Massey Research Online - Browsing by Author "Jauregui R"

Browsing by Author "Jauregui R"

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Complete Genome Sequence of Paenibacillus sp. Strain E222, a Bacterial Symbiont of an Epichloë Fungal Endophyte of Ryegrass.
(American Society for Microbiology, 2020-10-08) Bastías DA; Jauregui R; Applegate ER; Altermann E; Card SD; Johnson LJ; Stajich JE
We report on the whole-genome sequence of Paenibacillus sp. strain E222, a bacterium isolated from a fresh culture of Epichloë festucae var. lolii, a mutualistic fungal endophyte of perennial ryegrass. The genome has a size of 7.8 Mb and a G+C content of 46% and encodes 6,796 putative protein-coding genes.
Culture and genome-based analysis of four soil Clostridium isolates reveal their potential for antimicrobial production
(BioMed Central Ltd, 2021-12) Pahalagedara ASNW; Jauregui R; Maclean P; Altermann E; Flint S; Palmer J; Brightwell G; Gupta TB
BACKGROUND: Soil bacteria are a major source of specialized metabolites including antimicrobial compounds. Yet, one of the most diverse genera of bacteria ubiquitously present in soil, Clostridium, has been largely overlooked in bioactive compound discovery. As Clostridium spp. thrive in extreme environments with their metabolic mechanisms adapted to the harsh conditions, they are likely to synthesize molecules with unknown structures, properties, and functions. Therefore, their potential to synthesize small molecules with biological activities should be of great interest in the search for novel antimicrobial compounds. The current study focused on investigating the antimicrobial potential of four soil Clostridium isolates, FS01, FS2.2 FS03, and FS04, using a genome-led approach, validated by culture-based methods. RESULTS: Conditioned/spent media from all four Clostridium isolates showed varying levels of antimicrobial activity against indicator microorganism; all four isolates significantly inhibited the growth of Pseudomonas aeruginosa. FS01, FS2.2, and FS04 were active against Bacillus mycoides and FS03 reduced the growth of Bacillus cereus. Phylogenetic analysis together with DNA-DNA hybridization (dDDH), average nucleotide identity (ANI), and functional genome distribution (FGD) analyses confirmed that FS01, FS2.2, and FS04 belong to the species Paraclostridium bifermentans, Clostridium cadaveris, and Clostridium senegalense respectively, while FS03 may represent a novel species of the genus Clostridium. Bioinformatics analysis using antiSMASH 5.0 predicted the presence of eight biosynthetic gene clusters (BGCs) encoding for the synthesis of ribosomally synthesized post-translationally modified peptides (RiPPs) and non-ribosomal peptides (NRPs) in four genomes. All predicted BGCs showed no similarity with any known BGCs suggesting novelty of the molecules from those predicted gene clusters. In addition, the analysis of genomes for putative virulence factors revealed the presence of four putative Clostridium toxin related genes in FS01 and FS2.2 genomes. No genes associated with the main Clostridium toxins were identified in the FS03 and FS04 genomes. CONCLUSIONS: The presence of BGCs encoding for uncharacterized RiPPs and NRPSs in the genomes of antagonistic Clostridium spp. isolated from farm soil indicated their potential to produce novel secondary metabolites. This study serves as a basis for the identification and characterization of potent antimicrobials from these soil Clostridium spp. and expands the current knowledge base, encouraging future research into bioactive compound production in members of the genus Clostridium.
Draft Genome Sequence of Clostridium estertheticum subsp. laramiense DSM 14864T, Isolated from Spoiled Uncooked Beef.
(American Society for Microbiology, 2019-11-21) Palevich N; Palevich FP; Maclean PH; Jauregui R; Altermann E; Mills J; Brightwell G; Newton ILG
Clostridium estertheticum subsp. laramiense type strain DSM 14864 (ATCC 51254) was isolated from vacuum-packaged refrigerated spoiled beef. This report describes the generation and annotation of the 5.0-Mb draft genome sequence of C. estertheticum subsp. laramiense DSM 14864T.
Draft Genome Sequence of Clostridium estertheticum-Like Strain FP3, Isolated from Spoiled Uncooked Lamb.
(American Society for Microbiology, 2020-05-14) Palevich N; Palevich FP; Maclean PH; Jauregui R; Altermann E; Mills J; Brightwell G; Gill SR
Clostridium estertheticum-like strain FP3 was isolated from vacuum-packaged refrigerated spoiled lamb. This bacterium is psychrotrophic, Gram positive, spore-forming, and a strict anaerobe. Here, we report the generation and annotation of the 5.6-Mb draft genome sequence of C. estertheticum-like strain FP3.
Draft Genome Sequence of Clostridium estertheticum-like Strain FP4, Isolated from Spoiled Uncooked Lamb.
(American Society for Microbiology, 2020-05-07) Palevich N; Palevich FP; Maclean PH; Jauregui R; Altermann E; Mills J; Brightwell G; Rasco D
In order to improve the phylogenetic resolution of the genus Clostridium and our limited knowledge of meat spoilage caused by Clostridium estertheticum, the genome of C. estertheticum-like strain FP4 was sequenced. Here, we describe the 4.1-Mb draft genome sequence of C. estertheticum-like strain FP4, isolated from vacuum-packaged refrigerated spoiled lamb.
Draft Genome Sequence of Clostridium sp. Strain FP1, with Similarity to Clostridium tagluense, Isolated from Spoiled Lamb.
(American Society for Microbiology, 2020-04-30) Palevich N; Palevich FP; Maclean PH; Jauregui R; Altermann E; Mills J; Brightwell G; Hotopp JCD
Clostridium sp. strain FP1 was isolated from vacuum-packaged refrigerated spoiled lamb, and this article describes its 5.4-Mb draft genome sequence. The FP1 genome was sequenced to facilitate source tracking and attribution studies, adding to our understanding of the role of Clostridium species in premature spoilage of red meats.
Draft Genome Sequence of Psychrotolerant Clostridium sp. Strain M14, Isolated from Spoiled Uncooked Venison.
(American Society for Microbiology, 2020-04-16) Palevich N; Palevich FP; Maclean PH; Jauregui R; Altermann E; Mills J; Brightwell G; Hotopp JCD
Clostridium sp. strain M14 was isolated from vacuum-packaged refrigerated spoiled venison, and this report describes the generation and annotation of its 3.9-Mb draft genome sequence.
Genetic regulation of antibody responsiveness to immunization in substrains of BALB/c mice.
(John Wiley and Sons Inc., 2019-01-01) Poyntz HC; Jones A; Jauregui R; Young W; Gestin A; Mooney A; Lamiable O; Altermann E; Schmidt A; Gasser O; Weyrich L; Jolly CJ; Linterman MA; Gros GL; Hawkins ED; Forbes-Blom E
Antibody-mediated immunity is highly protective against disease. The majority of current vaccines confer protection through humoral immunity, but there is high variability in responsiveness across populations. Identifying immune mechanisms that mediate low antibody responsiveness may provide potential strategies to boost vaccine efficacy. Here, we report diverse antibody responsiveness to unadjuvanted as well as adjuvanted immunization in substrains of BALB/c mice, resulting in high and low antibody response phenotypes. Furthermore, these antibody phenotypes were not affected by changes in environmental factors such as the gut microbiota composition. Antigen-specific B cells following immunization had a marked difference in capability to class switch, resulting in perturbed IgG isotype antibody production. In vitro, a B-cell intrinsic defect in the regulation of class-switch recombination was identified in mice with low IgG antibody production. Whole genome sequencing identified polymorphisms associated with the magnitude of antibody produced, and we propose candidate genes that may regulate isotype class-switching capability. This study highlights that mice sourced from different vendors can have significantly altered humoral immune response profiles, and provides a resource to interrogate genetic regulators of antibody responsiveness. Together these results further our understanding of immune heterogeneity and suggest additional research on the genetic influences of adjuvanted vaccine strategies is warranted for enhancing vaccine efficacy.
Genomic insights into the physiology of Quinella, an iconic uncultured rumen bacterium.
(Nature Portfolio, 2022-10-20) Kumar S; Altermann E; Leahy SC; Jauregui R; Jonker A; Henderson G; Kittelmann S; Attwood GT; Kamke J; Waters SM; Patchett ML; Janssen PH
Quinella is a genus of iconic rumen bacteria first reported in 1913. There are no cultures of these bacteria, and information on their physiology is scarce and contradictory. Increased abundance of Quinella was previously found in the rumens of some sheep that emit low amounts of methane (CH4) relative to their feed intake, but whether Quinella contributes to low CH4 emissions is not known. Here, we concentrate Quinella cells from sheep rumen contents, extract and sequence DNA, and reconstruct Quinella genomes that are >90% complete with as little as 0.20% contamination. Bioinformatic analyses of the encoded proteins indicate that lactate and propionate formation are major fermentation pathways. The presence of a gene encoding a potential uptake hydrogenase suggests that Quinella might be able to use free hydrogen (H2). None of the inferred metabolic pathways is predicted to produce H2, a major precursor of CH4, which is consistent with the lower CH4 emissions from those sheep with high abundances of this bacterium.
Genomic selection shows improved expected genetic gain over phenotypic selection of agronomic traits in allotetraploid white clover.
(Springer Nature, 2025-01-23) Ehoche OG; Arojju SK; Jahufer MZZ; Jauregui R; Larking AC; Cousins G; Tate JA; Lockhart PJ; Griffiths AG
Genomic selection using white clover multi-year-multi-site data showed predicted genetic gains through integrating among-half-sibling-family phenotypic selection and within-family genomic selection were up to 89% greater than half-sibling-family phenotypic selection alone. Genomic selection, an effective breeding tool used widely in plants and animals for improving low-heritability traits, has only recently been applied to forages. We explored the feasibility of implementing genomic selection in white clover (Trifolium repens L.), a key forage legume which has shown limited genetic improvement in dry matter yield (DMY) and persistence traits. We used data from a training population comprising 200 half-sibling (HS) families evaluated in a cattle-grazed field trial across three years and two locations. Combining phenotype and genotyping-by-sequencing (GBS) data, we assessed different two-stage genomic prediction models, including KGD-GBLUP developed for low-depth GBS data, on DMY, growth score, leaf size and stolon traits. Predictive abilities were similar among the models, ranging from -0.17 to 0.44 across traits, and remained stable for most traits when reducing model input to 100-120 HS families and 5500 markers, suggesting genomic selection is viable with fewer resources. Incorporating a correlated trait with a primary trait in multi-trait prediction models increased predictive ability by 28-124%. Deterministic modelling showed integrating among-HS-family phenotypic selection and within-family genomic selection at different selection pressures estimated up to 89% DMY genetic gain compared to phenotypic selection alone, despite a modest predictive ability of 0.3. This study demonstrates the potential benefits of combining genomic and phenotypic selection to boost genetic gains in white clover. Using cost-effective GBS paired with a prediction model optimized for low read-depth data, the approach can achieve prediction accuracies comparable to traditional models, providing a viable path for implementing genomic selection in white clover.
Investigation of post-vaccinal canine distemper involving the Rockborn-like strain in nine puppies in New Zealand
(Taylor and Francis Group on behalf of the New Zealand Veterinary Association, 2025-04-09) Gulliver E; Taylor H; Eames M; Chernyavtseva A; Jauregui R; Wilson A; Bestbier M; O’Connell J; Buckle K; Castillo-Alcala F
Case history: This report details investigations into nine cases of neurological disease and/or sudden death in 8–13-week-old puppies between 2021 and 2024. Aside from two pairs of littermates, cases were unrelated. The puppies had an onset of clinical signs 9–23 days following at least one “on-label” dose of a commercially available quadrivalent vaccine containing live attenuated canine distemper virus (CDV). Clinical findings: Eight of the nine cases displayed signs typical of “classic distemper,” including seizures, circling, tremors, hypersalivation, progressive neurological deficits, pyrexia, and/or respiratory and gastrointestinal signs. Pathological and molecular investigations were undertaken in eight cases. Mononuclear/lymphohistiocytic encephalitis or meningoencephalitis with or without neuronal intranuclear inclusion bodies was present in seven cases. Five cases had bronchopneumonia. Other lesions included poliomyelitis, necrotising enteritis and myocardial necrosis or myocarditis. PCR for CDV was positive on tissues from seven cases, and immunohistochemistry for CDV was positive on neural tissues in six cases. Whole genome sequencing of PCR amplicons demonstrated a Rockborn-like strain with 99.9% homogeneity between samples from four cases and a vial of vaccine. Diagnosis: Based on the combination of case history, pathological findings, molecular test results and/or whole genome sequencing, a diagnosis of post-vaccinal canine distemper was confirmed in six cases and presumed in two. Clinical relevance: Outbreaks of canine distemper have been stemmed by widespread vaccination starting in the mid-twentieth century. Consequently, confirmed cases of natural CDV have not been reported in New Zealand since an outbreak in the 1980s, and CDV is considered a “notifiable organism” as per the Biosecurity Act 1993. This is the first case series to report genomic investigation of post-vaccinal canine distemper in New Zealand puppies and highlights a rare adverse event associated with routine vaccination. Our results suggest that puppies with neurological, respiratory and/or gastrointestinal disease with an onset within 6 weeks of vaccination with live attenuated CDV should be reported and investigated accordingly.
Methylobacterium, a major component of the culturable bacterial endophyte community of wild Brassica seed
(PeerJ, Inc, 2020-07-10) Roodi D; Millner JP; McGill C; Johnson RD; Jauregui R; Card SD; Souza V
BACKGROUND: Plants are commonly colonized by a wide diversity of microbial species and the relationships created can range from mutualistic through to parasitic. Microorganisms that typically form symptomless associations with internal plant tissues are termed endophytes. Endophytes associate with most plant species found in natural and managed ecosystems. They are extremely important plant partners that provide improved stress tolerance to the host compared with plants that lack this symbiosis. Plant domestication has reduced endophyte diversity and therefore the wild relatives of many crop species remain untapped reservoirs of beneficial microbes. Brassica species display immense diversity and consequently provide the greatest assortment of products used by humans from a single plant genus important for agriculture, horticulture, bioremediation, medicine, soil conditioners, composting crops, and in the production of edible and industrial oils. Many endophytes are horizontally transmitted, but some can colonize the plant's reproductive tissues, and this gives these symbionts an efficient mechanism of propagation via plant seed (termed vertical transmission). METHODS: This study surveyed 83 wild and landrace Brassica accessions composed of 14 different species with a worldwide distribution for seed-originating bacterial endophytes. Seed was stringently disinfected, sown within sterile tissue culture pots within a sterile environment and incubated. After approximately 1-month, direct isolation techniques were used to recover bacterial endophytes from roots and shoots of symptomless plants. Bacteria were identified based on the PCR amplification of partial 16S rDNA gene sequences and annotated using the BLASTn program against the NCBI rRNA database. A diversity index was used as a quantitative measure to reflect how many different bacterial species there were in the seed-originating microbial community of the Brassica accessions sampled. RESULTS: Bacterial endophytes were recovered from the majority of the Brassica accessions screened. 16S rDNA gene sequencing identified 19 different bacterial species belonging to three phyla, namely Actinobacteria, Firmicutes and Proteobacteria with the most frequently isolated species being Methylobacterium fujisawaense, Stenotrophomonas rhizophila and Pseudomonas lactis. Methylobacterium was the dominant genus composing 56% of the culturable isolated bacterial community and was common in 77% of accessions possessing culturable bacterial endophytes. Two selected isolates of Methylobacterium significantly promoted plant growth when inoculated into a cultivar of oilseed rape and inhibited the growth of the pathogen Leptosphaeria maculans in dual culture. This is the first report that investigates the seed-originating endophytic microorganisms of wild Brassica species and highlights the Brassica microbiome as a resource for plant growth promoting bacteria and biological control agents.
Outlier analyses and genome-wide association study identify glgC and ERD6-like 4 as candidate genes for foliar water-soluble carbohydrate accumulation in Trifolium repens.
(Frontiers Media S.A., 2022-01-09) Pearson SM; Griffiths AG; Maclean P; Larking AC; Hong SW; Jauregui R; Miller P; McKenzie CM; Lockhart PJ; Tate JA; Ford JL; Faville MJ; Xie W; Rodriguez VM
Increasing water-soluble carbohydrate (WSC) content in white clover is important for improving nutritional quality and reducing environmental impacts from pastoral agriculture. Elucidation of genes responsible for foliar WSC variation would enhance genetic improvement by enabling molecular breeding approaches. The aim of the present study was to identify single nucleotide polymorphisms (SNPs) associated with variation in foliar WSC in white clover. A set of 935 white clover individuals, randomly sampled from five breeding pools selectively bred for divergent (low or high) WSC content, were assessed with 14,743 genotyping-by-sequencing SNPs, using three outlier detection methods: PCAdapt, BayeScan and KGD-FST. These analyses identified 33 SNPs as discriminating between high and low WSC populations and putatively under selection. One SNP was located in the intron of ERD6-like 4, a gene coding for a sugar transporter located on the vacuole membrane. A genome-wide association study using a subset of 605 white clover individuals and 5,757 SNPs, identified a further 12 SNPs, one of which was associated with a starch biosynthesis gene, glucose-1-phosphate adenylyltransferase, glgC. Our results provide insight into genomic regions underlying WSC accumulation in white clover, identify candidate genomic regions for further functional validation studies, and reveal valuable information for marker-assisted or genomic selection in white clover.
Using meta-analysis to understand the impacts of dietary protein and fat content on the composition of fecal microbiota of domestic dogs (Canis lupus familiaris): A pilot study
(John Wiley and Sons Ltd, 2024-04) Phimister FD; Anderson RC; Thomas DG; Farquhar MJ; Maclean P; Jauregui R; Young W; Butowski CF; Bermingham EN
The interplay between diet and fecal microbiota composition is garnering increased interest across various host species, including domestic dogs. While the influence of dietary macronutrients and their associated microbial communities have been extensively reviewed, these reviews are descriptive and do not account for differences in microbial community analysis, nor do they standardize macronutrient content across studies. To address this, a meta-analysis was performed to assess the impact of dietary crude protein ("protein") and dietary crude fat ("fat") on the fecal microbiota composition in healthy dogs. Sixteen publications met the eligibility criteria for the meta-analysis, yielding a final data set of 314 dogs. Diets were classed as low, moderate, high, or supra in terms of protein or fat content. Sequence data from each publication were retrieved from public databases and reanalyzed using consistent bioinformatic pipelines. Analysis of community diversity indices and unsupervised clustering of the data with principal coordinate analysis revealed a small effect size and complete overlap between protein and fat levels at the overall community level. Supervised clustering through random forest analysis and partial least squares-discriminant analysis indicated alterations in the fecal microbiota composition at a more individual taxonomic level, corresponding to the levels of protein or fat. The Prevotellaceae Ga6A1 group and Enterococcus were associated with increasing levels of protein, while Allobaculum and Clostridium sensu stricto 13 were associated with increasing levels of fat. Interestingly, the random forest analyses revealed that Sharpea, despite its low relative abundance in the dog's fecal microbiome, was primarily responsible for the separation of the microbiome for both protein and fat. Future research should focus on validating and understanding the functional roles of these relatively low-abundant genera.
Whole-Genome Sequencing of Clostridium sp. Strain FP2, Isolated from Spoiled Venison.
(American Society for Microbiology, 2020-04-30) Palevich N; Palevich FP; Maclean PH; Jauregui R; Altermann E; Mills J; Brightwell G; Cuomo CA
Clostridium sp. strain FP2 was isolated from vacuum-packaged refrigerated spoiled venison in New Zealand. This report describes the generation and annotation of the 5.6-Mb draft genome sequence of Clostridium sp. FP2, which will facilitate future functional genomic studies to improve our understanding of premature spoilage of red meats.

Browsing by Author "Jauregui R"

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