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Palevich, N.

Publications and source records attributed to Palevich, N..

11 recordsLinked to original sources
bioRxiv2021

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 [~]3.54 Mb, while X503 and XB500-5 genome sizes were [~]3.24 Mb and [~]3.27 Mb, respectively. Only 68.28% of total orthologous clusters were shared among three genomes, and 40-44% of genes were identified as hypothetical proteins. The presence of genes encoding diverse carbohydrate-active enzymes (CAZymes) exhibited the lignocellulolytic potential of these strains. Further, the genome annotations revealed the metabolic pathways for monosaccharide fermentation to acetate, butyrate, lactate, ethanol, and hydrogen. The presence of genes for chemotaxis, antibiotic resistance, antimicrobial activity, synthesis of vitamins, and essential fatty acid suggested the versatile metabolic nature of these Butyrivibrio strains in the rumen environment.

genomics↗
bioRxiv2021

Genome sequence of Pseudopithomyces chartarum, causal agent of facial eczema (pithomycotoxicosis) in ruminants, and identification of the putative sporidesmin toxin gene cluster

Facial eczema (FE) in grazing ruminants is a debilitating liver syndrome induced by ingestion of sporidesmin, a toxin belonging to the epipolythiodioxopiperazine class of compounds. Sporidesmin is produced in spores of the fungus Pseudopithomyces chartarum, a microbe which colonises leaf litter in pastures. New Zealand has a high occurrence of FE in comparison to other countries as animals are fed predominantly on ryegrass, a species that supports high levels of Pse. chartarum spores. The climate is also particularly conducive for Pse. chartarum growth. Here, we present the genome of Pse. chartarum and identify the putative sporidesmin gene cluster. The Pse. chartarum genome was sequenced using single molecule real-time sequencing (PacBio) and gene models identified. Loci containing genes with homology to the aspirochlorine, sirodesmin PL and gliotoxin cluster genes of Aspergillus oryzae, Leptosphaeria maculans and Aspergillus fumigatus, respectively, were identified by tBLASTn. We identified and annotated an epipolythiodioxopiperazine cluster at a single locus with all the functionality required to synthesise sporidesmin. HighlightsO_LIThe whole genome of Pseudopithomyces chartarum has been sequenced and assembled. C_LIO_LIThe genome is 39.13 Mb, 99% complete, and contains 11,711 protein coding genes. C_LIO_LIA putative sporidesmin A toxin (cause of facial eczema) gene cluster is described. C_LIO_LIThe genomes of Pse. chartarum and the Leptosphaerulina chartarum teleomorph differ. C_LIO_LIComparative genomics is required to further resolve the Pseudopithomyces clade. C_LI

genomics↗
bioRxiv2021

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 Calliphora vicina, collected from Ashhurst, New Zealand (May 2020). The three dominant genera among adult male and female C. vicina were Serratia and Morganella (phylum Proteobacteria) and Carnobacterium (phylum Firmicutes), while the larvae were also dominated by the genera Lactobacillus (phylum Firmicutes).

molecular biology↗
bioRxiv2021

Good host - bad host: 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. Consequently, parasitic organisms have adopted a rich display of traits associated with survival that guarantees an effective "communication" with the host immunity and a balance with surrounding microbiome. However, gain/loss of hosts along the evolutionary axis represents a complex scenario that as contemporary onlookers, we can observe only after a long time displacement. The zoonotic and monophyletic Anisakidae diverged from its terrestrial sister group Ascarididae 150-250 Ma, although a split from their common ancestral host, a terrestrial amniote, seemingly happened already in Early Carboniferous (360.47 Ma). Faced with the sea-level rise during the Permian-Triassic extinction (215 Ma), anisakids acquired a semiaquatic tetrapod host, and as a result of lateral host-switches in Cenozoic, colonised marine mammals, co-evolving with their "new hosts". Although contemporary anisakids have lost the ability to propagate in terrestrial hosts, they can survive for a limited time in humans. To scrutinize anisakid versatility to infect evolutionary-distant host, we performed transcriptomic profiling of larvae infecting the accidental host (rat) and compared it to that of larvae infecting an evolutionary-familiar, paratenic host (fish). Identified differences and the modeling of handful of shared transcripts, provides the first insights into evolution of larval nematode virulence, warranting further investigation of shared transcript as potential drug therapy targets. Our findings have also revealed some key intrinsic cues that direct larval fate during infection.

molecular biology↗
bioRxiv2021

A multimodal metabolomics approach to elucidate the trigger components of rumen fluid for larval exsheathment in a model gastrointestinal parasitic nematode, Haemonchus contortus.

From an animal production and health perspective, our understanding of the metabolites in ruminant biofluids, particularly rumen fluid across different host species is poorly understood. Metabolomics is a powerful and sensitive approach for investigating low molecular weight metabolite profiles present in rumen biofluids. It can be used to identify potential roles of metabolites in the rumen microbiome and provide and understanding of host-level regulatory mechanisms associated with animal production. The rumen is a strictly anaerobic environment enriched with a complex community of bacteria, protozoa, fungi, archaea and bacteriophages. Here, we present a metabolomic dataset generated using hydrophilic interaction liquid chromatography (HILIC) and semi-polar (C18) chromatography methods coupled to high resolution mass spectrometry (MS), collected in both positive and negative ionization modes, of ovine rumen samples that were fractionated based on molecular weight (20 kDa, 8-10 kDa and 100 Da). This study highlights the potential of HILIC and C18 chromatography combined with non-targeted mass spectrometric methods to detect the polar and semi-polar metabolite species of the ruminal fluid metabolome.

molecular biology↗
bioRxiv2020

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

In the present study, the complete mitochondrial genome of the New Zealand parasitic blowfly Calliphora vicina (blue bottle blowfly) field strain NZ_CalVic_NP was generated using next-generation sequencing technology and annotated. The 16,518 bp mitochondrial genome consists of 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and a 1,689 bp non-coding region, similar to most metazoan mitochondrial genomes. Phylogenetic analysis showed that C. vicina NZ_CalVic_NP does not form a monophyletic cluster with the remaining three Calliphorinae species. The complete mitochondrial genome sequence of C. vicina NZ_CalVic_NP is a resource to facilitate future species identification research within the Calliphoridae.

zoology↗
bioRxiv2020

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

Bacterial species belonging to the Clostridium genera have been recognized as causative agents of blown pack spoilage (BPS) in vacuum packed meat products. Whole-genome sequencing of six New Zealand psychrotolerant Clostridium 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. BPS-associated Clostridia encode a large and diverse spectrum of degradative carbohydrate-active enzymes (CAZymes). In total, 516 glycoside hydrolases (GHs), 93 carbohydrate esterases (CEs), 21 polysaccharide lyases (PLs), 434 glycosyl transferases (GTs) and 211 carbohydrate-binding protein modules (CBM) with predicted activities involved in the breakdown and transport of carbohydrates were identified. Clostridia genomes have different patterns of CAZyme families and vary greatly in the number of genes within each CAZy category, suggesting some level of functional redundancy. These results suggest that BPS-associated Clostridia occupy similar environmental niches but apply different carbohydrate metabolism strategies to be able to co-exist and cause meat spoilage.

microbiology↗
bioRxiv2020

Teladorsagia circumcincta 1,6 bisphosphate aldolase: molecular and biochemical characterisation, structure analysis and recognition by immune hosts.

A 1095 bp full length cDNA encoding Teladorsagia circumcincta aldolase (TciALDO) was cloned, expressed in Escherichia coli, the recombinant protein purified and its kinetic properties determined. A phylogenetic tree was constructed using helminth aldolase sequences. The predicted protein consisted of 365 amino acids and was present as a single band of about 44 kDa on SDS-PAGE. Multiple alignments of the protein sequence of TciALDO with homologues from other helminths showed that the greatest similarity (93%) to the aldolases of Haemonchus contortus and Dictyocaulus viviparus, 82-86% similarity to the other nematode sequences and 68-71% similarity to cestode and trematode enzymes. Substrate binding sites and conserved regions were identified and were completely conserved in other homologues. At 25 {degrees}C, the optimum pH for TciALDO activity was pH 7.5, the Vmax was 432 {+/-} 23 nmoles.min-1.mg-1 protein and the apparent Km for the substrate fructose 1,6-bisphosphate was 0.24 {+/-} 0.01 M (mean {+/-} SEM, n = 3). Antibodies in both serum and saliva from field-immune, but not nematode-naive, sheep recognised recombinant TciALDO in enzyme-linked immunosorbent assays. The recognition of the recombinant protein by antibodies generated by exposure of sheep to native aldolase indicates similar antigenicity of the two proteins.

molecular biology↗
bioRxiv2020

Characterisation of a Teladorsagia circumcincta glutathione transferase.

A 615 bp full length cDNA encoding a Teladorsagia circumcincta glutathione transferase (TcGST) was cloned, expressed in Escherichia coli and the recombinant protein purified and its kinetic properties determined. The predicted protein consisted of 205 amino acids and was present as a single band of about 24 kDa on SDS-PAGE. Multiple alignments of the protein sequence of TcGST with homologues from other helminths showed that the highest identity of 53-68% with haem-binding nematode proteins designated as members of the nu class of GSTs. Substrate binding sites and conserved regions were identified and were generally conserved. The predicted 3-dimensional structures of TcGST and HcGST revealed highly open binding cavities typical of this class of GST, considered to allow greater accessibility to diverse ligands compared with other classes of GST. At 25 {degrees}C, the optimum pH for TcGST activity was pH 7, the Vmax was 1535 {+/-} 33 nmoles.min-1.mg-1 protein and the apparent Km for the substrate 1-chloro-2,4-dinitrobenzene (CDNB) was 0.22 {+/-} 0.01 mM (mean {+/-} SD, n = 2). Antibodies in both serum and saliva from field-immune, but not nematode-naIve, sheep, recognised recombinant TcGST in enzyme-linked immunosorbent assays. The recognition of the recombinant protein by antibodies generated by exposure of sheep to the native enzyme indicates similar antigenicity of the two proteins. These findings could aid in the design of novel drugs and vaccine antigens for economically important parasites of livestock.

molecular biology↗
bioRxiv2018

Butyrivibrio hungatei MB2003 competes effectively for soluble sugars released by Butyrivibrio proteoclasticus B316T from growth on xylan or pectin

Rumen bacterial species belonging to the genera Butyrivibrio are important degraders of plant polysaccharides, particularly hemicelluloses (arabinoxylans) and pectin. Currently, four distinct species are recognized which have very similar substrate utilization profiles, but little is known about how these microorganisms are able to co-exist in the rumen. To investigate this question, Butyrivibrio hungatei (MB2003) and Butyrivibrio proteoclasticus (B316T) were grown alone or in co-culture on the insoluble substrates, xylan or pectin, and their growth, release of sugars, fermentation end products and transcriptomes were examined. In single cultures, B316T was able to degrade and grow well on xylan and pectin, while B. hungatei MB2003 was unable to utilize either of these insoluble substrates to support significant growth. Co-cultures of B316T grown with MB2003 revealed that MB2003 showed almost equivalent growth to B316T when either xylan or pectin were supplied as substrates. The effect of co-culture on the transcriptomes of B316T and MB2003 was very marked; B316T transcription was largely unaffected by the presence MB2003, but MB2003 expressed a wide range of genes encoding carbohydrate degradation/metabolism and oligosaccharide transport/assimilation in order to compete with B316T for the released sugars. These results suggest that B316T has a role as an initiator of the primary solubilization of xylan and pectin, while MB2003 competes effectively as a scavenger for the released soluble sugars to enable its growth and maintenance in the rumen.\n\nIMPORTANCEFeeding a global population of nine billion people and climate change are the primary challenges facing agriculture today. Determining the roles of rumen microbes involved in plant polysaccharide breakdown is fundamental to understanding digestion and maximizing productivity of ruminant livestock. Butyrivibrio are abundant rumen bacteria and are a substantial source of polysaccharide-degrading enzymes with biotechnological applications for the depolymerization of lignocellulosic material. Our findings suggest that closely related species of Butyrivibrio have developed unique strategies for the degradation of plant fibre and the subsequent assimilation of carbohydrates in order to coexist in the competitive rumen environment. The identification of genes related to their enzymatic machinery by which these bacteria work in concert to degrade these different forms of polysaccharides contributes to our understanding of carbon flow in the rumen.

microbiology↗