Transcriptomic and proteomic changes associated with cobalamin-dependent propionate production by the rumen bacterium .

Unlabelled: is an abundant rumen bacterium that produces propionate in a cobalamin (vitamin B)-dependent manner via the succinate pathway. However, the extent to which this occurs across ruminal 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.

Genome sequences of three plastic-debris-inhabiting fungi isolated from New Zealand waste and recycling management plants.

and are cosmopolitan fungi of the class Dothideomycetes with few cultured and genomic representatives. Here, we report draft reference genome sequences of sp. F181 (GenBank accession number JAJSLS01), sp.

Complete genome sequence of the rumen bacterium D1.

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

Complete genome sequence of sp. ISO3-F5, a rumen methylotrophic methanogen.

spp. are methylotrophic methanogenic archaea and members of the order Methanobacteriales with few cultured representatives. sp.

Multiple genome sequences of lactic acid bacteria, and strains, isolated from vacuum-packaged lamb meat.

Here, we report the whole-genome sequences of 11 and 2 bacteria isolated from vacuum-packed chill-stored lamb meat in New Zealand. Examination of these lactic acid bacteria (LAB) genomes will improve our knowledge of their potential antimicrobial activities and spoilage mechanisms of importance to the meat industry.

Crystal Structures of Bacterial Pectin Methylesterases Pme8A and PmeC2 from Rumen .

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 (CH). Members of the genus 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.

Non-targeted multimodal metabolomics data from ovine rumen fluid fractions.

From an animal health perspective, our understanding of the metabolites in rumen fluid across different host species is poorly understood. Here, we present a metabolomic data set generated using hydrophilic interaction liquid chromatography and semi-polar (C18) chromatography methods coupled to high-resolution mass spectrometry of fractionated ovine rumen samples.

gen. nov. sp. nov. and sp. nov., two rumen bacterial species of a novel proposed family, fam. nov.

Two strains of Gram-negative, anaerobic, rod-shaped bacteria, from an abundant but uncharacterized rumen bacterial group of the order ', were phylogenetically and phenotypically characterized. These strains, designated R-7 and WTE2008, shared 98.6-99.

Multi-Omic Profiling, Structural Characterization, and Potent Inhibitor Screening of Evasion-Related Proteins of a Parasitic Nematode, , Surviving Vaccine Treatment.

The emergence of drug-resistant parasitic nematodes in both humans and livestock calls for development of alternative and cost-effective control strategies. Barbervax is the only registered vaccine for the economically important ruminant strongylid . In this study, we compared the microbiome, genome-wide diversity, and transcriptome of adult male populations that survived vaccination with an experimental vaccine after inoculation in sheep.

Genome collection of spp. isolated from spoiled lamb.

The diversity of the genus and their roles across a variety of ecological niches is largely unknown highlighting the phylogenetic diversity of these bacteria. From a food safety perspective, species have been recognized as causative spoilage agents of vacuum-packed meat products. However, the genetic basis and metabolic pathways for the spoilage mechanism are yet to be explored due to the unavailability of relevant strains and genomic resources.

Untargeted Multimodal Metabolomics Investigation of the Exsheathment Secretome.

In nematodes that invade the gastro-intestinal tract of the ruminant, the process of larval exsheathment marks the transition from the free-living to the parasitic stages of these parasites. To investigate the secretome associated with larval exsheathment, a closed in vitro system that effectively reproduces the two basic components of an anaerobic rumen environment (CO and 39 °C) was developed to trigger exsheathment in one of the most pathogenic and model gastrointestinal parasitic nematodes, (barber's pole worm). This study reports the use of multimodal untargeted metabolomics and lipidomics methodologies to identify the metabolic signatures and compounds secreted during in vitro larval exsheathment in the infective third-stage larva (iL3).

Soil Nitrogen Treatment Alters Microbiome Networks Across Farm Niches.

Agriculture is fundamental for food production, and microbiomes support agriculture through multiple essential ecosystem services. Despite the importance of individual (i.e.

Occurrence of genes encoding spore germination in species that cause meat spoilage.

Members of the genus are frequently associated with meat spoilage. The ability for low numbers of spores of certain species to germinate in cold-stored vacuum-packed meat can result in blown pack spoilage. However, little is known about the germination process of these clostridia, despite this characteristic being important for their ability to cause spoilage.

Genomic architecture of three newly isolated unclassified Butyrivibrio species elucidate their potential role in the rumen ecosystem.

One cellulose-degrading strain CB08 and two xylan-degrading strains XB500-5 and X503 were isolated from buffalo rumen. All the strains were designated as putative novel species of Butyrivibrio based on phylogeny, phylogenomy, digital DNA-DNA hybridization, and average nucleotide identity with their closest type strains. The draft genome length of CB08 was ~3.

Draft Genome Sequence of Clostridium bowmanii DSM 14206, Isolated from an Antarctic Microbial Mat.

Clostridium bowmanii type strain DSM 14206 (ATCC BAA-581) was isolated from a microbial mat sample retrieved from Lake Fryxell, Antarctica. This report describes the generation and annotation of the 4.9-Mb draft genome sequence of C.

Sequencing and Reconstructing Helminth Mitochondrial Genomes Directly from Genomic Next-Generation Sequencing Data.

We present a detailed method for extraction of high-molecular weight genomic DNA suitable for numerous DNA sequencing applications, and a straightforward in silico approach for reconstructing novel mitochondrial (mt) genomes directly from total genomic DNA extracts derived from next-generation sequencing (NGS) data sets. The in silico post-sequencing pipeline described is fast, accurate, and highly efficient, with modest memory requirements that can be performed using a standard desktop computer. The approach is particularly effective for obtaining mitochondrial genomes for species with little or no mitochondrial sequence information currently available and overcomes many of the limitations of traditional strategies.

Complete Genome Sequences of Three R-7 Group Strains Isolated from the Bovine Rumen in New Zealand.

Members of the R-7 group are abundant bacterial residents of the rumen microbiome; however, they are poorly characterized. We report the complete genome sequences of three members of the R-7 group, FE2010, FE2011, and XBB3002, isolated from the ruminal contents of pasture-grazed dairy cows in New Zealand.

Molecular and evolutionary basis for survival, its failure, and virulence factors of the zoonotic nematode Anisakis pegreffii.

Parasitism is a highly successful life strategy and a driving force in genetic diversity that has evolved many times over. Accidental infections of non-targeted hosts represent an opportunity for lateral host switches and parasite niche expansion. However, if directed toward organisms that are phylogenetically distant from parasite's natural host, such as humans, it may present a dead-end environment where the parasite fails to mature or is even killed by host immunity.

Bacterial Diversity Profiling of the New Zealand Parasitic Blowfly Lucilia sericata Based on 16S rRNA Gene Amplicon Sequencing.

Here, we present a 16S rRNA gene amplicon sequence data set and profiles demonstrating the bacterial diversity of larval and adult , collected from Ashhurst, New Zealand (May 2020). The two dominant genera among adult male and female were and (phylum ), while the larvae were also dominated by the genera , , and (phylum ).

16S rRNA Gene Amplicon Profiling of the New Zealand Parasitic Blowfly Calliphora vicina.

Here, we present a 16S rRNA gene amplicon sequence data set and profiles demonstrating the bacterial diversity of larval and adult , collected from Ashhurst, New Zealand (May 2020). The three dominant genera among the adult male and female blowflies were and (phylum ) and (phylum ), while the larvae were also dominated by the genera (phylum ).

Characterization of the complete mitochondrial genome of the New Zealand parasitic blowfly (Insecta: Diptera: Calliphoridae).

In this study, the complete mitochondrial (mt) genome of the New Zealand parasitic blowfly (blue bottle blowfly) field strain NZ_CalVic_NP was generated using next-generation sequencing technology and annotated. The 16,518 bp mt genome consists of 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and a 1689 bp non-coding region, similar to the two other available and most metazoan mt genomes. Phylogenetic analysis showed that NZ_CalVic_NP forms a monophyletic cluster with the remaining three Calliphorinae species.

The complete mitochondrial genome of the New Zealand parasitic blowfly (Insecta: Diptera: Calliphoridae).

In this study, the complete mitochondrial (mt) genome of the New Zealand parasitic blowfly (green bottle blowfly) field strain NZ_LucSer_NP was generated using next-generation sequencing technology. The length of complete the mt genome is 15,938 bp, with 39.4% A, 13.

Comparative genomics of Clostridium species associated with vacuum-packed meat spoilage.

Bacterial species belonging to the genus Clostridium have been recognized as causative agents of blown pack spoilage (BPS) in vacuum packed meat products. Whole-genome sequencing of six New Zealand psychrotolerant clostridia isolates derived from three meat production animal types and their environments was performed to examine their roles in BPS. Comparative genome analyses have provided insight into the genomic diversity and physiology of these bacteria and divides clostridia into two separate species clusters.