed ecosystem to understand larger truths. Our understanding of characteristics of the ruminal microbial population has opened new avenues of microbial ecology, such as the existence of hyperammonia-producing bacteria and how they can be used to improve N efficiency in ruminants. In this review, we examine some of the contributions to science that were first made in the rumen, which have not been recognized in a broader sense.

Metagenomic analysis of methanogen populations in three full-scale mesophilic anaerobic manure digesters operated on dairy farms in Vermont, USA

The microbial communities that produce biogas as a result of anaerobic digestion of manure remain poorly understood. Using next-generation sequencing, methanogen populations were investigated in three full scale mesophilic anaerobic digesters operated on dairy farms. A combined 50 246 non-chimeric sequence reads covering the V1-V3 hypervariable regions of the methanogen 16S rRNA gene were assigned to 307 species-level operational taxonomic units (OTUs). The Blue Spruce Farms (BSF) and Green Mountain Dairy (GMD) anaerobic digesters were found to have nearly identical methanogen profiles, with the overwhelming predominance of OTU 1 (98.5% and 99.7%, respectively), which showed 99.2% sequence identity to Methanosarcina thermophila. In contrast, methanogens from the Chaput Family Farms (CFF) anaerobic digester were more diverse, with five major OTUs belonging to four distinct phylogenetic groups (Methanomicrobiales, Methanosarcinales, Methanoplasmatales, and Methanobacteriales). Differences in management practices and years of operation were hypothesized as potential factors responsible for differences in the methanogen profiles.

Biodiversity and molecular phylogeny of Australian Clevelandella species (Class Armophorea, Order Clevelandellida, Family Clevelandellidae), intestinal endosymbiotic ciliates in the wood-feeding roach Panesthia cribrata Saussure, 1864

There are over 100 species in the Order Clevelandellida distributed in many hosts. The majority is assigned to one of the five families, the Nyctotheridae. Our knowledge of clevelandellid genetic diversity is limited to species of Nyctotherus and Nyctotheroides. To increase our understanding of clevelandellid genetic diversity, species were isolated from intestines of the Australian wood-feeding roach Panesthia cribrata Saussure, 1864 from August to October, 2008. Four morphospecies, similar to those reported in Java and Japan by Kidder [Parasitologica, 29:163-205], were identified: Clevelandella constricta, Clevelandella nipponensis, Clevelandella parapanesthiae, and Clevelandella panesthiae. Small subunit rRNA gene sequences assigned all species to a "family" clade that was sister to the clade of species assigned to the Family Nyctotheridae in the Order Clevelandellida. Genetics and morphology were consistent for the first three Clevelandella species, but isolates assigned to C. panesthiae were assignable to three different genotypes, suggesting that this may be a cryptic species complex.

Comparison of methanogen diversity of yak (Bos grunniens) and cattle (Bos taurus) from the Qinghai-Tibetan plateau, China

BACKGROUND

Methane emissions by methanogen from livestock ruminants have significantly contributed to the agricultural greenhouse gas effect. It is worthwhile to compare methanogen from "energy-saving" animal (yak) and normal animal (cattle) in order to investigate the link between methanogen structure and low methane production.

RESULTS

Diversity of methanogens from the yak and cattle rumen was investigated by analysis of 16S rRNA gene sequences from rumen digesta samples from four yaks (209 clones) and four cattle (205 clones) from the Qinghai-Tibetan Plateau area (QTP). Overall, a total of 414 clones (i.e. sequences) were examined and assigned to 95 operational taxonomic units (OTUs) using MOTHUR, based upon a 98% species-level identity criterion. Forty-six OTUs were unique to the yak clone library and 34 OTUs were unique to the cattle clone library, while 15 OTUs were found in both libraries. Of the 95 OTUs, 93 putative new species were identified. Sequences belonging to the Thermoplasmatales-affiliated Linage C (TALC) were found to dominate in both libraries, accounting for 80.9% and 62.9% of the sequences from the yak and cattle clone libraries, respectively. Sequences belonging to the Methanobacteriales represented the second largest clade in both libraries. However, Methanobrevibacter wolinii (QTPC 110) was only found in the cattle library. The number of clones from the order Methanomicrobiales was greater in cattle than in the yak clone library. Although the Shannon index value indicated similar diversity between the two libraries, the Libshuff analysis indicated that the methanogen community structure of the yak was significantly different than those from cattle.

CONCLUSION

This study revealed for the first time the molecular diversity of methanogen community in yaks and cattle in Qinghai-Tibetan Plateau area in China. From the analysis, we conclude that yaks have a unique rumen microbial ecosystem that is significantly different from that of cattle, this may also help to explain why yak produce less methane than cattle.

Insight into the bacterial gut microbiome of the North American moose (Alces alces)

Background

The work presented here provides the first intensive insight into the bacterial populations in the digestive tract of the North American moose (Alces alces). Eight free-range moose on natural pasture were sampled, producing eight rumen samples and six colon samples. Second generation (G2) PhyloChips were used to determine the presence of hundreds of operational taxonomic units (OTUs), representing multiple closely related species/strains (>97% identity), found in the rumen and colon of the moose.

Results

A total of 789 unique OTUs were used for analysis, which passed the fluorescence and the positive fraction thresholds. There were 73 OTUs, representing 21 bacterial families, which were found exclusively in the rumen samples: Lachnospiraceae, Prevotellaceae and several unclassified families, whereas there were 71 OTUs, representing 22 bacterial families, which were found exclusively in the colon samples: Clostridiaceae, Enterobacteriaceae and several unclassified families. Overall, there were 164 OTUs that were found in 100% of the samples. The Firmicutes were the most dominant bacteria phylum in both the rumen and the colon. Microarray data available at ArrayExpress, accession number E-MEXP-3721.

Conclusions

Using PhyloTrac and UniFrac computer software, samples clustered into two distinct groups: rumen and colon, confirming that the rumen and colon are distinct environments. There was an apparent correlation of age to cluster, which will be validated by a larger sample size in future studies, but there were no detectable trends based upon gender.

Analysis of rumen methanogen diversity in water buffaloes (Bubalus bubalis) under three different diets

The water buffalo (Bubalus bubalis) is a prominent livestock species for the production of milk and meat in many countries. We investigated the diversity of rumen methanogens in Mediterranean water buffaloes maintained in Brazil under different diets: corn silage, grazing pasture, or sugar cane. A total of 467 clones were isolated from three methanogen 16S rRNA gene clone libraries that each represented a distinct feed type. The 467 clones were assigned to 19 species-level operational taxonomic units (OTUs). Four OTUs were represented in all three libraries, eight OTUs were library-specific, six OTUs were found in only the corn silage and pasture grazing libraries, and one OTU was shared only between pasture grazing and sugar cane libraries. We found that Methanobrevibacter-related sequences were the most abundant in the water buffaloes sampled for our analysis, in contrast to previously reported studies showing that Methanomicrobium mobile-like methanogens were the most abundant methanogens in water buffaloes of Murrah and Surti breeds sampled in India. Considering the worldwide distribution of water buffaloes and the likely wide variety of diets provided, our results combined with studies from other groups support that larger scope analyses of microbiomes for this livestock species would provide great insight into the contribution of geographical location, breed, and diet in determining the population structure of rumen microorganisms.

Molecular analysis of methanogenic archaea in the forestomach of the alpaca (Vicugna pacos)

Background

Methanogens 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.

Results

We 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.

Conclusion

From 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.

Molecular diversity of the foregut bacteria community in the dromedary camel (Camelus dromedarius)

The molecular diversity of the foregut bacterial community in the dromedary camel (Camelus dromedarius) in Central Australia was investigated through comparative analyses of 16S rRNA gene sequences prepared from the foregut contents of 12 adult feral camels fed on native vegetation. A total of 267 full-length 16S rRNA gene clones were examined, with 151 operational taxonomic units (OTUs) identified at a 99% species-level identity cut-off criterion. The prediction of actual diversity in the foregut of the dromedary camel using the Chaol approach was 238 OTUs, while the richness and evenness of the diversity estimated using Shannon index was 4.84. The majority of bacteria in the current study were affiliated with the bacterial phylum Firmicutes (67% of total clones) and were related to the classes Clostridia, Bacilli and Mollicutes, followed by the Bacteroidetes (25%) that were mostly represented by the family Prevotellaceae. The remaining phyla were represented by Actinobacteria, Chloroflexi, Cynophyta, Lentisphaerae, Planctomycetes, Proteobacteria and Sphirochaetes. Moreover, 11 clones of cultivated bacteria were identified as Brevundimonas sp., Butyrivibrio fibrisolvens, Prevotella sp. and Ruminococcus flavefaciens. The novelty in this foregut environment is remarkable where 97% of the OTUs were distantly related to any known sequence in the public database.

Impact of subacute ruminal acidosis (SARA) adaptation and recovery on the density and diversity of bacteria in the rumen of dairy cows

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.

Impact of high-concentrate feeding and low ruminal pH on methanogens and protozoa in the rumen of dairy cows

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.

Methanogens: methane producers of the rumen and mitigation strategies

Methanogens are the only known microorganisms capable of methane production, making them of interest when investigating methane abatement strategies. A number of experiments have been conducted to study the methanogen population in the rumen of cattle and sheep, as well as the relationship that methanogens have with other microorganisms. The rumen methanogen species differ depending on diet and geographical location of the host, as does methanogenesis, which can be reduced by modifying dietary composition, or by supplementation of monensin, lipids, organic acids, or plant compounds within the diet. Other methane abatement strategies that have been investigated are defaunation and vaccines. These mitigation methods target the methanogen population of the rumen directly or indirectly, resulting in varying degrees of efficacy. This paper describes the methanogens identified in the rumens of cattle and sheep, as well as a number of methane mitigation strategies that have been effective in vivo.

Ecological characterisation of the colonic microbiota in arctic and sub-arctic seals

Dominant colonic bacteria in wild hooded (n = 9), harbour (n = 1) and grey (n = 1) seals were identified using 16S rRNA gene clone libraries (313 clones), revealing 52.7% Bacteroidetes, 41.5% Firmicutes, 4.5% Proteobacteria and 1.0% Fusobacteria. Thirty (77%) of the 39 phylotypes identified were novel, showing <97% sequence similarity to their nearest cultivated relatives. Mean colonic bacterial cell density, determined by real-time PCR, was high (12.8 log(10) cells/g wet wt) for the hooded seals, while the number of methanogenic Archea was low (4.0 log(10) cells/g wet wt). The level of ampicillin (amp(r)) and tetracycline-resistant (tet(r)) isolates was investigated by cultivation. Aerobic amp(r) isolates were only detected in colon contents from four hooded seals, whereas aerobic tet(r) isolates were found in seven of the nine hooded seals. These data provide novel insight to the gut microbiota of Arctic and sub-Arctic seals living in the wild.

Molecular diversity of the rumen microbiome of Norwegian reindeer on natural summer pasture

The molecular diversity of the rumen microbiome was investigated in five semi-domesticated adult female Norwegian reindeer (Rangifer tarandus tarandus) grazing on natural summer pastures on the coast of northern Norway (71.00 degrees N, 25.30 degrees E). Mean population densities (numbers per gram wet weight) of methanogenic archaea, rumen bacteria and ciliate protozoa, estimated using quantitative real-time polymerase chain reaction (PCR), were 3.17x10(9), 5.17x10(11) and 4.02x10(7), respectively. Molecular diversity of rumen methanogens was revealed using a 16S rRNA gene library (54 clones) constructed using pooled PCR products from the whole rumen contents of the five individual reindeer. Based upon a similarity criterion of <97%, a total of 19 distinct operational taxonomic units (OTUs) were identified, nine of which are potential new species. The 16S rRNA sequences generated from the reindeer rumen exhibited a high degree of sequence similarity to methanogens affiliated with the families Methanobacteriaceae (14 OTUs) and Methanosarcinaceae (one OTU). Four of the OTUs detected belonged to a group of uncultivated archaea previously found in domestic ruminants and thought to be dominant in the rumen together with Methanobrevibacter spp. Denaturing gradient gel electrophoresis profiling of the rumen bacterial 16S rRNA gene and the protozoal 18S rRNA gene indicated a high degree of animal variation, although some bands were common to all individuals. Automated ribosomal intergenic spacer analysis (ARISA) profiling of the ruminal Neocallimastigales population indicated that the reindeer are likely to contain more than one type of anaerobic fungus. The ARISA profile from one animal was distinct from the other four. This is the first molecular investigation of the ruminal methanogenic archaea in reindeer, revealing higher numbers than expected based on methane emission data available. Also, many of the reindeer archaeal 16S rRNA gene sequences were similar to those reported in domesticated ruminants in Australia, Canada, China, New Zealand and Venezuela, supporting previous findings that there seems to be no host type or geographical effect on the methanogenic archaea community structure in ruminants.

Methanobrevibacter phylotypes are the dominant methanogens in sheep from Venezuela

Rumen methanogens in sheep from Venezuela were examined using 16S rRNA gene libraries and denaturing gradient gel electrophoresis (DGGE) profiles prepared from pooled and individual PCR products from the rumen contents from 10 animals. A total of 104 clones were examined, revealing 14 different 16S rRNA gene sequences or phylotypes. Of the 14 phylotypes, 13 (99 of 104 clones) belonged to the genus Methanobrevibacter, indicating that the genus Methanobrevibacter is the most dominant component of methanogen populations in sheep in Venezuela. The largest group of clones (41 clones) was 97.9-98.5% similar to Methanobrevibacter gottschalkii. Two sequences were identified as possible new species, one belonging to the genus Methanobrevibacter and the other belonging to the genus Methanobacterium. DGGE analysis of the rumen contents from individual animals also revealed 14 different bands with a range of 4-9 bands per animal.

Reponses of sheep to a vaccination of entodinial or mixed rumen protozoal antigens to reduce rumen protozoal numbers

Two rumen protozoa vaccine formulations containing either whole fixed Entodinium or mixed rumen protozoa cells were tested on Merino sheep with the aim of decreasing the number and/or activity of protozoa in the rumen. Negative control (no antigen) and positive control (Tetrahymena corlissi antigens) treatments were also included in the experiment. Blood and saliva were sampled to measure the specific immune response. Protozoal numbers in the rumen were monitored by microscopic counts. Vaccination with protozoal formulations resulted in the presence of specific IgG in plasma and saliva, but saliva titres were low. Titres after secondary vaccination were higher (P < 0·05) than after primary vaccination. There was a moderate (r2 0·556) relationship (P < 0·05) between plasma and saliva titres for the rumen protozoal vaccine formulations. Rumen protozoa were not decreased (P>0·05) by the vaccination and there was also no difference (P>0·05) between treatments in rumen fluid ammonia-N concentration or wool growth. In vitro studies investigated the binding ability of the antibodies and estimated the amount of antibody required to reduce cell numbers in the rumen. The studies showed that the antibodies did bind to and reduced protozoa numbers, but the amount of antibody generated by vaccination was not enough to produce results in an in vivo system. It is suggested that the vaccine could be improved if specific protozoal antigens are determined and isolated and that improved understanding of the actions of protozoa antibodies in rumen fluid and the relationships between levels of antibodies and numbers of protozoa in the rumen is needed.

Molecular diversity of methanogens in feedlot cattle from Ontario and Prince Edward Island, Canada

The molecular diversity of rumen methanogens in feedlot cattle and the composition of the methanogen populations in these animals from two geographic locations were investigated using 16S rRNA gene libraries prepared from pooled PCR products from 10 animals in Ontario (127 clones) and 10 animals from Prince Edward Island (114 clones). A total of 241 clones were examined, with Methanobrevibacter ruminantium accounting for more than one-third (85 clones) of the clones identified. From these 241 clones, 23 different 16S rRNA phylotypes were identified. Feedlot cattle from Ontario, which were fed a corn-based diet, revealed 11 phylotypes (38 clones) not found in feedlot cattle from Prince Edward Island, whereas the Prince Edward Island cattle, which were fed potato by-products as a finishing diet, had 7 phylotypes (42 clones) not found in cattle from Ontario. Five sequences, representing the remaining 161 clones (67% of the clones), were common in both herds. Of the 23 different sequences, 10 sequences (136 clones) were 89.8 to 100% similar to those from cultivated methanogens belonging to the orders Methanobacteriales, Methanomicrobiales, and Methanosarcinales, and the remaining 13 sequences (105 clones) were 74.1 to 75.8% similar to those from Thermoplasma volcanium and Thermoplasma acidophilum. Overall, nine possible new species were identified from the two clone libraries, including two new species belonging to the order Methanobacteriales and a new genus/species within the order Methanosarcinales. From the present survey, it is difficult to conclude whether the geographical isolation between these two herds or differences between the two finishing diets directly influenced community structure in the rumen. Further studies are warranted to properly assess the differences between these two finishing diets.

Methanobrevibacter millerae sp. nov. and Methanobrevibacter olleyae sp. nov., methanogens from the ovine and bovine rumen that can utilize formate for growth

Four formate-utilizing methanogens were isolated from ovine (strain KM1H5-1PT) and bovine (strains AK-87, OCP and ZA-10T) rumen contents. Based on 16S rRNA gene sequence analysis, the methanogen strains were found to belong to the order Methanobacteriales in the genus Methanobrevibacter. Strains ZA-10T and KM1H5-1PT gained energy for growth by the reduction of CO2 to CH4 using H2 or formate exclusively as electron donors. Increasing formate concentrations to 220 mM in batch cultures increased the growth of strain KM1H5-1PT but did not affect the growth of strain ZA-10T. Substrate specificity and resistance to cell-wall lysis supported the affiliation of the strains to the genus Methanobrevibacter. Strains ZA-10T and KM1H5-1PT showed 16S rRNA gene sequence similarity of 98.0 and 98.6 % to their closest recognized relatives, Methanobrevibacter thaueri CWT and Methanobrevibacter ruminantium M1T, respectively. DNA–DNA hybridization experiments indicated that the strains were not affiliated at the species level to their closest recognized relatives, with DNA reassociation values of only 28 % between strains ZA-10T and Methanobrevibacter thaueri CWT and <25 % between strains KM1H5-1PT and Methanobrevibacter ruminantium M1T. Based on the data presented, the new strains are considered to represent two novel species of the genus Methanobrevibacter, for which the names Methanobrevibacter millerae sp. nov. (type strain ZA-10T=DSM 16643T=OCM 820T) and Methanobrevibacter olleyae sp. nov. (type strain KM1H5-1PT=DSM 16632T=OCM 841T) are proposed.

Molecular identification of methanogenic archaea from sheep in Queensland, Australia reveal more uncultured novel archaea

Molecular diversity of rumen methanogens in sheep in Queensland, Australia was investigated using 16S rRNA gene libraries prepared from pooled rumen contents from nine merino sheep. A total of 78 clones were identified revealing 26 different sequences. Of these 26 sequences, eight sequences (15 clones) were 95-100% similar to cultivated methanogens belonging to the orders Methanobacteriales and Methanomicrobiales, and the remaining 18 phylotypes (63 clones) were 72-75% similar to Thermoplasma acidophilum and Thermoplasma volcanium. These unique sequences clustered within a distinct and strongly supported (100% bootstrap support) phylogenetic group, exclusively composed of sequences from uncharacterized archaea from very diverse anaerobic environments. Members of this unique group that were previously considered atypical for the rumen environment were the predominant clones.

Development and validation of a real-time PCR method to quantify rumen protozoa and examination of variability between entodinium populations in sheep offered a hay-based diet

PCR and real-time PCR primers for the 18S rRNA gene of rumen protozoa (Entodinium and Dasytricha spp.) were designed, and their specificities were tested against a range of rumen microbes and protozoal groups. External standards were prepared from DNA extracts of a rumen matrix containing known numbers and species of protozoa. The efficiency of PCR (epsilon) was calculated following amplification of serial dilutions of each standard and was used to calculate the numbers of protozoa in each sample collected; serial dilutions of DNA were used similarly to calculate PCR efficiency. Species of Entodinium, the most prevalent of the rumen protozoa, were enumerated in rumen samples collected from 100 1-year-old merino wethers by microscopy and real-time PCR. Both the counts developed by the real-time PCR method and microscopic counts were accurate and repeatable, with a strong correlation between them (R2= 0.8), particularly when the PCR efficiency was close to optimal (i.e., two copies per cycle). The advantages and disadvantages of each procedure are discussed. Entodinium represented on average 98% of the total protozoa, and populations within the same sheep were relatively stable, but greater variation occurred between different sheep (10(0) and 10(6) entodinia per gram of rumen contents). With this inherent variability, it was estimated that, to detect a statistically significant (P = 0.05) 20% change in Entodinium populations, 52 sheep per treatment group would be required.