Understanding the intricate nexus between cattle health and microbiome dynamics holds profound implications for enhancing animal productivity and welfare. However, our understanding of the role of these microbial communities is limited in beef cattle, especially in understudied body sites such as the oral and nasal microbiome. Here, using a genome-centric metagenomics approach, we recovered substantial metagenome-assembled genomes (MAGs) from the faecal, oral and nasal microbiome of Australian Angus cattle from different herds and life stages. The MAGs recovered from faecal samples were dominated by Bacillota and Bacteroidota, while the MAGs from saliva and nasal mucus samples were mainly associated with Pseudomonadota, Actinomycetota and Bacteroidota. Functional annotation of the MAGs revealed enriched pathways involved in the production of some amino acids, nucleic acids and short chain fatty acids (SCFA). The metabolic capacities of the MAGs were correlated with their taxonomy, notably at the phylum level. Overall, this study provides a comprehensive catalogue of MAGs to further our understanding of their role in the health and fitness of beef cattle.

Context Between animal variation in performance is a determinant of productivity in the northern Australian beef industry. Understanding factors that contribute to this variation is critical for selection of superior genotypes and optimising the pasture animal interface. Aim To determine factors that influence performance of cattle grazing tropical pastures through co-ordinated grazing and pen studies. Methods Within a cohort of 56 yearling heifers, 32 were allocated to an 11-month grazing trial, whereas 24 were grazed, then individually fed hay in pens. At the end of the trial, pasture cattle were ranked according to liveweight (LW) gain and the top- and bottom-ranked animals were allocated to high-performance (HP) or low-performance (LP) groups. Residual feed intake (RFI) of heifers in pens was determined and correlations between pasture and pen performance were estimated. Pasture and diets were characterised using the Botanal method (pasture only) and near-infrared reflectance spectroscopy analysis. Activity on pasture was measured using global positioning system (GPS) collars. Pasture data were divided into dry and wet seasons and the grazing trial was analysed as a factorial, with performance group and season as the two factors. Key results There were seasonal differences in most measured variables of animal production, behaviour and rumen fermentation consistent with changes in diet quality. Diet selection, activity on pasture and rumen fermentation characteristics did not to differ between LP and HP groups. Differences in RFI of hay-fed heifers were attributed to variation in feed intake. There was a correlation (r2 = 0.5) between performance of heifers in pens and on pasture in the wet season. Conclusion Seasonal variations in pasture biomass and nutritive value had an overriding effect on LW change in growing beef cattle, but among-animal variation in LW gain was still apparent. This could not be attributed to any of the measured variables on pasture; however, RFI data suggested a genetic influence on intake, which was supported by estimated breeding values. Implications Several possible reasons for differences in performance of grazing cattle were ruled out by this research. Methods for measuring intake and efficiency of grazing cattle are required to understand and manage the grazing animal.

The ruminant livestock industry is the largest agricultural emissions source of anthropogenic greenhouse gases, primarily from enteric methane. Several technologies, both natural and synthetic are being investigated to mitigate enteric methane emissions. Macroalgae derived feed ingredients that contain bromoform, a recognised inhibitor of methanogenesis, are an effective natural approach for methane mitigation. However, producing sufficient biomass economically to satisfy the livestock industry at a global scale is challenging. Here we demonstrate that a Curvularia soil fungi isolate can be cultured to produce bromoform and subsequently inhibit methanogenesis in pure cultures of Methanobrevibacter smithii and in mixed cultures of ovine rumen fluid. This highly culturable fungal species produces no known toxins and creates an exciting new, scalable and natural alternative for reducing ruminant livestock emissions.

The objective of this study was to improve understandings of the rumen microbial ecosystem during ruminal acidosis and responses to feed additives to improve prudent use strategies for ruminal acidosis control. Rumen bacterial and archaeal community composition (BCC) and its associations with rumen fermentation measures were examined in Holstein heifers fed feed additives and challenged with starch and fructose. Heifers (n = 40) were randomly allocated to 5 treatment groups: (1) control (no additives); (2) virginiamycin (VM; 200 mg/d); (3) monensin (MT; 200 mg/d) + tylosin (110 mg/d); (4) monensin (MLY; 220 mg/d) + live yeast (5.0 × 1012 cfu/d); (5) sodium bicarbonate (BUF; 200 g/d) + magnesium oxide (30 g/d). Heifers were fed twice daily a 62% forage:38% concentrate total mixed ration at 1.25% of body weight (BW) dry matter (DM)/d for a 20-d adaptation period with their additive(s). Fructose (0.1% of BW/d) was added to the ration for the last 10 d of adaptation. On d 21 heifers were challenged once with a ration consisting of 1.0% of BW DM wheat and 0.2% of BW fructose plus their additive(s). A rumen sample was collected from each heifer via stomach tube weekly (d 0, 7, 14) and 5 times over a 3.6 h period at 5, 65, 115, 165, and 215 min after consumption of the challenge ration (d 21) and analyzed for pH, and ammonia, d- and l-lactate, volatile fatty acids (VFA), and histamine concentrations and total bacteria and archaea. The 16S rRNA gene spanning the V4 region was PCR amplified and sequenced. Alpha and β diversity and associations of relative abundances of taxa with rumen fermentation measures were evaluated. Rumen BCC shifted among treatment groups in the adaptation period and across the challenge sampling period, indicating the feed additives had different modes of action. The monensin-containing treatment groups, MT and MLY often had similar relative abundances of rumen bacterial phyla and families. The MLY treatment group was characterized in the challenge period by increased relative abundances of the lactate utilizing genera Anaerovibrio and Megasphaera. The MLY treatment group also had increased diversity of ruminal bacteria which may provide resilience to changes in substrates. The control and BUF treatment groups were most similar in BCC. A redundancy analysis showed the MLY treatment group differed from all other treatment groups and concentrations of histamine and valerate in the rumen were associated with the most variation in the microbiota, 5.3% and 4.8%, respectively. It was evident from the taxa common to all treatment groups that cattle have a core microbiota. Functional redundancy of rumen bacteria which was reflected in the greater sensitivity for the rumen BCC than rumen fermentation measures likely provide resilience to changes in substrate. This functional redundancy of microbes in cattle suggests that there is no single optimal ruminal microbial population and no universally superior feed additive(s). In summary, differences in modes of action suggest the potential for more targeted and improved prudent use of feed additives with no single feed additive(s) providing an optimal BCC in all heifers.

Heifers (n = 40) were randomly allocated to 5 treatment groups: (1) control (no additives); (2) virginiamycin (VM; 200 mg/d); (3) monensin (MT; 200 mg/d) + tylosin (110 mg/d); (4) monensin (MLY; 220 mg/d) + live yeast (5.0 × 108 cfu/d); (5) sodium bicarbonate (BUF; 200 g/d) + magnesium oxide (30 g/d).

AbstractThe aim of this study was to establish a distinctive rumen microbial and fermentation profile using the anti-methanogenic compound 3-NOP to assess dam effect, and nutritional intervention of the juvenile offspring on microbial structure and function of rumen up to 12 months of age, once the treatment was withdrawn. Forty-eight pregnant heifers (H) and their future offspring (C) were allocated to either Control (-) or 3-NOP (+) treatment resulting in four experimental groups: H+/C+, H+/C-, H-/C + and H-/C-. Animals were treated from 6 weeks prior to calving until weaning, with the offspring monitored until 12 months of age. Rumen fluid samples and methane measurements using the Greenfeed system were collected during the trial. Results supported the mode of action of the compound, with a shift in fermentation from acetate to propionate, increases in branched chain fatty acids and formic acid in the 3-NOP treated animals. Similar shifts in microbial populations occurred in 3-NOP treated animals with lower abundances of rumen methanogen populations, increases of bacterial groups Succiniclasticum spp, Candidatus Saccharimonas. Fibrobacter and the families Prevotellaceae and Succinivibrioacea. and the protozoa Entodinium. Early life intervention had an enduring impact on the rumen microbial structure of young animals up to 28 weeks post weaning, however the effect was diminished once 3-NOP was withdrawn. Interestingly, a group of young animals emitted significantly less methane (15%) than the animals that did not receive the treatment during their juvenile stage. Our results suggest a higher resemblance of the young calf microbiome to a low methane adult and that early life colonisation of the rumen persists through to later life with the pre-weaning microbiome comprising ~ 65% of the yearling animal. Further research needs to be performed to determine the timing and dose of 3-NOP for new-born calves that can sustain a reduction in methane emissions after the treatment is withdrawn, under extensive grazing or controlled conditions.

Nitrogen use efficiency is an important index in ruminants and can be indirectly evaluated through the N isotopic discrimination between the animal and its diet (Δ15Nanimal-diet). The concentration and source of N may determine both the extent of the N isotopic discrimination in bacteria and N use efficiency. We hypothesised that the uptake and release of ammonia by rumen bacteria will affect the natural 15N enrichment of the bacterial biomass over their substrates (Δ15Nbacteria-substrate) and thereby further impacting Δ15Nanimal-diet. To test this hypothesis, two independent in vitro experiments were conducted using two contrasting N sources (organic vs inorganic) at different levels either in pure rumen bacteria culture incubations (Experiment #1) or in mixed rumen cultures (Experiment #2). In Experiment #1, tryptone casein or ammonium chloride were tested at low (1 mM N) and high (11.5 mM N) concentrations on three rumen bacterial strains (Fibrobacter succinogenes, Eubacterium limosum and Xylanibacter ruminicola) incubated in triplicate in anaerobic batch monocultures during 48h. In Experiment #2 mixed rumen cultures were incubated during 120 h with peptone or ammonium chloride at five different levels of N (1.5, 3, 4.5, 6 and 12-mM). In experiment #1, Δ15Nbacteria-substrate was lowest when the ammonia-consumer bacterium Fibrobacter succinogenes was grown on ammonium chloride, and highest when the proteolytic bacterial strain Xylanibacter ruminicola was grown on tryptone. In experiment #2, Δ15Nbacteria-substrate was lower with inorganic (ammonium chloride) vs organic (peptone) N source. A strong negative correlation between Δ15Nbacteria-substrate and Rikenellaceae_RC9_gut_group, a potential fibrolytic rumen bacterium, was detected. Together, our results showed that Δ15Nbacteria-substrate may change according to the balance between synthesis of microbial protein from ammonia versus non-ammonia N sources and confirm the key role of rumen bacteria as modulators of Δ15Nanimal-diet.

OBJECTIVE:Monofluoroacetate (MFA) is a potent toxin that blocks ATP production via the Krebs cycle and causes acute toxicity in ruminants consuming MFA-containing plants. The rumen bacterium, Cloacibacillus porcorum strain MFA1 belongs to the phylum Synergistota and can produce fluoride and acetate from MFA as the end-products of dehalorespiration. The aim of this study was to identify the genomic basis for the metabolism of MFA by this bacterium.METHODS:A draft genome sequence for C. porcorum strain MFA1 was assembled and quantitative transcriptomic analysis was performed thus highlighting a candidate operon encoding four proteins that are responsible for the carbon-fluorine bond cleavage. Comparative genome analysis of this operon was undertaken with three other species of closely related Synergistota bacteria.RESULTS:Two of the genes in this operon are related to the substrate-binding components of the glycine reductase protein B (GrdB) complex. Glycine shares a similar structure to MFA suggesting a role for these proteins in binding MFA. The remaining two genes in the operon, an antiporter family protein and an oxidoreductase belonging to the radical S-adenosyl methionine superfamily, are hypothesised to transport and activate the GrdB-like protein respectively. Similar operons were identified in a small number of other Synergistota bacteria including type strains of Cloacibacillus porcorum, C. evryensis, and Pyramidobacter piscolens, suggesting lateral transfer of the operon as these genera belong to separate families. We confirmed that all three species can degrade MFA, however, substrate degradation in P. piscolens was notably reduced compared to Cloacibacillus isolates possibly reflecting the loss of the oxidoreductase and antiporter in the P. piscolens operon.CONCLUSION:Identification of this unusual anaerobic fluoroacetate metabolism extends the known substrates for dehalorespiration and indicates the potential for substrate plasticity in amino acid-reducing enzymes to include xenobiotics.

Ruminants are able to produce large quantities of saliva which enter into the rumen. Although previous research has indicated that salivary immunoglobulins can partially modulate the rumen microbial activity, the role of the salivary components other than ions on the rumen microbial ecosystem has not been thoroughly investigated in ruminants. A total of 16 semi-continuous in vitro cultures were used to incubate rumen fluid from 4 donor goats inoculated with autoclaved saliva (AUT) as negative control, saliva from the same rumen fluid donor (OWN) as positive control, and either GOAT or SHEEP saliva as experimental interventions. Fermentation was monitored throughout the 7 days of incubation and the prokaryotic communities and metabolome were analysed at day 7 of incubation. Characterization of the salivas used prior to incubation showed a high degree of individual variability in terms of the salivary metabolites and proteins, including immunoglobulins. The prokaryotic community composition in AUT incubators was the most divergent across treatments, suggesting a modulatory effect of active salivary components, which were not affected in the other treatments (OWN, GOAT and SHEEP). The differences across treatments in microbial diversity were mostly caused by a greater abundance of Proteobacteria and Rikenellacea and lower of Prevotellaceae, a key rumen bacterium with greater abundance in GOAT and SHEEP treatments. These results suggest that specific salivary components contribute to host-associated role in selecting the rumen commensal microbiota and its activity.

Summary Background Carbohydrate fermentation plays a pivotal role in maintaining colonic health with excessive proximal and deficient distal fermentation being detrimental. Aims To utilise telemetric gas‐ and pH‐sensing capsule technologies for defining patterns of regional fermentation following dietary manipulations, alongside conventional techniques of measuring fermentation. Methods In a double‐blind crossover trial, 20 patients with irritable bowel syndrome were fed low FODMAP diets that included no extra fibre (total fibre content 24 g/day), or additional poorly fermented fibre, alone (33 g/day) or with fermentable fibre (45 g/day) for 2 weeks. Plasma and faecal biochemistry, luminal profiles defined by tandem gas‐ and pH‐sensing capsules, and faecal microbiota were assessed. Results Plasma short‐chain fatty acid (SCFA) concentrations (μmol/L) were median (IQR) 121 (100–222) with fibre combination compared with 66 (44–120) with poorly fermented fibre alone ( p = 0.028) and 74 (55–125) control ( p = 0.069), but no differences in faecal content were observed. Luminal hydrogen concentrations (%), but not pH, were higher in distal colon (mean 4.9 [95% CI: 2.2–7.5]) with fibre combination compared with 1.8 (0.8–2.8) with poorly fermented fibre alone ( p = 0.003) and 1.9 (0.7–3.1) control ( p = 0.003). Relative abundances of saccharolytic fermentative bacteria were generally higher in association with supplementation with the fibre combination. Conclusions A modest increase in fermentable plus poorly fermented fibres had minor effects on faecal measures of fermentation, despite increases in plasma SCFA and abundance of fermentative bacteria, but the gas‐sensing capsule, not pH‐sensing capsule, detected the anticipated propagation of fermentation distally in the colon. The gas‐sensing capsule technology provides unique insights into localisation of colonic fermentation. Trial registration: ACTRN12619000691145.

Enteric methane (CH4) emissions from sheep contribute to global greenhouse gas emissions from livestock. However, as already available for dairy and beef cattle, empirical models are needed to predict CH4 emissions from sheep for accounting purposes. The objectives of this study were to: 1) collate an intercontinental database of enteric CH4 emissions from individual sheep; 2) identify the key variables for predicting enteric sheep CH4 absolute production (g/d per animal) and yield [g/kg dry matter intake (DMI)] and their respective relationships; and 3) develop and cross-validate global equations as well as the potential need for age-, diet-, or climatic region-specific equations. The refined intercontinental database included 2,135 individual animal data from 13 countries. Linear CH4 prediction models were developed by incrementally adding variables. A universal CH4 production equation using only DMI led to a root mean square prediction error (RMSPE, % of observed mean) of 25.4% and an RMSPE-standard deviation ratio (RSR) of 0.69. Universal equations that, in addition to DMI, also included body weight (DMI + BW), and organic matter digestibility (DMI + OMD + BW) improved the prediction performance further (RSR, 0.62 and 0.60), whereas diet composition variables had negligible effects. These universal equations had lower prediction error than the extant IPCC 2019 equations. Developing age-specific models for adult sheep (>1-year-old) including DMI alone (RSR = 0.66) or in combination with rumen propionate molar proportion (for research of more refined purposes) substantially improved prediction performance (RSR = 0.57) on a smaller dataset. On the contrary, for young sheep (<1-year-old), the universal models could be applied, instead of age-specific models, if DMI and BW were included. Universal models showed similar prediction performances to the diet- and region-specific models. However, optimal prediction equations led to different regression coefficients (i.e. intercepts and slopes) for universal, age-specific, diet-specific, and region-specific models with predictive implications. Equations for CH4 yield led to low prediction performances, with DMI being negatively and BW and OMD positively correlated with CH4 yield. In conclusion, predicting sheep CH4 production requires information on DMI and prediction accuracy will improve national and global inventories if separate equations for young and adult sheep are used with the additional variables BW, OMD and rumen propionate proportion. Appropriate universal equations can be used to predict CH4 production from sheep across different diets and climatic conditions.

Mitigation of methane emission, a potent greenhouse gas, is a worldwide priority to limit global warming. A substantial part of anthropogenic methane is emitted by the livestock sector, as methane is a normal product of ruminant digestion. We present the latest developments and challenges ahead of the main efficient mitigation strategies of enteric methane production in ruminants. Numerous mitigation strategies have been developed in the last decades, from dietary manipulation and breeding to targeting of methanogens, the microbes that produce methane. The most recent advances focus on specific inhibition of key enzymes involved in methanogenesis. But these inhibitors, although efficient, are not affordable and not adapted to the extensive farming systems prevalent in low- and middle-income countries. Effective global mitigation of methane emissions from livestock should be based not only on scientific progress but also on the feasibility and accessibility of mitigation strategies.

The red macroalgae Asparagopsis taxiformis has been identified as a promising feed supplement to inhibit enteric methane formation during ruminant livestock production and thereby contribute to GHG emissions reduction. Some studies also suggest improvements to animal weight gain through enhanced feed conversion efficiency. In this study, the potential GHG emissions reduction benefits were assessed from a life cycle perspective and in an actual industry context - the large Australian beef cattle sector, where feed supplementation occurred during feedlot finishing, when farmers have greatest control over animal diets. Seven adoption scenarios were compared to a baseline emissions inventory that was extrapolated to 2030. Feed supplementation with A. taxiformis had the potential to reduce the sector's carbon footprint by 1-4% in 2030, which due to the scale of the industry is a relevant emissions reduction (0.6-2.0 Mt CO(2)e), but modest in relation to the industry's goal of carbon neutrality by 2030. When emissions were assessed using alternative climate metrics that are more sensitive to changes in the rate of methane emission than the GWP100 climate metric (i.e. GWP*, radiative forcing climate footprint), larger potential benefits were found. Considering only the feedlot subsector, the radiative forcing climate footprint reached a plateau under most scenarios, indicating that climate neutrality is realistically achievable for the feedlot subsector within 5 years. That said, concurrent action on CO2 and N2O emissions will be needed, as even steep reductions in methane emissions at the expense of additional long-lived emissions will only achieve a short-term climate benefit and will make long-term climate stabilization more difficult.

Lumpy wool (dermatophilosis) develops following prolonged wetting of sheep when bacterial proliferation in wool and on skin induce an exudative dermatitis, causing a superficial skin lesion and damage to wool follicles and fibres. The incidence of dermatophilosis is strongly dependent on wet and warm weather and, hence, infection is sporadic. While older animals are less at risk than are lambs, it is unclear whether this reflects naturally acquired immune resistance or the maturation of skin and wool fibres. Dermatophilosis directly causes wool production losses and it also is a risk factor for blowfly strike, which has a substantial economic impact and increasing challenges associated with current control procedures. This review assessed research on the bacterial causes of lumpy wool, the characteristics of the resulting immune defence reactions in sheep, current control strategies, and limitations of previous attempts to control lumpy wool by sheep vaccination.

Context The Qinghai Tibetan plateau (QTP) is characterised as a harsh high-altitude environment inhabited by a large number of ruminants. Rumen microorganisms potentially play a vital role in the adaptation of indigenous ruminants to this harsh environment. Aims The present study aimed to investigate the diversity of rumen bacteria in ruminants (yak and Tibetan sheep) indigenous to the QTP and introduced species (cattle and crossbred sheep). Methods Rumen bacterial composition and α and β diversity of indigenous and introduced ruminants were analysed based on 16s rDNA sequence data. Key results Most of the sequences from all animals were affiliated with phylum Bacteroidetes (67.6–84.0%), followed by Firmicutes (11.6–21.0%). The β diversity (Bray–Curtis and weighted-Unifrac distance matrices) of bacteria was significantly different among ruminant species yak (Bos grunniens), cattle (Bos taurus) and sheep (Ovis aries), but there were no differences between the indigenous and introduced sheep breeds. At the genus level, Fibrobacter, Lachnospira and Pseudobutyrivibrio were more abundant (P < 0.05) in the rumen of yak, while Prevotella was significantly (P < 0.05) more abundant in cattle than in the other ruminants; enterotypes affiliated with the uncultured Ruminococcaceae and Prevotella was more dominant in the indigenous and introduced ruminants respectively. Conclusions The ruminant species was the main factor distinguishing the rumen bacterial diversity among the ruminants grazing on the QTP, although there were differences in discrete populations of bacteria between indigenous and introduced ruminants. It appears that yak, which has evolved as a distinctive species with specialised physiological and anatomical adaptations, has a rumen bacterial population that favours its survival in this extreme environment. Implications This work extends the findings of previous studies comparing microbiota from different ruminants in the QTP, and provides a basis for exploration of the interactions governing the tri-partite relationship among host, rumen microbiota and the harsh environment, and indicates the potential of rumen microbiota in assisting the adaptation of host to the harsh environment.

Fleece rot develops following prolonged wetting of sheep when bacterial proliferation in wool and on skin induces exudation of serum proteins onto the skin surface and causes damage to wool follicles and fibres. These processes create an attractive environment for blowflies to lay eggs, leading to body strike. Current reliance on insecticides for prevention and treatment of fly strike is being increasingly challenged by development of insecticide resistance. This review examines the large body of past research on the bacterial causes of fleece rot, the genetics of sheep susceptibility and resistance, the characteristics of the resulting immune defence reactions, and attempts to control fleece rot by vaccination. The high dependence on weather conditions for expression of fleece rot hampers studies on the disease. Normal skin and wool are populated by a dynamic microbial community. During adverse environmental conditions, natural resistance to fleece rot associated with physical characteristics of wool and skin can be overwhelmed and a complex mix of bacteria flourishes. Prolonged hydration alone, and in combination with bacterial exoproducts, induces dermatitis and exudation of immunoglobulins and other serum proteins onto the skin surface. Pathogens do not usually penetrate the epidermis. Nonetheless, during prolonged skin hydration, sheep can become sensitised to fleece rot pathogens and produce antibodies. Antibody titres rise late within a typical (3 week) case of fleece rot. High naturally acquired antibody titres may contribute to resistance to fleece rot. In contrast to some evidence for a protective role of antibody, there is little evidence for innate or adaptive cellular immune responses contributing to protection against fleece rot pathogens. Previous attempts to develop vaccines have met with mixed success. Nonetheless, there remain prospects for development of a new vaccine to control fleece rot. Further knowledge on the microbial ecology of normal and wet skin would assist this endeavour and may help identify other control strategies.

During prolonged wetting of the fleece, proliferation of bacterial flora often dominated by Pseudomonas aeruginosa or Dermatophilus congolensis can induce dermatitis and fleece damage termed fleece rot and dermatophilosis respectively, which predispose sheep to blowfly strike. A large research effort in the 1980s and 1990s on vaccines to control fleece rot and dermatophilosis met with limited success. This review examines theoretical and technological advances in microbial ecology, pathogenesis, immunology, vaccine development and the characterisation of microbial virulence factors that create new opportunities for development of vaccines against these diseases. Genomic technologies have now created new opportunities for examining microbial dynamics and pathogen virulence in dermatitis. An effective vaccine requires the combination of appropriate antigens with an adjuvant that elicits a protective immune response that ideally provides long-lasting protection in the field. A clinical goal informed by epidemiological, economic and animal welfare values is needed as a measure of vaccine efficacy. Due to dependence of fleece rot and dermatophilosis on sporadic wet conditions for their expression, vaccine development would be expedited by in vitro correlates of immune protection. The efficacy of vaccines is influenced by genetic and phenotypic characteristics of the animal. Advances in understanding vaccine responsiveness, immune defence in skin and immune competence in sheep should also inform any renewed efforts to develop new fleece rot and dermatophilosis vaccines. The commercial imperatives for new vaccines are likely to continue to increase as the animal welfare expectations of society intensify and reliance on pharmacotherapeutics decrease due to chemical resistance, market pressures and societal influences. Vaccines should be considered part of an integrated disease control strategy, in combination with genetic selection for general immune competence and resistance to specific diseases, as well as management practices that minimise stress and opportunities for disease transmission. The strategy could help preserve the efficacy of pharmacotherapeutics as tactical interventions to alleviate compromised welfare when adverse environmental conditions lead to a break down in integrated strategic disease control. P. aeruginosa and D. congolensis are formidable pathogens and development of effective vaccines remains a substantial challenge.

Aims Yak is a dominant ruminant, well adapted to grazing on pasture year around in the harsh climate of the 3000-meter-high Qinghai-Tibetan Plateau. The complex microbial community that resides within the yak rumen is responsible for fermentation and contributes to its climatic adaptation. This study aimed to characterize the rumen microbiota responses to wide seasonal variations, especially those necessary for survival in the cold seasons. Methods and Results In the present study, we performed 16s rRNA gene sequencing to investigate the seasonal variations in microbiota composition, diversity and associated volatile fatty acids (VFAs) in yak rumen. The results showed that rumen microbiota were dominated by Bacteroides (72.13%-78.54%) and Firmicutes; the relative abundance of Firmicutes was higher in summer (17.44%) than in winter (10.67%; p < 0.05). The distribution of taxa differed among spring, summer and winter rumen communities (PERMANOVA, p = 0.001), whereas other taxa (e.g., Fibrobacter, Verrucomicrobia, Anaerostipes and Paludibacter), which could potentially help overcome harsh climate conditions were observed in higher abundance during the cold spring and winter seasons. The highest total VFA concentration in the yak rumen was obtained in summer (p < 0.05), followed by spring and winter, and both positive and negative correlations between VFAs and specific genera were revealed. Conclusions Microbiota in yak rumen appear to be highly responsive to seasonal variations. Considering environmental factors, we suggest that seasonal adaptation by microbial communities in rumen enables their hosts to survive seasonal scarcity and cold stress in the spring and winter. Significance and Impact of Study The present study furthers our understanding of how microbial adaptation to seasonal variations in nutrient availability and climate may function in high plateau ruminants, providing insights into the tripartite relationship between the environment, host and microbiota.

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Methane production from rumen methanogenesis contributes approximately 71% of greenhouse gas emissions from the agricultural sector. This study has performed genomic predictions for methane production from 99 sheep across 3 yr using a residual methane phenotype that is log methane yield corrected for live weight, rumen volume, and feed intake. Using genomic relationships, the prediction accuracies (as determined by the correlation between predicted and observed residual methane production) ranged from 0.058 to 0.220 depending on the time point being predicted. The best linear unbiased prediction algorithm was then applied to relationships between animals that were built on the rumen metabolome and microbiome. Prediction accuracies for the metabolome-based relationships for the two available time points were 0.254 and 0.132; the prediction accuracy for the first microbiome time point was 0.142. The second microbiome time point could not successfully predict residual methane production. When the metabolomic relationships were added to the genomic relationships, the accuracy of predictions increased to 0.274 (from 0.201 when only the genomic relationship was used) and 0.158 (from 0.081 when only the genomic relationship was used) for the two time points, respectively. When the microbiome relationships from the first time point were added to the genomic relationships, the maximum prediction accuracy increased to 0.247 (from 0.216 when only the genomic relationship was used), which was achieved by giving the genomic relationships 10 times more weighting than the microbiome relationships. These accuracies were higher than the genomic, metabolomic, and microbiome relationship matrixes achieved alone when identical sets of animals were used.