Stuart Edward Denman

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.

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.

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.

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.

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.

We have found one inadvertent error in our paper published in Microorganisms

This study aimed to characterize the rumen microbiota structure of cattle grazing in tropical rangelands throughout seasons and their responses in rumen ecology and productivity to a N-based supplement during the dry season. Twenty pregnant heifers grazing during the dry season of northern Australia were allocated to either N-supplemented or un-supplemented diets and monitored through the seasons. Rumen fluid, blood, and feces were analyzed before supplementation (mid-dry season), after two months supplementation (late-dry season), and post supplementation (wet season). Supplementation increased average daily weight gain (ADWG), rumen NH₃–N, branched fatty acids, butyrate and acetic:propionic ratio, and decreased plasma δ¹⁵N. The supplement promoted bacterial populations involved in hemicellulose and pectin degradation and ammonia assimilation: Bacteroidales BS11, Cyanobacteria, and Prevotella spp. During the dry season, fibrolytic populations were promoted: the bacteria Fibrobacter, Cyanobacteria and Kiritimatiellaeota groups; the fungi Cyllamyces; and the protozoa Ostracodinium. The wet season increased the abundances of rumen protozoa and fungi populations, with increases of bacterial families Lachnospiraceae, Ruminococcaceae, and Muribaculaceae; the protozoa Entodinium and Eudiplodinium; the fungi Pecoramyces; and the archaea Methanosphera. In conclusion, the rumen microbiota of cattle grazing in a tropical grassland is distinctive from published studies that mainly describe ruminants consuming better quality diets.

Lick-blocks that are used in northern Australian beef enterprises contain varying levels of macro-nutrients (crude protein, sulfur and phosphorus) to correct deficiencies in the forage. It is thought that organic forms of nitrogen and sulfur are used more efficiently for growth and function of the rumen than the inorganic nutrients. A trial was undertaken in pregnant heifers grazing a poor-quality dry season diet in the Northern Territory. The animals received three lick supplements containing varying forms of organic and inorganic N. No significant differences on animal performance and rumen fermentation parameters were observed between supplements. Animals were initially deficient for rumen ammonia-N (15.8 mg/L) and BUN (4.7 mg/100 mL) concentration. All nitrogen supplements led to a significant improvement in ammonia N (24.7–31.8 mg/L) but levels remained deficient until the wet season and availability of higher quality pasture. Even though the rumen ammonia levels were sub-optimal, the supplemented animals gained approximately 650 g liveweight daily compared with a weight loss of 330 g daily in unsupplemented animals. The increased availability of N in either an organic or inorganic form had a similar influence on the rumen microbiome and rumen fermentation products with increases in ammonia, branched fatty acids, butyrate and the acetic: propionic ratio. All three N supplements showed the same significant increase in species of Ruminocococcus, Bacteroidetes and Cyanobacteria (Melainabacteria) involved in cellulose and hemicellulose digestion. It appears inorganic N is as effective as organic N in improving rumen efficiency when there is a gross deficiency of N for microbial growth.

We report the genome sequence of Sporanaerobacter acetigenes strain F-12, isolated from the rumen of a steer grazing on Rhodes grass in Townsville (Lansdown Research Station), Queensland, Australia. This draft genome consists of 2,866,191 bp, with 31.23% G+C content and 2,889 predicted coding sequences.

Keynote paper presented at the International Leucaena Conference, 1‒3 November 2018, Brisbane, Queensland, Australia.Leucaena leucocephala is a nutritionally rich forage tree legume that contains a toxic non-protein amino acid, mimosine, from which other toxic compounds 3,4-dihydroxypyridone (3,4-DHP) and 2,3-DHP are formed in the rumen. The rumen bacterium Synergistes jonesii is able to degrade these DHP isomers into non-toxic end products. In this study we developed new PCR-based assays to improve the specificity and sensitivity of detection of S. jonesii in the rumen. Using these new assays in a survey of ruminants from different countries showed S. jonesii appeared to be ubiquitous rather than isolated geographically. The bacterium was present as a minor population (<106 cells/mL) in the rumen and was usually comprised of several genetic variants of the species. Although the indigenous nature of S. jonesii could imply animals are protected from toxicity, the relative abundance of the bacterium, potential variation in DHP degrading ability of genetic variants of the species, and amount of leucaena in the diet may determine the ability of the resident population in the rumen to protect the animal from toxicity.