Browsing by Author "Janssen PH"

Now showing 1 - 6 of 6
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    A protocol combining breath testing and ex vivo fermentations to study the human gut microbiome
    (Elsevier Inc, 2021-03-19) Payling L; Roy NC; Fraser K; Loveday SM; Sims IM; Janssen PH; Hill SJ; Raymond LG; McNabb WC
    This protocol describes the application of breath testing and ex vivo fermentations to study the association between breath methane and the composition and functionality of the gut microbiome. The protocol provides a useful systems biology approach for studying the gut microbiome in humans, which combines standardized methods in human breath testing and fecal sampling. The model described is accessible and easy to repeat, but its relative simplicity means that it can deviate from human physiological conditions.
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    Aristaeella hokkaidonensis gen. nov. sp. nov. and Aristaeella lactis sp. nov., two rumen bacterial species of a novel proposed family, Aristaeellaceae fam. nov.
    (Microbiology Society, 2023-05-12) Mahoney-Kurpe SC; Palevich N; Noel SJ; Gagic D; Biggs PJ; Soni P; Reid PM; Koike S; Kobayashi Y; Janssen PH; Attwood GT; Moon CD
    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-7T and WTE2008T, shared 98.6-99.0 % sequence identity between their 16S rRNA gene sequences. R-7T and WTE2008T clustered together on a distinct branch from other Christensenellaceae strains and had <88.1 % sequence identity to the closest type-strain sequence from Luoshenia tenuis NSJ-44T. The genome sequences of R-7T and WTE2008T 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-7T and WTE2008T 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 C16 : 0, C16 : 0 iso, C17 : 0 anteiso, C18 : 0 and C15 : 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-7T produced considerably more hydrogen than WTE2008T, 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-7T (=DSM 112795T=JCM 34733T) and WTE2008T (=DSM 112788T=JCM 34734T) are the proposed type strains for Aristaeella hokkaidonensis sp. nov. and Aristaeella lactis sp. nov., respectively.
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    Complete genome sequence of Methanosphaera sp. ISO3-F5, a rumen methylotrophic methanogen.
    (American Society for Microbiology, 2024-04-11) Palevich N; Jeyanathan J; Reilly K; Palevich FP; Maclean PH; Li D; Altermann E; Kelly WJ; Leahy SC; Attwood GT; Ronimus RS; Henderson G; Janssen PH; Stedman KM
    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).
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    Complete Genome Sequences of Three Clostridiales R-7 Group Strains Isolated from the Bovine Rumen in New Zealand
    (American Society for Microbiology, 2021-07-01) Mahoney-Kurpe SC; Palevich N; Noel SJ; Kumar S; Gagic D; Biggs PJ; Janssen PH; Attwood GT; Moon CD; Putonti C
    Members of the Clostridiales 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.
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    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.
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    Mapping immunogenic epitopes of an adhesin-like protein from Methanobrevibacter ruminantium M1 and comparison of empirical data with in silico prediction methods.
    (Springer Nature Limited, 2022-06-21) Khanum S; Carbone V; Gupta SK; Yeung J; Shu D; Wilson T; Parlane NA; Altermann E; Estein SM; Janssen PH; Wedlock DN; Heiser A
    In silico prediction of epitopes is a potentially time-saving alternative to experimental epitope identification but is often subject to misidentification of epitopes and may not be useful for proteins from archaeal microorganisms. In this study, we mapped B- and T-cell epitopes of a model antigen from the methanogen Methanobrevibacter ruminantium M1, the Big_1 domain (AdLP-D1, amino acids 19-198) of an adhesin-like protein. A series of 17 overlapping 20-mer peptides was selected to cover the Big_1 domain. Peptide-specific antibodies were produced in mice and measured by ELISA, while an in vitro splenocyte re-stimulation assay determined specific T-cell responses. Overall, five peptides of the 17 peptides were shown to be major immunogenic epitopes of AdLP-D1. These immunogenic regions were examined for their localization in a homology-based model of AdLP-D1. Validated epitopes were found in the outside region of the protein, with loop like secondary structures reflecting their flexibility. The empirical data were compared with epitope predictions made by programmes based on a range of algorithms. In general, the epitopes identified by in silico predictions were not comparable to those determined empirically.