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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. Complete genome sequence of Methanosphaera sp. ISO3-F5, a rumen methylotrophic methanogen. Microbiol Resour Announc 2024; 13:e0004324. [PMID: 38426731 PMCID: PMC11008217 DOI: 10.1128/mra.00043-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 02/13/2024] [Indexed: 03/02/2024] Open
Abstract
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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Affiliation(s)
- Nikola Palevich
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
| | - Jeyamalar Jeyanathan
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
- Laboratory for Animal Nutrition and Animal Product Quality, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Kerri Reilly
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
| | - Faith P. Palevich
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
- AgResearch Ltd., Hopkirk Research Institute, Palmerston North, New Zealand
| | - Paul H. Maclean
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
| | - Dong Li
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
| | - Eric Altermann
- School of Veterinary Science and Centre for Bioparticle Applications, Massey University, Palmerston North, New Zealand
- Blue Barn Life Sciences Ltd., Feilding, New Zealand
| | - William J. Kelly
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
| | - Sinead C. Leahy
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
- New Zealand Agricultural Greenhouse Gas Research Centre (NZAGRC), Palmerston North, New Zealand
| | - Graeme T. Attwood
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
| | - Ron S. Ronimus
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
| | - Gemma Henderson
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
- Bacthera AG, Basel, Switzerland
| | - Peter H. Janssen
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
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Li Y, Crouzet L, Kelly WJ, Reid P, Leahy SC, Attwood GT. Methanobrevibacter boviskoreani JH1T growth on alcohols allows development of a high throughput bioassay to detect methanogen inhibition. Current Research in Microbial Sciences 2023; 4:100189. [PMID: 37122845 PMCID: PMC10139955 DOI: 10.1016/j.crmicr.2023.100189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023] Open
Abstract
Rumen methanogenic archaea use by-products of fermentation to carry out methanogenesis for energy generation. A key fermentation by-product is hydrogen (H2), which acts as the source of reducing potential for methane (CH4) formation in hydrogenotrophic methanogens. The in vitro cultivation of hydrogenotrophic rumen methanogens requires pressurised H2 which limits the ability to conduct high-throughput screening experiments with these organisms. The genome of the hydrogenotrophic methanogen Methanobrevibacter boviskoreani JH1T harbors genes encoding an NADP-dependent alcohol dehydrogenase and a F420-dependent NADP reductase, which may facilitate the transfer of reducing potential from ethanol to F420 via NADP. The aim of this study was to explore the anaerobic culturing of JH1T without pressurised H2, using a variety of short chain alcohols. The results demonstrate that in the absence of H2, JHIT can use ethanol, 1-propanol, and 1-butanol but not methanol, as a source of reducing potential for methanogenesis. The ability to use ethanol to drive CH4 formation in JH1T makes it possible to develop a high throughput culture-based bioassay enabling screening of potential anti-methanogen compounds. The development of this resource will help researchers globally to accelerate the search for methane mitigation technologies for ruminant animals. Global emissions pathways that are consistent with the temperature goal of the Paris Agreement, rely on substantial reductions of agricultural greenhouse gasses, particularly from ruminant animals.
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Kelly WJ, Mackie RI, Attwood GT, Janssen PH, McAllister TA, Leahy SC. Hydrogen and formate production and utilisation in the rumen and the human colon. Anim Microbiome 2022; 4:22. [PMID: 35287765 PMCID: PMC8919644 DOI: 10.1186/s42523-022-00174-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/02/2022] [Indexed: 12/31/2022] Open
Abstract
Molecular hydrogen (H2) and formate (HCOO−) are metabolic end products of many primary fermenters in the mammalian gut. Both play a vital role in fermentation where they are electron sinks for individual microbes in an anaerobic environment that lacks external electron acceptors. If H2 and/or formate accumulate within the gut ecosystem, the ability of primary fermenters to regenerate electron carriers may be inhibited and microbial metabolism and growth disrupted. Consequently, H2- and/or formate-consuming microbes such as methanogens and homoacetogens play a key role in maintaining the metabolic efficiency of primary fermenters. There is increasing interest in identifying approaches to manipulate mammalian gut environments for the benefit of the host and the environment. As H2 and formate are important mediators of interspecies interactions, an understanding of their production and utilisation could be a significant entry point for the development of successful interventions. Ruminant methane mitigation approaches are discussed as a model to help understand the fate of H2 and formate in gut systems.
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Leahy SC, Janssen PH, Attwood GT, Mackie RI, McAllister TA, Kelly WJ. Electron flow: key to mitigating ruminant methanogenesis. Trends Microbiol 2022; 30:209-212. [PMID: 35027237 DOI: 10.1016/j.tim.2021.12.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 10/19/2022]
Abstract
Disposal of electrons generated during the fermentation of ingested feed is a fundamental feature of anaerobic microbial gut ecosystems. Here, we focus on the well-studied rumen environment to highlight how electrons are transferred through anaerobic fermentation pathways and how manipulating this electron flow is important to reducing methane emissions from ruminants. Priorities for research that can accelerate understanding in this area are highlighted.
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Affiliation(s)
- Sinead C Leahy
- New Zealand Agricultural Greenhouse Gas Research Centre (NZAGRC), Palmerston North, New Zealand.
| | - Peter H Janssen
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - Graeme T Attwood
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | | | | | - William J Kelly
- New Zealand Agricultural Greenhouse Gas Research Centre (NZAGRC), Palmerston North, New Zealand
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5
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Palevich N, Maclean PH, Kelly WJ, Leahy SC, Rakonjac J, Attwood GT. Complete Genome Sequence of the Polysaccharide-Degrading Rumen Bacterium Pseudobutyrivibrio xylanivorans MA3014 Reveals an Incomplete Glycolytic Pathway. Genome Biol Evol 2021; 12:1566-1572. [PMID: 32770231 PMCID: PMC7523725 DOI: 10.1093/gbe/evaa165] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2020] [Indexed: 11/24/2022] Open
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.
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Affiliation(s)
- Nikola Palevich
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand.,Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Paul H Maclean
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | | | - Sinead C Leahy
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Jasna Rakonjac
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Graeme T Attwood
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
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Kelly WJ, Leahy SC, Kamke J, Soni P, Koike S, Mackie R, Seshadri R, Cook GM, Morales SE, Greening C, Attwood GT. Occurrence and expression of genes encoding methyl-compound production in rumen bacteria. Anim Microbiome 2019; 1:15. [PMID: 33499937 PMCID: PMC7807696 DOI: 10.1186/s42523-019-0016-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 10/17/2019] [Indexed: 12/22/2022] Open
Abstract
Background Digestive processes in the rumen lead to the release of methyl-compounds, mainly methanol and methylamines, which are used by methyltrophic methanogens to form methane, an important agricultural greenhouse gas. Methylamines are produced from plant phosphatidylcholine degradation, by choline trimethylamine lyase, while methanol comes from demethoxylation of dietary pectins via pectin methylesterase activity. We have screened rumen metagenomic and metatranscriptomic datasets, metagenome assembled genomes, and the Hungate1000 genomes to identify organisms capable of producing methyl-compounds. We also describe the enrichment of pectin-degrading and methane-forming microbes from sheep rumen contents and the analysis of their genomes via metagenomic assembly. Results Screens of metagenomic data using the protein domains of choline trimethylamine lyase (CutC), and activator protein (CutD) found good matches only to Olsenella umbonata and to Caecibacter, while the Hungate1000 genomes and metagenome assembled genomes from the cattle rumen found bacteria within the phyla Actinobacteria, Firmicutes and Proteobacteria. The cutC and cutD genes clustered with genes that encode structural components of bacterial microcompartment proteins. Prevotella was the dominant genus encoding pectin methyl esterases, with smaller numbers of sequences identified from other fibre-degrading rumen bacteria. Some large pectin methyl esterases (> 2100 aa) were found to be encoded in Butyrivibrio genomes. The pectin-utilising, methane-producing consortium was composed of (i) a putative pectin-degrading bacterium (phylum Tenericutes, class Mollicutes), (ii) a galacturonate-using Sphaerochaeta sp. predicted to produce acetate, lactate, and ethanol, and (iii) a methylotrophic methanogen, Methanosphaera sp., with the ability to form methane via a primary ethanol-dependent, hydrogen-independent, methanogenesis pathway. Conclusions The main bacteria that produce methyl-compounds have been identified in ruminants. Their enzymatic activities can now be targeted with the aim of finding ways to reduce the supply of methyl-compound substrates to methanogens, and thereby limit methylotrophic methanogenesis in the rumen.
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Affiliation(s)
| | - Sinead C Leahy
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
| | - Janine Kamke
- Horizons Regional Council, Palmerston North, New Zealand
| | - Priya Soni
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
| | | | | | - Rekha Seshadri
- Department of Energy, Joint Genome Institute, San Francisco, CA, USA
| | | | | | | | - Graeme T Attwood
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand.
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Attwood GT, Wakelin SA, Leahy SC, Rowe S, Clarke S, Chapman DF, Muirhead R, Jacobs JME. Applications of the Soil, Plant and Rumen Microbiomes in Pastoral Agriculture. Front Nutr 2019; 6:107. [PMID: 31380386 PMCID: PMC6646666 DOI: 10.3389/fnut.2019.00107] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/27/2019] [Indexed: 12/14/2022] Open
Abstract
The production of dairy, meat, and fiber by ruminant animals relies on the biological processes occurring in soils, forage plants, and the animals' rumens. Each of these components has an associated microbiome, and these have traditionally been viewed as distinct ecosystems. However, these microbiomes operate under similar ecological principles and are connected via water, energy flows, and the carbon and nitrogen nutrient cycles. Here, we summarize the microbiome research that has been done in each of these three environments (soils, forage plants, animals' rumen) and investigate what additional benefits may be possible through understanding the interactions between the various microbiomes. The challenge for future research is to enhance microbiome function by appropriate matching of plant and animal genotypes with the environment to improve the output and environmental sustainability of pastoral agriculture.
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Affiliation(s)
| | | | - Sinead C Leahy
- Animal Science, AgResearch, Palmerston North, New Zealand
| | - Suzanne Rowe
- Animal Science, AgResearch, Invermay, New Zealand
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Greening C, Geier R, Wang C, Woods LC, Morales SE, McDonald MJ, Rushton-Green R, Morgan XC, Koike S, Leahy SC, Kelly WJ, Cann I, Attwood GT, Cook GM, Mackie RI. Diverse hydrogen production and consumption pathways influence methane production in ruminants. ISME J 2019; 13:2617-2632. [PMID: 31243332 PMCID: PMC6776011 DOI: 10.1038/s41396-019-0464-2] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 06/03/2019] [Accepted: 06/07/2019] [Indexed: 01/17/2023]
Abstract
Farmed ruminants are the largest source of anthropogenic methane emissions globally. The methanogenic archaea responsible for these emissions use molecular hydrogen (H2), produced during bacterial and eukaryotic carbohydrate fermentation, as their primary energy source. In this work, we used comparative genomic, metatranscriptomic and co-culture-based approaches to gain a system-wide understanding of the organisms and pathways responsible for ruminal H2 metabolism. Two-thirds of sequenced rumen bacterial and archaeal genomes encode enzymes that catalyse H2 production or consumption, including 26 distinct hydrogenase subgroups. Metatranscriptomic analysis confirmed that these hydrogenases are differentially expressed in sheep rumen. Electron-bifurcating [FeFe]-hydrogenases from carbohydrate-fermenting Clostridia (e.g., Ruminococcus) accounted for half of all hydrogenase transcripts. Various H2 uptake pathways were also expressed, including methanogenesis (Methanobrevibacter), fumarate and nitrite reduction (Selenomonas), and acetogenesis (Blautia). Whereas methanogenesis-related transcripts predominated in high methane yield sheep, alternative uptake pathways were significantly upregulated in low methane yield sheep. Complementing these findings, we observed significant differential expression and activity of the hydrogenases of the hydrogenogenic cellulose fermenter Ruminococcus albus and the hydrogenotrophic fumarate reducer Wolinella succinogenes in co-culture compared with pure culture. We conclude that H2 metabolism is a more complex and widespread trait among rumen microorganisms than previously recognised. There is evidence that alternative hydrogenotrophs, including acetogenic and respiratory bacteria, can prosper in the rumen and effectively compete with methanogens for H2. These findings may help to inform ongoing strategies to mitigate methane emissions by increasing flux through alternative H2 uptake pathways, including through animal selection, dietary supplementation and methanogenesis inhibitors.
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Affiliation(s)
- Chris Greening
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia.
| | - Renae Geier
- Department of Animal Sciences and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Cecilia Wang
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Laura C Woods
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Sergio E Morales
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Michael J McDonald
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Rowena Rushton-Green
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Xochitl C Morgan
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Satoshi Koike
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Sinead C Leahy
- Grasslands Research Centre, AgResearch Ltd., Palmerston North, 4410, New Zealand
| | | | - Isaac Cann
- Department of Animal Sciences and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Graeme T Attwood
- Grasslands Research Centre, AgResearch Ltd., Palmerston North, 4410, New Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Roderick I Mackie
- Department of Animal Sciences and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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Henderson G, Yilmaz P, Kumar S, Forster RJ, Kelly WJ, Leahy SC, Guan LL, Janssen PH. Improved taxonomic assignment of rumen bacterial 16S rRNA sequences using a revised SILVA taxonomic framework. PeerJ 2019; 7:e6496. [PMID: 30863673 PMCID: PMC6407505 DOI: 10.7717/peerj.6496] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 01/21/2019] [Indexed: 11/20/2022] Open
Abstract
The taxonomy and associated nomenclature of many taxa of rumen bacteria are poorly defined within databases of 16S rRNA genes. This lack of resolution results in inadequate definition of microbial community structures, with large parts of the community designated as incertae sedis, unclassified, or uncultured within families, orders, or even classes. We have begun resolving these poorly-defined groups of rumen bacteria, based on our desire to name these for use in microbial community profiling. We used the previously-reported global rumen census (GRC) dataset consisting of >4.5 million partial bacterial 16S rRNA gene sequences amplified from 684 rumen samples and representing a wide range of animal hosts and diets. Representative sequences from the 8,985 largest operational units (groups of sequence sharing >97% sequence similarity, and covering 97.8% of all sequences in the GRC dataset) were used to identify 241 pre-defined clusters (mainly at genus or family level) of abundant rumen bacteria in the ARB SILVA 119 framework. A total of 99 of these clusters (containing 63.8% of all GRC sequences) had no unique or had inadequate taxonomic identifiers, and each was given a unique nomenclature. We assessed this improved framework by comparing taxonomic assignments of bacterial 16S rRNA gene sequence data in the GRC dataset with those made using the original SILVA 119 framework, and three other frameworks. The two SILVA frameworks performed best at assigning sequences to genus-level taxa. The SILVA 119 framework allowed 55.4% of the sequence data to be assigned to 751 uniquely identifiable genus-level groups. The improved framework increased this to 87.1% of all sequences being assigned to one of 871 uniquely identifiable genus-level groups. The new designations were included in the SILVA 123 release (https://www.arb-silva.de/documentation/release-123/) and will be perpetuated in future releases.
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Affiliation(s)
- Gemma Henderson
- Grasslands Research Centre, AgResearch, Palmerston North, New Zealand
| | - Pelin Yilmaz
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sandeep Kumar
- Grasslands Research Centre, AgResearch, Palmerston North, New Zealand
| | - Robert J Forster
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - William J Kelly
- Grasslands Research Centre, AgResearch, Palmerston North, New Zealand
| | - Sinead C Leahy
- Grasslands Research Centre, AgResearch, Palmerston North, New Zealand
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Peter H Janssen
- Grasslands Research Centre, AgResearch, Palmerston North, New Zealand
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10
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Gilbert RA, Kelly WJ, Altermann E, Leahy SC, Minchin C, Ouwerkerk D, Klieve AV. Toward Understanding Phage:Host Interactions in the Rumen; Complete Genome Sequences of Lytic Phages Infecting Rumen Bacteria. Front Microbiol 2017; 8:2340. [PMID: 29259581 PMCID: PMC5723332 DOI: 10.3389/fmicb.2017.02340] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 11/13/2017] [Indexed: 11/18/2022] Open
Abstract
The rumen is known to harbor dense populations of bacteriophages (phages) predicted to be capable of infecting a diverse range of rumen bacteria. While bacterial genome sequencing projects are revealing the presence of phages which can integrate their DNA into the genome of their host to form stable, lysogenic associations, little is known of the genetics of phages which utilize lytic replication. These phages infect and replicate within the host, culminating in host lysis, and the release of progeny phage particles. While lytic phages for rumen bacteria have been previously isolated, their genomes have remained largely uncharacterized. Here we report the first complete genome sequences of lytic phage isolates specifically infecting three genera of rumen bacteria: Bacteroides, Ruminococcus, and Streptococcus. All phages were classified within the viral order Caudovirales and include two phage morphotypes, representative of the Siphoviridae and Podoviridae families. The phage genomes displayed modular organization and conserved viral genes were identified which enabled further classification and determination of closest phage relatives. Co-examination of bacterial host genomes led to the identification of several genes responsible for modulating phage:host interactions, including CRISPR/Cas elements and restriction-modification phage defense systems. These findings provide new genetic information and insights into how lytic phages may interact with bacteria of the rumen microbiome.
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Affiliation(s)
- Rosalind A Gilbert
- Department of Agriculture and Fisheries, EcoSciences Precinct, Brisbane, QLD, Australia.,Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, Australia
| | | | - Eric Altermann
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand.,Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Sinead C Leahy
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand.,New Zealand Agricultural Greenhouse Gas Research Centre, Palmerston North, New Zealand
| | - Catherine Minchin
- Department of Agriculture and Fisheries, EcoSciences Precinct, Brisbane, QLD, Australia
| | - Diane Ouwerkerk
- Department of Agriculture and Fisheries, EcoSciences Precinct, Brisbane, QLD, Australia.,Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, Australia
| | - Athol V Klieve
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, Australia.,School of Agriculture and Food Sciences, University of Queensland, Gatton Campus, Gatton, QLD, Australia
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11
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Kamke J, Soni P, Li Y, Ganesh S, Kelly WJ, Leahy SC, Shi W, Froula J, Rubin EM, Attwood GT. Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep. BMC Res Notes 2017; 10:367. [PMID: 28789673 PMCID: PMC5549432 DOI: 10.1186/s13104-017-2671-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 07/22/2017] [Indexed: 11/28/2022] Open
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 CH4/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. Electronic supplementary material The online version of this article (doi:10.1186/s13104-017-2671-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Janine Kamke
- AgResearch Limited, Grasslands Research Centre, Tennent Drive, Palmerston North, 4442, New Zealand
| | - Priya Soni
- AgResearch Limited, Grasslands Research Centre, Tennent Drive, Palmerston North, 4442, New Zealand
| | - Yang Li
- AgResearch Limited, Grasslands Research Centre, Tennent Drive, Palmerston North, 4442, New Zealand
| | - Siva Ganesh
- AgResearch Limited, Grasslands Research Centre, Tennent Drive, Palmerston North, 4442, New Zealand
| | - William J Kelly
- AgResearch Limited, Grasslands Research Centre, Tennent Drive, Palmerston North, 4442, New Zealand
| | - Sinead C Leahy
- AgResearch Limited, Grasslands Research Centre, Tennent Drive, Palmerston North, 4442, New Zealand
| | - Weibing Shi
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.,Genomic Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jeff Froula
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.,Genomic Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Edward M Rubin
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.,Genomic Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Graeme T Attwood
- AgResearch Limited, Grasslands Research Centre, Tennent Drive, Palmerston North, 4442, New Zealand.
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Finn TJ, Shewaramani S, Leahy SC, Janssen PH, Moon CD. Dynamics and genetic diversification of Escherichia coli during experimental adaptation to an anaerobic environment. PeerJ 2017; 5:e3244. [PMID: 28480139 PMCID: PMC5419217 DOI: 10.7717/peerj.3244] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 03/29/2017] [Indexed: 01/25/2023] Open
Abstract
Background Many bacteria are facultative anaerobes, and can proliferate in both anoxic and oxic environments. Under anaerobic conditions, fermentation is the primary means of energy generation in contrast to respiration. Furthermore, the rates and spectra of spontaneous mutations that arise during anaerobic growth differ to those under aerobic growth. A long-term selection experiment was undertaken to investigate the genetic changes that underpin how the facultative anaerobe, Escherichia coli, adapts to anaerobic environments. Methods Twenty-one populations of E. coli REL4536, an aerobically evolved 10,000th generation descendent of the E. coli B strain, REL606, were established from a clonal ancestral culture. These were serially sub-cultured for 2,000 generations in a defined minimal glucose medium in strict aerobic and strict anaerobic environments, as well as in a treatment that fluctuated between the two environments. The competitive fitness of the evolving lineages was assessed at approximately 0, 1,000 and 2,000 generations, in both the environment of selection and the alternative environment. Whole genome re-sequencing was performed on random colonies from all lineages after 2,000-generations. Mutations were identified relative to the ancestral genome, and based on the extent of parallelism, traits that were likely to have contributed towards adaptation were inferred. Results There were increases in fitness relative to the ancestor among anaerobically evolved lineages when tested in the anaerobic environment, but no increases were found in the aerobic environment. For lineages that had evolved under the fluctuating regime, relative fitness increased significantly in the anaerobic environment, but did not increase in the aerobic environment. The aerobically-evolved lineages did not increase in fitness when tested in either the aerobic or anaerobic environments. The strictly anaerobic lineages adapted more rapidly to the anaerobic environment than did the fluctuating lineages. Two main strategies appeared to predominate during adaptation to the anaerobic environment: modification of energy generation pathways, and inactivation of non-essential functions. Fermentation pathways appeared to alter through selection for mutations in genes such as nadR, adhE, dcuS/R, and pflB. Mutations were frequently identified in genes for presumably dispensable functions such as toxin-antitoxin systems, prophages, virulence and amino acid transport. Adaptation of the fluctuating lineages to the anaerobic environments involved mutations affecting traits similar to those observed in the anaerobically evolved lineages. Discussion There appeared to be strong selective pressure for activities that conferred cell yield advantages during anaerobic growth, which include restoring activities that had previously been inactivated under long-term continuous aerobic evolution of the ancestor.
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Affiliation(s)
- Thomas J Finn
- Grasslands Research Centre, AgResearch Ltd, Palmerston North, New Zealand.,New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand.,Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Sonal Shewaramani
- Grasslands Research Centre, AgResearch Ltd, Palmerston North, New Zealand.,New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand.,Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States of America
| | - Sinead C Leahy
- Grasslands Research Centre, AgResearch Ltd, Palmerston North, New Zealand
| | - Peter H Janssen
- Grasslands Research Centre, AgResearch Ltd, Palmerston North, New Zealand
| | - Christina D Moon
- Grasslands Research Centre, AgResearch Ltd, Palmerston North, New Zealand
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Shewaramani S, Finn TJ, Leahy SC, Kassen R, Rainey PB, Moon CD. Anaerobically Grown Escherichia coli Has an Enhanced Mutation Rate and Distinct Mutational Spectra. PLoS Genet 2017; 13:e1006570. [PMID: 28103245 PMCID: PMC5289635 DOI: 10.1371/journal.pgen.1006570] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 02/02/2017] [Accepted: 01/04/2017] [Indexed: 12/21/2022] Open
Abstract
Oxidative stress is a major cause of mutation but little is known about how growth in the absence of oxygen impacts the rate and spectrum of mutations. We employed long-term mutation accumulation experiments to directly measure the rates and spectra of spontaneous mutation events in Escherichia coli populations propagated under aerobic and anaerobic conditions. To detect mutations, whole genome sequencing was coupled with methods of analysis sufficient to identify a broad range of mutational classes, including structural variants (SVs) generated by movement of repetitive elements. The anaerobically grown populations displayed a mutation rate nearly twice that of the aerobic populations, showed distinct asymmetric mutational strand biases, and greater insertion element activity. Consistent with mutation rate and spectra observations, genes for transposition and recombination repair associated with SVs were up-regulated during anaerobic growth. Together, these results define differences in mutational spectra affecting the evolution of facultative anaerobes.
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Affiliation(s)
- Sonal Shewaramani
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
| | - Thomas J. Finn
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
| | - Sinead C. Leahy
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
| | - Rees Kassen
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Paul B. Rainey
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI ParisTech), CNRS UMR 8231, PSL Research University, Paris, France
| | - Christina D. Moon
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
- * E-mail:
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Li Y, Leahy SC, Jeyanathan J, Henderson G, Cox F, Altermann E, Kelly WJ, Lambie SC, Janssen PH, Rakonjac J, Attwood GT. The complete genome sequence of the methanogenic archaeon ISO4-H5 provides insights into the methylotrophic lifestyle of a ruminal representative of the Methanomassiliicoccales. Stand Genomic Sci 2016; 11:59. [PMID: 27602181 PMCID: PMC5011839 DOI: 10.1186/s40793-016-0183-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 08/22/2016] [Indexed: 12/03/2022] Open
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.
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Affiliation(s)
- Yang Li
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand ; Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Sinead C Leahy
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | | | - Gemma Henderson
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Faith Cox
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Eric Altermann
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - William J Kelly
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Suzanne C Lambie
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Peter H Janssen
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Jasna Rakonjac
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Graeme T Attwood
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
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Kelly WJ, Pacheco DM, Li D, Attwood GT, Altermann E, Leahy SC. The complete genome sequence of the rumen methanogen Methanobrevibacter millerae SM9. Stand Genomic Sci 2016; 11:49. [PMID: 27536339 PMCID: PMC4987999 DOI: 10.1186/s40793-016-0171-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Accepted: 08/04/2016] [Indexed: 12/04/2022] Open
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-10T) 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.
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Affiliation(s)
- William J Kelly
- Rumen Microbiology, Animal Science, AgResearch Limited, Tennent Drive, Private Bag 11008, Palmerston North, 4442 New Zealand
| | - Diana M Pacheco
- Rumen Microbiology, Animal Science, AgResearch Limited, Tennent Drive, Private Bag 11008, Palmerston North, 4442 New Zealand
| | - Dong Li
- Rumen Microbiology, Animal Science, AgResearch Limited, Tennent Drive, Private Bag 11008, Palmerston North, 4442 New Zealand
| | - Graeme T Attwood
- Rumen Microbiology, Animal Science, AgResearch Limited, Tennent Drive, Private Bag 11008, Palmerston North, 4442 New Zealand
| | - Eric Altermann
- Rumen Microbiology, Animal Science, AgResearch Limited, Tennent Drive, Private Bag 11008, Palmerston North, 4442 New Zealand
| | - Sinead C Leahy
- Rumen Microbiology, Animal Science, AgResearch Limited, Tennent Drive, Private Bag 11008, Palmerston North, 4442 New Zealand
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Kelly WJ, Henderson G, Pacheco DM, Li D, Reilly K, Naylor GE, Janssen PH, Attwood GT, Altermann E, Leahy SC. The complete genome sequence of Eubacterium limosum SA11, a metabolically versatile rumen acetogen. Stand Genomic Sci 2016; 11:26. [PMID: 26981167 PMCID: PMC4791908 DOI: 10.1186/s40793-016-0147-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Accepted: 03/07/2016] [Indexed: 12/22/2022] Open
Abstract
Acetogens are a specialized group of anaerobic bacteria able to produce acetate from CO2 and H2 via the Wood-Ljungdahl pathway. In some gut environments acetogens can compete with methanogens for H2, and as a result rumen acetogens are of interest in the development of microbial approaches for methane mitigation. The acetogen Eubacterium limosum SA11 was isolated from the rumen of a New Zealand sheep and its genome has been sequenced to examine its potential application in methane mitigation strategies, particularly in situations where hydrogenotrophic methanogens are inhibited resulting in increased H2 levels in the rumen. The 4.15 Mb chromosome of SA11 has an average G + C content of 47 %, and encodes 3805 protein-coding genes. There is a single prophage inserted in the chromosome, and several other gene clusters appear to have been acquired by horizontal transfer. These include genes for cell wall glycopolymers, a type VII secretion system, cell surface proteins and chemotaxis. SA11 is able to use a variety of organic substrates in addition to H2/CO2, with acetate and butyrate as the principal fermentation end-products, and genes involved in these metabolic pathways have been identified. An unusual feature is the presence of 39 genes encoding trimethylamine methyltransferase family proteins, more than any other bacterial genome. Overall, SA11 is a metabolically versatile organism, but its ability to grow on such a wide range of substrates suggests it may not be a suitable candidate to take the place of hydrogen-utilizing methanogens in the rumen.
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Affiliation(s)
- William J. Kelly
- Rumen Microbiology, Animal Science, AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, 4442 New Zealand
| | - Gemma Henderson
- Rumen Microbiology, Animal Science, AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, 4442 New Zealand
| | - Diana M. Pacheco
- Rumen Microbiology, Animal Science, AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, 4442 New Zealand
| | - Dong Li
- Rumen Microbiology, Animal Science, AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, 4442 New Zealand
| | - Kerri Reilly
- Rumen Microbiology, Animal Science, AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, 4442 New Zealand
| | - Graham E. Naylor
- Rumen Microbiology, Animal Science, AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, 4442 New Zealand
| | - Peter H. Janssen
- Rumen Microbiology, Animal Science, AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, 4442 New Zealand
| | - Graeme T. Attwood
- Rumen Microbiology, Animal Science, AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, 4442 New Zealand
| | - Eric Altermann
- Rumen Microbiology, Animal Science, AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, 4442 New Zealand
| | - Sinead C. Leahy
- Rumen Microbiology, Animal Science, AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, 4442 New Zealand
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Dunne JC, Kelly WJ, Leahy SC, Li D, Bond JJ, Peng L, Attwood GT, Jordan TW. The Cytosolic Oligosaccharide-Degrading Proteome of Butyrivibrio Proteoclasticus. Proteomes 2015; 3:347-368. [PMID: 28248275 PMCID: PMC5217386 DOI: 10.3390/proteomes3040347] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 10/15/2015] [Accepted: 10/19/2015] [Indexed: 11/16/2022] Open
Abstract
The growth and productivity of ruminants depends on a complex microbial community found in their fore-stomach (rumen), which is able to breakdown plant polysaccharides and ferment the released sugars. Butyrivibrio proteoclasticus B316T is a Gram-positive polysaccharide-degrading, butyrate-producing bacterium that is present at high numbers in the rumen of animals consuming pasture or grass silage based diets. B316T is one of a small number of rumen fibrolytic microbes capable of efficiently degrading and utilizing xylan, as well as being capable of utilizing arabinose, xylose, pectin and starch. We have therefore carried out a proteomic analysis of B316T to identify intracellular enzymes that are implicated in the metabolism of internalized xylan. Three hundred and ninety four proteins were identified including enzymes that have potential to metabolize assimilated products of extracellular xylan digestion. Identified enzymes included arabinosidases, esterases, an endoxylanase, and β-xylosidase. The presence of intracellular debranching enzymes indicated that some hemicellulosic side-chains may not be removed until oligosaccharides liberated by extracellular digestion have been assimilated by the cells. The results support a model of extracellular digestion of hemicellulose to oligosaccharides that are then transported to the cytoplasm for further digestion by intracellular enzymes.
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Affiliation(s)
- Jonathan C Dunne
- Rumen Microbiology, Animal Science Group, AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand.
- Centre for Biodiscovery and School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand.
- AgResearch Limited/Victoria University of Wellington Proteomics Laboratory, Victoria University of Wellington, Wellington 6140, New Zealand.
| | - William J Kelly
- Rumen Microbiology, Animal Science Group, AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand.
| | - Sinead C Leahy
- Rumen Microbiology, Animal Science Group, AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand.
| | - Dong Li
- Rumen Microbiology, Animal Science Group, AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand.
| | - Judy J Bond
- Rumen Microbiology, Animal Science Group, AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand.
- Centre for Biodiscovery and School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand.
- AgResearch Limited/Victoria University of Wellington Proteomics Laboratory, Victoria University of Wellington, Wellington 6140, New Zealand.
| | - Lifeng Peng
- Centre for Biodiscovery and School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand.
| | - Graeme T Attwood
- Rumen Microbiology, Animal Science Group, AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand.
| | - T William Jordan
- Centre for Biodiscovery and School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand.
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Lambie SC, Kelly WJ, Leahy SC, Li D, Reilly K, McAllister TA, Valle ER, Attwood GT, Altermann E. The complete genome sequence of the rumen methanogen Methanosarcina barkeri CM1. Stand Genomic Sci 2015; 10:57. [PMID: 26413197 PMCID: PMC4582637 DOI: 10.1186/s40793-015-0038-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 07/09/2015] [Indexed: 01/05/2023] Open
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.
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Affiliation(s)
- Suzanne C Lambie
- Rumen Microbiology, Animal Nutrition and Health, AgResearch Limited, Tennent Drive, Private Bag 11008, Palmerston North, 4442 New Zealand
| | - William J Kelly
- Rumen Microbiology, Animal Nutrition and Health, AgResearch Limited, Tennent Drive, Private Bag 11008, Palmerston North, 4442 New Zealand
| | - Sinead C Leahy
- Rumen Microbiology, Animal Nutrition and Health, AgResearch Limited, Tennent Drive, Private Bag 11008, Palmerston North, 4442 New Zealand ; New Zealand Agricultural Greenhouse Gas Research Centre, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, 4442 New Zealand
| | - Dong Li
- Rumen Microbiology, Animal Nutrition and Health, AgResearch Limited, Tennent Drive, Private Bag 11008, Palmerston North, 4442 New Zealand
| | - Kerri Reilly
- Rumen Microbiology, Animal Nutrition and Health, AgResearch Limited, Tennent Drive, Private Bag 11008, Palmerston North, 4442 New Zealand
| | - Tim A McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, Alberta T1J 4B1 Canada
| | - Edith R Valle
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, Alberta T1J 4B1 Canada
| | - Graeme T Attwood
- Rumen Microbiology, Animal Nutrition and Health, AgResearch Limited, Tennent Drive, Private Bag 11008, Palmerston North, 4442 New Zealand ; New Zealand Agricultural Greenhouse Gas Research Centre, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, 4442 New Zealand
| | - Eric Altermann
- Rumen Microbiology, Animal Nutrition and Health, AgResearch Limited, Tennent Drive, Private Bag 11008, Palmerston North, 4442 New Zealand ; Riddet Institute, Massey University, Palmerston North, 4442 New Zealand
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Kelly WJ, Leahy SC, Li D, Perry R, Lambie SC, Attwood GT, Altermann E. The complete genome sequence of the rumen methanogen Methanobacterium formicicum BRM9. Stand Genomic Sci 2014; 9:15. [PMID: 25780506 PMCID: PMC4335013 DOI: 10.1186/1944-3277-9-15] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 10/29/2014] [Indexed: 01/09/2023] Open
Abstract
Methanobacterium formicicum BRM9 was isolated from the rumen of a New Zealand Friesan 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 2.45 Mb BRM9 chromosome has an average G + C content of 41%, and encodes 2,352 protein-coding genes. The genes involved in methanogenesis are comparable to those found in other members of the Methanobacteriaceae with the exception that there is no [Fe]-hydrogenase dehydrogenase (Hmd) which links the methenyl-H4MPT reduction directly with the oxidation of H2. Compared to the rumen Methanobrevibacter strains, BRM9 has a much larger complement of genes involved in determining oxidative stress response, signal transduction and nitrogen fixation. BRM9 also has genes for the biosynthesis of the compatible solute ectoine that has not been reported to be produced by methanogens. The BRM9 genome has a prophage and two CRISPR repeat regions. Comparison to the genomes of other Methanobacterium strains shows a core genome of ~1,350 coding sequences and 190 strain-specific genes in BRM9, most of which are hypothetical proteins or prophage related.
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Affiliation(s)
- William J Kelly
- Rumen Microbiology, Animal Nutrition and Health, AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
| | - Sinead C Leahy
- Rumen Microbiology, Animal Nutrition and Health, AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
- New Zealand Agricultural Greenhouse Gas Research Centre, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
| | - Dong Li
- Rumen Microbiology, Animal Nutrition and Health, AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
| | - Rechelle Perry
- Rumen Microbiology, Animal Nutrition and Health, AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
| | - Suzanne C Lambie
- Rumen Microbiology, Animal Nutrition and Health, AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
| | - Graeme T Attwood
- Rumen Microbiology, Animal Nutrition and Health, AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
- New Zealand Agricultural Greenhouse Gas Research Centre, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
| | - Eric Altermann
- Rumen Microbiology, Animal Nutrition and Health, AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
- Riddet Institute, Massey University, Palmerston North 4442, New Zealand
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Creevey CJ, Kelly WJ, Henderson G, Leahy SC. Determining the culturability of the rumen bacterial microbiome. Microb Biotechnol 2014; 7:467-79. [PMID: 24986151 PMCID: PMC4229327 DOI: 10.1111/1751-7915.12141] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 05/14/2014] [Accepted: 06/02/2014] [Indexed: 11/25/2022] Open
Abstract
The goal of the Hungate1000 project is to generate a reference set of rumen microbial genome sequences. Toward this goal we have carried out a meta-analysis using information from culture collections, scientific literature, and the NCBI and RDP databases and linked this with a comparative study of several rumen 16S rRNA gene-based surveys. In this way we have attempted to capture a snapshot of rumen bacterial diversity to examine the culturable fraction of the rumen bacterial microbiome. Our analyses have revealed that for cultured rumen bacteria, there are many genera without a reference genome sequence. Our examination of culture-independent studies highlights that there are few novel but many uncultured taxa within the rumen bacterial microbiome. Taken together these results have allowed us to compile a list of cultured rumen isolates that are representative of abundant, novel and core bacterial species in the rumen. In addition, we have identified taxa, particularly within the phylum Bacteroidetes, where further cultivation efforts are clearly required. This information is being used to guide the isolation efforts and selection of bacteria from the rumen microbiota for sequencing through the Hungate1000.
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Affiliation(s)
- Christopher J Creevey
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland; Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, UK
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Shi W, Moon CD, Leahy SC, Kang D, Froula J, Kittelmann S, Fan C, Deutsch S, Gagic D, Seedorf H, Kelly WJ, Atua R, Sang C, Soni P, Li D, Pinares-Patiño CS, McEwan JC, Janssen PH, Chen F, Visel A, Wang Z, Attwood GT, Rubin EM. Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome. Genome Res 2014; 24:1517-25. [PMID: 24907284 PMCID: PMC4158751 DOI: 10.1101/gr.168245.113] [Citation(s) in RCA: 222] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Ruminant livestock represent the single largest anthropogenic source of the potent greenhouse gas methane, which is generated by methanogenic archaea residing in ruminant digestive tracts. While differences between individual animals of the same breed in the amount of methane produced have been observed, the basis for this variation remains to be elucidated. To explore the mechanistic basis of this methane production, we measured methane yields from 22 sheep, which revealed that methane yields are a reproducible, quantitative trait. Deep metagenomic and metatranscriptomic sequencing demonstrated a similar abundance of methanogens and methanogenesis pathway genes in high and low methane emitters. However, transcription of methanogenesis pathway genes was substantially increased in sheep with high methane yields. These results identify a discrete set of rumen methanogens whose methanogenesis pathway transcription profiles correlate with methane yields and provide new targets for CH4 mitigation at the levels of microbiota composition and transcriptional regulation.
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Affiliation(s)
- Weibing Shi
- Department of Energy, Joint Genome Institute, Walnut Creek, California 94598, USA; Genomic Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Christina D Moon
- AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - Sinead C Leahy
- AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - Dongwan Kang
- Department of Energy, Joint Genome Institute, Walnut Creek, California 94598, USA; Genomic Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jeff Froula
- Department of Energy, Joint Genome Institute, Walnut Creek, California 94598, USA; Genomic Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Sandra Kittelmann
- AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - Christina Fan
- Department of Energy, Joint Genome Institute, Walnut Creek, California 94598, USA; Genomic Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Samuel Deutsch
- Department of Energy, Joint Genome Institute, Walnut Creek, California 94598, USA; Genomic Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Dragana Gagic
- AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - Henning Seedorf
- AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - William J Kelly
- AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - Renee Atua
- AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - Carrie Sang
- AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - Priya Soni
- AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - Dong Li
- AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | | | - John C McEwan
- AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - Peter H Janssen
- AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - Feng Chen
- Department of Energy, Joint Genome Institute, Walnut Creek, California 94598, USA; Genomic Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Axel Visel
- Department of Energy, Joint Genome Institute, Walnut Creek, California 94598, USA; Genomic Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; School of Natural Sciences, University of California, Merced, California 95343, USA
| | - Zhong Wang
- Department of Energy, Joint Genome Institute, Walnut Creek, California 94598, USA; Genomic Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; School of Natural Sciences, University of California, Merced, California 95343, USA
| | - Graeme T Attwood
- AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - Edward M Rubin
- Department of Energy, Joint Genome Institute, Walnut Creek, California 94598, USA; Genomic Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
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22
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Ciric M, Moon CD, Leahy SC, Creevey CJ, Altermann E, Attwood GT, Rakonjac J, Gagic D. Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community. BMC Genomics 2014; 15:356. [PMID: 24886150 PMCID: PMC4035507 DOI: 10.1186/1471-2164-15-356] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 04/29/2014] [Indexed: 11/22/2022] Open
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, cell-surface 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. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-356) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | - Jasna Rakonjac
- Animal Nutrition and Health, AgResearch Ltd, Palmerston North 4442, New Zealand.
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23
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Kelly WJ, Altermann E, Lambie SC, Leahy SC. Interaction between the genomes of Lactococcus lactis and phages of the P335 species. Front Microbiol 2013; 4:257. [PMID: 24009606 PMCID: PMC3757294 DOI: 10.3389/fmicb.2013.00257] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2013] [Accepted: 08/13/2013] [Indexed: 11/28/2022] Open
Abstract
Phages of the P335 species infect Lactococcus lactis and have been particularly studied because of their association with strains of L. lactis subsp. cremoris used as dairy starter cultures. Unlike other lactococcal phages, those of the P335 species may have a temperate or lytic lifestyle, and are believed to originate from the starter cultures themselves. We have sequenced the genome of L. lactis subsp. cremoris KW2 isolated from fermented corn and found that it contains an integrated P335 species prophage. This 41 kb prophage (Φ KW2) has a mosaic structure with functional modules that are highly similar to several other phages of the P335 species associated with dairy starter cultures. Comparison of the genomes of 26 phages of the P335 species, with either a lytic or temperate lifestyle, shows that they can be divided into three groups and that the morphogenesis gene region is the most conserved. Analysis of these phage genomes in conjunction with the genomes of several L. lactis strains shows that prophage insertion is site specific and occurs at seven different chromosomal locations. Exactly how induced or lytic phages of the P335 species interact with carbohydrate cell surface receptors in the host cell envelope remains to be determined. Genes for the biosynthesis of a variable cell surface polysaccharide and for lipoteichoic acids (LTAs) are found in L. lactis and are the main candidates for phage receptors, as the genes for other cell surface carbohydrates have been lost from dairy starter strains. Overall, phages of the P335 species appear to have had only a minor role in the adaptation of L. lactis subsp. cremoris strains to the dairy environment, and instead they appear to be an integral part of the L. lactis chromosome. There remains a great deal to be discovered about their role, and their contribution to the evolution of the bacterial genome.
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Affiliation(s)
- William J Kelly
- AgResearch Limited, Grasslands Research Centre Palmerston North, New Zealand
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24
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Abstract
Methanobrevibacter sp. AbM4 was originally isolated from the abomasal contents of a sheep and was chosen as a representative of the Methanobrevibacter wolinii clade for genome sequencing. The AbM4 genome is smaller than that of the rumen methanogen M. ruminantium M1 (2.0 Mb versus 2.93 Mb), encodes fewer open reading frames (ORFs) (1,671 versus 2,217) and has a lower G+C percentage (29% versus 33%). Overall, the composition of the AbM4 genome is very similar to that of M1 suggesting that the methanogenesis pathway and central metabolism of these strains are highly similar, and both organisms are likely to be amenable to inhibition by small molecule inhibitors and vaccine-based methane mitigation technologies targeting these conserved features. The main differences compared to M1 are that AbM4 has a complete coenzyme M biosynthesis pathway and does not contain a prophage or non-ribosomal peptide synthase genes. However, AbM4 has a large CRISPR region and several type I and type II restriction-modification system components. Unusually, DNA-directed RNA polymerase B' and B'' subunits of AbM4 are joined, a feature only previously observed in some thermophilic archaea. AbM4 has a much reduced complement of genes encoding adhesin-like proteins which suggests it occupies a ruminal niche different from that of M1.
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Affiliation(s)
- S C Leahy
- New Zealand Agricultural Greenhouse Gas Research Centre ; Rumen Microbiology, Animal Nutrition and Health, AgResearch Limited, Grasslands Research Centre, New Zealand
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25
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Bond JJ, Dunne JC, Kwan FYS, Li D, Zhang K, Leahy SC, Kelly WJ, Attwood GT, Jordan TW. Carbohydrate transporting membrane proteins of the rumen bacterium, Butyrivibrio proteoclasticus. J Proteomics 2011; 75:3138-44. [PMID: 22200676 DOI: 10.1016/j.jprot.2011.12.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 10/19/2011] [Accepted: 12/06/2011] [Indexed: 11/24/2022]
Abstract
The research was aimed at finding which membrane proteins of the rumen bacterium Butyrivibrio proteoclasticus are involved in the uptake of carbohydrates resulting from extracellular enzymatic degradation of hemicellulose and fructan. The proteomic analysis of cells grown with fructose or xylan as the sole substrate identified 13 membrane proteins predicted to function as carbohydrate transporters. One protein detected was the membrane component of a fructose-specific phosphoenolpyruvate:sugar phosphotransferase system believed to be involved in the fructose uptake following extracellular fructan breakdown. The other 12 proteins were all ABC transport system substrate-binding proteins, nine of which belong to functional category COG1653 that includes proteins predicted to transport oligosaccharides. Four of the SBPs were significantly upregulated in xylan grown cells, and three of these were found in polysaccharide utilisation loci where they are clustered with other genes involved in hemicellulose breakdown and metabolism. It is possible that the carbon source available regulates a wider network of genes. The information on the mechanisms used by rumen bacteria to take up carbohydrates from their environment may improve our understanding of the ruminant digestion and facilitate strategies for improved pasture and stored feed utilisation.
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Affiliation(s)
- Jude J Bond
- AgResearch Ltd, Grasslands Research Centre, Tennent Drive, Palmerston North, New Zealand.
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26
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Dunne JC, Li D, Kelly WJ, Leahy SC, Bond JJ, Attwood GT, Jordan TW. Extracellular polysaccharide-degrading proteome of Butyrivibrio proteoclasticus. J Proteome Res 2011; 11:131-42. [PMID: 22060546 DOI: 10.1021/pr200864j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Plant polysaccharide-degrading rumen microbes are fundamental to the health and productivity of ruminant animals. Butyrivibrio proteoclasticus B316(T) is a gram-positive, butyrate-producing anaerobic bacterium with a key role in hemicellulose degradation in the rumen. Gel-based proteomics was used to examine the growth-phase-dependent abundance patterns of secreted proteins recovered from cells grown in vitro with xylan or xylose provided as the sole supplementary carbon source. Five polysaccharidases and two carbohydrate-binding proteins (CBPs) were among 30 identified secreted proteins. The endo-1,4-β-xylanase Xyn10B was 17.5-fold more abundant in the culture medium of xylan-grown cells, which suggests it plays an important role in hemicellulose degradation. The secretion of three nonxylanolytic enzymes and two CBPs implies they augment hemicellulose degradation by hydrolysis or disruption of associated structural polysaccharides. Sixteen ATP-binding cassette (ABC) transporter substrate-binding proteins were identified, several of which had altered relative abundance levels between growth conditions, which suggests they are important for oligosaccharide uptake. This study demonstrates that B. proteoclasticus modulates the secretion of hemicellulose-degrading enzymes and ATP-dependent sugar uptake systems in response to growth substrate and supports the notion that this organism makes an important contribution to polysaccharide degradation in the rumen.
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Affiliation(s)
- Jonathan C Dunne
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand
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27
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O'Connell Motherway M, Zomer A, Leahy SC, Reunanen J, Bottacini F, Claesson MJ, O'Brien F, Flynn K, Casey PG, Moreno Munoz JA, Kearney B, Houston AM, O'Mahony C, Higgins DG, Shanahan F, Palva A, de Vos WM, Fitzgerald GF, Ventura M, O'Toole PW, van Sinderen D. Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor. Proc Natl Acad Sci U S A 2011; 108:11217-22. [PMID: 21690406 PMCID: PMC3131351 DOI: 10.1073/pnas.1105380108] [Citation(s) in RCA: 281] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Development of the human gut microbiota commences at birth, with bifidobacteria being among the first colonizers of the sterile newborn gastrointestinal tract. To date, the genetic basis of Bifidobacterium colonization and persistence remains poorly understood. Transcriptome analysis of the Bifidobacterium breve UCC2003 2.42-Mb genome in a murine colonization model revealed differential expression of a type IVb tight adherence (Tad) pilus-encoding gene cluster designated "tad(2003)." Mutational analysis demonstrated that the tad(2003) gene cluster is essential for efficient in vivo murine gut colonization, and immunogold transmission electron microscopy confirmed the presence of Tad pili at the poles of B. breve UCC2003 cells. Conservation of the Tad pilus-encoding locus among other B. breve strains and among sequenced Bifidobacterium genomes supports the notion of a ubiquitous pili-mediated host colonization and persistence mechanism for bifidobacteria.
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MESH Headings
- Amino Acid Sequence
- Animals
- Bacterial Proteins/genetics
- Bacterial Proteins/physiology
- Base Sequence
- Bifidobacterium/genetics
- Bifidobacterium/growth & development
- Bifidobacterium/physiology
- Bifidobacterium/ultrastructure
- Comparative Genomic Hybridization
- DNA, Bacterial/genetics
- Female
- Fimbriae, Bacterial/genetics
- Fimbriae, Bacterial/physiology
- Fimbriae, Bacterial/ultrastructure
- Gastrointestinal Tract/microbiology
- Gene Expression Regulation, Bacterial
- Genome, Bacterial
- Germ-Free Life
- Humans
- Male
- Metagenome
- Mice
- Mice, Inbred BALB C
- Microscopy, Electron, Transmission
- Microscopy, Immunoelectron
- Molecular Sequence Data
- Multigene Family
- Mutation
- Sequence Homology, Amino Acid
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Affiliation(s)
| | - Aldert Zomer
- Alimentary Pharmabiotic Centre and Departments of
| | - Sinead C. Leahy
- Alimentary Pharmabiotic Centre and Departments of
- Microbiology
| | - Justus Reunanen
- Division of Microbiology and Epidemiology, Department of Basic Veterinary Medicine, University of Helsinki, FIN-00014, Helsinki, Finland
| | - Francesca Bottacini
- Alimentary Pharmabiotic Centre and Departments of
- Microbiology
- Laboratory of Probiogenomics, Department of Genetics, Biology of Microorganisms, Anthropology, and Evolution, University of Parma, 43100 Parma, Italy
| | | | | | - Kiera Flynn
- Alimentary Pharmabiotic Centre and Departments of
| | | | | | | | | | | | - Des G. Higgins
- Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland; and
| | - Fergus Shanahan
- Alimentary Pharmabiotic Centre and Departments of
- Medicine, and
| | - Airi Palva
- Division of Microbiology and Epidemiology, Department of Basic Veterinary Medicine, University of Helsinki, FIN-00014, Helsinki, Finland
| | - Willem M. de Vos
- Division of Microbiology and Epidemiology, Department of Basic Veterinary Medicine, University of Helsinki, FIN-00014, Helsinki, Finland
- Laboratory of Microbiology, Wageningen University, 6703 HB, Wageningen, The Netherlands
| | - Gerald F. Fitzgerald
- Alimentary Pharmabiotic Centre and Departments of
- Microbiology
- Food and Nutritional Sciences, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Genetics, Biology of Microorganisms, Anthropology, and Evolution, University of Parma, 43100 Parma, Italy
| | - Paul W. O'Toole
- Alimentary Pharmabiotic Centre and Departments of
- Microbiology
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28
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Cookson AL, Noel S, Hussein H, Perry R, Sang C, Moon CD, Leahy SC, Altermann E, Kelly WJ, Attwood GT. Transposition of Tn916 in the four replicons of the Butyrivibrio proteoclasticus B316(T) genome. FEMS Microbiol Lett 2011; 316:144-51. [PMID: 21204937 DOI: 10.1111/j.1574-6968.2010.02204.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The rumen bacterium Butyrivibrio proteoclasticus B316(T) has a 4.4-Mb genome composed of four replicons (approximately 3.55 Mb, 361, 302 and 186 kb). Mutagenesis of B316(T) was performed with the broad host-range conjugative transposon Tn916 to screen for functionally important characteristics. The insertion sites of 123 mutants containing a single copy of Tn916 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 Tn916 integration into B316(T) . A search of the B316(T) genome using the modelled target consensus sequence (up to two mismatches) identified 39 theoretical Tn916 insertion sites (19 coding, 20 noncoding), of which nine corresponded to Tn916 insertions identified in B316(T) mutants during our conjugation experiments.
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Affiliation(s)
- Adrian L Cookson
- Agri-Foods & Health Section Ruminant Nutrition & Microbiology, Food & Health Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand.
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29
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Abstract
A large collection of Lactococcus lactis strains, including wild-type isolates and dairy starter cultures, were screened on the basis of their phenotype and the macrorestriction patterns produced from pulsed-field gel electrophoresis (PFGE) analysis of SmaI digests of genomic DNA. Three groups of dairy starter cultures, used for different purposes in the dairy industry, and a fourth group made up of strains isolated from the environment were selected for analysis of their chromosomal diversity using the endonuclease I-CeuI. Chromosome architecture was largely conserved with each strain having six copies of the rRNA genes, and the chromosome size of individual strains ranged between 2,240 and 2,688 kb. The origin of L. lactis strains showed the greatest correlation with chromosome size, and dairy strains, particularly those with the cremoris phenotype, had smaller chromosomes than wild-type strains. Overall, this study, coupled with analysis of the sequenced L. lactis genomes, provides evidence that defined strain dairy starter cultures have arisen from plant L. lactis strains. Adaptation of these strains to the dairy environment has involved loss of functions resulting in smaller chromosomes and acquisition of genes (usually plasmid associated) that facilitate growth in milk. We conclude that dairy starter cultures generally and the industrially used cremoris and diacetylactis phenotype strains in particular comprise a specialized group of L. lactis strains that have been selected to become an essential component of industrial processes and have evolved accordingly, so that they are no longer fit to survive outside the dairy environment.
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Affiliation(s)
- William J Kelly
- Rumen Microbial Genomics, AgResearch Limited, Grasslands Research Center, Palmerston North, New Zealand.
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30
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Kelly WJ, Leahy SC, Altermann E, Yeoman CJ, Dunne JC, Kong Z, Pacheco DM, Li D, Noel SJ, Moon CD, Cookson AL, Attwood GT. The glycobiome of the rumen bacterium Butyrivibrio proteoclasticus B316(T) highlights adaptation to a polysaccharide-rich environment. PLoS One 2010; 5:e11942. [PMID: 20689770 PMCID: PMC2914790 DOI: 10.1371/journal.pone.0011942] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Accepted: 07/07/2010] [Indexed: 12/22/2022] Open
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 Gram-positive, 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.
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Affiliation(s)
- William J. Kelly
- Rumen Microbial Genomics, AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - Sinead C. Leahy
- Rumen Microbial Genomics, AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - Eric Altermann
- Rumen Microbial Genomics, AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - Carl J. Yeoman
- Rumen Microbial Genomics, AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
- Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand
| | - Jonathan C. Dunne
- Rumen Microbial Genomics, AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
- Centre for Biodiscovery and School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Zhanhao Kong
- Rumen Microbial Genomics, AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - Diana M. Pacheco
- Rumen Microbial Genomics, AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - Dong Li
- Rumen Microbial Genomics, AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - Samantha J. Noel
- Rumen Microbial Genomics, AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - Christina D. Moon
- Rumen Microbial Genomics, AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - Adrian L. Cookson
- Rumen Microbial Genomics, AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - Graeme T. Attwood
- Rumen Microbial Genomics, AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
- * E-mail:
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31
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Leahy SC, Kelly WJ, Altermann E, Ronimus RS, Yeoman CJ, Pacheco DM, Li D, Kong Z, McTavish S, Sang C, Lambie SC, Janssen PH, Dey D, Attwood GT. The genome sequence of the rumen methanogen Methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions. PLoS One 2010; 5:e8926. [PMID: 20126622 PMCID: PMC2812497 DOI: 10.1371/journal.pone.0008926] [Citation(s) in RCA: 197] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Accepted: 12/07/2009] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Methane (CH(4)) is a potent greenhouse gas (GHG), having a global warming potential 21 times that of carbon dioxide (CO(2)). 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 peptide-directed 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 (H(2)) 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.
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Affiliation(s)
- Sinead C. Leahy
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - William J. Kelly
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Eric Altermann
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Ron S. Ronimus
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Carl J. Yeoman
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Diana M. Pacheco
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Dong Li
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Zhanhao Kong
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Sharla McTavish
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Carrie Sang
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Suzanne C. Lambie
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Peter H. Janssen
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Debjit Dey
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Graeme T. Attwood
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
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Affiliation(s)
- S C Leahy
- Department of Microbiology, National University of Ireland, Western Road, Cork, Ireland
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