Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

Seshadri, Rekha; Leahy, Sinead C.; Attwood, Graeme T.; Teh, Koon Hoong; Lambie, Suzanne C.; Cookson, Adrian L.; Eloe-Fadrosh, Emiley A.; Pavlopoulos, Georgios A.; Hadjithomas, Michalis; Varghese, Neha J.; Paez-Espino, David; Palevich, Nikola; Janssen, Peter H.; Ronimus, Ron S.; Noel, Samantha; Soni, Priya; Reilly, Kerri; Atherly, Todd; Ziemer, Cherie; Wright, Andre-Denis; Ishaq, Suzanne; Cotta, Michael; Thompson, Stephanie; Crosley, Katie; McKain, Nest; Wallace, R. John; Flint, Harry J.; Martin, Jennifer C.; Forster, Robert J.; Gruninger, Robert J.; McAllister, Tim; Gilbert, Rosalind; Ouwerkerk, Diane; Klieve, Athol; Jassim, Rafat Al; Denman, Stuart; McSweeney, Chris; Rosewarne, Carly; Koike, Satoshi; Kobayashi, Yasuo; Mitsumori, Makoto; Shinkai, Takumi; Cravero, Silvio; Cucchi, María Cerón; Perry, Rechelle; Henderson, Gemma; Creevey, Christopher J.; Terrapon, Nicolas; Lapebie, Pascal; Drula, Elodie; Lombard, Vincent; Rubin, Edward; Kyrpides, Nikos C.; Henrissat, Bernard; Woyke, Tanja; Ivanova, Natalia N.; Kelly, William J.

doi:10.1038/nbt.4110

Title: Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

Journal Article · Mon Mar 19 00:00:00 EDT 2018 · Nature Biotechnology

DOI:https://doi.org/10.1038/nbt.4110· OSTI ID:1489281

;

; Attwood, Graeme T.; Teh, Koon Hoong; Lambie, Suzanne C.; Cookson, Adrian L.; Eloe-Fadrosh, Emiley A.; Pavlopoulos, Georgios A.; Hadjithomas, Michalis; Varghese, Neha J.;

; Palevich, Nikola; Janssen, Peter H.; Ronimus, Ron S.; Noel, Samantha; Soni, Priya; Reilly, Kerri; Atherly, Todd; Ziemer, Cherie; Wright, Andre-Denis more »

Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B 12, ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents ~75% of the genus-level bacterial and archaeal taxa present in the rumen.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Contributing Organization:: Hungate1000 Project Collaborators

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1489281

Alternate ID(s):: OSTI ID: 1542309

Journal Information:: Nature Biotechnology, Vol. 36, Issue 4; ISSN 1087-0156

Publisher:: Springer NatureCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 248 works

Citation information provided by
Web of Science

References (77)

Biome engineering-2020 Brüssow, Harald Microbial Biotechnology, Vol. 9, Issue 5 https://doi.org/10.1111/1751-7915.12391	journal	July 2016
Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements Mukherjee, Supratim; Stamatis, Dimitri; Bertsch, Jon Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw992	journal	October 2016
Toward a standard in structural genome annotation for prokaryotes Tripp, H. James; Sutton, Granger; White, Owen Standards in Genomic Sciences, Vol. 10, Issue 1 https://doi.org/10.1186/s40793-015-0034-9	journal	July 2015
1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life Mukherjee, Supratim; Seshadri, Rekha; Varghese, Neha J. Nature Biotechnology, Vol. 35, Issue 7 https://doi.org/10.1038/nbt.3886	journal	June 2017
Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation Browne, Hilary P.; Forster, Samuel C.; Anonye, Blessing O. Nature, Vol. 533, Issue 7604 https://doi.org/10.1038/nature17645	journal	May 2016
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data Chin, Chen-Shan; Alexander, David H.; Marks, Patrick Nature Methods, Vol. 10, Issue 6 https://doi.org/10.1038/nmeth.2474	journal	May 2013
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A. Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402 https://doi.org/10.1093/nar/25.17.3389	journal	September 1997
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P. PLoS ONE, Vol. 5, Issue 3 https://doi.org/10.1371/journal.pone.0009490	journal	March 2010
metaSPAdes: a new versatile metagenomic assembler Nurk, Sergey; Meleshko, Dmitry; Korobeynikov, Anton Genome Research, Vol. 27, Issue 5 https://doi.org/10.1101/gr.213959.116	journal	March 2017
Prodigal: prokaryotic gene recognition and translation initiation site identification Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-119	journal	March 2010
Computational approaches to predict bacteriophage–host relationships Edwards, Robert A.; McNair, Katelyn; Faust, Karoline FEMS Microbiology Reviews, Vol. 40, Issue 2 https://doi.org/10.1093/femsre/fuv048	journal	December 2015
MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences Luo, Chengwei; Rodriguez-R, Luis M.; Konstantinidis, Konstantinos T. Nucleic Acids Research, Vol. 42, Issue 8 https://doi.org/10.1093/nar/gku169	journal	March 2014
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T. Genome Research, Vol. 25, Issue 7 https://doi.org/10.1101/gr.186072.114	journal	May 2015
Ribosomal Database Project: data and tools for high throughput rRNA analysis Cole, James R.; Wang, Qiong; Fish, Jordan A. Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1244	journal	November 2013
Fast and accurate long-read alignment with Burrows–Wheeler transform Li, Heng; Durbin, Richard Bioinformatics, Vol. 26, Issue 5 https://doi.org/10.1093/bioinformatics/btp698	journal	January 2010
Prepartum and Postpartum Rumen Fluid Microbiomes: Characterization and Correlation with Production Traits in Dairy Cows Lima, Fabio S.; Oikonomou, Georgios; Lima, Svetlana F. Applied and Environmental Microbiology, Vol. 81, Issue 4 https://doi.org/10.1128/AEM.03138-14	journal	December 2014
Vitamin B 12 as a Modulator of Gut Microbial Ecology Degnan, Patrick H.; Taga, Michiko E.; Goodman, Andrew L. Cell Metabolism, Vol. 20, Issue 5 https://doi.org/10.1016/j.cmet.2014.10.002	journal	November 2014
PULDB: the expanded database of Polysaccharide Utilization Loci Terrapon, Nicolas; Lombard, Vincent; Drula, Élodie Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx1022	journal	October 2017
Microbiome Data Science: Understanding Our Microbial Planet Kyrpides, Nikos C.; Eloe-Fadrosh, Emiley A.; Ivanova, Natalia N. Trends in Microbiology, Vol. 24, Issue 6 https://doi.org/10.1016/j.tim.2016.02.011	journal	June 2016
Global Survey of the Bovine Salivary Proteome: Integrating Multidimensional Prefractionation, Targeted, and Glycocapture Strategies Ang, Ching-Seng; Binos, Steve; Knight, Matthew I. Journal of Proteome Research, Vol. 10, Issue 11 https://doi.org/10.1021/pr200516d	journal	November 2011
Adaptive seeds tame genomic sequence comparison Kielbasa, S. M.; Wan, R.; Sato, K. Genome Research, Vol. 21, Issue 3 https://doi.org/10.1101/gr.113985.110	journal	January 2011
Uncovering Earth’s virome Paez-Espino, David; Eloe-Fadrosh, Emiley A.; Pavlopoulos, Georgios A. Nature, Vol. 536, Issue 7617 https://doi.org/10.1038/nature19094	journal	August 2016
Status of the phylogenetic diversity census of ruminal microbiomes: Status of microbial census in rumen Kim, Minseok; Morrison, Mark; Yu, Zhongtang FEMS Microbiology Ecology, Vol. 76, Issue 1 https://doi.org/10.1111/j.1574-6941.2010.01029.x	journal	January 2011
Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes Solomon, Kevin V.; Haitjema, Charles H.; Henske, John K. Science, Vol. 351, Issue 6278 https://doi.org/10.1126/science.aad1431	journal	February 2016
The carbohydrate-active enzymes database (CAZy) in 2013 Lombard, Vincent; Golaconda Ramulu, Hemalatha; Drula, Elodie Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1178	journal	November 2013
Complex pectin metabolism by gut bacteria reveals novel catalytic functions Ndeh, Didier; Rogowski, Artur; Cartmell, Alan Nature, Vol. 544, Issue 7648 https://doi.org/10.1038/nature21725	journal	March 2017
RUMINANT NUTRITION SYMPOSIUM: How to use data on the rumen microbiome to improve our understanding of ruminant nutrition1,2 Firkins, J. L.; Yu, Z. Journal of Animal Science, Vol. 93, Issue 4 https://doi.org/10.2527/jas.2014-8754	journal	April 2015
The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota Lagkouvardos, Ilias; Pukall, Rüdiger; Abt, Birte Nature Microbiology, Vol. 1, Issue 10 https://doi.org/10.1038/nmicrobiol.2016.131	journal	August 2016
antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters Weber, Tilmann; Blin, Kai; Duddela, Srikanth Nucleic Acids Research, Vol. 43, Issue W1 https://doi.org/10.1093/nar/gkv437	journal	May 2015
Mosaic Evolution of Ruminant Stomach Lysozyme Genes Wen, Yi; Irwin, David M. Molecular Phylogenetics and Evolution, Vol. 13, Issue 3 https://doi.org/10.1006/mpev.1999.0651	journal	December 1999
Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range Henderson, Gemma; Cox, Faith; Ganesh, Siva Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep14567	journal	October 2015
IMG/M: integrated genome and metagenome comparative data analysis system Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw929	journal	October 2016
Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions Mistry, Jaina; Finn, Robert D.; Eddy, Sean R. Nucleic Acids Research, Vol. 41, Issue 12 https://doi.org/10.1093/nar/gkt263	journal	April 2013
The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation Mavromatis, Konstantinos; Land, Miriam L.; Brettin, Thomas S. PLoS ONE, Vol. 7, Issue 12 https://doi.org/10.1371/journal.pone.0048837	journal	December 2012
Gluconeogenesis in dairy cows: The secret of making sweet milk from sour dough Aschenbach, Jörg R.; Kristensen, Niels B.; Donkin, Shawn S. IUBMB Life, Vol. 62, Issue 12 https://doi.org/10.1002/iub.400	journal	December 2010
GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes Pati, Amrita; Ivanova, Natalia N.; Mikhailova, Natalia Nature Methods, Vol. 7, Issue 6 https://doi.org/10.1038/nmeth.1457	journal	May 2010
Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples White, James Robert; Nagarajan, Niranjan; Pop, Mihai PLoS Computational Biology, Vol. 5, Issue 4 https://doi.org/10.1371/journal.pcbi.1000352	journal	April 2009
RUMINANT NUTRITION SYMPOSIUM: Use of genomics and transcriptomics to identify strategies to lower ruminal methanogenesis1,2,3 McAllister, T. A.; Meale, S. J.; Valle, E. Journal of Animal Science, Vol. 93, Issue 4 https://doi.org/10.2527/jas.2014-8329	journal	April 2015
Genome Project Standards in a New Era of Sequencing Chain, P. S. G.; Grafham, D. V.; Fulton, R. S. Science, Vol. 326, Issue 5950 https://doi.org/10.1126/science.1180614	journal	October 2009
A Catalog of Reference Genomes from the Human Microbiome Nelson, K. E.; Weinstock, G. M.; Highlander, S. K. Science, Vol. 328, Issue 5981 https://doi.org/10.1126/science.1183605	journal	May 2010
Real-Time DNA Sequencing from Single Polymerase Molecules Eid, John; Fehr, Adrian; Gray, Jeremy Science, Vol. 323, Issue 5910, p. 133-138 https://doi.org/10.1126/science.1162986	journal	January 2009
Biomass use, production, feed efficiencies, and greenhouse gas emissions from global livestock systems Herrero, M.; Havlik, P.; Valin, H. Proceedings of the National Academy of Sciences, Vol. 110, Issue 52 https://doi.org/10.1073/pnas.1308149110	journal	December 2013
Ultrafast clustering algorithms for metagenomic sequence analysis Li, W.; Fu, L.; Niu, B. Briefings in Bioinformatics, Vol. 13, Issue 6 https://doi.org/10.1093/bib/bbs035	journal	July 2012
Agriculture: Steps to sustainable livestock Eisler, Mark C.; Lee, Michael R. F.; Tarlton, John F. Nature, Vol. 507, Issue 7490 https://doi.org/10.1038/507032a	journal	March 2014
The Jalview Java alignment editor Clamp, M.; Cuff, J.; Searle, S. M. Bioinformatics, Vol. 20, Issue 3 https://doi.org/10.1093/bioinformatics/btg430	journal	January 2004
Cellulose Degradation by Ruminal Microorganisms Weimer, Paul J. Critical Reviews in Biotechnology, Vol. 12, Issue 3 https://doi.org/10.3109/07388559209069192	journal	January 1992
An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography Nayfach, Stephen; Rodriguez-Mueller, Beltran; Garud, Nandita Genome Research, Vol. 26, Issue 11 https://doi.org/10.1101/gr.201863.115	journal	October 2016
Cellulosomes: bacterial nanomachines for dismantling plant polysaccharides Artzi, Lior; Bayer, Edward A.; Moraïs, Sarah Nature Reviews Microbiology, Vol. 15, Issue 2 https://doi.org/10.1038/nrmicro.2016.164	journal	December 2016
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs Zerbino, D. R.; Birney, E. Genome Research, Vol. 18, Issue 5 https://doi.org/10.1101/gr.074492.107	journal	February 2008
Rumen microbial (meta)genomics and its application to ruminant production Morgavi, D. P.; Kelly, W. J.; Janssen, P. H. animal, Vol. 7, Issue s1 https://doi.org/10.1017/S1751731112000419	journal	March 2012
Vitamin B12 in meat and dairy products Gille, D.; Schmid, A. Nutrition Reviews, Vol. 73, Issue 2 https://doi.org/10.1093/nutrit/nuu011	journal	January 2015
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees Letunic, Ivica; Bork, Peer Nucleic Acids Research, Vol. 44, Issue W1 https://doi.org/10.1093/nar/gkw290	journal	April 2016
Factors affecting intestinal starch digestion in ruminants: A review Harmon, D. L.; Yamka, R. M.; Elam, N. A. Canadian Journal of Animal Science, Vol. 84, Issue 3 https://doi.org/10.4141/A03-077	journal	September 2004
IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses Paez-Espino, David; Chen, I. -Min A.; Palaniappan, Krishna Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw1030	journal	October 2016
A Meta-analysis of Bacterial Diversity in the Feces of Cattle Kim, Minseok; Wells, James. E. Current Microbiology, Vol. 72, Issue 2 https://doi.org/10.1007/s00284-015-0931-6	journal	November 2015
Toward a Predictive Understanding of Earth’s Microbiomes to Address 21st Century Challenges Blaser, Martin J.; Cardon, Zoe G.; Cho, Mildred K. mBio, Vol. 7, Issue 3 https://doi.org/10.1128/mBio.00714-16	journal	May 2016
ALLPATHS: De novo assembly of whole-genome shotgun microreads Butler, J.; MacCallum, I.; Kleber, M. Genome Research, Vol. 18, Issue 5 https://doi.org/10.1101/gr.7337908	journal	February 2008
The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4) Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos Standards in Genomic Sciences, Vol. 11, Issue 1 https://doi.org/10.1186/s40793-016-0138-x	journal	February 2016
Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs Eloe-Fadrosh, Emiley A.; Paez-Espino, David; Jarett, Jessica Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms10476	journal	January 2016
Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpea-enriched microbiome characterised by lactic acid formation and utilisation Kamke, Janine; Kittelmann, Sandra; Soni, Priya Microbiome, Vol. 4, Issue 1 https://doi.org/10.1186/s40168-016-0201-2	journal	October 2016
Reducing emissions from agriculture to meet the 2 °C target Wollenberg, Eva; Richards, Meryl; Smith, Pete Global Change Biology, Vol. 22, Issue 12 https://doi.org/10.1111/gcb.13340	journal	July 2016
Bovine Host Genetic Variation Influences Rumen Microbial Methane Production with Best Selection Criterion for Low Methane Emitting and Efficiently Feed Converting Hosts Based on Metagenomic Gene Abundance Roehe, Rainer; Dewhurst, Richard J.; Duthie, Carol-Anne PLOS Genetics, Vol. 12, Issue 2 https://doi.org/10.1371/journal.pgen.1005846	journal	February 2016
Determining the culturability of the rumen bacterial microbiome: Targeting rumen bacteria for genome sequencing Creevey, Christopher J.; Kelly, William J.; Henderson, Gemma Microbial Biotechnology, Vol. 7, Issue 5 https://doi.org/10.1111/1751-7915.12141	journal	July 2014
Invited review: Enteric methane in dairy cattle production: Quantifying the opportunities and impact of reducing emissions Knapp, J. R.; Laur, G. L.; Vadas, P. A. Journal of Dairy Science, Vol. 97, Issue 6 https://doi.org/10.3168/jds.2013-7234	journal	June 2014
PhyloSift: phylogenetic analysis of genomes and metagenomes Darling, Aaron E.; Jospin, Guillaume; Lowe, Eric PeerJ, Vol. 2 https://doi.org/10.7717/peerj.243	journal	January 2014
Composition and Similarity of Bovine Rumen Microbiota across Individual Animals Jami, Elie; Mizrahi, Itzhak PLoS ONE, Vol. 7, Issue 3 https://doi.org/10.1371/journal.pone.0033306	journal	March 2012
Metagenomics of rumen bacteriophage from thirteen lactating dairy cattle Ross, Elizabeth M.; Petrovski, Steve; Moate, Peter J. BMC Microbiology, Vol. 13, Issue 1 https://doi.org/10.1186/1471-2180-13-242	journal	January 2013
Sporulation in Bacteria: Beyond the Standard Model Hutchison, Elizabeth A.; Miller, David A.; Angert, Esther R. Microbiology Spectrum, Vol. 2, Issue 5 https://doi.org/10.1128/microbiolspec.TBS-0013-2012	journal	October 2014
Sporulation capability and amylosome conservation among diverse human colonic and rumen isolates of the keystone starch-degrader Ruminococcus bromii : Comparative genomics of Mukhopadhya, Indrani; Moraïs, Sarah; Laverde-Gomez, Jenny Environmental Microbiology, Vol. 20, Issue 1 https://doi.org/10.1111/1462-2920.14000	journal	December 2017
Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen Hess, M.; Sczyrba, A.; Egan, R. Science, Vol. 331, Issue 6016 https://doi.org/10.1126/science.1200387	journal	January 2011
Food Security: The Challenge of Feeding 9 Billion People Godfray, H. C. J.; Beddington, J. R.; Crute, I. R. Science, Vol. 327, Issue 5967 https://doi.org/10.1126/science.1185383	journal	January 2010
How much do direct livestock emissions actually contribute to global warming? Reisinger, Andy; Clark, Harry Global Change Biology, Vol. 24, Issue 4 https://doi.org/10.1111/gcb.13975	journal	November 2017
Evolution by gene loss Albalat, Ricard; Cañestro, Cristian Nature Reviews Genetics, Vol. 17, Issue 7 https://doi.org/10.1038/nrg.2016.39	journal	April 2016
Bacterial Species of the Rumen Bryant, Marvin P. Bacteriological Reviews, Vol. 23, Issue 3 https://doi.org/10.1128/MMBR.23.3.125-153.1959	journal	January 1959
Massilia aromaticivorans sp. nov., a BTEX Degrading Bacterium Isolated from Arctic Soil Son, Jigwan; Lee, Hyosun; Kim, Mincheol Current Microbiology, Vol. 78, Issue 5 https://doi.org/10.1007/s00284-021-02379-y	journal	April 2021
Production of viable chicken by allogeneic transplantation of primordial germ cells induced from somatic cells Zhao, Ruifeng; Zuo, Qisheng; Yuan, Xia Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-23242-5	journal	May 2021
Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range Henderson, Gemma; Cox, Faith; Ganesh, Siva ETH Zurich https://doi.org/10.3929/ethz-b-000164426	text	January 2015

Cited By (57)

Metagenomic insights into the roles of Proteobacteria in the gastrointestinal microbiomes of healthy dogs and cats Moon, Christina D.; Young, Wayne; Maclean, Paul H. MicrobiologyOpen, Vol. 7, Issue 5 https://doi.org/10.1002/mbo3.677	journal	June 2018
Bacterial colonisation of reeds and cottonseed hulls in the rumen of Tarim red deer (Cervus elaphus yarkandensis) Qian, Wenxi; Ao, Weiping; Jia, Cunhui Antonie van Leeuwenhoek, Vol. 112, Issue 9 https://doi.org/10.1007/s10482-019-01260-0	journal	April 2019
Metatranscriptomics: an approach for retrieving novel eukaryotic genes from polluted and related environments Mukherjee, Arkadeep; Reddy, M. Sudhakara 3 Biotech, Vol. 10, Issue 2 https://doi.org/10.1007/s13205-020-2057-1	journal	January 2020
Review: The application of omics to rumen microbiota function Denman, S. E.; Morgavi, D. P.; McSweeney, C. S. animal, Vol. 12, Issue s2 https://doi.org/10.1017/s175173111800229x	journal	September 2018
Taxonomic and functional assessment using metatranscriptomics reveals the effect of Angus cattle on rumen microbial signatures Neves, A. L. A.; Chen, Y.; Lê Cao, K. -A. animal, Vol. 14, Issue 4 https://doi.org/10.1017/s1751731119002453	journal	October 2019
Review: Fifty years of research on rumen methanogenesis: lessons learned and future challenges for mitigation Beauchemin, K. A.; Ungerfeld, E. M.; Eckard, R. J. animal, Vol. 14, Issue S1 https://doi.org/10.1017/s1751731119003100	journal	February 2020
Review: Ruminal microbiome and microbial metabolome: effects of diet and ruminant host Newbold, C. J.; Ramos-Morales, E. animal, Vol. 14, Issue S1 https://doi.org/10.1017/s1751731119003252	journal	February 2020
Diverse hydrogen production and consumption pathways influence methane production in ruminants Greening, Chris; Geier, Renae; Wang, Cecilia The ISME Journal, Vol. 13, Issue 10 https://doi.org/10.1038/s41396-019-0464-2	journal	June 2019
Characterization of antibiotic resistance genes in the species of the rumen microbiota Sabino, Yasmin Neves Vieira; Santana, Mateus Ferreira; Oyama, Linda Boniface Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-13118-0	journal	November 2019
Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem Solden, Lindsey M.; Naas, Adrian E.; Roux, Simon Nature Microbiology, Vol. 3, Issue 11 https://doi.org/10.1038/s41564-018-0225-4	journal	October 2018
Common principles and best practices for engineering microbiomes Lawson, Christopher E.; Harcombe, William R.; Hatzenpichler, Roland Nature Reviews Microbiology, Vol. 17, Issue 12 https://doi.org/10.1038/s41579-019-0255-9	journal	September 2019
Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery Stewart, Robert D.; Auffret, Marc D.; Warr, Amanda Nature Biotechnology, Vol. 37, Issue 8 https://doi.org/10.1038/s41587-019-0202-3	journal	August 2019
Exploring the rumen fluid metabolome using liquid chromatography-high-resolution mass spectrometry and Molecular Networking de Almeida, Rafaela Takako Ribeiro; do Prado, Rodolpho Martin; Porto, Carla Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-36196-4	journal	December 2018
Whole rumen metagenome sequencing allows classifying and predicting feed efficiency and intake levels in cattle Delgado, Beatriz; Bach, Alex; Guasch, Isabel Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-018-36673-w	journal	January 2019
Energy conservation involving 2 respiratory circuits Schoelmerich, Marie Charlotte; Katsyv, Alexander; Dönig, Judith Proceedings of the National Academy of Sciences, Vol. 117, Issue 2 https://doi.org/10.1073/pnas.1914939117	journal	December 2019
A meta-analysis of the bovine gastrointestinal tract microbiota Holman, Devin B.; Gzyl, Katherine E. FEMS Microbiology Ecology, Vol. 95, Issue 6 https://doi.org/10.1093/femsec/fiz072	journal	May 2019
The first complete genomic structure of Butyrivibrio fibrisolvens and its chromid Rodríguez Hernáez, Javier; Cerón Cucchi, Maria Esperanza; Cravero, Silvio Microbial Genomics, Vol. 4, Issue 10 https://doi.org/10.1099/mgen.0.000216	journal	October 2018
Comparative Genomics of Rumen Butyrivibrio spp. Uncovers a Continuum of Polysaccharide-Degrading Capabilities Palevich, Nikola; Kelly, William J.; Leahy, Sinead C. Applied and Environmental Microbiology, Vol. 86, Issue 1 https://doi.org/10.1128/aem.01993-19	journal	October 2019
Use of a Fluorescent Analog of Glucose (2-NBDG) To Identify Uncultured Rumen Bacteria That Take Up Glucose Tao, Junyi; McCourt, Courtney; Sultana, Halima Applied and Environmental Microbiology, Vol. 85, Issue 7 https://doi.org/10.1128/aem.03018-18	journal	February 2019
Draft Genome Sequence and Annotation of Oribacterium sp. Strain C9, Isolated from a Cattle Rumen Kang, Seungha; Denman, Stuart; McSweeney, Chris Microbiology Resource Announcements, Vol. 8, Issue 13 https://doi.org/10.1128/mra.01562-18	journal	March 2019
Diversity and community of methanogens in the large intestine of finishing pigs Mi, Jiandui; Peng, Haiyan; Wu, Yinbao BMC Microbiology, Vol. 19, Issue 1 https://doi.org/10.1186/s12866-019-1459-x	journal	April 2019
Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation Bickhart, Derek M.; Watson, Mick; Koren, Sergey Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1760-x	journal	August 2019
Development and characterization of stable anaerobic thermophilic methanogenic microbiomes fermenting switchgrass at decreasing residence times Liang, Xiaoyu; Whitham, Jason M.; Holwerda, Evert K. Biotechnology for Biofuels, Vol. 11, Issue 1 https://doi.org/10.1186/s13068-018-1238-1	journal	September 2018
Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle Li, Fuyong; Li, Changxi; Chen, Yanhong Microbiome, Vol. 7, Issue 1 https://doi.org/10.1186/s40168-019-0699-1	journal	June 2019
Ruminal microbiome-host crosstalk stimulates the development of the ruminal epithelium in a lamb model Lin, Limei; Xie, Fei; Sun, Daming Microbiome, Vol. 7, Issue 1 https://doi.org/10.1186/s40168-019-0701-y	journal	June 2019
Can rumen bacteria communicate to each other? Won, Mi-Young; Oyama, Linda B.; Courtney, Stephen J. Microbiome, Vol. 8, Issue 1 https://doi.org/10.1186/s40168-020-00796-y	journal	February 2020
Occurrence and expression of genes encoding methyl-compound production in rumen bacteria Kelly, William J.; Leahy, Sinead C.; Kamke, Janine Animal Microbiome, Vol. 1, Issue 1 https://doi.org/10.1186/s42523-019-0016-0	journal	November 2019
Temporal stability of the rumen microbiota in beef cattle, and response to diet and supplements Snelling, Timothy J.; Auffret, Marc D.; Duthie, Carol-Anne Animal Microbiome, Vol. 1, Issue 1 https://doi.org/10.1186/s42523-019-0018-y	journal	November 2019
Domesticated equine species and their derived hybrids differ in their fecal microbiota Edwards, J. E.; Schennink, A.; Burden, F. Animal Microbiome, Vol. 2, Issue 1 https://doi.org/10.1186/s42523-020-00027-7	journal	March 2020
Evaluating Established Methods for Rumen 16S rRNA Amplicon Sequencing With Mock Microbial Populations McGovern, Emily; Waters, Sinéad M.; Blackshields, Gordon Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.01365	journal	June 2018
Insights Into Culturomics of the Rumen Microbiome Zehavi, Tamar; Probst, Maraike; Mizrahi, Itzhak Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.01999	journal	August 2018
Applications of the Soil, Plant and Rumen Microbiomes in Pastoral Agriculture Attwood, Graeme T.; Wakelin, Steve A.; Leahy, Sinead C. Frontiers in Nutrition, Vol. 6 https://doi.org/10.3389/fnut.2019.00107	journal	July 2019
Comparative Genomics Analysis of Lactobacillus mucosae from Different Niches Jia, Yan; Yang, Bo; Ross, Paul Genes, Vol. 11, Issue 1 https://doi.org/10.3390/genes11010095	journal	January 2020
Effects of Chestnut Tannin Extract, Vescalagin and Gallic Acid on the Dimethyl Acetals Profile and Microbial Community Composition in Rumen Liquor: An In Vitro Study Mannelli, Federica; Daghio, Matteo; Alves, Susana P. Microorganisms, Vol. 7, Issue 7 https://doi.org/10.3390/microorganisms7070202	journal	July 2019
Cowpi: A Rumen Microbiome Focussed Version Of The Picrust Functional Inference Software Wilkinson, Toby James; Huws, Sharon Ann; Elizabeth, Edwards. Joan Zenodo https://doi.org/10.5281/zenodo.1252857	text	January 2018
Improved taxonomic assignment of rumen bacterial 16S rRNA sequences using a revised SILVA taxonomic framework Henderson, Gemma; Yilmaz, Pelin; Kumar, Sandeep PeerJ, Vol. 7 https://doi.org/10.7717/peerj.6496	journal	January 2019
Islands in the stream: from individual to communal fiber degradation in the rumen ecosystem Moraïs, Sarah; Mizrahi, Itzhak FEMS Microbiology Reviews, Vol. 43, Issue 4 https://doi.org/10.1093/femsre/fuz007	journal	April 2019
A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment Li, Junhua; Zhong, Huanzi; Ramayo-Caldas, Yuliaxis GigaScience, Vol. 9, Issue 6 https://doi.org/10.1093/gigascience/giaa057	journal	May 2020
CAMITAX: Taxon labels for microbial genomes Bremges, Andreas; Fritz, Adrian; McHardy, Alice C. GigaScience, Vol. 9, Issue 1 https://doi.org/10.1093/gigascience/giz154	journal	January 2020
A microbial sea of possibilities: current knowledge and prospects for an improved understanding of the fish microbiome Legrand, Thibault P. R. A.; Wynne, James W.; Weyrich, Laura S. Reviews in Aquaculture, Vol. 12, Issue 2 https://doi.org/10.1111/raq.12375	journal	August 2019
Medium-Chain Fatty Acid Synthesis by “ Candidatus Weimeria bifida” gen. nov., sp. nov., and “ Candidatus Pseudoramibacter fermentans” sp. nov. Scarborough, Matthew J.; Myers, Kevin S.; Donohue, Timothy J. Applied and Environmental Microbiology, Vol. 86, Issue 3 https://doi.org/10.1128/aem.02242-19	journal	November 2019
Molecular Dating of the Emergence of Anaerobic Rumen Fungi and the Impact of Laterally Acquired Genes Wang, Yan; Youssef, Noha H.; Couger, Matthew Brian mSystems, Vol. 4, Issue 4 https://doi.org/10.1128/mSystems.00247-19	journal	August 2019
Metagenomic biomarker discovery and explanation Segata, Nicola; Izard, Jacques; Waldron, Levi Genome Biology, Vol. 12, Issue 6 https://doi.org/10.1186/gb-2011-12-6-r60	journal	January 2011
Heterogeneous development of methanogens and the correlation with bacteria in the rumen and cecum of sika deer (Cervus nippon) during early life suggest different ecology relevance Li, Zhipeng; Wang, Xiaoxu; Zhang, Ting BMC Microbiology, Vol. 19, Issue 1 https://doi.org/10.1186/s12866-019-1504-9	journal	June 2019
Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle Li, Fuyong; Hitch, Thomas C. A.; Chen, Yanhong Microbiome, Vol. 7, Issue 1 https://doi.org/10.1186/s40168-019-0618-5	journal	January 2019
Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future Huws, Sharon A.; Creevey, Christopher J.; Oyama, Linda B. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.02161	journal	September 2018
Cowpi: A Rumen Microbiome Focussed Version Of The Picrust Functional Inference Software Wilkinson, Toby James; Huws, Sharon Ann; Elizabeth, Edwards. Joan Zenodo https://doi.org/10.5281/zenodo.1252858	text	January 2018
Diets with and without edible cricket support a similar level of diversity in the gut microbiome of dogs Jarett, Jessica K.; Carlson, Anne; Rossoni Serao, Mariana PeerJ, Vol. 7 https://doi.org/10.7717/peerj.7661	journal	January 2019
Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber Hagen, Live H.; Brooke, Charles G.; Shaw, Claire A. The ISME Journal, Vol. 15, Issue 2 https://doi.org/10.1038/s41396-020-00769-x	journal	September 2020
Comparing the Microbial Community in Four Stomach of Dairy Cattle, Yellow Cattle and Three Yak Herds in Qinghai-Tibetan Plateau Xin, Jinwei; Chai, Zhixin; Zhang, Chengfu Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01547	journal	July 2019
CowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software Wilkinson, Toby J.; Huws, Sharon A.; Edwards, Joan E. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.01095	journal	May 2018
Co-abundance analysis reveals hidden players associated with high methane yield phenotype in sheep rumen microbiome Ghanbari Maman, Leila; Palizban, Fahimeh; Fallah Atanaki, Fereshteh Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-61942-y	journal	March 2020
IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes Paez-Espino, David; Roux, Simon; Chen, I-Min A. Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky1127	journal	November 2018
Genomic insights into ruminant evolution: from past to future prospects Wang, Bao; Chen, Lei; Wang, Wen Zool. Res., Vol. 40, Issue 6 https://doi.org/10.24272/j.issn.2095-8137.2019.061	journal	January 2019
Humic Substances Alter Ammonia Production and the Microbial Populations Within a RUSITEC Fed a Mixed Hay – Concentrate Diet Terry, Stephanie A.; Ramos, Aline F. O.; Holman, Devin B. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.01410	journal	July 2018
Use of Lactic Acid Bacteria to Reduce Methane Production in Ruminants, a Critical Review Doyle, Natasha; Mbandlwa, Philiswa; Kelly, William J. Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.02207	journal	October 2019
Comparison of Ruminal Degradability, Indigestible Neutral Detergent Fiber, and Total-Tract Digestibility of Three Main Crop Straws with Alfalfa Hay and Corn Silage Wang, Erdan; Wang, Jidong; Lv, Jiaying Animals, Vol. 11, Issue 11 https://doi.org/10.3390/ani11113218	journal	November 2021

Similar Records

Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome

Journal Article · Fri Jun 06 00:00:00 EDT 2014 · Genome Research · OSTI ID:1489281

Shi, Weibing; Moon, Christina D.; Leahy, Sinead C.; +20 more

Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpea-enriched microbiome characterised by lactic acid formation and utilisation

Journal Article · Wed Oct 19 00:00:00 EDT 2016 · Microbiome · OSTI ID:1489281

Kamke, Janine; Kittelmann, Sandra; Soni, Priya; +8 more

Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep

Journal Article · Tue Aug 08 00:00:00 EDT 2017 · BMC Research Notes · OSTI ID:1489281

Kamke, Janine; Soni, Priya; Li, Yang; +7 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES

Title: Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

Citation Formats

References (77)

Cited By (57)

Similar Records

Related Subjects