Graeme Trevor Attwood

Background: Methane emissions from enteric fermentation in ruminant livestock make up 27% of anthropogenic methane emissions. Results: Screening > 1,700 lactic acid bacteria identified Lacticaseibacillus rhamnosus FNZ118 (Kowbucha™ FNZ118) and L. rhamnosus FNZ142, (Kowbucha™ FNZ142) as capable of inhibiting rumen methanogens and methane production in vitro. FNZ118 or FNZ142 fed daily to Friesian heifer calves from birth to 14 weeks substantially lowered methane production through the first year of life compared to control animals. These strains also decreased feed intake and reduced ruminal metabolite concentrations without affecting animal live weight, suggesting an improvement in feed conversion efficiency. The observed effects did not cause major changes in the structure of the rumen microbiome. Conclusions: These findings demonstrate that early life provision of specific L. rhamnosus strains lower CH ₄ production and have potential for the mitigation of enteric greenhouse gas emissions from growing dairy cattle.

Pectin is a dynamic and complex polysaccharide that forms a substantial proportion of the primary plant cell wall and middle lamella of forage ingested by grazing ruminants. Pectin methylesterases (PMEs) are enzymes that belongs to the carbohydrate esterase family 8 (CE8) and catalyze the demethylesterification of pectin, a key polysaccharide in cell walls. Here we present the crystal structure of the catalytic domain of PmeC5 that is associated with a gene from Butyrivibrio fibrisolvens D1^T that encodes a large secreted pectinesterase family protein (2089 aa) determined to a resolution of 1.33 Å. Protein in silico modelling of the secreted pectinesterase confirmed the presence of an additional pectate lyase (PL9) and adhesin-like domains. The structure of PmeC5 was the characteristic right-handed parallel β-helical topology and active site residues of Asp231, Asp253, and Arg326 typical of the enzyme class. PmeC5 is a large modular enzyme that is characteristic of rumen B. fibrisolvens megaplasmids and plays a central role in degrading plant cell wall components and releasing methanol in the rumen environment. Such secreted PMEs are significant contributors to plant fiber digestion and methane production, making them attractive targets for both methane mitigation strategies and livestock productivity enhancement.

Xylanibacter ruminicola is an abundant rumen bacterium that produces propionate in a cobalamin (vitamin B ₁₂ )-dependent manner via the succinate pathway. However, the extent to which this occurs across ruminal Xylanibacter and closely related bacteria, and the effect of cobalamin supplementation on the expression of propionate pathway genes and enzymes has yet to be investigated. To assess this, we screened 14 strains and found that almost all strains produced propionate when supplemented with cobalamin. X. ruminicola KHP1 was selected for further study, including complete genome sequencing, and comparative transcriptomics and proteomics of KHP1 cultures grown with and without supplemented cobalamin. The complete KHP1 genome was searched for cobalamin-binding riboswitches and four were predicted, though none were closely located to any of the succinate pathway genes, which were dispersed at numerous genomic loci. Cobalamin supplementation led to the differential expression of 17.5% of genes, including genes encoding the cobalamin-dependent methylmalonyl-CoA mutase and some methylmalonyl-CoA decarboxylase subunits, but most propionate biosynthesis pathway genes were not differentially expressed. The effect of cobalamin supplementation on the KHP1 proteome was much less pronounced, with the only differentially abundant propionate pathway enzyme being methylmalonyl-CoA mutase, which had greater abundance when supplemented with cobalamin. Our results demonstrate that cobalamin supplementation does not result in induction of the entire propionate biosynthesis pathway, but consistently increased expression of methylmalonyl-CoA mutase at transcriptome and proteome levels. The magnitude of the differential expression of propionate pathway genes observed was minor compared to that of genes proximate to predicted cobalamin riboswitches. IMPORTANCE: In ruminants, the rumen microbial community plays a critical role in nutrition through the fermentation of feed to provide vital energy substrates for the host animal. Propionate is a major rumen fermentation end-product and increasing its production is desirable given its importance in host glucose production and impact on greenhouse gas production. Vitamin B ₁₂ (cobalamin) can induce propionate production in the prominent rumen bacterium Xylanibacter ruminicola , but it is not fully understood how cobalamin regulates propionate pathway activity. Contrary to expectation, we found that cobalamin supplementation had little effect on propionate pathway expression at transcriptome and proteome levels, with minor upregulation of genes encoding the cobalamin-dependent enzyme of the pathway. These findings provide new insights into factors that regulate propionate production and suggest that cobalamin-dependent propionate production by X. ruminicola is controlled post-translationally.

Cladosporium and Epicoccum are cosmopolitan fungi of the class Dothideomycetes with few cultured and genomic representatives. Here, we report draft reference genome sequences of Epicoccum sp. F181 (GenBank accession number JAJSLS01 ), Cladosporium sp. F165 ( JAJSLR01 ), and F190 ( JAJSLT01 ) isolated from recycling and waste management facilities in New Zealand.

Butyrivibrio are anaerobic bacteria and members of the family Lachnospiraceae with important roles in fiber digestion in both animals and humans. This report describes the complete genome of Butyrivibrio fibrisolvens type strain D1 ^T (DSM 3071) consisting of a chromosome ( CP146963 ), megaplasmid (pNP243), and small plasmid (pNP21).

Methanosphaera spp. are methylotrophic methanogenic archaea and members of the order Methanobacteriales with few cultured representatives. Methanosphaera sp. ISO3-F5 was isolated from sheep rumen contents in New Zealand. Here, we report its complete genome, consisting of a large chromosome and a megaplasmid (GenBank accession numbers CP118753 and CP118754 , respectively).

Pectin is a complex polysaccharide that forms a substantial proportion of the plant’s middle lamella of forage ingested by grazing ruminants. Methanol in the rumen is derived mainly from methoxy groups released from pectin by the action of pectin methylesterase (PME) and is subsequently used by rumen methylotrophic methanogens that reduce methanol to produce methane (CH₄). Members of the genus Butyrivibrio are key pectin-degrading rumen bacteria that contribute to methanol formation and have important roles in fibre breakdown, protein digestion, and the biohydrogenation of fatty acids. Therefore, methanol release from pectin degradation in the rumen is a potential target for CH₄ mitigation technologies. Here, we present the crystal structures of PMEs belonging to the carbohydrate esterase family 8 (CE8) from Butyrivibrio proteoclasticus and Butyrivibrio fibrisolvens, determined to a resolution of 2.30 Å. These enzymes, like other PMEs, are right-handed β-helical proteins with a well-defined catalytic site and reaction mechanisms previously defined in insect, plant, and other bacterial pectin methylesterases. Potential substrate binding domains are also defined for the enzymes.

Two strains of Gram-negative, anaerobic, rod-shaped bacteria, from an abundant but uncharacterized rumen bacterial group of the order ‘Christensenellales’, were phylogenetically and phenotypically characterized. These strains, designated R-7^T and WTE2008^T, shared 98.6–99.0 % sequence identity between their 16S rRNA gene sequences. R-7^T and WTE2008^T clustered together on a distinct branch from other Christensenellaceae strains and had Luoshenia tenuis NSJ-44^T. The genome sequences of R-7^T and WTE2008^T had 83.6 % average nucleotide identity to each other, and taxonomic assignment using the Genome Taxonomy Database indicates these are separate species within a novel family of the order ‘Christensenellales’. Cells of R-7^T and WTE2008^T lacked any obvious appendages and their cell wall ultra-structures were characteristic of Gram-negative bacteria. The five most abundant cellular fatty acids of both strains were C_16 : 0, C_16 : 0 iso, C_17 : 0 anteiso, C_18 : 0 and C_15 : 0 anteiso. The strains used a wide range of the 23 soluble carbon sources tested, and grew best on cellobiose, but not on sugar-alcohols. Xylan and pectin were fermented by both strains, but not cellulose. Acetate, hydrogen, ethanol and lactate were the major fermentation end products. R-7^T produced considerably more hydrogen than WTE2008^T, which produced more lactate. Based on these analyses, Aristaeellaceae fam. nov. and Aristaeella gen. nov., with type species Aristaeella hokkaidonensis sp. nov., are proposed. Strains R-7^T (=DSM 112795^T=JCM 34733^T) and WTE2008^T (=DSM 112788^T=JCM 34734^T) are the proposed type strains for Aristaeella hokkaidonensis sp. nov. and Aristaeella lactis sp. nov., respectively.

It is with much sadness that we report the death of Dr Neville Donovan Grace (1939–2022). Neville was a long-standing member of the Editorial Board of the New Zealand Veterinary Journal, serving fo...