Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

resource OPEN © 2018 Nature America, Inc., part of Springer Nature. All rights reserved. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection Rekha Seshadri1,9    , Sinead C Leahy2,8,9    , Graeme T Attwood2, Koon Hoong Teh2,8, Suzanne C Lambie2,8, Adrian L Cookson2, Emiley A Eloe-Fadrosh1, Georgios A Pavlopoulos1, Michalis Hadjithomas1, Neha J Varghese1, David Paez-Espino1    , Hungate1000 project collaborators3, Rechelle Perry2, Gemma Henderson2,8, Christopher J Creevey4, Nicolas Terrapon5,6    , Pascal Lapebie5,6, Elodie Drula5,6, Vincent Lombard5,6, Edward Rubin1,8, Nikos C Kyrpides1, Bernard Henrissat5–7, Tanja Woyke1    , Natalia N Ivanova1, William J Kelly2,8     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 B12, 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. Climate change and feeding a growing global population are the two biggest challenges facing agriculture1. Ruminant livestock have an important role in food security2; they convert low-value lignocellulosic plant material into high-value animal proteins that include milk, meat and fiber products. Microorganisms present in the rumen3,4 ferment polysaccharides to yield short-chain fatty acids (SCFAs; acetate, butyrate and propionate) that are absorbed across the rumen epithelium and used by the ruminant for maintenance and growth. The rumen represents one of the most rapid and efficient lignocellulose depolymerization and utilization systems known, and is a promising source of enzymes for application in lignocellulose-based biofuel production5. Enteric fermentation in ruminants is also the single largest anthropogenic source of methane (CH4)6, and each year these animals release ~125 million tonnes of CH4 into the atmosphere. Targets to reduce agricultural carbon emissions have been proposed7, with >100 countries pledging to reduce agricultural greenhouse gas emissions in the 2015 Paris Agreement of the United Nations Framework Convention on Climate Change. Consequently, improved knowledge of the flow of carbon through the rumen by lignocellulose degradation and fermentation to SCFAs and CH4 is relevant to food security, sustainability and greenhouse gas emissions. Understanding the functions of the rumen microbiome is crucial to the development of technologies and practices that support efficient global food production from ruminants while minimizing greenhouse gas emissions. The Rumen Microbial Genomics Network (http://www.rmgnetwork.org/) was launched under the auspices of the Livestock Research Group of the Global Research Alliance (http:// globalresearchalliance.org/research/livestock/) to further this understanding, with the generation of a reference microbial genome catalog—the Hungate1000 project—as a primary collaborative objective. Although the microbial ecology of the rumen has long been the focus of research8,9, at the beginning of the project reference genomes were available for only 14 bacteria and one methanogen, so that genomic diversity was largely unexplored. The Hungate1000 project was initiated as a community resource in 2012, and the collection assembled includes virtually all the bacterial 1Department of Energy, Joint Genome Institute, Walnut Creek, California, USA. 2AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand. 3A comprehensive list of authors and affiliations is at the end of the paper. 4Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Wales, UK. 5Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Marseille, France. 6Institut National de la Recherche Agronomique, Marseille, France. 7Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia. 8Present addresses: New Zealand Agricultural Greenhouse Gas Research Centre, Palmerston North, New Zealand (S.C.Leahy); Massey University, Auckland, New Zealand (K.H.T.); Chr. Hansen A/S, Hørsholm, Denmark (G.H.); Metabiota, San Francisco California, USA (E.R.); Donvis Ltd, Palmerston North, New Zealand (W.J.K.);. Hill Laboratories, Blenheim, New Zealand (S.C.Lambie). 9These authors contributed equally to this work. Correspondence should be addressed to W.J.K. (), S.C.L. () or R.S. (). Received 16 August 2017; accepted 23 February 2018; published online 19 March 2018; doi:10.1038/nbt.4110 nature biotechnology VOLUME 36 NUMBER 4 APRIL 2018 359 © 2018 Nature America, Inc., part of Springer Nature. All rights reserved. resource and archaeal species that have been cultivated from the rumens of a diverse group of animals10. We surveyed Members of the Rumen Microbial Genomics Network and requested they provide cultures of interest. We supplemented these with additional cultures purchased from culture collections to generate the most comprehensive collection possible. These cultures are available to researchers, and we envisage that additional organisms will have their genome sequences included as more rumen microbes are able to be cultivated. Large-scale reference genome catalogs, including the Human Microbiome Project (HMP)11 and the Genomic Encyclopedia of Bacteria and Archaea (GEBA)12 have helped to improve our understanding of microbiome functions, diversity and interactions with the host. The success of these efforts has resulted in calls for continued development of high-quality reference genome catalogs13,14, and led to a resurgence in efforts to cultivate microorganisms15–17. This high-quality reference genome catalog for rumen bacteria and archaea increases our understanding of rumen functions by revealing degradative and physiological capabilities, and identifying potential rumen-specific adaptations. RESULTS Reference rumen genomes Members of nine phyla, 48 families and 82 genera (Supplementary Table 1 and Supplementary Note 1) are present in the Hungate Collection. The organisms were chosen to make the (...truncated)