145 results on '"Attwood, Graeme T."'
Search Results
2. Methanobrevibacter boviskoreani JH1T growth on alcohols allows development of a high throughput bioassay to detect methanogen inhibition
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Li, Yang, Crouzet, Laureen, Kelly, William J., Reid, Peter, Leahy, Sinead C., and Attwood, Graeme T.
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- 2023
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3. Hydrogen and formate production and utilisation in the rumen and the human colon
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Kelly, William J., Mackie, Roderick I., Attwood, Graeme T., Janssen, Peter H., McAllister, Tim A., and Leahy, Sinead C.
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- 2022
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4. Genomic insights into the physiology of Quinella, an iconic uncultured rumen bacterium
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Kumar, Sandeep, Altermann, Eric, Leahy, Sinead C., Jauregui, Ruy, Jonker, Arjan, Henderson, Gemma, Kittelmann, Sandra, Attwood, Graeme T., Kamke, Janine, Waters, Sinéad M., Patchett, Mark L., and Janssen, Peter H.
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- 2022
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5. Electron flow: key to mitigating ruminant methanogenesis
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Leahy, Sinead C., Janssen, Peter H., Attwood, Graeme T., Mackie, Roderick I., McAllister, Tim A., and Kelly, William J.
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- 2022
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- View/download PDF
6. Farm-scale carbon and nitrogen fluxes in pastoral dairy production systems using different nitrogen fertilizer regimes
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Beukes, Pierre C., Gregorini, Pablo, Cameron, Keith, and Attwood, Graeme T.
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- 2020
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7. Diverse hydrogen production and consumption pathways influence methane production in ruminants
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Greening, Chris, Geier, Renae, Wang, Cecilia, Woods, Laura C., Morales, Sergio E., McDonald, Michael J., Rushton-Green, Rowena, Morgan, Xochitl C., Koike, Satoshi, Leahy, Sinead C., Kelly, William J., Cann, Isaac, Attwood, Graeme T., Cook, Gregory M., and Mackie, Roderick I.
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- 2019
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8. Sharpea and Kandleria are lactic acid producing rumen bacteria that do not change their fermentation products when co-cultured with a methanogen
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Kumar, Sandeep, Treloar, Bryan P., Teh, Koon Hoong, McKenzie, Catherine M., Henderson, Gemma, Attwood, Graeme T., Waters, Sinéad M., Patchett, Mark L., and Janssen, Peter H.
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- 2018
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9. Occurrence and expression of genes encoding methyl-compound production in rumen bacteria
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Kelly, William J., Leahy, Sinead C., Kamke, Janine, Soni, Priya, Koike, Satoshi, Mackie, Roderick, Seshadri, Rekha, Cook, Gregory M., Morales, Sergio E., Greening, Chris, and Attwood, Graeme T.
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- 2019
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10. Crystal Structures of Bacterial Pectin Methylesterases Pme8A and PmeC2 from Rumen Butyrivibrio.
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Carbone, Vincenzo, Reilly, Kerri, Sang, Carrie, Schofield, Linley R., Ronimus, Ron S., Kelly, William J., Attwood, Graeme T., and Palevich, Nikola
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PECTINS ,CRYSTAL structure ,PECTINESTERASE ,METHOXY group ,POLYSACCHARIDES ,PROTEOLYSIS - Abstract
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
4 ). 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. [ABSTRACT FROM AUTHOR]- Published
- 2023
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11. Carbohydrate transporting membrane proteins of the rumen bacterium, Butyrivibrio proteoclasticus
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Bond, Jude J., Dunne, Jonathan C., Kwan, Fiona Y-S, Li, Dong, Zhang, Kunkun, Leahy, Sinead C., Kelly, William J., Attwood, Graeme T., and Jordan, T. William
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- 2012
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12. Strategies to reduce methane emissions from farmed ruminants grazing on pasture
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Buddle, Bryce M., Denis, Michel, Attwood, Graeme T., Altermann, Eric, Janssen, Peter H., Ronimus, Ron S., Pinares-Patiño, Cesar S., Muetzel, Stefan, and Neil Wedlock, D.
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- 2011
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13. Phenotypic characterization of transposon-inserted mutants of Clostridium proteoclasticum B316 T using extracellular metabolomics
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Villas-Bôas, Silas G., Moon, Christina D., Noel, Samantha, Hussein, Hassan, Kelly, William J., Cao, Mingshu, Lane, Geoffrey A., Cookson, Adrian L., and Attwood, Graeme T.
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- 2008
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14. Molecular subtyping and genetic analysis of the enterohemolysin gene (ehxA) from Shiga toxin-producing Escherichia coli and atypical enteropathogenic E. coli
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Cookson, Adrian L., Bennett, Jenny, Thomson-Carter, Fiona, and Attwood, Graeme T.
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Hemolysis and hemolysins -- Research ,Escherichia coli -- Research ,Escherichia coli -- Physiological aspects ,Biological sciences - Abstract
The distribution of enterohemolysin subtypes, a plasmid-encoded toxin, among Escherichia coli isolates from various human and animal sources is assessed. No apparent difference that can indicate specific roles for enterohemolysin in the separate hosts is found.
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- 2007
15. Soil Nitrogen Treatment Alters Microbiome Networks Across Farm Niches.
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Wang, XinYue, Reilly, Kerri, Heathcott, Rosemary, Biswas, Ambarish, Johnson, Linda J., Teasdale, Suliana, Grelet, Gwen-Aëlle, Podolyan, Anastasija, Gregorini, Pablo, Attwood, Graeme T., Palevich, Nikola, and Morales, Sergio E.
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NITROGEN in soils ,RYEGRASSES ,WHITE clover ,FARMS ,ECOSYSTEM services - Abstract
Agriculture is fundamental for food production, and microbiomes support agriculture through multiple essential ecosystem services. Despite the importance of individual (i.e., niche specific) agricultural microbiomes, microbiome interactions across niches are not well-understood. To observe the linkages between nearby agricultural microbiomes, multiple approaches (16S, 18S, and ITS) were used to inspect a broad coverage of niche microbiomes. Here we examined agricultural microbiome responses to 3 different nitrogen treatments (0, 150, and 300 kg/ha/yr) in soil and tracked linked responses in other neighbouring farm niches (rumen, faecal, white clover leaf, white clover root, rye grass leaf, and rye grass root). Nitrogen treatment had little impact on microbiome structure or composition across niches, but drastically reduced the microbiome network connectivity in soil. Networks of 16S microbiomes were the most sensitive to nitrogen treatment across amplicons, where ITS microbiome networks were the least responsive. Nitrogen enrichment in soil altered soil and the neighbouring microbiome networks, supporting our hypotheses that nitrogen treatment in soil altered microbiomes in soil and in nearby niches. This suggested that agricultural microbiomes across farm niches are ecologically interactive. Therefore, knock-on effects on neighbouring niches should be considered when management is applied to a single agricultural niche. [ABSTRACT FROM AUTHOR]
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- 2022
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16. Addressing global ruminant agricultural challenges through understanding the rumen microbiome: Past, present and future
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Huws, Sharon A., Creevey, Christopher J., Oyama, Linda B., Mizrahi, Itzhak, Denman, Stuart E., Popova, Milka, Muñoz-Tamayo, Rafael, Forano, Evelyne, Waters, Sinead M., Hess, Matthias, Tapio, Ilma, Smidt, Hauke, Krizsan, Sophie J., Yáñez-Ruiz, David R., Belanche, Alejandro, Guan, Leluo, Gruninger, Robert J., McAllister, Tim A., Newbold, C.J., Roehe, Rainer, Dewhurst, Richard J., Snelling, Tim J., Watson, Mick, Suen, Garret, Hart, Elizabeth H., Kingston-Smith, Alison H., Scollan, Nigel D., Do Prado, Rodolpho M., Pilau, Eduardo J., Mantovani, Hilario C., Attwood, Graeme T., Edwards, Joan E., McEwan, Neil R., Morrisson, Steven, Mayorga, Olga L., Elliott, Christopher, Morgavi, Diego P., European Commission, Ministerio de Economía y Competitividad (España), Biotechnology and Biological Sciences Research Council (UK), Institute for Global Food Security [Belfast], Queen's University [Belfast] (QUB), Department of Life Sciences and The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev (BGU), Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Queensland Bioscience Precinct, Unité Mixte de Recherches sur les Herbivores - UMR 1213 (UMRH), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Modélisation Systémique Appliquée aux Ruminants (MoSAR), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Animal and Grassland Research and Innovation Centre (AGRICE), College of Agricultural and Environmental Sciences, University of California [Davis] (UC Davis), University of California-University of California, Natural Resources Institute Finland (LUKE), Department of Agrotechnology and Food Sciences [Wageningen], Wageningen University and Research [Wageningen] (WUR), Department of Agricultural Research for Northern Sweden, Swedish University of Agricultural Sciences (SLU), Consejo Superior de Investigaciones Científicas [Spain] (CSIC), Department of Agricultural, Food and Nutritional Science, University of Alberta, Lethbridge Research Centre, Agriculture and Agri-Food Canada, Scotland's Rural College (SRUC), The Rowett Institute, University of Aberdeen, The Roslin Institute and the Royal (Dick) School of Veterinary Studies (R(D)SVS), University of Edinburgh, Departments of Botany and Bacteriology, University of Wisconsin-Madison, Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Laboratório de Biomoléculas e Espectrometria de Massas-Labiomass, Departamento de Química, Universidade Estadual de Maringá, Universidade Federal de Viçosa (UFC), AgResearch Limited, School of Pharmacy and Life Sciences, Robert Gordon University (RGU), Sustainable Livestock, Agri-Food and Bio-Sciences Institute, Agri-Food and Biosciences Institute, Colombian Agricultural Research Corporation, European Project: 640384 ,RuMicroPlas, European Project: 706899,EQUIANFUN, Institute for Global Food Security, Department of Life Sciences and the National Institute for Biotechnology in the Negev, VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne (UCA), Animal and Bioscience Research Department, Irish Agriculture and Food Development Authority, Natural Resources Institute Finland, Department of Agrotechnology and Food Sciences, Wageningen University and Research Centre [Wageningen] (WUR), Estacion Experimental del Zaidin, Spanish National Research Council (CSIC), Lethbridge Research and Development Centre, Agriculture and Agri-Food [Ottawa] (AAFC), Scotland's Rural College (SCUR), Department of Microbiology, Nippon Dental University, Grasslands Research Centre, Laboratory of Microbiology, Northern Regional Institution of Hungarian National Public Health and Medical Officer Service, Robert Gordon University, Sustainable Livestock, Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Microbiologie Environnement Digestif Santé (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Estación Experimental del Zaidín (EEZ), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), EU H2020 Marie Curie Fellowship 706899, European Project: 640384,H2020,ERC-2014-STG,RuMicroPlas(2016), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), University of California (UC)-University of California (UC), Agriculture and Agri-Food (AAFC), and Biotechnology and Biological Sciences Research Council (BBSRC)-Aberystwyth University
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Microbiology (medical) ,animal structures ,Rumen ,Environmental Science and Management ,alimentation animale ,[SDV]Life Sciences [q-bio] ,lcsh:QR1-502 ,microbiome ,Omics ,ruminant ,Review ,Microbiology ,lcsh:Microbiology ,modèle mathématique ,Microbiologie ,Genetics ,VLAG ,métagénomique ,metagenomics ,rumen ,WIMEK ,methane ,Host ,Human Genome ,host ,diet ,production ,omics ,Production ,[SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology ,Diet ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,Soil Sciences ,biomarker ,Zero Hunger ,animal feeding ,Microbiome ,biomarqueur ,Methane ,mathematical model - Abstract
The rumen is a complex ecosystem composed of anaerobic bacteria, protozoa, fungi, methanogenic archaea and phages. These microbes interact closely to breakdown plant material that cannot be digested by humans, whilst providing metabolic energy to the host and, in the case of archaea, producing methane. Consequently, ruminants produce meat and milk, which are rich in high-quality protein, vitamins and minerals, and therefore contribute to food security. As the world population is predicted to reach approximately 9.7 billion by 2050, an increase in ruminant production to satisfy global protein demand is necessary, despite limited land availability, and whilst ensuring environmental impact is minimized. Although challenging, these goals can be met, but depend on our understanding of the rumen microbiome. Attempts to manipulate the rumen microbiome to benefit global agricultural challenges have been ongoing for decades with limited success, mostly due to the lack of a detailed understanding of this microbiome and our limited ability to culture most of these microbes outside the rumen. The potential to manipulate the rumen microbiome and meet global livestock challenges through animal breeding and introduction of dietary interventions during early life have recently emerged as promising new technologies. Our inability to phenotype ruminants in a high-throughput manner has also hampered progress, although the recent increase in >omic> data may allow further development of mathematical models and rumen microbial gene biomarkers as proxies. Advances in computational tools, high-throughput sequencing technologies and cultivation-independent >omics> approaches continue to revolutionize our understanding of the rumen microbiome. This will ultimately provide the knowledge framework needed to solve current and future ruminant livestock challenges., SH, DM, MP, RM-T, SW, IT, HS, JE, SK, GA, and CC acknowledge the support of ERA-net gas co-fund for funding (Project name: RumenPredict). SH, HM and CC acknowledge support from BBSRC (BBL/L026716/1 and BBL/L026716/2) and a British Council Newton Institutional Links funding (Grant 172629373). IM acknowledges funding from the European Research Council under the European Union's Horizon 2020 research and innovation program (Grant 640384). JE acknowledges funding from an EU H2020 Marie Curie Fellowship (706899). CC, AK-S, and EH were supported by the Biotechnology and Biological Sciences Research Council (Grants BBS/OS/GC/000011B and BBS/E/W/0012843D). CN and OM acknowledge the support of the British Council Newton Institutional Links funding (Grant 216425215). SRUC receives financial support from the Scottish Government's Rural and Environment Science and Analytical Services Division (RESAS). RD and RR acknowledge financial support from the Biotechnology and Biological Sciences Research Council (BBSRC BB/N01720X/1). DY-R and AB acknowledge funding from MINECO, Spain (Grant AGL2017-86938-R). GS acknowledges funding from the U.S. Department of Agriculture National Institute of Food and Agriculture foundational (Grant 2015-67015-23246). EP acknowledges funding from CNPq (Grant 401590/2014-3). All authors are also members of the Global Research Alliance Rumen Microbial Genomics network.
- Published
- 2018
17. Methanobrevibacter ruminantium genome sequencing
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Attwood, Graeme T
- Published
- 2008
18. Future directions for methanogen genomics
- Author
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Attwood, Graeme T
- Published
- 2008
19. The use of PCR for the identification and characterisation of bacteriocin genes from bacterial strains isolated from rumen or caecal contents of cattle and sheep
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Cookson, Adrian L., Noel, Samantha J., Kelly, William J., and Attwood, Graeme T.
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- 2004
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20. Genetic diversity in ruminal isolates ofSelenomonas ruminantium
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Ning, Zhang, Attwood, Graeme T., Lockington, Robin A., and Brooker, John D.
- Published
- 1991
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21. Opportunities to improve fiber degradation in the rumen: microbiology, ecology, and genomics
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Krause, Denis O, Denman, Stuart E, Mackie, Roderick I, Morrison, Mark, Rae, Ann L, Attwood, Graeme T, and McSweeney, Christopher S
- Published
- 2003
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22. Retraction: An endo-β-1,4-glucanase gene (celA) from the rumen anaerobe Ruminococcus albus 8: cloning, sequencing, and transcriptional analysis
- Author
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Attwood, Graeme T, Herrera, Felicitas, Weissenstein, Lee A, and White, Bryan A
- Published
- 1998
23. Complete Genome Sequence of the Polysaccharide-Degrading Rumen Bacterium Pseudobutyrivibrio xylanivorans MA3014 Reveals an Incomplete Glycolytic Pathway.
- Author
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Palevich, Nikola, Maclean, Paul H, Kelly, William J, Leahy, Sinead C, Rakonjac, Jasna, and Attwood, Graeme T
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PECTINS ,NUCLEOTIDE sequencing ,GLYCOSIDASES ,TRANSFERASES ,OLIGOSACCHARIDES ,CARBOHYDRATES - Abstract
Bacterial species belonging to the genus Pseudobutyrivibrio are important members of the rumen microbiome contributing to the degradation of complex plant polysaccharides. Pseudobutyrivibrio xylanivorans MA3014 was selected for genome sequencing to examine its ability to breakdown and utilize plant polysaccharides. The complete genome sequence of MA3014 is 3.58 Mb, consists of three replicons (a chromosome, chromid, and plasmid), has an overall G + C content of 39.6%, and encodes 3,265 putative protein-coding genes (CDS). Comparative pan-genomic analysis of all cultivated and currently available P. xylanivorans genomes has revealed a strong correlation of orthologous genes within this rumen bacterial species. MA3014 is metabolically versatile and capable of growing on a range of simple mono- or oligosaccharides derived from complex plant polysaccharides such as pectins, mannans, starch, and hemicelluloses, with lactate, butyrate, and formate as the principal fermentation end products. The genes encoding these metabolic pathways have been identified and MA3014 is predicted to encode an extensive range of Carbohydrate-Active enZYmes with 78 glycoside hydrolases, 13 carbohydrate esterases, and 54 glycosyl transferases, suggesting an important role in solubilization of plant matter in the rumen. [ABSTRACT FROM AUTHOR]
- Published
- 2020
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24. Relationship between virulence gene profiles of atypical enteropathogenic Escherichia coli and shiga toxin-producing E. coli isolates from cattle and sheep in New Zealand
- Author
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Cookson, Adrian L., Mingshu Cao, Bennett, Jenny, Nicol, Carolyn, Thomson-Carter, Fiona, and Attwood, Graeme T.
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Escherichia coli -- Physiological aspects ,Shigella -- Physiological aspects ,Virulence (Microbiology) -- Research ,Biological sciences - Abstract
Virulence gene profiles of atypical enteropathogenic Escherichia coli (aEPEC) and Shiga toxin-producing E. coli (STEC) from cattle, sheep, and humans were examined to determine the relationship between pathotypes. The identified shared virulence factors such as intimin, EHEC hemolysin, serine protease, and a type II secretion system indicated a dynamic evolutionary relationship between aEPEC and STEC.
- Published
- 2010
25. Erratum: Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range
- Author
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Henderson, Gemma, Cox, Faith, Ganesh, Siva, Jonker, Arjan, Young, Wayne, Abecia, Leticia, Angarita, Erika, Aravena, Paula, Nora Arenas, Graciela, Ariza, Claudia, Attwood, Graeme T., Mauricio Avila, Jose, Avila-stagno, Jorge, Bannink, André, Barahona, Rolando, Batistotti, Mariano, Bertelsen, Mads F., Brown-Kav, Aya, Carvajal, Andres M., Cersosimo, Laura, Vieira Chaves, Alexandre, Church, John, Clipson, Nicholas, Cobos-peralta, Mario A., Cookson, Adrian L., Cravero, Silvio, Cristobal Carballo, Omar, Crosley, Katie, Cruz, Gustavo, Cerón Cucchi, María, de la Barra, Rodrigo, de Menezes, Alexandre B., Detmann, Edenio, Dieho, Kasper, Dijkstra, Jan, Dos Reis, William L.S., Dugan, Mike E.R., Hadi Ebrahimi, Seyed, Eythórsdóttir, Emma, Nde Fon, Fabian, Fraga, Martín, Franco, Francisco, Friedeman, Chris, Fukuma, Naoki, Gagić, Dragana, Gangnat, Isabelle, Javier Grilli, Diego, Guan, Le Luo, Heidarian Miri, Vahideh, Hernandez-Sanabria, Emma, Gomez, Alma Ximena Ibarra, Isah, Olubukola A., Ishaq, Suzanne, Jami, Elie, Jelincic, Juan, Kantanen, Juha, Kelly, William J., Kim, Seon-Ho, Klieve, Athol, Kobayashi, Yasuo, Koike, Satoshi, Kopecny, Jan, Nygaard Kristensen, Torsten, Julie Krizsan, Sophie, Lachance, Hannah, Lachman, Medora, Lamberson, William R., Lambie, Suzanne, Lassen, Jan, Leahy, Sinead C., Lee, Sang-Suk, Leiber, Florian, Lewis, Eva, Lin, Bo, Lira, Raúl, Lund, Peter, Macipe, Edgar, Mamuad, Lovelia L., Cuquetto Mantovani, Hilário, Marcoppido, Gisela Ariana, Márquez, Cristian, Martin, Cécile, Martinez, Gonzalo, Eugenia Martinez, Maria, Lucía Mayorga, Olga, McAllister, Tim A., McSweeney, Chris, Mestre, Lorena, Minnee, Elena, Mitsumori, Makoto, Mizrahi, Itzhak, Molina, Isabel, Muenger, Andreas, Muñoz, Camila, Murovec, Bostjan, Newbold, John, Nsereko, Victor, O’donovan, Michael, Okunade, Sunday, O’neill, Brendan, Ospina, Sonia, Ouwerkerk, Diane, Parra, Diana, Pereira, Luiz Gustavo Ribeiro, Pinares-patiño, Cesar, Pope, Phil B., Poulsen, Morten, Rodehutscord, Markus, Rodriguez, Tatiana, Saito, Kunihiko, Sales, Francisco, Sauer, Catherine, Shingfield, Kevin, Shoji, Noriaki, Simunek, Jiri, Stojanović-Radić, Zorica, Stres, Blaz, Sun, Xuezhao, Swartz, Jeffery, Liang Tan, Zhi, Tapio, Ilma, Taxis, Tasia M., Tomkins, Nigel, Ungerfeld, Emilio, Valizadeh, Reza, van Adrichem, Peter, van Hamme, Jonathan, van Hoven, Woulter, Waghorn, Garry, Wallace, John R., Wang, Min, Waters, Sinéad M., Keogh, Kate, Witzig, Maren, Wright, Andre-Denis G., Yamano, Hidehisa, Yan, Tianhai, Yáñez-ruiz, David R., Yeoman, Carl J., Zambrano, Ricardo, Zeitz, Johanna, Zhou, Mi, Wei Zhou, Hua, Xia Zou, Cai, Zunino, Pablo, and Janssen, Peter H.
- Subjects
Multidisciplinary ,Animal Nutrition ,WIAS ,Life Science ,Laboratorium voor Plantenfysiologie ,Diervoeding ,Laboratory of Plant Physiology - Abstract
Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific.
- Published
- 2016
26. Molecular subtyping and distribution of the serine protease from shiga toxin-producing Escherichia coli among atypical enteropathogenic E. coli strains
- Author
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Cookson, Adrian L., Bennett, Jenny, Nicol, Carolyn, Thomson-Carter, Fiona, and Attwood, Graeme T.
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Bacterial toxins -- Research ,Nucleotide sequence -- Analysis ,Escherichia coli -- Physiological aspects ,Escherichia coli -- Genetic aspects ,Proteases -- Chemical properties ,Serine -- Chemical properties ,Biological sciences - Abstract
Atypical enteropathogenic Escherichia coli (aEPEC) and Shiga toxin-producing E. coli (STEC) were characterized to determine the prevalence and sequence of espP which encodes a serine protease. The shared espP sequence types observed between the two E. coli pathotypes provide better insight into the evolution of aEPEC and STEC.
- Published
- 2009
27. A REFERENCE SET OF RUMEN MICROBIAL GENOMES: THE HUNGATE1000 PROJECT
- Author
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Kelly, William J, Attwood, Graeme T, Janssen, Peter H, Cookson, Adrian L, Henderson, Gemma, Lambie, Suzanne C, Rechelle Perry, Teh, Kenneth, Palevich, Nikola, Noel, Samantha, Goodwin, Lynne A, Shapiro, Nicole, Woyke, Tanja, Creevey, Christopher J, and Sinead C Leahy
- Published
- 2014
- Full Text
- View/download PDF
28. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection.
- Author
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Seshadri, Rekha, Leahy, Sinead C, Attwood, Graeme T, Teh, Koon Hoong, Lambie, Suzanne C, Cookson, Adrian L, Eloe-Fadrosh, Emiley A, Pavlopoulos, Georgios A, Hadjithomas, Michalis, Varghese, Neha J, Paez-Espino, David, Perry, Rechelle, Henderson, Gemma, Creevey, Christopher J, Terrapon, Nicolas, Lapebie, Pascal, Drula, Elodie, Lombard, Vincent, Rubin, Edward, and Kyrpides, Nikos C
- Abstract
Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B
12 , ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents ∼75% of the genus-level bacterial and archaeal taxa present in the rumen. [ABSTRACT FROM AUTHOR]- Published
- 2018
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- View/download PDF
29. The complete genome sequence of the rumen bacterium Butyrivibrio hungatei MB2003.
- Author
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Palevich, Nikola, Kelly, William J., Leahy, Sinead C., Altermann, Eric, Rakonjac, Jasna, and Attwood, Graeme T.
- Subjects
RUMEN (Ruminants) ,BUTYRIVIBRIO ,CHROMOSOMES ,XYLANS ,MONOSACCHARIDES - Abstract
Butyrivibrio hungatei MB2003 was isolated from the plant-adherent fraction of rumen contents from a pasturegrazed New Zealand dairy cow, and was selected for genome sequencing in order to examine its ability to degrade plant polysaccharides. The genome of MB2003 is 3.39 Mb and consists of four replicons; a chromosome, a secondary chromosome or chromid, a megaplasmid and a small plasmid. The genome has an average G + C content of 39.7%, and encodes 2983 putative protein-coding genes. MB2003 is able to use a variety of monosaccharide substrates for growth, with acetate, butyrate and formate as the principal fermentation endproducts, and the genes encoding these metabolic pathways have been identified. MB2003 is predicted to encode an extensive repertoire of CAZymes with 78 GHs, 7 CEs, 1 PL and 78 GTs. MB2003 is unable to grow on xylan or pectin, and its role in the rumen appears to be as a utilizer of monosaccharides, disaccharides and oligosaccharides made available by the degradative activities of other bacterial species. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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30. Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep.
- Author
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Kamke, Janine, Soni, Priya, Yang Li, Ganesh, Siva, Kelly, William J., Leahy, Sinead C., Weibing Shi, Froula, Jeff, Rubin, Edward M., and Attwood, Graeme T.
- Subjects
RUMEN microbiology ,METHANE ,RUMINANTS ,GENETIC transcription in bacteria ,SHEEP - Abstract
Background: Ruminants are important contributors to global methane emissions via microbial fermentation in their reticulo-rumens. This study is part of a larger program, characterising the rumen microbiomes of sheep which vary naturally in methane yield (g CH
4 /kg DM/day) and aims to define differences in microbial communities, and in gene and transcript abundances that can explain the animal methane phenotype. Methods: Rumen microbiome metagenomic and metatranscriptomic data were analysed by Gene Set Enrichment, sparse partial least squares regression and the Wilcoxon Rank Sum test to estimate correlations between specific KEGG bacterial pathways/genes and high methane yield in sheep. KEGG genes enriched in high methane yield sheep were reassembled from raw reads and existing contigs and analysed by MEGAN to predict their phylogenetic origin. Protein coding sequences from Succinivibrio dextrinosolvens strains were analysed using Effective DB to predict bacterial type III secreted proteins. The effect of S. dextrinosolvens strain H5 growth on methane formation by rumen methanogens was explored using co-cultures. Results: Detailed analysis of the rumen microbiomes of high methane yield sheep shows that gene and transcript abundances of bacterial type III secretion system genes are positively correlated with methane yield in sheep. Most of the bacterial type III secretion system genes could not be assigned to a particular bacterial group, but several genes were affiliated with the genus Succinivibrio, and searches of bacterial genome sequences found that strains of S. dextrinosolvens were part of a small group of rumen bacteria that encode this type of secretion system. In co-culture experiments, S. dextrinosolvens strain H5 showed a growth-enhancing effect on a methanogen belonging to the order Methanomassiliicoccales, and inhibition of a representative of the Methanobrevibacter gottschalkii clade. Conclusions: This is the first report of bacterial type III secretion system genes being associated with high methane emissions in ruminants, and identifies these secretions systems as potential new targets for methane mitigation research. The effects of S. dextrinosolvens on the growth of rumen methanogens in co-cultures indicate that bacteria-methanogen interactions are important modulators of methane production in ruminant animals. [ABSTRACT FROM AUTHOR]- Published
- 2017
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31. Seasonal changes in the digesta-adherent rumen bacterial communities of dairy cattle grazing pasture.
- Author
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Noel, Samantha J., Attwood, Graeme T., Rakonjac, Jasna, Moon, Christina D., Waghorn, Garry C., and Janssen, Peter H.
- Subjects
- *
DAIRY cattle behavior , *RUMEN microbiology , *GRAZING , *CLIMATE change , *RIBOSOMAL RNA - Abstract
The complex microbiota that resides within the rumen is responsible for the break-down of plant fibre. The bacteria that attach to ingested plant matter within the rumen are thought to be responsible for initial fibre degradation. Most studies examining the ecology of this important microbiome only offer a ‘snapshot’ in time. We monitored the diversity of rumen bacteria in four New Zealand dairy cows, grazing a rye-grass and clover pasture over five consecutive seasons, using high throughput pyrosequencing of bacterial 16S rRNA genes. We chose to focus on the digesta-adherent bacterial community to learn more about the stability of this community over time. 16S rRNA gene sequencing showed a high level of bacterial diversity, totalling 1539 operational taxonomic units (OTUs, grouped at 96% sequence similarity) across all samples, and ranging from 653 to 926 OTUs per individual sample. The nutritive composition of the pasture changed with the seasons as did the production phase of the animals. Sequence analysis showed that, overall, the bacterial communities were broadly similar between the individual animals. The adherent bacterial community was strongly dominated by members of Firmicutes (82.1%), followed by Bacteroidetes (11.8%). This community differed between the seasons, returning to close to that observed in the same season one year later. These seasonal differences were only small, but were statistically significant (p < 0.001), and were probably due to the seasonal differences in the diet. These results demonstrate a general invariability of the ruminal bacterial community structure in these grazing dairy cattle. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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32. Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpeaenriched microbiome characterised by lactic acid formation and utilisation.
- Author
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Kamke, Janine, Kittelmann, Sandra, Soni, Priya, Yang Li, Tavendale, Michael, Ganesh, Siva, Janssen, Peter H., Weibing Shi, Froula, Jeff, Rubin, Edward M., and Attwood, Graeme T.
- Published
- 2016
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33. The complete genome sequence of the methanogenic archaeon ISO4-H5 provides insights into the methylotrophic lifestyle of a ruminal representative of the Methanomassiliicoccales.
- Author
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Yang Li, Leahy, Sinead C., Jeyanathan, Jeyamalar, Henderson, Gemma, Cox, Faith, Altermann, Eric, Kelly, William J., Lambie, Suzanne C., Janssen, Peter H., Rakonjac, Jasna, and Attwood, Graeme T.
- Subjects
NUCLEOTIDE sequencing ,METHANOGENS ,METHYLOTROPHIC microorganisms ,PYRROLYSINE ,COENZYME M ,RUMINANTS - Abstract
Methane emissions from agriculture represent around 9% of global anthropogenic greenhouse emissions. The single largest source of this methane is animal enteric fermentation, predominantly from ruminant livestock where it is produced mainly in their fermentative forestomach (or reticulo-rumen) by a group of archaea known as methanogens. In order to reduce methane emissions from ruminants, it is necessary to understand the role of methanogenic archaea in the rumen, and to identify their distinguishing characteristics that can be used to develop methane mitigation technologies. To gain insights into the role of methylotrophic methanogens in the rumen environment, the genome of a methanogenic archaeon has been sequenced. This isolate, strain ISO4-H5, was isolated from the ovine rumen and belongs to the order Methanomassiliicoccales. Genomic analysis suggests ISO4-H5 is an obligate hydrogen-dependent methylotrophic methanogen, able to use methanol and methylamines as substrates for methanogenesis. Like other organisms within this order, ISO4-H5 does not possess genes required for the first six steps of hydrogenotrophic methanogenesis. Comparison between the genomes of different members of the order Methanomassiliicoccales revealed strong conservation in energy metabolism, particularly in genes of the methylotrophic methanogenesis pathway, as well as in the biosynthesis and use of pyrrolysine. Unlike members of Methanomassiliicoccales from human sources, ISO4-H5 does not contain the genes required for production of coenzyme M, and so likely requires external coenzyme M to survive. [ABSTRACT FROM AUTHOR]
- Published
- 2016
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34. An adhesin from hydrogen-utilizing rumen methanogen M ethanobrevibacter ruminantium M1 binds a broad range of hydrogen-producing microorganisms.
- Author
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Ng, Filomena, Kittelmann, Sandra, Patchett, Mark L., Attwood, Graeme T., Janssen, Peter H., Rakonjac, Jasna, and Gagic, Dragana
- Subjects
METHANOGENS ,BREVIBACTERIUM ,HYDROGEN bacteria ,BACTERIAL mutation ,HYDROGEN transfer reactions - Abstract
Symbiotic associations are ubiquitous in the microbial world and have a major role in shaping the evolution of both partners. One of the most interesting mutualistic relationships exists between protozoa and methanogenic archaea in the fermentative forestomach (rumen) of ruminant animals. Methanogens reside within and on the surface of protozoa as symbionts, and interspecies hydrogen transfer is speculated to be the main driver for physical associations observed between the two groups. In silico analyses of several rumen methanogen genomes have previously shown that up to 5% of genes encode adhesin-like proteins, which may be central to rumen interspecies attachment. We hypothesized that adhesin-like proteins on methanogen cell surfaces facilitate attachment to protozoal hosts. Using phage display technology, we have identified a protein ( Mru_1499) from M ethanobrevibacter ruminantium M1 as an adhesin that binds to a broad range of rumen protozoa (including the genera E pidinium and E ntodinium). This unique adhesin also binds the cell surface of the bacterium B utyrivibrio proteoclasticus, suggesting a broad adhesion spectrum for this protein. [ABSTRACT FROM AUTHOR]
- Published
- 2016
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- View/download PDF
35. The complete genome sequence of the rumen methanogen Methanobrevibacter millerae SM9.
- Author
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Kelly, William J., Pacheco, Diana M., Dong Li, Attwood, Graeme T., Altermann, Eric, and Leahy, Sinead C.
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NUCLEOTIDE sequencing ,METHANOGENS ,RUMINANTS ,NONRIBOSOMAL peptide synthetases ,LACTOBACILLUS plantarum ,COENZYMES - Abstract
Methanobrevibacter millerae SM9 was isolated from the rumen of a sheep maintained on a fresh forage diet, and its genome has been sequenced to provide information on the phylogenetic diversity of rumen methanogens with a view to developing technologies for methane mitigation. It is the first rumen isolate from the Methanobrevibacter gottschalkii clade to have its genome sequence completed. The 2.54 Mb SM9 chromosome has an average G + C content of 31.8%, encodes 2269 protein-coding genes, and harbors a single prophage. The overall gene content is comparable to that of Methanobrevibacter ruminantium M1 and the type strain of M. millerae (ZA-10
T ) suggesting that the basic metabolism of these two hydrogenotrophic rumen methanogen species is similar. However, M. millerae has a larger complement of genes involved in methanogenesis including genes for methyl coenzyme M reductase II (mrtAGDB) which are not found in M1. Unusual features of the M. millerae genomes include the presence of a tannase gene which shows high sequence similarity with the tannase from Lactobacillus plantarum, and large non-ribosomal peptide synthase genes. The M. millerae sequences indicate that methane mitigation strategies based on the M. ruminantium M1 genome sequence are also likely to be applicable to members of the M. gottschalkii clade. [ABSTRACT FROM AUTHOR]- Published
- 2016
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36. The Cytosolic Oligosaccharide-Degrading Proteome of Butyrivibrio Proteoclasticus.
- Author
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Dunne, Jonathan C., Kelly, William J., Leahy, Sinead C., Li, Dong, Bond, Judy J., Peng, Lifeng, Attwood, Graeme T., and Jordan, T. William
- Published
- 2015
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37. The complete genome sequence of the rumen methanogen Methanosarcina barkeri CM1.
- Author
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Lambie, Suzanne C., Kelly, William J., Leahy, Sinead C., Dong Li, Reilly, Kerri, McAllister, Tim A., Valle, Edith R., Attwood, Graeme T., and Altermann, Eric
- Subjects
RUMEN microbiology ,NUCLEOTIDE sequencing ,METHANOSARCINA barkeri ,ARCHAEBACTERIA metabolism ,METHANE synthesis ,GENETIC code - Abstract
Methanosarcina species are the most metabolically versatile of the methanogenic Archaea and can obtain energy for growth by producing methane via the hydrogenotrophic, acetoclastic or methylotrophic pathways. Methanosarcina barkeri CM1 was isolated from the rumen of a New Zealand Friesian cow grazing a ryegrass/clover pasture, and its genome has been sequenced to provide information on the phylogenetic diversity of rumen methanogens with a view to developing technologies for methane mitigation. The 4.5 Mb chromosome has an average G + C content of 39%, and encodes 3523 protein-coding genes, but has no plasmid or prophage sequences. The gene content is very similar to that of M. barkeri Fusaro which was isolated from freshwater sediment. CM1 has a full complement of genes for all three methanogenesis pathways, but its genome shows many differences from those of other sequenced rumen methanogens. Consequently strategies to mitigate ruminant methane need to include information on the different methanogens that occur in the rumen. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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38. Improving the genetic representation of rare taxa within complex microbial communities using DNA normalization methods.
- Author
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Gagic, Dragana, Maclean, Paul H., Li, Dong, Attwood, Graeme T., and Moon, Christina D.
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MICROORGANISMS ,BIODIVERSITY ,NUCLEOTIDE sequencing ,BIOSPHERE ,METAGENOMICS ,HYDROXYAPATITE ,CHROMATOGRAPHIC analysis - Abstract
Complex microbial communities typically contain a large number of low abundance species, which collectively, comprise a considerable proportion of the community. This 'rare biosphere' has been speculated to contain keystone species and act as a repository of genomic diversity to facilitate community adaptation. Many environmental microbes are currently resistant to cultivation, and can only be accessed via culture-independent approaches. To enhance our understanding of the role of the rare biosphere, we aimed to improve their metagenomic representation using DNA normalization methods, and assess normalization success via shotgun DNA sequencing. A synthetic metagenome was constructed from the genomic DNA of five bacterial species, pooled in a defined ratio spanning three orders of magnitude. The synthetic metagenome was fractionated and thermally renatured, allowing the most abundant sequences to hybridize. Double-stranded DNA was removed either by hydroxyapatite chromatography, or by a duplex-specific nuclease ( DSN). The chromatographic method failed to enrich for the genomes present in low starting abundance, whereas the DSN method resulted in all genomes reaching near equimolar abundance. The representation of the rarest member was increased by approximately 450-fold. De novo assembly of the normalized metagenome enabled up to 18.0% of genes from the rarest organism to be assembled, in contrast to the un-normalized sample, where genes were not able to be assembled at the same sequencing depth. This study has demonstrated that the application of normalization methods to metagenomic samples is a powerful tool to enrich for sequences from rare taxa, which will shed further light on their ecological niches. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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39. Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community.
- Author
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Ciric, Milica, Moon, Christina D., Leahy, Sinead C., Creevey, Christopher J., Altermann, Eric, Attwood, Graeme T., Rakonjac, Jasna, and Gagic, Dragana
- Subjects
BACTERIOPHAGE genetics ,VIRAL genetics ,GENOMICS ,BACTERIAL genetics ,RUMEN microbiology - Abstract
Background In silico, secretome proteins can be predicted from completely sequenced genomes using various available algorithms that identify membrane-targeting sequences. For metasecretome (collection of surface, secreted and transmembrane proteins from environmental microbial communities) this approach is impractical, considering that the metasecretome open reading frames (ORFs) comprise only 10% to 30% of total metagenome, and are poorly represented in the dataset due to overall low coverage of metagenomic gene pool, even in large-scale projects. Results By combining secretome-selective phage display and next-generation sequencing, we focused the sequence analysis of complex rumen microbial community on the metasecretome component of the metagenome. This approach achieved high enrichment (29 fold) of secreted fibrolytic enzymes from the plant-adherent microbial community of the bovine rumen. In particular, we identified hundreds of heretofore rare modules belonging to cellulosomes, cellsurface complexes specialised for recognition and degradation of the plant fibre. Conclusions As a method, metasecretome phage display combined with next-generation sequencing has a power to sample the diversity of low-abundance surface and secreted proteins that would otherwise require exceptionally large metagenomic sequencing projects. As a resource, metasecretome display library backed by the dataset obtained by next-generation sequencing is ready for i) affinity selection by standard phage display methodology and ii) easy purification of displayed proteins as part of the virion for individual functional analysis. [ABSTRACT FROM AUTHOR]
- Published
- 2014
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40. Structure and function of an acetyl xylan esterase (Est2A) from the rumen bacterium Butyrivibrio proteoclasticus.
- Author
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Till, Marisa, Goldstone, David C., Attwood, Graeme T., Moon, Christina D., Kelly, Willam J., and Arcus, Vickery L.
- Abstract
Butyrivibrio proteoclasticus is a significant component of the microbial population of the rumen of dairy cattle. It is a xylan-degrading organism whose genome encodes a large number of open reading frames annotated as fiber-degrading enzymes. We have determined the three-dimensional structure of Est2A, an acetyl xylan esterase from B. proteoclasticus, at 2.1 Å resolution, along with the structure of an inactive mutant (H351A) at 2.0 Å resolution. The structure reveals two domains-a C-terminal SGNH domain and an N-terminal jelly-roll domain typical of CE2 family structures. The structures are accompanied by experimentally determined enzymatic parameters against two model substrates, para-nitrophenyl acetate and para-nitrophenyl butyrate. The suite of fiber-degrading enzymes produced by B. proteoclasticus provides a rich source of new enzymes of potential use in industrial settings. Proteins 2013. © 2012 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]
- Published
- 2013
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41. Transposition of Tn 916 in the four replicons of the Butyrivibrio proteoclasticus B316.
- Author
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Cookson, Adrian L., Noel, Samantha, Hussein, Hassan, Perry, Rechelle, Sang, Carrie, Moon, Christina D., Leahy, Sinead C., Altermann, Eric, Kelly, William J., and Attwood, Graeme T.
- Subjects
BACTERIOLOGY ,TRANSPOSONS ,CHROMOSOMAL translocation ,MOBILE genetic elements ,RADIOGENETICS - Abstract
The rumen bacterium Butyrivibrio proteoclasticus B316 has a 4.4-Mb genome composed of four replicons (approximately 3.55 Mb, 361, 302 and 186 kb). Mutagenesis of B316 was performed with the broad host-range conjugative transposon Tn 916 to screen for functionally important characteristics. The insertion sites of 123 mutants containing a single copy of Tn 916 were identified and corresponded to 53 different insertion points, of which 18 (34.0%), representing 39 mutants (31.7%), were in ORFs and 12 were where transposition occurred in both directions (top and bottom DNA strand). Up to eight mutants from several independent conjugation experiments were found to have the same integration site. Although transposition occurred in all four replicons, the number of specific insertion sites, transposition frequency and the average intertransposon distance between insertions varied between the four replicons. In silico analysis of the 53 insertion sites was used to model a target consensus sequence for Tn 916 integration into B316. A search of the B316 genome using the modelled target consensus sequence (up to two mismatches) identified 39 theoretical Tn 916 insertion sites (19 coding, 20 noncoding), of which nine corresponded to Tn 916 insertions identified in B316 mutants during our conjugation experiments. [ABSTRACT FROM AUTHOR]
- Published
- 2011
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42. The Glycobiome of the Rumen Bacterium Butyrivibrio proteoclasticus B316T Highlights Adaptation to a Polysaccharide-Rich Environment.
- Author
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Kelly, William J., Leahy, Sinead C., Altermann, Eric, Yeoman, Carl J., Dunne, Jonathan C., Kong, Zhanhao, Pacheco, Diana M., Li, Dong, Noel, Samantha J., Moon, Christina D., Cookson, Adrian L., and Attwood, Graeme T.
- Subjects
RUMEN (Ruminants) ,BACTERIA ,PLANT enzymes ,POLYSACCHARIDES ,RUMINANTS ,PECTINS ,STARCH ,SUBTILISINS ,PROTEASE inhibitors ,PLANT proteins - Abstract
Determining the role of rumen microbes and their enzymes in plant polysaccharide breakdown is fundamental to understanding digestion and maximising productivity in ruminant animals. Butyrivibrio proteoclasticus B316T is a Grampositive, butyrate-forming rumen bacterium with a key role in plant polysaccharide degradation. The 4.4Mb genome consists of 4 replicons; a chromosome, a chromid and two megaplasmids. The chromid is the smallest reported for all bacteria, and the first identified from the phylum Firmicutes. B316 devotes a large proportion of its genome to the breakdown and reassembly of complex polysaccharides and has a highly developed glycobiome when compared to other sequenced bacteria. The secretion of a range of polysaccharide-degrading enzymes which initiate the breakdown of pectin, starch and xylan, a subtilisin family protease active against plant proteins, and diverse intracellular enzymes to break down oligosaccharides constitute the degradative capability of this organism. A prominent feature of the genome is the presence of multiple gene clusters predicted to be involved in polysaccharide biosynthesis. Metabolic reconstruction reveals the absence of an identifiable gene for enolase, a conserved enzyme of the glycolytic pathway. To our knowledge this is the first report of an organism lacking an enolase. Our analysis of the B316 genome shows how one organism can contribute to the multi-organism complex that rapidly breaks down plant material in the rumen. It can be concluded that B316, and similar organisms with broad polysaccharide-degrading capability, are well suited to being early colonizers and degraders of plant polysaccharides in the rumen environment. [ABSTRACT FROM AUTHOR]
- Published
- 2010
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43. Structural and functional characterization of a promiscuous feruloyl esterase (Est1E) from the rumen bacterium Butyrivibrio proteoclasticus.
- Author
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Goldstone, David C., Villas-Bôas, Silas G., Till, Marisa, Kelly, William J., Attwood, Graeme T., and Arcus, Vickery L.
- Abstract
The release of polysaccharide from the plant cell wall is a key process to release the stored energy from plant biomass. Within the ruminant digestive system, a host of commensal microorganisms speed the breakdown of plant cell matter releasing fermentable sugars. The presence of phenolic compounds, most notably ferulic acid (FA), esterified within the cell wall is thought to pose a significant impediment to the degradation of the plant cell wall. The structure of a FA esterase from the ruminant bacterium Butyrivibrio proteoclasticus has been determined in two different space groups, in both the apo-form, and the ligand bound form with FA located in the active site. The structure reveals a new lid domain that has no structural homologues in the PDB. The flexibility of the lid domain is evident by the presence of three different conformations adopted by different molecules in the crystals. In the FA-bound structures, these conformations show sequential binding and closing of the lid domain over the substrate. Enzymatic activity assays demonstrate a broad activity against plant-derived hemicellulose, releasing at least four aromatic compounds including FA, coumaric acid, coumarin-3-carboxylic acid, and cinnamic acid. The rumen is a complex ecosystem that efficiently degrades plant biomass and the genome of B. proteoclasticus contains greater than 130 enzymes, which are potentially involved in this process of which Est1E is the first to be well characterized. Proteins 2010. © 2009 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]
- Published
- 2010
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44. The Genome Sequence of the Rumen Methanogen Methanobrevibacter ruminantium Reveals New Possibilities for Controlling Ruminant Methane Emissions.
- Author
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Leahy, Sinead C., Kelly, William J., Altermann, Eric, Ronimus, Ron S., Yeoman, Carl J., Pacheco, Diana M., Dong Li, Zhanhao Kong, McTavish, Sharla, Sang, Carrie, Lambie, Suzanne C., Janssen, Peter H., Dey, Debjit, and Attwood, Graeme T.
- Subjects
GENOMES ,RUMEN (Ruminants) ,METHANE ,CARBON dioxide ,GREENHOUSE gases ,AGRICULTURE ,LIVESTOCK ,ALCOHOLS (Chemical class) ,GENES - Abstract
Background: Methane (CH
4 ) is a potent greenhouse gas (GHG), having a global warming potential 21 times that of carbon dioxide (CO2 ). Methane emissions from agriculture represent around 40% of the emissions produced by human-related activities, the single largest source being enteric fermentation, mainly in ruminant livestock. Technologies to reduce these emissions are lacking. Ruminant methane is formed by the action of methanogenic archaea typified by Methanobrevibacter ruminantium, which is present in ruminants fed a wide variety of diets worldwide. To gain more insight into the lifestyle of a rumen methanogen, and to identify genes and proteins that can be targeted to reduce methane production, we have sequenced the 2.93 Mb genome of M. ruminantium M1, the first rumen methanogen genome to be completed. Methodology/Principal Findings: The M1 genome was sequenced, annotated and subjected to comparative genomic and metabolic pathway analyses. Conserved and methanogen-specific gene sets suitable as targets for vaccine development or chemogenomic-based inhibition of rumen methanogens were identified. The feasibility of using a synthetic peptidedirected vaccinology approach to target epitopes of methanogen surface proteins was demonstrated. A prophage genome was described and its lytic enzyme, endoisopeptidase PeiR, was shown to lyse M1 cells in pure culture. A predicted stimulation of M1 growth by alcohols was demonstrated and microarray analyses indicated up-regulation of methanogenesis genes during co-culture with a hydrogen (H2 ) producing rumen bacterium. We also report the discovery of non-ribosomal peptide synthetases in M. ruminantium M1, the first reported in archaeal species. Conclusions/Significance: The M1 genome sequence provides new insights into the lifestyle and cellular processes of this important rumen methanogen. It also defines vaccine and chemogenomic targets for broad inhibition of rumen methanogens and represents a significant contribution to worldwide efforts to mitigate ruminant methane emissions and reduce production of anthropogenic greenhouse gases. [ABSTRACT FROM AUTHOR]- Published
- 2010
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- View/download PDF
45. Intimin subtyping of Escherichia coli: concomitant carriage of multiple intimin subtypes from forage-fed cattle and sheep.
- Author
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Cookson, Adrian L., Bennett, Jenny, Thomson-Carter, Fiona, and Attwood, Graeme T.
- Subjects
ESCHERICHIA coli ,CATTLE ,SHEEP ,POLYMERASE chain reaction ,GENETIC polymorphisms ,FORAGE - Abstract
The outer membrane protein, intimin ( eae), which mediates bacterial attachment to epithelial cells, is associated with enteropathogenic Escherichia coli and some Shiga toxin-producing E. coli. The eae subtype of E. coli strains isolated from healthy cattle and sheep was identified using a rapid PCR-restriction fragment length polymorphism (RFLP) method to produce profiles that were compared with those generated in silico. The 139 eae-positive E. coli strains were separated into 11 different PCR-RFLP profiles. The most common eae PCR-RFLP type was β (23.7%), followed by ζ (20.1%), θ (16.5%), ι (12.2%), κ (8.6%), ℇ (7.2%), γ (2.9%), ν and β2 (2.2%) and ι2 (1.4%). Four isolates did not yield a PCR-RFLP amplification product but complete sequencing of the eae gene matched subtype ρ. Two different eae variants were isolated from the same swab from 18 different animals and subtype ι was the most ‘promiscuous’, being isolated with four other eae subtypes from seven separate animals. None of the eae-positive STEC were subtype γ, which is associated with STEC serogroup O157. This method allowed the rapid identification of eae subtypes and indicates that forage-fed animals possessed a wide diversity of bacterial eae subtypes with a low frequency of eae subtype γ. [ABSTRACT FROM AUTHOR]
- Published
- 2007
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46. Ammonia-hyperproducing bacteria from New Zealand ruminants.
- Author
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Attwood, Graeme T., Klieve, Athol V., Ouwerkerk, Diane, and Patel, Bharat K.C.
- Subjects
- *
BACTERIA , *RUMEN microbiology - Abstract
Examines the isolation of the ammonia-hyperproducing (HAP) bacteria from the rumen of various New Zealand pasture-grazed animals. Representation of the colonies able to grow on the medium containing tryptone casamino acids; Purification of the 14 morphologically distinct colonies; What the carbon source utilization experiments showed.
- Published
- 1998
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47. Rumen Lachnospiraceae isolate NK3A20 exhibits metabolic flexibility in response to substrate and coculture with a methanogen.
- Author
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Kaminsky, Rachel A., Reid, Peter M., Altermann, Eric, Kenters, Nikki, Kelly, William J., Noel, Samantha J., Attwood, Graeme T., and Janssen, Peter H.
- Subjects
- *
GALACTURONIC acid , *PARTIAL pressure , *BUTYRATES , *MICROBIAL physiology , *ELECTRON donors , *MICROBIAL genomics , *DEHYDROGENASES - Abstract
Hydrogen (H2) is the primary electron donor for methane formation in ruminants, but the H2-producing organisms involved are largely uncharacterized. This work integrated studies of microbial physiology and genomics to characterize rumen bacterial isolate NK3A20 of the family Lachnospiraceae. Isolate NK3A20 was the first recognized isolate of the NK3A20 group, which is among the ten most abundant bacterial genera in 16S rRNA gene surveys of rumen microbiota. NK3A20 produced acetate, butyrate, H2, and formate from glucose. The end product ratios varied when grown with different substrates and at different H2 partial pressures. NK3A20 produced butyrate as a major product using glucose or under high H2 partial pressures and switched to mainly acetate in the presence of galacturonic acid (an oxidized sugar) or in coculture with a methanogen. Growth with galacturonic acid was faster at elevated H2 concentrations, while elevated H2 slowed growth with glucose. Genome analyses revealed the presence of multiple hydrogenases including a membrane-bound Ech hydrogenase, an electron bifurcating butyryl-CoA dehydrogenase (Bcd-Etf), and an Rnf complex that may be involved in modulating the observed metabolic pathway changes, providing insight into H2 formation in the rumen. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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48. A new growth medium for rapid selection and purification of Clostridium proteoclasticum transposon mutants
- Author
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Hussein, Hassan M., Cookson, Adrian L., and Attwood, Graeme T.
- Subjects
- *
CLOSTRIDIUM , *TRANSPOSONS , *HEMICELLULOSE , *CIPROFLOXACIN - Abstract
Abstract: Clostridium proteoclasticum is commonly associated with the rumen microflora of pasture-fed cattle and sheep and has significant hemicellulose degradation abilities. Genes involved in plant fibre breakdown are commonly identified by producing site-specific mutations. However, the genetics of C. proteoclasticum and other closely-related Butyrivibrio/Pseudobutyrivibrio species is not well-established. Therefore random transposon mutants of C. proteoclasticum were generated by conjugation with Enterococcus faecalis containing Tn916. A new counter-selection agar medium was developed containing L-arabinose and D-raffinose as carbon sources, both of which are utilized by C. proteoclasticum only, and also ciprofloxacin, an antibiotic that suppresses the growth of E. faecalis. With this new medium the enhanced growth and more rapid separation of C. proteoclasticum transposon mutants from the background of E. faecalis cells was made, thereby facilitating the selection of transposon mutants and the identification of their Tn916 insertion sites. [Copyright &y& Elsevier]
- Published
- 2008
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49. Comparative Genomics of Rumen Butyrivibrio spp. Uncovers a Continuum of Polysaccharide-Degrading Capabilities.
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Palevich, Nikola, Kelly, William J., Leahy, Sinead C., Denman, Stuart, Altermann, Eric, Rakonjac, Jasna, and Attwood, Graeme T.
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RIBOSOMAL RNA , *COMPARATIVE genomics , *CARBOHYDRATE-binding proteins , *SHORT-chain fatty acids , *MONOSACCHARIDES , *CARRIER proteins , *GLYCOSIDASES , *POLYSACCHARIDES - Abstract
Plant polysaccharide breakdown by microbes in the rumen is fundamental to digestion in ruminant livestock. Bacterial species belonging to the rumen genera Butyrivibrio and Pseudobutyrivibrio are important degraders and utilizers of lignocellulosic plant material. These bacteria degrade polysaccharides and ferment the released monosaccharides to yield short-chain fatty acids that are used by the ruminant for growth and the production of meat, milk, and fiber products. Although rumen Butyrivibrio and Pseudobutyrivibrio species are regarded as common rumen inhabitants, their polysaccharide-degrading and carbohydrate-utilizing enzymes are not well understood. In this study, we analyzed the genomes of 40 Butyrivibrio and 6 Pseudobutyrivibrio strains isolated from the plant-adherent fraction of New Zealand dairy cows to explore the polysaccharide-degrading potential of these important rumen bacteria. Comparative genome analyses combined with phylogenetic analysis of their 16S rRNA genes and short-chain fatty acid production patterns provide insight into the genomic diversity and physiology of these bacteria and divide Butyrivibrio into 3 species clusters. Rumen Butyrivibrio bacteria were found to encode a large and diverse spectrum of degradative carbohydrate-active enzymes (CAZymes) and binding proteins. In total, 4,421 glycoside hydrolases (GHs), 1,283 carbohydrate esterases (CEs), 110 polysaccharide lyases (PLs), 3,605 glycosyltransferases (GTs), and 1,706 carbohydrate-binding protein modules (CBM) with predicted activities involved in the depolymerization and transport of the insoluble plant polysaccharides were identified. Butyrivibrio genomes had similar patterns of CAZyme families but varied greatly in the number of genes within each category in the Carbohydrate-Active Enzymes database (CAZy), suggesting some level of functional redundancy. These results suggest that rumen Butyrivibrio species occupy similar niches but apply different degradation strategies to be able to coexist in the rumen. [ABSTRACT FROM AUTHOR]
- Published
- 2020
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50. Butyrivibrio hungatei MB2003 competes effectively for soluble sugars released by Butyrivibrio proteoclasticus B316T from growth on xylan or pectin.
- Author
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Palevich, Nikola, Kelly, William J., Ganesh, Siva, Rakonjac, Jasna, and Attwood, Graeme T.
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BUTYRIVIBRIO , *XYLANS , *SUGAR analysis , *PECTINS , *TRANSCRIPTOMES , *ARABINOXYLANS - Abstract
Rumen bacterial species belonging to the genus Butyrivibrio are important degraders of plant polysaccharides, particularly hemicelluloses (arabinoxylans) and pectin. Currently, four 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 xylan or pectin, and their growth, release of sugars, fermentation end products and transcriptomes were examined. In mono-cultures, B316T was able to grow well on xylan and pectin, while 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 assessed; B316T transcription was largely unaffected by the presence of MB2003, but MB2003 expressed a wide range of genes encoding carbohydrate degradation, central metabolism, oligosaccharide transport and substrate assimilation in order to compete with B316T for the released sugars. These results suggest that B316T has a role as an initiator of primary solubilization of xylan and pectin, while MB2003 competes effectively for the released soluble sugars to enable its growth and maintenance in the rumen. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
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