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French National Institute for Agricultural Research
(Contribution by Rafael Muñoz-Tamayo)
My name is Rafael Muñoz-Tamayo and I am from Colombia. I am a researcher at the French National Institute for Agricultural Research (INRA) joining the MoSAR (Systemic modelling applied to ruminants) team in 2014.
I am a mathematical modeller of biological systems with a background in chemical engineering and automatic control. The aim of my research project is to enhance understanding of the dynamic interplay between the diet, the rumen microbiota and the ruminant animal via an interdisciplinary approach covering microbiology, chemistry, thermodynamics, animal nutrition and mathematical modelling. To attain this goal, I collaborate with scientists from different domains including rumen microbiology.
The type of mathematical models we develop are known as dynamic models. We focus on models that can predict the dynamic pattern of metabolism by rumen microbes (Muñoz-Tamayo et al., 2016; Munoz-Tamayo et al., 2018) with the ultimate goal of developing mathematical tools that can guide the design of microbial manipulation strategies to improve ruminant function and promote a healthy microbial ecosystem for sustainable livestock farming. While we have mainly focused on rumen in vitro fermentation, we are starting to build models to tackle the in vivo scenario (Muñoz-Tamayo et al., 2019). Very recently, we have been interested in genome-scale metabolic modelling approaches. I believe that integrating modelling with microbiology is a great approach for improving our knowledge of the rumen microbiota. Being part of the RMG network is a great opportunity to build up exciting collaborations.
I participated in the European projects
· RumenPredict FACCE ERA-GAS project: Predicting appropriate GHG mitigation strategies based on modelling variables that contribute to ruminant environmental impact
· H2020 MASTER project: Microbiome applications for sustainable food systems through technologies and enterprise
Last but not least, I am very happy to be leading the open initiative 'Peer Community in Animal Science' (https://animsci.peercommunityin.org/) and to have so many RMG members participating!
Key publications
Muñoz-Tamayo R, Giger-Reverdin S and Sauvant D 2016. Mechanistic modelling of in vitro fermentation by rumen microbiota. Anim. Feed Sci. Technol. 220, 1–21. https://doi.org/10.1016/j.anifeedsci.2016.07.005
Munoz-Tamayo R, Popova M, Tillier M, Morgavi DP, Morel J-P, Fonty G and Morel-Desrosiers N 2018. Hydrogenotrophic methanogens of the mammalian gut: functionally similar, thermodynamically different. A modelling approach. bioRxiv. https://doi.org/10.1101/445171
Muñoz-Tamayo R, Ramirez Agudelo JF, Dewhurst RJ, Miller G, Vernon T and Kettle H 2019. A parsimonious software sensor for estimating the individual dynamic pattern of methane emissions from cattle. Animal 13, 1180–1187. https://doi.org/10.1017/S1751731118002550
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The Functional Microbiome Research Group in Aachen
(Contribution by Thomas Hitch)
The Functional Microbiome Research Group headed by Prof. Thomas Clavel is based at the RWTH University Hospital in Aachen, Germany. Whilst the group focuses on the human, pig and mouse gut microbiomes and their interaction with the host, a large section of our research is on anaerobic cultivation of novel bacterial species.
Currently the group has culture collections for multiple species including mice, pig, chicken and humans. A major contribution of our group to bacterial taxonomy is the description of the family Muribaculaceae, previously S24-7. The publication of the mouse intestinal bacterial collection (miBC; see www.dsmz.de/miBC) included Muribaculum instestinale, the type species for this family (Lagkouvardos et al., 2016). 16S rRNA gene-based ecological analysis identified the rodent gut as the most common host for this family; ~40% of bovine gut samples and ~30% of 'ruminant stomach' samples contained a member of this family (Lagkouvardos et al., 2019). Muribaculaceae species have also been suggested to contribute to a core rumen microbiota in beef cattle (Li et al., 2019).
Along with the application of classical cultivation methods for the isolation of novel bacteria, our group is also interested in new technologies to address old issues. For instance, PhD student Afrizal has been working on microfluidic-based workflows for rapid isolation of anaerobic bacteria.
Additionally our group studies the functional potential of the microbiome. Of particular interests are lipolytic enzymes (Thomas Hitch) (Hitch and Clavel, 2019) and the production of secondary bile acids and their effect on the host (David Wylensek, Esther Wortmann and Theresa Streidl).
Process Infographic
The team
References: 1. Hitch, T. C. A. and Clavel, T. (2019) 'A proposed update for the classification and description of bacterial lipolytic enzymes', PeerJ, 7(e7249). doi: 10.7717/peerj.7249.; 2. Lagkouvardos, I. et al. (2016) 'The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota', Nature Microbiology. Nature Publishing Group, 1(10), p. 16131. doi: 10.1038/nmicrobiol.2016.131.; 3. Lagkouvardos, I. et al. (2019) 'Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family', Microbiome. Microbiome, 7(1), pp. 1–15. doi: 10.1186/s40168-019-0637-2.; 4. Li, F. et al. (2019) 'Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle', Microbiome. Microbiome, 7(1), pp. 1–17. doi: 10.1186/s40168-019-0699-1.
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AgResearch- New Zealand & Rumen microbiology
(Contribution by Sinead Leahy)
Agriculture is a major contributor to New Zealand's economy and each year the sector generates around 35% of the country's export revenue. New Zealand exports are sought after internationally and most of the meat, wool, and milk that is produced is exported. New Zealand operates predominantly grass-based livestock systems, in which animals graze outside all year round. Ruminant animals such as cows, sheep and deer are our most important farmed animals, and there is a population of over 38 million ruminants (Stats NZ, 2017). However, the agricultural sector in New Zealand is facing some stern challenges. While farming has long been the backbone of New Zealand's economy, and is a significant part of its cultural and aesthetic landscape (Image 1), it is also a significant contributor to some of the nation's environmental issues. For example, almost half of New Zealand's greenhouse gas emissions (48% in 2017) come from agriculture, comprising methane and nitrous oxide from mainly ruminant sources. It is therefore critical that New Zealand scientists remain at the forefront in the development of environmentally sustainable pastoral production systems. Understanding the functions of rumen microbes has an important role in this development, and as such, has had a long history and focus in New Zealand.
Image 1
Historical Background
The first report of rumen microbiology research in New Zealand starts 70 years years ago in 1949, investigating propionate formation in the rumen2. Subsequent records of research in rumen microbiology related to New Zealand are from three papers published by Alan Johns in the early 1950s3-5. This created interest in the field and, in the 1960s, Dr Richard Clarke and Mr Graham Naylor continued to investigate the relationship between microbes living in the cattle rumen and a condition called "bloat". After the development of the Hungate anaerobic culturing technique, work was continued by Dr Tom Bauchop, who used this technique to develop methods for isolating and identifying anaerobic rumen fungi. Dr Keith Joblin was also interested in the digestion of fibre, and for over two decades he continued to investigate how the interactions among fungi, bacteria and methanogens contributed to fibre digestion. In 1982, Dr Bill Kelly joined the rumen microbiology team and with Dr Rod Asmundson focused on developing the genetic basis for better understanding the ability of rumen bacteria to digest fibre. However, by the mid-1980s, the field of rumen microbiology very nearly collapsed altogether in New Zealand, in part because of a shift in government policy towards "user pays," whereby scientists were encouraged to move into other areas of research in an effort to generate more direct funding. Fortunately, Naylor and Joblin stuck to investigating fibre digestion in the rumen and, by the late 1980s, new technologies had become widely available which allowed investigation of the rumen microbes at the molecular level. In the early 1990s, Dr Marc Ulyatt began to link work in the rumen back to animal nutrition. Ulyatt took a holistic approach and began to connect forage research with studies of the rumen and its microbial contents and further related this to protein uptake and animal nutrition generally. Within this programme, Dr Graeme Attwood worked on characterising protein-degrading bacteria from the rumen. The knowledge generated in this area was key to understanding how animal feeds and rumen microbial processes contribute to product quality aspects (off flavours in milk and meat). In 2002, Attwood started the Rumen Microbial Genomics Programme. The group developed expertise in sequencing the genomes of rumen microorganisms, targeting key players in two main processes in the rumen: the breakdown of plant polysaccharides by adherent rumen bacteria, and methane formation by rumen methanogens. This research continues today.
Today
Since the mid-2000s the Rumen Microbiology Team based at AgResearch Limited's Grasslands campus, Palmerston North, has continued to expand and grow. Today the team consists of over 15 scientists, technicians and students (Image 2). Recent research highlights from the team include the first genome sequence of a rumen methanogen published in 20106. This work has helped underpin the downstream development of methane mitigation technologies such as methane inhibitors and vaccines which the team actively contributes to. The team has been active in the development of tools required to work with methanogens7,8 and has made valuable contributions to the structures of enzymes from methanogens9. In 2014, the team was involved in understanding the microbial component of sheep which had been selectively bred for both a high and low methane emissions phenotype5. New Zealand has been the first country in the world to directly breed for a low emissions trait in ruminants. In 2015, the Global Rumen Census project was led and published6 by the team. It represents the most extensive exploration of rumen microbial communities to date and was supported by 140 scientists from 73 research institutions worldwide. In 2018, the team continued its international collaborations, 57 researchers from 14 research organisations and led and published the Hungate collection7. This project represented the single largest effort to provide a catalogued and curated culture and genome resource for rumen microbes. Both the Global Rumen Census and Hungate collection have been collaborations among members of the Rumen Microbial Genomic network and would not have been possible without the support of the global rumen microbial research community.
A snapshot in time - some past and present members of the Rumen Microbiology team
References: 1. AgResearch Science Review (2010) The biology of rumen microflora, pp 59-63.; 2. Craig AS (1989) Jubilee History of the Biotechnology Division, 1938-1988. Biotechnology Division, DSIR, Palmerston North, New Zealand.; 3. Johns AT (1951) The mechanism of propionic acid formation by Veillonella gazogenes. Journal of General Microbiology 5: 326-336.; 4. Johns AT (1951) Isolation of a bacterium, producing propionic acid, from the rumen of sheep. Journal of General Microbiology 5: 317-325.; 5. AT Johns (1952) The mechanism of propionic acid formation by Clostridium propionicum. Journal of General Microbiology 6: 123-127.; 6. Leahy SC et al. (2010) The genome sequence of the rumen methanogen Methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions. PLoS One 5: e8926.; 7. Weimar MR et al. (2017) Development of multiwell-plate methods using pure cultures of methanogens to identify new inhibitors for suppressing ruminant methane emissions. Applied Environmental Microbiology 83:15.; 8. Muetzel S et al.(2018) A small scale rumen incubation system to screen chemical libraries for potential methane inhibitors, Animal Feed Science and Technology 244:88-92; 9. Carbone V et al. (2015) Structure and evolution of the archaeal lipid synthesis enzyme sn-glycerol-1-phosphate dehydrogenase. Journal of Biologial Chemistry 290:21690-21704.; 10. Shi W et al. (2014) Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome. Genome Research 24:1517-1525.; 11. Henderson G et al. (2015) Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Scientific Reports 6:19175.; 12. Seshadri R et al. (2018) Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnology 36:359-367.
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