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Roques S, Martinez-Fernandez G, Ramayo-Caldas Y, Popova M, Denman S, Meale SJ, Morgavi DP. Recent Advances in Enteric Methane Mitigation and the Long Road to Sustainable Ruminant Production. Annu Rev Anim Biosci 2024; 12:321-343. [PMID: 38079599 DOI: 10.1146/annurev-animal-021022-024931] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Mitigation of methane emission, a potent greenhouse gas, is a worldwide priority to limit global warming. A substantial part of anthropogenic methane is emitted by the livestock sector, as methane is a normal product of ruminant digestion. We present the latest developments and challenges ahead of the main efficient mitigation strategies of enteric methane production in ruminants. Numerous mitigation strategies have been developed in the last decades, from dietary manipulation and breeding to targeting of methanogens, the microbes that produce methane. The most recent advances focus on specific inhibition of key enzymes involved in methanogenesis. But these inhibitors, although efficient, are not affordable and not adapted to the extensive farming systems prevalent in low- and middle-income countries. Effective global mitigation of methane emissions from livestock should be based not only on scientific progress but also on the feasibility and accessibility of mitigation strategies.
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Affiliation(s)
- Simon Roques
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, Saint-Genes-Champanelle, France; , ,
| | | | - Yuliaxis Ramayo-Caldas
- Animal Breeding and Genetics Program, Institute of Agrifood Research and Technology (IRTA), Torre Marimon, Caldes de Montbui, Spain;
| | - Milka Popova
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, Saint-Genes-Champanelle, France; , ,
| | - Stuart Denman
- Agriculture and Food, CSIRO, St. Lucia, Queensland, Australia; ,
| | - Sarah J Meale
- School of Agriculture and Food Sustainability, Faculty of Science, University of Queensland, Gatton, Queensland, Australia;
| | - Diego P Morgavi
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, Saint-Genes-Champanelle, France; , ,
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2
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Monteiro A, Barreto-Mendes L, Fanchone A, Morgavi DP, Pedreira BC, Magalhães CAS, Abdalla AL, Eugène M. Crop-livestock-forestry systems as a strategy for mitigating greenhouse gas emissions and enhancing the sustainability of forage-based livestock systems in the Amazon biome. Sci Total Environ 2024; 906:167396. [PMID: 37778569 DOI: 10.1016/j.scitotenv.2023.167396] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/21/2023] [Accepted: 09/24/2023] [Indexed: 10/03/2023]
Abstract
Intensification of livestock systems becomes essential to meet the food demand of the growing world population, but it is important to consider the environmental impact of these systems. To assess the potential of forage-based livestock systems to offset greenhouse gas (GHG) emissions, the net carbon (C) balance of four systems in the Brazilian Amazon Biome was estimated: livestock (L) with a monoculture of Marandu palisade grass [Brachiaria brizantha (Hochst. ex A. Rich.) R. D. Webster]; livestock-forestry (LF) with palisade grass intercropped with three rows of eucalyptus at 128 trees/ha; crop-livestock (CL) with soybeans and then corn + palisade grass, rotated with livestock every two years; and crop-livestock-forestry (CLF) with CL + one row of eucalyptus at 72 trees/ha. Over the four years studied, the systems with crops (CL and CLF) produced more human-edible protein than those without them (L and LF) (3010 vs. 755 kg/ha). Methane contributed the most to total GHG emissions: a mean of 85 % for L and LF and 67 % for CL and CLF. Consequently, L and LF had greater total GHG emissions (mean of 30 Mg CO2eq/ha/year). Over the four years, the system with the most negative net C balance (i.e., C storage) was LF when expressed per ha (-53.3 Mg CO2eq/ha), CLF when expressed per kg of carcass (-26 kg CO2eq/kg carcass), and LF when expressed per kg of human-edible protein (-72 kg CO2eq/kg human-edible protein). Even the L system can store C if well managed, leading to benefits such as increased meat as well as improved soil quality. Moreover, including crops and forestry in these livestock systems enhances these benefits, emphasizing the potential of integrated systems to offset GHG emissions.
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Affiliation(s)
- Alyce Monteiro
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France; University of São Paulo, Center for Nuclear Energy in Agriculture, Laboratory of Animal Nutrition, Av. Centenário, 303, São Dimas, 13400-970 Piracicaba, SP, Brazil
| | - Luciano Barreto-Mendes
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - Audrey Fanchone
- INRAE, ASSET, Centre Antilles-Guyane, Domaine Duclos, Prise d'Eau, 97170 Petit Bourg, Guadeloupe, France
| | - Diego P Morgavi
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - Bruno C Pedreira
- Department of Plant Science, University of Tennessee, Knoxville, TN, 37996, USA.
| | - Ciro A S Magalhães
- Brazilian Agricultural Research Corporation (Embrapa Agrossilvipastoril), 78550-970 Sinop, MT, Brazil
| | - Adibe L Abdalla
- University of São Paulo, Center for Nuclear Energy in Agriculture, Laboratory of Animal Nutrition, Av. Centenário, 303, São Dimas, 13400-970 Piracicaba, SP, Brazil
| | - Maguy Eugène
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
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Xu Q, Ungerfeld EM, Morgavi DP, Waters SM, Liu J, Du W, Zhao S. Editorial: Rumen microbiome: interacting with host genetics, dietary nutrients metabolism, animal production, and environment. Front Microbiol 2023; 14:1267149. [PMID: 37779689 PMCID: PMC10539901 DOI: 10.3389/fmicb.2023.1267149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 08/28/2023] [Indexed: 10/03/2023] Open
Affiliation(s)
- Qingbiao Xu
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Emilio M. Ungerfeld
- Centro Regional de Investigación Carillanca, Instituto de Investigaciones Agropecuarias, Vilcún, La Araucanía, Chile
| | - Diego P. Morgavi
- INRAE, VetAgro Sup, UMR Herbivores, Université Clermont Auvergne, Saint-Genès-Champanelle, France
| | - Sinead M. Waters
- Teagasc, Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Dunsany, Ireland
| | - Jinxin Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Wenjuan Du
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shengguo Zhao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Morgavi DP, Cantalapiedra-Hijar G, Eugène M, Martin C, Noziere P, Popova M, Ortigues-Marty I, Muñoz-Tamayo R, Ungerfeld EM. Review: Reducing enteric methane emissions improves energy metabolism in livestock: is the tenet right? Animal 2023; 17 Suppl 3:100830. [PMID: 37263815 DOI: 10.1016/j.animal.2023.100830] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/21/2022] [Accepted: 12/30/2022] [Indexed: 06/03/2023] Open
Abstract
The production of enteric methane in the gastrointestinal tract of livestock is considered as an energy loss in the equations for estimating energy metabolism in feeding systems. Therefore, the spared energy resulting from specific inhibition of methane emissions should be re-equilibrated with other factors of the equation. And, it is commonly assumed that net energy from feeds increases, thus benefitting production functions, particularly in ruminants due to the important production of methane in the rumen. Notwithstanding, we confirm in this work that inhibition of emissions in ruminants does not transpose into consistent improvements in production. Theoretical calculations of energy flows using experimental data show that the expected improvement in net energy for production is small and difficult to detect under the prevailing, moderate inhibition of methane production (≈25%) obtained using feed additives inhibiting methanogenesis. Importantly, the calculation of energy partitioning using canonical models might not be adequate when methanogenesis is inhibited. There is a lack of information on various parameters that play a role in energy partitioning and that may be affected under provoked abatement of methane. The formula used to calculate heat production based on respiratory exchanges should be validated when methanogenesis is inhibited. Also, a better understanding is needed of the effects of inhibition on fermentation products, fermentation heat, and microbial biomass. Inhibition induces the accumulation of H2, the main substrate used to produce methane, that has no energetic value for the host, and it is not extensively used by the majority of rumen microbes. Currently, the fate of this excess of H2 and its consequences on the microbiota and the host are not well known. All this additional information will provide a better account of energy transactions in ruminants when enteric methanogenesis is inhibited. Based on the available information, it is concluded that the claim that enteric methane inhibition will translate into more feed-efficient animals is not warranted.
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Affiliation(s)
- D P Morgavi
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France.
| | - G Cantalapiedra-Hijar
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France
| | - M Eugène
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France
| | - C Martin
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France
| | - P Noziere
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France
| | - M Popova
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France
| | - I Ortigues-Marty
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France
| | - R Muñoz-Tamayo
- Université Paris-Saclay, INRAE, AgroParisTech, UMR Modélisation Systémique Appliquée aux Ruminants, 91120 Palaiseau, France
| | - E M Ungerfeld
- Centro Regional de Investigación Carillanca, Instituto de Investigaciones Agropecuarias INIA, Temuco 4880000, Chile
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Mariadassou M, Nouvel LX, Constant F, Morgavi DP, Rault L, Barbey S, Helloin E, Rué O, Schbath S, Launay F, Sandra O, Lefebvre R, Le Loir Y, Germon P, Citti C, Even S. Microbiota members from body sites of dairy cows are largely shared within individual hosts throughout lactation but sharing is limited in the herd. Anim Microbiome 2023; 5:32. [PMID: 37308970 DOI: 10.1186/s42523-023-00252-w] [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: 09/22/2022] [Accepted: 06/06/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Host-associated microbes are major determinants of the host phenotypes. In the present study, we used dairy cows with different scores of susceptibility to mastitis with the aim to explore the relationships between microbiota composition and different factors in various body sites throughout lactation as well as the intra- and inter-animal microbial sharing. RESULTS Microbiotas from the mouth, nose, vagina and milk of 45 lactating dairy cows were characterized by metataxonomics at four time points during the first lactation, from 1-week pre-partum to 7 months post-partum. Each site harbored a specific community that changed with time, likely reflecting physiological changes in the transition period and changes in diet and housing. Importantly, we found a significant number of microbes shared among different anatomical sites within each animal. This was between nearby anatomic sites, with up to 32% of the total number of Amplicon Sequence Variants (ASVs) of the oral microbiota shared with the nasal microbiota but also between distant ones (e.g. milk with nasal and vaginal microbiotas). In contrast, the share of microbes between animals was limited (< 7% of ASVs shared by more than 50% of the herd for a given site and time point). The latter widely shared ASVs were mainly found in the oral and nasal microbiotas. These results thus indicate that despite a common environment and diet, each animal hosted a specific set of bacteria, supporting a tight interplay between each animal and its microbiota. The score of susceptibility to mastitis was slightly but significantly related to the microbiota associated to milk suggesting a link between host genetics and microbiota. CONCLUSIONS This work highlights an important sharing of microbes between relevant microbiotas involved in health and production at the animal level, whereas the presence of common microbes was limited between animals of the herd. This suggests a host regulation of body-associated microbiotas that seems to be differently expressed depending on the body site, as suggested by changes in the milk microbiota that were associated to genotypes of susceptibility to mastitis.
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Affiliation(s)
| | | | - Fabienne Constant
- Ecole Nationale Vétérinaire d'Alfort, Université Paris-Saclay, UVSQ, INRAE, BREED, Maisons-Alfort, France
| | - Diego P Morgavi
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, Saint-Genes-Champanelle, France
| | - Lucie Rault
- INRAE, Institut Agro, UMR1253 STLO, Rennes, France
| | - Sarah Barbey
- INRAE, UE326 Unité Expérimentale du Pin, Gouffern en Auge, France
| | | | - Olivier Rué
- Université Paris-Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics Facility, Jouy-en-Josas, France
| | - Sophie Schbath
- Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
| | - Frederic Launay
- INRAE, UE326 Unité Expérimentale du Pin, Gouffern en Auge, France
| | - Olivier Sandra
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France
| | - Rachel Lefebvre
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Yves Le Loir
- INRAE, Institut Agro, UMR1253 STLO, Rennes, France
| | - Pierre Germon
- INRAE, Université de Tours, UMR ISP, 37380, Nouzilly, France
| | | | - Sergine Even
- INRAE, Institut Agro, UMR1253 STLO, Rennes, France.
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6
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Li RW, Moon CD, Morgavi DP. Editorial: Rumen microbiome dynamics and their implications in health and environment. Front Microbiol 2023; 14:1223885. [PMID: 37346751 PMCID: PMC10280159 DOI: 10.3389/fmicb.2023.1223885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 05/18/2023] [Indexed: 06/23/2023] Open
Affiliation(s)
- Robert W. Li
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Beltsville, MD, United States
| | - Christina D. Moon
- AgResearch Ltd., Grassland Research Centre, Palmerston North, New Zealand
| | - Diego P. Morgavi
- INRAE, Clermont-Auvergne-Rhône-Alpes, Saint-Genès-Champanelle, France
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Andersen TO, Altshuler I, Vera-Ponce de León A, Walter JM, McGovern E, Keogh K, Martin C, Bernard L, Morgavi DP, Park T, Li Z, Jiang Y, Firkins JL, Yu Z, Hvidsten TR, Waters SM, Popova M, Arntzen MØ, Hagen LH, Pope PB. Metabolic influence of core ciliates within the rumen microbiome. ISME J 2023:10.1038/s41396-023-01407-y. [PMID: 37169869 DOI: 10.1038/s41396-023-01407-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 05/13/2023]
Abstract
Protozoa comprise a major fraction of the microbial biomass in the rumen microbiome, of which the entodiniomorphs (order: Entodiniomorphida) and holotrichs (order: Vestibuliferida) are consistently observed to be dominant across a diverse genetic and geographical range of ruminant hosts. Despite the apparent core role that protozoal species exert, their major biological and metabolic contributions to rumen function remain largely undescribed in vivo. Here, we have leveraged (meta)genome-centric metaproteomes from rumen fluid samples originating from both cattle and goats fed diets with varying inclusion levels of lipids and starch, to detail the specific metabolic niches that protozoa occupy in the context of their microbial co-habitants. Initial proteome estimations via total protein counts and label-free quantification highlight that entodiniomorph species Entodinium and Epidinium as well as the holotrichs Dasytricha and Isotricha comprise an extensive fraction of the total rumen metaproteome. Proteomic detection of protozoal metabolism such as hydrogenases (Dasytricha, Isotricha, Epidinium, Enoploplastron), carbohydrate-active enzymes (Epidinium, Diplodinium, Enoploplastron, Polyplastron), microbial predation (Entodinium) and volatile fatty acid production (Entodinium and Epidinium) was observed at increased levels in high methane-emitting animals. Despite certain protozoal species having well-established reputations for digesting starch, they were unexpectedly less detectable in low methane emitting-animals fed high starch diets, which were instead dominated by propionate/succinate-producing bacterial populations suspected of being resistant to predation irrespective of host. Finally, we reaffirmed our abovementioned observations in geographically independent datasets, thus illuminating the substantial metabolic influence that under-explored eukaryotic populations have in the rumen, with greater implications for both digestion and methane metabolism.
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Affiliation(s)
- Thea O Andersen
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Ianina Altshuler
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Arturo Vera-Ponce de León
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Juline M Walter
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Emily McGovern
- Teagasc, Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, County, Meath, Ireland
| | - Kate Keogh
- Teagasc, Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, County, Meath, Ireland
| | - Cécile Martin
- INRAE, VetAgro Sup, UMR Herbivores, Université Clermont Auvergne, Saint-Genes-Champanelle, France
| | - Laurence Bernard
- INRAE, VetAgro Sup, UMR Herbivores, Université Clermont Auvergne, Saint-Genes-Champanelle, France
| | - Diego P Morgavi
- INRAE, VetAgro Sup, UMR Herbivores, Université Clermont Auvergne, Saint-Genes-Champanelle, France
| | - Tansol Park
- Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do, Republic of Korea
- Department of Animal Sciences, The Ohio State University, Columbus, OH, USA
| | - Zongjun Li
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China
| | - Yu Jiang
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China
| | - Jeffrey L Firkins
- Department of Animal Sciences, The Ohio State University, Columbus, OH, USA
| | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State University, Columbus, OH, USA
| | - Torgeir R Hvidsten
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Sinead M Waters
- Teagasc, Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, County, Meath, Ireland
| | - Milka Popova
- INRAE, VetAgro Sup, UMR Herbivores, Université Clermont Auvergne, Saint-Genes-Champanelle, France
| | - Magnus Ø Arntzen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Live H Hagen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Phillip B Pope
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
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Romero P, Huang R, Jiménez E, Palma-Hidalgo JM, Ungerfeld EM, Popova M, Morgavi DP, Belanche A, Yáñez-Ruiz DR. Evaluating the effect of phenolic compounds as hydrogen acceptors when ruminal methanogenesis is inhibited in vitro – Part 2. Dairy goats. Animal 2023; 17:100789. [PMID: 37087998 DOI: 10.1016/j.animal.2023.100789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 03/31/2023] Open
Abstract
Most mitigation strategies to reduce enteric methane (CH4) production in the rumen induce an excess of rumen dihydrogen (H2) that is expelled and consequently not redirected to the synthesis of metabolites that can be utilised by the ruminant. We hypothesised that phenolic compounds can be potential H2 acceptors when added to the diet, as they can be degraded to compounds that may be beneficial for the animal, using part of the H2 available when ruminal methanogenesis is inhibited. We performed four in vitro incubation experiments using rumen inoculum from Murciano-Granadina adult goats: Experiment 1 examined the inhibitory potential of Asparagopsis taxiformis (AT) at different concentrations (0, 1, 2, 3, 4 and 5% of the substrate on a DM basis) in 24 h incubations; Experiment 2 investigated the effect of a wide range of phenolic compounds (phenol, catechol, resorcinol, hydroquinone, pyrogallol, phloroglucinol, gallic acid and formic acid) at different doses (0, 2, 4, and 6 mM) on rumen fermentation for 24 h; Experiment 3 evaluated the combined effect of each phenolic compound at 6 mM with AT at 2% DM in sequential batch cultures for 5 days; and Experiment 4 examined the dose-response effect of phloroglucinol at different concentrations (0, 6, 16, 26 and 36 mM) combined with AT in sequential batch cultures for 5 days. Results from Experiment 1 confirmed that AT at 2% DM substantially inhibited CH4 production while significantly increasing H2 accumulation and decreasing the acetate:propionate ratio. Results from Experiment 2 showed that phenolic compounds did not negatively affect rumen fermentation at any dose. In Experiment 3, each phenolic compound at 6 mM combined with AT at 2% DM inhibited CH4 production. Phloroglucinol numerically decreased H2 accumulation and significantly increased total gas production (TGP), volatile fatty acid (VFA) production and the acetate:propionate ratio. In Experiment 4, phloroglucinol at increasing doses supplemented with AT at 2% DM significantly decreased H2 accumulation and the abundances of archaea, protozoa and fungi abundances, and increased TGP, total VFA production and the acetate:propionate ratio in a dose-dependent way. In conclusion, combined treatment with AT and phloroglucinol was successful to mitigate CH4 production while preventing the accumulation of H2, leading to an increase in acetate and total VFA production and therefore an improvement in rumen fermentation in goats.
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Affiliation(s)
- P Romero
- Estación Experimental del Zaidín (CSIC), Profesor Albareda, 1, 18008 Granada, Spain
| | - R Huang
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès Champanelle, France
| | - E Jiménez
- Estación Experimental del Zaidín (CSIC), Profesor Albareda, 1, 18008 Granada, Spain
| | - J M Palma-Hidalgo
- Estación Experimental del Zaidín (CSIC), Profesor Albareda, 1, 18008 Granada, Spain
| | - E M Ungerfeld
- Centro Regional de Investigación Carillanca, Instituto de Investigaciones Agropecuarias INIA, Temuco 4880000, Chile
| | - M Popova
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès Champanelle, France
| | - D P Morgavi
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès Champanelle, France
| | - A Belanche
- Estación Experimental del Zaidín (CSIC), Profesor Albareda, 1, 18008 Granada, Spain; Departamento de Producción Animal y Ciencia de los Alimentos, Universidad de Zaragoza, Miguel Servet 177, 50013 Zaragoza, Spain
| | - D R Yáñez-Ruiz
- Estación Experimental del Zaidín (CSIC), Profesor Albareda, 1, 18008 Granada, Spain.
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9
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Muñoz-Tamayo R, Gagaoua M, Gondret F, Hess M, Morgavi DP, Olsson IAS, Taghipoor M, Tedeschi LO, Veissier I. 177 Peer Community in Animal Science: A Free Publication Model for Transparent and Open Science. J Anim Sci 2022. [DOI: 10.1093/jas/skac247.158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
The scientific publication system should evolve into practices that enhance free dissemination and full access to research findings. At the same time, it should ensure reproducibility and transparency and safeguard scientific integrity from the detrimental effects of the current “publish or perish” culture. The objective of this contribution is to introduce the Peer Community In (PCI) Animal Science initiative (https://animsci.peercommunityin.org/), which represents an alternative to the current publication system under the umbrella of the “Peer Community In” project (https://peercommunityin.org/ ). PCI Animal Science is an international community of researchers working in animal science and related areas and it promotes open science and research transparency. Although PCI Animal Science is not a scientific journal, it operates similarly with editors (here: recommenders) and reviewers. Currently, the PCI Animal Science community has 64 recommenders from 20 countries. PCI Animal Science is a non-profit initiative, run and managed by researchers. The PCI Animal Science community performs, at no cost, rigorous open reviews of preprints that have been deposited on repositories such as bioRxiv and Zenodo from a wide range of research areas related to animal science. Based on independent reviews, a recommender decides whether a paper is recommended or not. Recommended preprints are peer-reviewed and citable stand-alone articles of high scientific value that do not need publication in traditional journals. However, if the authors wish, they can also publish their recommended preprint in the Diamond Open Access Peer Community Journal (https://peercommunityjournal.org/section/animsci/) at no cost. Authors can also submit their recommended manuscript to PCI-friendly journals (i.e., journals that consider the PCI evaluation in their own review processes) or to other journals. This contribution shows the workflow of the evaluation of manuscripts by PCI Animal Science and the advantages of adopting this new publishing model.
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Affiliation(s)
- Rafael Muñoz-Tamayo
- Université Paris-Saclay, INRAE, AgroParisTech, UMR Modélisation Systémique Appliquée aux Ruminants
| | | | | | - Matthias Hess
- Department of Animal Science, University of California
| | - Diego P Morgavi
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores
| | - I Anna S Olsson
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen
| | - Masoomeh Taghipoor
- Université Paris-Saclay, INRAE, AgroParisTech, UMR Modélisation Systémique Appliquée aux Ruminants
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10
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Popova M, Ferlay A, Bougouin A, Eugène M, Martin C, Morgavi DP. Associating changes in the bacterial community of rumen and faeces and milk fatty acid profiles in dairy cows fed high-starch or starch and oil-supplemented diets. J DAIRY RES 2022; 89:1-10. [PMID: 36039952 DOI: 10.1017/s0022029922000498] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The experiment reported in this research paper aimed to evaluate the effects of high-starch or starch and oil-supplemented diets on rumen and faecal bacteria, and explore links between the structure of bacterial communities and milk fatty acid (FA) profiles. We used four Holstein dairy cows in a 4 × 4 Latin square design. Cows were fed a diet rich in cereals (high-starch diet with 23% starch content on dry matter (DM) basis), a diet supplemented with saturated FA from Ca salts of palm oil + 18% DM starch, a diet with high content of monounsaturated FA (from extruded rapeseeds) + 18% DM starch or a diet rich in polyunsaturated FA (from extruded sunflower seeds) + 17% DM starch. At the end of each experimental period, cows were sampled for rumen and faecal contents, which were used for DNA extraction and amplicon sequencing. Partial least squares (PLS) regression analysis highlighted diet-related changes in both rumen and faecal bacterial structures. Sparse PLS discriminant analysis was further employed to identify biologically relevant operational taxonomical units (OTUs) driving these differences. Our results show that Butyrivibrio discriminated the high-starch diet and linked positively with higher concentrations of milk odd- and branched-chain FA. YS2-related OTUs were key taxa distinguishing diets supplemented with Ca salts of palm oil or sunflower seeds and correlated positively with linoleic acid in milk. Similarly, diets modulated faecal bacterial composition. However, correlations between changes in faecal and rumen bacteria were poor. With this work, we demonstrated that high-starch or lipid-supplemented diets affect rumen and faecal bacterial community structure, and these changes could have a knock-on effect on milk FA profiles.
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Affiliation(s)
- Milka Popova
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France
| | - Anne Ferlay
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France
| | - Adeline Bougouin
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France
| | - Maguy Eugène
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France
| | - Cécile Martin
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France
| | - Diego P Morgavi
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France
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11
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Muñoz-Tamayo R, Nielsen BL, Gagaoua M, Gondret F, Krause ET, Morgavi DP, Olsson IAS, Pastell M, Taghipoor M, Tedeschi L, Veissier I, Nawroth C. Seven steps to enhance Open Science practices in animal science. PNAS Nexus 2022; 1:pgac106. [PMID: 36741429 PMCID: PMC9896936 DOI: 10.1093/pnasnexus/pgac106] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/30/2022] [Indexed: 04/14/2023]
Abstract
The Open Science movement aims at ensuring accessibility, reproducibility, and transparency of research. The adoption of Open Science practices in animal science, however, is still at an early stage. To move ahead as a field, we here provide seven practical steps to embrace Open Science in animal science. We hope that this paper contributes to the shift in research practices of animal scientists towards open, reproducible, and transparent science, enabling the field to gain additional public trust and deal with future challenges to guarantee reliable research. Although the paper targets primarily animal science researchers, the steps discussed here are also applicable to other research domains.
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Affiliation(s)
- Rafael Muñoz-Tamayo
- INRAE, AgroParisTech, Université Paris-Saclay, UMR Modélisation Systémique Appliquée aux Ruminants, 75005 Paris, France
| | - Birte L Nielsen
- Universities Federation for Animal Welfare (UFAW), The Old School, Brewhouse Hill, Wheathampstead, Hertfordshire AL4 8AN, UK
| | | | | | - E Tobias Krause
- Institute of Animal Welfare and Animal Husbandry, Friedrich-Loeffler-Institut, Dörnbergstr. 25/27, 29223 Celle, Germany
| | - Diego P Morgavi
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France
| | - I Anna S Olsson
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-180 Porto, Portugal
| | - Matti Pastell
- Natural Resources Institute Finland (Luke), Production Systems, Latokartanonkaari 9, FI-00790 Helsinki, Finland
| | - Masoomeh Taghipoor
- INRAE, AgroParisTech, Université Paris-Saclay, UMR Modélisation Systémique Appliquée aux Ruminants, 75005 Paris, France
| | - Luis Tedeschi
- Department of Animal Science, Texas A&M University, College Station, TX 77843-2471, USA
| | - Isabelle Veissier
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France
| | - Christian Nawroth
- Institute of Behavioural Physiology, Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
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12
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Sayd T, Chambon C, Popova M, Morgavi DP, Torrent A, Blinet S, Theron L, Niderkorn V. Impact of Tannin Supplementation on Proteolysis during Post-Ruminal Digestion in Wethers Using a Dynamic In Vitro System: A Plant ( Medicago sativa) Digestomic Approach. J Agric Food Chem 2022; 70:2221-2230. [PMID: 35157803 DOI: 10.1021/acs.jafc.1c07378] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The aim of this study was to characterize the effects of tannins on plant protein during sheep digestion using a digestomic approach combining in vivo (rumen) conditions and an in vitro digestive system (abomasum and small intestine). Ruminal fluid from wethers infused with a tannin solution or water (control) was introduced into the digester, and protein degradation was followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Tannin infusion in the rumen led to a clear decrease in protein degradation-related fermentation end-products, whereas ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCo) protein was more abundant than in control wethers. In the simulated abomasum, peptidomic analysis showed more degradation products of RuBisCo in the presence of tannins. The effect of RuBisCo protection by tannins continued to impact Rubisco digestion into early-stage intestinal digestion but was no longer detectable in late-stage intestinal digestion. The peptidomics approach proved a potent tool for identifying and quantifying the type of protein hydrolyzed throughout the gastrointestinal tract.
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Affiliation(s)
- Thierry Sayd
- INRAE, UR 370, Qualité des Produits Animaux (QuaPA), Site de Theix, 63122 Saint-Genès-Champanelle, France
| | - Christophe Chambon
- INRAE, UR 370, Plateforme Exploration du Métabolisme (PFEM) composante protéomique, UR 370, Qualité des Produits Animaux (QuaPA), Site de Theix, 63122 Saint-Genès-Champanelle, France
| | - Milka Popova
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France
| | - Diego P Morgavi
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France
| | - Angélique Torrent
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France
| | - Sylvie Blinet
- INRAE, UR 370, Qualité des Produits Animaux (QuaPA), Site de Theix, 63122 Saint-Genès-Champanelle, France
| | - Laetitia Theron
- INRAE, UR 370, Qualité des Produits Animaux (QuaPA), Site de Theix, 63122 Saint-Genès-Champanelle, France
| | - Vincent Niderkorn
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France
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13
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Boudra H, Noziere P, Cantalapiedra-Hijar G, Traikia M, Martin JF, Petera M, Lagree M, Doreau M, Morgavi DP. Spot urine collection: A valid alternative to total urine collection for metabolomic studies in dairy cattle. J Dairy Sci 2021; 105:301-312. [PMID: 34763916 DOI: 10.3168/jds.2021-20788] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 05/26/2021] [Accepted: 09/13/2021] [Indexed: 11/19/2022]
Abstract
Urine is a highly suitable biological matrix for metabolomics studies. Total collection for 24-h periods is the gold standard as it ensures the presence of all metabolites excreted throughout the day. However, in animal studies, it presents limitations related to animal welfare and also due to alterations of the metabolome originating from the use of acid for preventing microbial growth or microbial contamination. In this study, we investigated whether spot urine collection is a practical alternative to total collection for metabolomic studies in lactating cows. For this purpose, we collected urine samples from 4 lactating Holstein cows fed 4 diets in a 4 × 4 Latin square design. Urine was collected for 24 h using a collecting device (i.e., total collection) or collected once per day 4 h after the morning feeding (i.e., spot urine collection). Dietary treatments differed by the amount of nitrogen content (high vs. low) and by the nature of the energy (starch vs. fiber). Urine metabolome was analyzed by 2 untargeted complementary methods, nuclear magnetic resonance and hydrophilic-interaction liquid chromatography (HILIC) coupled to a time-of-flight mass spectrometer, and by 1 targeted method, HILIC-tandem mass spectrometry. Although sampling technique had an effect on the abundance of metabolites detected, spot urine samples were equally capable of showing differences in urine metabolome than samples from total collection. When considering nitrogen levels in the diet, the robustness and precision for discriminating high- and low-nitrogen diets was equally achieved with both sampling techniques. A total of 22 discriminant metabolites associated with the N level of diets were identified from untargeted HILIC coupled to a time-of-flight mass spectrometer (n = 9) and nuclear magnetic resonance (n = 11), and 2 from targeted HILIC-tandem mass spectrometry. Alternatively, starch or fiber in the diet induced less changes in the metabolome that were not clearly discriminated independently of the sampling technique. We concluded that spot urine collection can successfully reveal differences in the urine metabolome elicited by dietary N levels and be used as a substitute of total urinary 24-h collection for metabolomic studies.
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Affiliation(s)
- H Boudra
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France.
| | - P Noziere
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France
| | - G Cantalapiedra-Hijar
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France
| | - M Traikia
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, F-63000 Clermont-Ferrand, France
| | - J-F Martin
- INRAE, Toxalim, MetaboHub-Axiom, Metabo-Hub-ANR611-INBS-0010
| | - M Petera
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, F-63000 Clermont-Ferrand, France
| | - M Lagree
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, F-63000 Clermont-Ferrand, France
| | - M Doreau
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France
| | - D P Morgavi
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France.
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14
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Yanibada B, Hohenester U, Pétéra M, Canlet C, Durand S, Jourdan F, Ferlay A, Morgavi DP, Boudra H. Milk metabolome reveals variations on enteric methane emissions from dairy cows fed a specific inhibitor of the methanogenesis pathway. J Dairy Sci 2021; 104:12553-12566. [PMID: 34531049 DOI: 10.3168/jds.2021-20477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 04/01/2021] [Accepted: 07/26/2021] [Indexed: 11/19/2022]
Abstract
Metabolome profiling in biological fluids is an interesting approach for exploring markers of methane emissions in ruminants. In this study, a multiplatform metabolomics approach was used for investigating changes in milk metabolic profiles related to methanogenesis in dairy cows. For this purpose, 25 primiparous Holstein cows at similar lactation stage were fed the same diet supplemented with (treated, n = 12) or without (control, n = 13) a specific antimethanogenic additive that reduced enteric methane production by 23% with no changes in intake, milk production, and health status. The study lasted 6 wk, with sampling and measures performed in wk 5 and 6. Milk samples were analyzed using 4 complementary analytical methods, including 2 untargeted (nuclear magnetic resonance and liquid chromatography coupled to a quadrupole-time-of-flight mass spectrometer) and 2 targeted (liquid chromatography-tandem mass spectrometry and gas chromatography coupled to a flame ionization detector) approaches. After filtration, variable selection and normalization data from each analytical platform were then analyzed using multivariate orthogonal partial least square discriminant analysis. All 4 analytical methods were able to differentiate cows from treated and control groups. Overall, 38 discriminant metabolites were identified, which affected 10 metabolic pathways including methane metabolism. Some of these metabolites such as dimethylsulfoxide, dimethylsulfone, and citramalic acid, detected by nuclear magnetic resonance or liquid chromatography-mass spectrometry methods, originated from the rumen microbiota or had a microbial-host animal co-metabolism that could be associated with methanogenesis. Also, discriminant milk fatty acids detected by targeted gas chromatography were mostly of ruminal microbial origin. Other metabolites and metabolic pathways significantly affected were associated with AA metabolism. These findings provide new insight on the potential role of milk metabolites as indicators of enteric methane modifications in dairy cows.
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Affiliation(s)
- Bénédict Yanibada
- INRAE, Université Clermont Auvergne, Vetagro Sup, UMRH, 63122, Saint-Genès-Champanelle, France
| | - Ulli Hohenester
- INRAE, Université Clermont Auvergne, Vetagro Sup, UMRH, 63122, Saint-Genès-Champanelle, France
| | - Mélanie Pétéra
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, F-63000 Clermont-Ferrand, France
| | - Cécile Canlet
- Toxalim, Research Centre in Food Toxicology, Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, F-31027, Toulouse, France; Axiom Platform, MetaToul-MetaboHUB, National Infrastructure for Metabolomics and Fluxomics, F-31027, Toulouse, France
| | - Stéphanie Durand
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, F-63000 Clermont-Ferrand, France
| | - Fabien Jourdan
- Toxalim, Research Centre in Food Toxicology, Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, F-31027, Toulouse, France
| | - Anne Ferlay
- INRAE, Université Clermont Auvergne, Vetagro Sup, UMRH, 63122, Saint-Genès-Champanelle, France
| | - Diego P Morgavi
- INRAE, Université Clermont Auvergne, Vetagro Sup, UMRH, 63122, Saint-Genès-Champanelle, France.
| | - Hamid Boudra
- INRAE, Université Clermont Auvergne, Vetagro Sup, UMRH, 63122, Saint-Genès-Champanelle, France.
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15
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Belanche A, Patra AK, Morgavi DP, Suen G, Newbold CJ, Yáñez-Ruiz DR. Editorial: Gut Microbiome Modulation in Ruminants: Enhancing Advantages and Minimizing Drawbacks. Front Microbiol 2021; 11:622002. [PMID: 33505388 PMCID: PMC7829182 DOI: 10.3389/fmicb.2020.622002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/14/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Alejandro Belanche
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Amlan K Patra
- Department of Animal Nutrition, West Bengal University of Animal and Fishery Sciences, Kolkata, India
| | - Diego P Morgavi
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 1213 Herbivores Unit, Saint-Genès-Champanelle, France
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Charles J Newbold
- Scotland's Rural College, Edinburg Campus, Edinburgh, United Kingdom
| | - David R Yáñez-Ruiz
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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Li A, Laville E, Tarquis L, Lombard V, Ropartz D, Terrapon N, Henrissat B, Guieysse D, Esque J, Durand J, Morgavi DP, Potocki-Veronese G. Analysis of the diversity of the glycoside hydrolase family 130 in mammal gut microbiomes reveals a novel mannoside-phosphorylase function. Microb Genom 2020; 6:mgen000404. [PMID: 32667876 PMCID: PMC7660257 DOI: 10.1099/mgen.0.000404] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/20/2020] [Indexed: 12/04/2022] Open
Abstract
Mannoside phosphorylases are involved in the intracellular metabolization of mannooligosaccharides, and are also useful enzymes for the in vitro synthesis of oligosaccharides. They are found in glycoside hydrolase family GH130. Here we report on an analysis of 6308 GH130 sequences, including 4714 from the human, bovine, porcine and murine microbiomes. Using sequence similarity networks, we divided the diversity of sequences into 15 mostly isofunctional meta-nodes; of these, 9 contained no experimentally characterized member. By examining the multiple sequence alignments in each meta-node, we predicted the determinants of the phosphorolytic mechanism and linkage specificity. We thus hypothesized that eight uncharacterized meta-nodes would be phosphorylases. These sequences are characterized by the absence of signal peptides and of the catalytic base. Those sequences with the conserved E/K, E/R and Y/R pairs of residues involved in substrate binding would target β-1,2-, β-1,3- and β-1,4-linked mannosyl residues, respectively. These predictions were tested by characterizing members of three of the uncharacterized meta-nodes from gut bacteria. We discovered the first known β-1,4-mannosyl-glucuronic acid phosphorylase, which targets a motif of the Shigella lipopolysaccharide O-antigen. This work uncovers a reliable strategy for the discovery of novel mannoside-phosphorylases, reveals possible interactions between gut bacteria, and identifies a biotechnological tool for the synthesis of antigenic oligosaccharides.
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Affiliation(s)
- Ao Li
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31077 Toulouse, France
| | - Elisabeth Laville
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31077 Toulouse, France
| | - Laurence Tarquis
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31077 Toulouse, France
| | - Vincent Lombard
- AFMB, UMR 7257 CNRS, Aix-Marseille Université, F-13288 Marseille, France
- INRAE, USC 1408 AFMB, F-13288 Marseille, France
| | - David Ropartz
- INRAE, UR BIA, F-44316 Nantes, France
- INRAE, BIBS facility, F-44316 Nantes, France
| | - Nicolas Terrapon
- AFMB, UMR 7257 CNRS, Aix-Marseille Université, F-13288 Marseille, France
- INRAE, USC 1408 AFMB, F-13288 Marseille, France
| | - Bernard Henrissat
- AFMB, UMR 7257 CNRS, Aix-Marseille Université, F-13288 Marseille, France
- INRAE, USC 1408 AFMB, F-13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - David Guieysse
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31077 Toulouse, France
| | - Jeremy Esque
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31077 Toulouse, France
| | - Julien Durand
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31077 Toulouse, France
| | - Diego P. Morgavi
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, Saint-Genès-Champanelle, France
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17
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Zingaretti LM, Renand G, Morgavi DP, Ramayo-Caldas Y. Link-HD: a versatile framework to explore and integrate heterogeneous microbial communities. Bioinformatics 2020; 36:2298-2299. [PMID: 31738392 PMCID: PMC7141858 DOI: 10.1093/bioinformatics/btz862] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 06/19/2019] [Revised: 10/04/2019] [Accepted: 11/15/2019] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION We present Link-HD, an approach to integrate multiple datasets. Link-HD is a generalization of 'Structuration des Tableaux A Trois Indices de la Statistique-Analyse Conjointe de Tableaux', a family of methods designed to integrate information from heterogeneous data. Here, we extend the classical approach to deal with broader datasets (e.g. compositional data), methods for variable selection and taxon-set enrichment analysis. RESULTS The methodology is demonstrated by integrating rumen microbial communities from cows for which methane yield (CH4y) was individually measured. Our approach reproduces the significant link between rumen microbiota structure and CH4 emission. When analyzing the TARA's ocean data, Link-HD replicates published results, highlighting the relevance of temperature with members of phyla Proteobacteria on the structure and functionality of this ecosystem. AVAILABILITY AND IMPLEMENTATION The source code, examples and a complete manual are freely available in GitHub https://github.com/lauzingaretti/LinkHD and in Bioconductor https://bioconductor.org/packages/release/bioc/html/LinkHD.html.
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Affiliation(s)
- Laura M Zingaretti
- Plant and Animal Genomics, Statistical and Population Genomics Group, CSIC-IRTA-UAB-UB Consortium, Centre for Research in Agricultural Genomics (CRAG), 08193 Bellaterra, Spain.,IAPCBA and IAPCH, UNVM, Villa María, Córdoba 5900, Argentina
| | - Gilles Renand
- URM Animal Genetics and Integrative Biology, GABI, INRA, AgroParisTech, Université Paris-Saclay, 78352 Jouy-en-Josas, France
| | - Diego P Morgavi
- Animal Physiology and Livestock Systems Divisions, INRA, Herbivore Research Unit, Clermont Auvergne University, Saint Genès-Champanelle 63122, France
| | - Yuliaxis Ramayo-Caldas
- URM Animal Genetics and Integrative Biology, GABI, INRA, AgroParisTech, Université Paris-Saclay, 78352 Jouy-en-Josas, France.,Animal Breeding and Genetics Program, IRTA, 08140 Caldes de Montbui, Spain
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18
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Nasrollahi SM, Meale SJ, Morgavi DP, Schiphorst AM, Robins RJ, Ortigues-Marty I, Cantalapiedra-Hijar G. The origin of N isotopic discrimination and its relationship with feed efficiency in fattening yearling bulls is diet-dependent. PLoS One 2020; 15:e0234344. [PMID: 32502191 PMCID: PMC7274422 DOI: 10.1371/journal.pone.0234344] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 11/29/2019] [Accepted: 05/23/2020] [Indexed: 11/19/2022] Open
Abstract
Nitrogen (N) isotopic discrimination (i.e. the difference in natural 15N abundance between the animal proteins and the diet; Δ15N) is known to correlate with N use efficiency (NUE) and feed conversion efficiency (FCE) in ruminants. However, results from the literature are not always consistent across studies, likely due to isotopic discrimination pathways that may differ with the nature of diets. The objective of the present study was to assess at which level, from rumen to tissues, Δ15N originates and becomes related to NUE and FCE in fattening yearling bulls when they are fed two contrasted diets. Twenty-four Charolais yearling bulls were randomly divided into two groups and fed during 8 months, from weaning to slaughter, either 1) a high starch diet based on corn silage supplying a balanced N to energy ratio at the rumen level (starch) or 2) a high fiber diet based on grass silage supplying an excess of rumen degradable N (fiber). All animals were slaughtered and samples of different digestive pools (ruminal, duodenal, ileal and fecal contents), animal tissues (duodenum, liver and muscle), blood and urine were collected for each animal. Ruminal content was further used to isolate liquid-associated bacteria (LAB), protozoa and free ammonia, while plasma proteins were obtained from blood. All samples along with feed were analyzed for their N isotopic composition. For both diets, the digestive contribution (i.e. the N isotopic discrimination occurring before absorption) to the Δ15N observed in animal tissues accounted for 65 ± 11%, leaving only one third to the contribution of post-absorptive metabolism. Concerning the Δ15N in digestive pools, the majority of these changes occurred in the rumen (av. Δ15N = 2.12 ± 0.66‰), with only minor 15N enrichments thereafter (av. Δ15N = 2.24 ± 0.41‰), highlighting the key role of the rumen on N isotopic discrimination. A strong, significant overall relationship (n = 24) between Δ15N and FCE or NUE was found when using any post-absorptive metabolic pool (duodenum, liver, or muscle tissues, or plasma proteins; 0.52 < r < 0.73; P ≤ 0.01), probably as these pools reflect both digestive and post-absorptive metabolic phenomena. Fiber diet compared to starch diet had a lower feed efficiency and promoted higher (P ≤ 0.05) Δ15N values across all post-absorptive metabolic pools and some digestive pools (ruminal, duodenal, and ileal contents). The within-diet relationship (n = 12) between Δ15N and feed efficiency was not as strong and consistent as the overall relationship, with contrasted responses between the two diets for specific pools (diet x pool interaction; P ≤ 0.01). Our results highlight the contrasted use of N at the rumen level between the two experimental diets and suggests the need for different equations to predict FCE or NUE from Δ15N according to the type of diet. In conclusion, rumen digestion and associated microbial activity can play an important role on N isotopic discrimination so rumen effect related to diet may interfere with the relationship between Δ15N and feed efficiency in fattening yearling bulls.
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Affiliation(s)
| | - Sarah Jade Meale
- School of Agriculture and Food Sciences, The University of Queensland, Gatton Campus, Gatton, Australia
| | - Diego P. Morgavi
- INRAE, Université Clermont Auvergne, Vetagro Sup, UMRH, Saint-Genès-Champanelle, France
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19
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Li J, Zhong H, Ramayo-Caldas Y, Terrapon N, Lombard V, Potocki-Veronese G, Estellé J, Popova M, Yang Z, Zhang H, Li F, Tang S, Yang F, Chen W, Chen B, Li J, Guo J, Martin C, Maguin E, Xu X, Yang H, Wang J, Madsen L, Kristiansen K, Henrissat B, Ehrlich SD, Morgavi DP. A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment. Gigascience 2020; 9:5849033. [PMID: 32473013 PMCID: PMC7260996 DOI: 10.1093/gigascience/giaa057] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [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: 05/02/2019] [Revised: 11/07/2019] [Accepted: 05/06/2020] [Indexed: 01/10/2023] Open
Abstract
Background The rumen microbiota provides essential services to its host and, through its role in ruminant production, contributes to human nutrition and food security. A thorough knowledge of the genetic potential of rumen microbes will provide opportunities for improving the sustainability of ruminant production systems. The availability of gene reference catalogs from gut microbiomes has advanced the understanding of the role of the microbiota in health and disease in humans and other mammals. In this work, we established a catalog of reference prokaryote genes from the bovine rumen. Results Using deep metagenome sequencing we identified 13,825,880 non-redundant prokaryote genes from the bovine rumen. Compared to human, pig, and mouse gut metagenome catalogs, the rumen is larger and richer in functions and microbial species associated with the degradation of plant cell wall material and production of methane. Genes encoding enzymes catalyzing the breakdown of plant polysaccharides showed a particularly high richness that is otherwise impossible to infer from available genomes or shallow metagenomics sequencing. The catalog expands the dataset of carbohydrate-degrading enzymes described in the rumen. Using an independent dataset from a group of 77 cattle fed 4 common dietary regimes, we found that only <0.1% of genes were shared by all animals, which contrast with a large overlap for functions, i.e., 63% for KEGG functions. Different diets induced differences in the relative abundance rather than the presence or absence of genes, which explains the great adaptability of cattle to rapidly adjust to dietary changes. Conclusions These data bring new insights into functions, carbohydrate-degrading enzymes, and microbes of the rumen to complement the available information on microbial genomes. The catalog is a significant biological resource enabling deeper understanding of phenotypes and biological processes and will be expanded as new data are made available.
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Affiliation(s)
- Junhua Li
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.,School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Huanzi Zhong
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - Yuliaxis Ramayo-Caldas
- INRAE, Génétique Animale et Biologie Intégrative, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.,Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, Caldes de Montbui 08140, Spain
| | - Nicolas Terrapon
- CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France.,INRAE, USC 1408 AFMB, 13288 Marseille, France
| | - Vincent Lombard
- CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France.,INRAE, USC 1408 AFMB, 13288 Marseille, France
| | | | - Jordi Estellé
- INRAE, Génétique Animale et Biologie Intégrative, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Milka Popova
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès Champanelle, France
| | - Ziyi Yang
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Hui Zhang
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Fang Li
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Shanmei Tang
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Fangming Yang
- BGI-Shenzhen, Shenzhen 518083, China.,School of Future Technology, University of Chinese Academy of Sciences, Beijing 101408, China
| | | | - Bing Chen
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Jiyang Li
- BGI-Shenzhen, Shenzhen 518083, China
| | - Jing Guo
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Cécile Martin
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès Champanelle, France
| | - Emmanuelle Maguin
- INRAE, Micalis Institute, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Lise Madsen
- BGI-Shenzhen, Shenzhen 518083, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark.,Institute of Marine Research (IMR), Postboks 1870 Nordnes, 5817 Bergen, Norway
| | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen 518083, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - Bernard Henrissat
- CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France.,INRAE, USC 1408 AFMB, 13288 Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Stanislav D Ehrlich
- BGI-Shenzhen, Shenzhen 518083, China.,MGP MetaGenoPolis, INRAE, Université Paris-Saclay, 78350 Jouy en Josas, France.,Centre for Host Microbiome Interactions, Dental Institute, King's College London, London, UK
| | - Diego P Morgavi
- BGI-Shenzhen, Shenzhen 518083, China.,Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès Champanelle, France
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20
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Belanche A, Newbold CJ, Morgavi DP, Bach A, Zweifel B, Yáñez-Ruiz DR. A Meta-analysis Describing the Effects of the Essential oils Blend Agolin Ruminant on Performance, Rumen Fermentation and Methane Emissions in Dairy Cows. Animals (Basel) 2020; 10:E620. [PMID: 32260263 PMCID: PMC7222807 DOI: 10.3390/ani10040620] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [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: 02/07/2020] [Revised: 03/05/2020] [Accepted: 03/30/2020] [Indexed: 01/29/2023] Open
Abstract
There is an increasing pressure to identify feed additives which increase productivity or decrease methane emissions. This paper aims to elucidate the effects of supplementing a specific essential oils blend Agolin® Ruminant on the productivity of dairy cows in comparison to non-treated animals. A total of 23 in vivo studies were identified in which Agolin was supplemented at 1 g/d per cow; then a meta-analysis was performed to determine the response ratio on milk yield, rumen fermentation, methane emissions and health. Results indicated that an adaptation period of at least 4 weeks of treatment is required. Whereas short-term studies showed minor and inconsistent effects of Agolin, long-term studies (>4 weeks of treatment) revealed that Agolin supplementation increases milk yield (+3.6%), fat and protein corrected milk (+4.1%) and feed efficiency (+4.4%) without further changes in milk composition and feed intake. Long-term treatment also decreased methane production per day (-8.8%), per dry matter intake (-12.9%) and per fat and protein corrected milk yield (-9.9%) without changes in rumen fermentation pattern. In conclusion, despite the mode of action is still unclear and the small number of studies considered, these findings show that Agolin represents an encouraging alternative to improve productivity in dairy cows.
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Affiliation(s)
- Alejandro Belanche
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Profesor Albareda 1, 18008 Granada, Spain;
| | - Charles J. Newbold
- Scotland’s Rural College (SRUC), Edinburg campus, Peter Wilson Building, King’s Buildings, Edinburgh EH9 3JG, UK;
| | - Diego P. Morgavi
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 1213 Herbivores unit, F-63122 Saint-Genès-Champanelle, France;
| | - Alex Bach
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08005 Barcelona, Spain;
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Department of Ruminant Production, 08140 Caldes de Montbui, Spain
| | | | - David R. Yáñez-Ruiz
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Profesor Albareda 1, 18008 Granada, Spain;
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21
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Ramayo‐Caldas Y, Zingaretti L, Popova M, Estellé J, Bernard A, Pons N, Bellot P, Mach N, Rau A, Roume H, Perez‐Enciso M, Faverdin P, Edouard N, Ehrlich D, Morgavi DP, Renand G. Identification of rumen microbial biomarkers linked to methane emission in Holstein dairy cows. J Anim Breed Genet 2020; 137:49-59. [PMID: 31418488 PMCID: PMC6972549 DOI: 10.1111/jbg.12427] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 07/12/2019] [Accepted: 07/13/2019] [Indexed: 12/29/2022]
Abstract
Mitigation of greenhouse gas emissions is relevant for reducing the environmental impact of ruminant production. In this study, the rumen microbiome from Holstein cows was characterized through a combination of 16S rRNA gene and shotgun metagenomic sequencing. Methane production (CH4 ) and dry matter intake (DMI) were individually measured over 4-6 weeks to calculate the CH4 yield (CH4 y = CH4 /DMI) per cow. We implemented a combination of clustering, multivariate and mixed model analyses to identify a set of operational taxonomic unit (OTU) jointly associated with CH4 y and the structure of ruminal microbial communities. Three ruminotype clusters (R1, R2 and R3) were identified, and R2 was associated with higher CH4 y. The taxonomic composition on R2 had lower abundance of Succinivibrionaceae and Methanosphaera, and higher abundance of Ruminococcaceae, Christensenellaceae and Lachnospiraceae. Metagenomic data confirmed the lower abundance of Succinivibrionaceae and Methanosphaera in R2 and identified genera (Fibrobacter and unclassified Bacteroidales) not highlighted by metataxonomic analysis. In addition, the functional metagenomic analysis revealed that samples classified in cluster R2 were overrepresented by genes coding for KEGG modules associated with methanogenesis, including a significant relative abundance of the methyl-coenzyme M reductase enzyme. Based on the cluster assignment, we applied a sparse partial least-squares discriminant analysis at the taxonomic and functional levels. In addition, we implemented a sPLS regression model using the phenotypic variation of CH4 y. By combining these two approaches, we identified 86 discriminant bacterial OTUs, notably including families linked to CH4 emission such as Succinivibrionaceae, Ruminococcaceae, Christensenellaceae, Lachnospiraceae and Rikenellaceae. These selected OTUs explained 24% of the CH4 y phenotypic variance, whereas the host genome contribution was ~14%. In summary, we identified rumen microbial biomarkers associated with the methane production of dairy cows; these biomarkers could be used for targeted methane-reduction selection programmes in the dairy cattle industry provided they are heritable.
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Affiliation(s)
- Yuliaxis Ramayo‐Caldas
- UMR 1313 GABIINRA, AgroParisTech, Université Paris‐SaclayJouy‐en‐JosasFrance
- Animal Breeding and Genetics ProgramIRTA Torre MarimonCaldes de MontbuiSpain
| | | | - Milka Popova
- VetAgro Sup, UMR 1213 HerbivoresINRA, Université Clermont AuvergneSaint‐Genès‐ChampanelleFrance
| | - Jordi Estellé
- UMR 1313 GABIINRA, AgroParisTech, Université Paris‐SaclayJouy‐en‐JosasFrance
| | - Aurelien Bernard
- VetAgro Sup, UMR 1213 HerbivoresINRA, Université Clermont AuvergneSaint‐Genès‐ChampanelleFrance
| | | | - Pau Bellot
- Department of Animal Genetics, CRAGUABBellaterraSpain
| | - Núria Mach
- UMR 1313 GABIINRA, AgroParisTech, Université Paris‐SaclayJouy‐en‐JosasFrance
| | - Andrea Rau
- UMR 1313 GABIINRA, AgroParisTech, Université Paris‐SaclayJouy‐en‐JosasFrance
| | - Hugo Roume
- INRA METAGENOPOLIS UnitJouy‐en‐JosasFrance
| | | | | | | | | | - Diego P. Morgavi
- VetAgro Sup, UMR 1213 HerbivoresINRA, Université Clermont AuvergneSaint‐Genès‐ChampanelleFrance
| | - Gilles Renand
- UMR 1313 GABIINRA, AgroParisTech, Université Paris‐SaclayJouy‐en‐JosasFrance
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22
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Muñoz-Tamayo R, Popova M, Tillier M, Morgavi DP, Morel JP, Fonty G, Morel-Desrosiers N. Hydrogenotrophic methanogens of the mammalian gut: Functionally similar, thermodynamically different-A modelling approach. PLoS One 2019; 14:e0226243. [PMID: 31826000 PMCID: PMC6905546 DOI: 10.1371/journal.pone.0226243] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 07/11/2019] [Accepted: 11/24/2019] [Indexed: 12/11/2022] Open
Abstract
Methanogenic archaea occupy a functionally important niche in the gut microbial ecosystem of mammals. Our purpose was to quantitatively characterize the dynamics of methanogenesis by integrating microbiology, thermodynamics and mathematical modelling. For that, in vitro growth experiments were performed with pure cultures of key methanogens from the human and ruminant gut, namely Methanobrevibacter smithii, Methanobrevibacter ruminantium and Methanobacterium formicium. Microcalorimetric experiments were performed to quantify the methanogenesis heat flux. We constructed an energetic-based mathematical model of methanogenesis. Our model captured efficiently the dynamics of methanogenesis with average concordance correlation coefficients of 0.95 for CO2, 0.98 for H2 and 0.97 for CH4. Together, experimental data and model enabled us to quantify metabolism kinetics and energetic patterns that were specific and distinct for each species despite their use of analogous methane-producing pathways. Then, we tested in silico the interactions between these methanogens under an in vivo simulation scenario using a theoretical modelling exercise. In silico simulations suggest that the classical competitive exclusion principle is inapplicable to gut ecosystems and that kinetic information alone cannot explain gut ecological aspects such as microbial coexistence. We suggest that ecological models of gut ecosystems require the integration of microbial kinetics with nonlinear behaviours related to spatial and temporal variations taking place in mammalian guts. Our work provides novel information on the thermodynamics and dynamics of methanogens. This understanding will be useful to construct new gut models with enhanced prediction capabilities and could have practical applications for promoting gut health in mammals and mitigating ruminant methane emissions.
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Affiliation(s)
- Rafael Muñoz-Tamayo
- UMR Modélisation Systémique Appliquée aux Ruminants, INRA, AgroParisTech, Université Paris-Saclay, Paris, France
- * E-mail:
| | - Milka Popova
- Institute National de la Recherche Agronomique, UMR1213 Herbivores, Clermont Université, VetAgro Sup, UMR Herbivores, Clermont-Ferrand, France
| | - Maxence Tillier
- Institute National de la Recherche Agronomique, UMR1213 Herbivores, Clermont Université, VetAgro Sup, UMR Herbivores, Clermont-Ferrand, France
| | - Diego P. Morgavi
- Institute National de la Recherche Agronomique, UMR1213 Herbivores, Clermont Université, VetAgro Sup, UMR Herbivores, Clermont-Ferrand, France
| | | | - Gérard Fonty
- Université Clermont Auvergne, CNRS, LMGE, Clermont-Ferrand, France
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23
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Rira M, Morgavi DP, Genestoux L, Djibiri S, Sekhri I, Doreau M. Methanogenic potential of tropical feeds rich in hydrolyzable tannins1,2. J Anim Sci 2019; 97:2700-2710. [PMID: 31192352 DOI: 10.1093/jas/skz199] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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: 01/07/2019] [Accepted: 03/20/2019] [Indexed: 11/14/2022] Open
Abstract
The present study was carried out to determine the effect of Acacia nilotica, a tropical plant rich in hydrolyzable tannins (HT), on rumen fermentation and methane (CH4) production in vitro. We used leaves and pods from A. nilotica alone and combined. The combination of HT from A. nilotica leaves and pods and condensed tannins (CT) from Calliandra calothyrsus and Leucaena leucocephala were also evaluated to assess potential differences in biological activity between HT and CT. Four series of 24-h incubations were performed using rumen contents of 4 sheep fed a tropical grass (natural grassland based on Dichanthium spp.). A first experiment tested different levels of replacement of this tropical forage (control [CTL] without tannins) by A. nilotica leaves or pods: 0:100, 25:75, 50:50, 75:25 and 100:0. A second experiment tested the mixture of A. nilotica leaves and pods in different proportions: 100:0, 75:25, 50:50, 25:75, and 0:100. A third experiment tested the 50:50 combination of A. nilotica leaves or pods with C. calothyrsus and L. leucocephala. Acacia nilotica pods and leaves had a high content of HT (350 and 178 g/kg DM, respectively), whereas C. calothyrsus and L. leucocephala had a high content of CT (361 and 180 g/kg DM, respectively). The inclusion of HT from A. nilotica leaves and pods decreased CH4 production dose-dependently (P < 0.01). Total replacement of the CTL by A. nilotica decreased CH4 production by 64 and 55% with leaves and pods, respectively. Pods were richer in HT than leaves, but their antimethanogenic effect did not differ (P > 0.05). Although A. nilotica leaves and pods inhibited fermentation, as indicated by the lower gas production and VFA production (P < 0.01), this effect was less pronounced than for CH4. Volatile fatty acid production decreased by 12% in leaves and by 30% in pods when compared with the CTL alone. Positive associative effect was reported for VFA, when HT-rich sources and CT-rich sources were mixed. Combining the 2 sources of HT did not show associative effects on fermentation or CH4 production (P > 0.05). Hydrolyzable tannin-rich sources were more effective in suppressing methanogenesis than CT-rich sources. Our results show that HT-rich A. nilotica leaves and pods have the potential to reduce ruminal CH4 production.
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Affiliation(s)
- Moufida Rira
- Ecole Nationale Supérieure de Biotechnologie, Ali Mendjli, Constantine, Algeria.,†INRA, VetAgro Sup, UMR1213 Herbivores, Saint-Genès-Champanelle, France
| | - Diego P Morgavi
- †INRA, VetAgro Sup, UMR1213 Herbivores, Saint-Genès-Champanelle, France
| | - Lucette Genestoux
- †INRA, VetAgro Sup, UMR1213 Herbivores, Saint-Genès-Champanelle, France
| | - Sihem Djibiri
- Ecole Nationale Supérieure de Biotechnologie, Ali Mendjli, Constantine, Algeria
| | - Ines Sekhri
- Ecole Nationale Supérieure de Biotechnologie, Ali Mendjli, Constantine, Algeria
| | - Michel Doreau
- †INRA, VetAgro Sup, UMR1213 Herbivores, Saint-Genès-Champanelle, France
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24
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Jeyanathan J, Martin C, Eugène M, Ferlay A, Popova M, Morgavi DP. Bacterial direct-fed microbials fail to reduce methane emissions in primiparous lactating dairy cows. J Anim Sci Biotechnol 2019; 10:41. [PMID: 31069075 PMCID: PMC6495644 DOI: 10.1186/s40104-019-0342-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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: 11/30/2018] [Accepted: 03/11/2019] [Indexed: 02/07/2023] Open
Abstract
Direct-fed microbials (DFM) are considered as a promising technique to improve animal productivity without affecting animal health or harming the environment. The potential of three bacterial DFM to reduce methane (CH4) emissions, modulate ruminal fermentation, milk production and composition of primiparous dairy cows was examined in this study. As previous reports have shown that DFM respond differently to different diets, two contrasting diets were used in this study. Eight lactating primiparous cows were randomly divided into two groups that were fed a corn silage-based, high-starch diet (HSD) or a grass silage-based, high-fiber diet (HFD). Cows in each dietary group were randomly assigned to four treatments in a 4 × 4 Latin square design. The bacterial DFM used were selected for their proven CH4-reducing effect in vitro. Treatments included control (without DFM) and 3 DFM treatments: Propionibacterium freudenreichii 53-W (2.9 × 1010 colony forming units (CFU)/cow per day), Lactobacillus pentosus D31 (3.6 × 1011 CFU/cow per day) and Lactobacillus bulgaricus D1 (4.6 × 1010 CFU/cow per day). Each experimental period included 4 weeks of treatment and 1 week of wash-out, with measures performed in the fourth week of the treatment period. Enteric CH4 emissions were measured during 3 consecutive days using respiration chambers. Rumen samples were collected for ruminal fermentation parameters and quantitative microbial analyses. Milk samples were collected for composition analysis. Body weight of cows were recorded at the end of each treatment period. Irrespective of diet, no mitigating effect of DFM was observed on CH4 emissions in dairy cows. In contrast, Propionibacterium increased CH4 intensity by 27% (g CH4/kg milk) in cows fed HSD. There was no effect of DFM on other fermentation parameters and on bacterial, archaeal and protozoal numbers. Similarly, the effect of DFM on milk fatty acid composition was negligible. Propionibacterium and L. pentosus DFM tended to increase body weight gain with HSD. We conclude that, contrary to the effect previously observed in vitro, bacterial DFM Propionibacterium freudenreichii 53-W, Lactobacillus pentosus D31 and Lactobacillus bulgaricus D1 did not alter ruminal fermentation and failed to reduce CH4 emissions in lactating primiparous cows fed high-starch or high-fiber diets.
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Affiliation(s)
- Jeyamalar Jeyanathan
- Université Clermont Auvergne, INRA, VetAgro Sup, UMR 1213 Herbivores, F-63122 Saint-Genès-Champanelle, France.,2Present address: Laboratory for Animal Nutrition and Animal Product Quality, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Cécile Martin
- Université Clermont Auvergne, INRA, VetAgro Sup, UMR 1213 Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - Maguy Eugène
- Université Clermont Auvergne, INRA, VetAgro Sup, UMR 1213 Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - Anne Ferlay
- Université Clermont Auvergne, INRA, VetAgro Sup, UMR 1213 Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - Milka Popova
- Université Clermont Auvergne, INRA, VetAgro Sup, UMR 1213 Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - Diego P Morgavi
- Université Clermont Auvergne, INRA, VetAgro Sup, UMR 1213 Herbivores, F-63122 Saint-Genès-Champanelle, France
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25
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Yanibada B, Boudra H, Debrauwer L, Martin C, Morgavi DP, Canlet C. Evaluation of sample preparation methods for NMR-based metabolomics of cow milk. Heliyon 2018; 4:e00856. [PMID: 30364606 PMCID: PMC6197446 DOI: 10.1016/j.heliyon.2018.e00856] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 04/16/2018] [Revised: 07/24/2018] [Accepted: 10/10/2018] [Indexed: 01/26/2023] Open
Abstract
The quality of milk metabolome analyzed by nuclear magnetic resonance (NMR) is greatly influenced by the way samples are prepared. Although this analytical method is increasingly used to study milk metabolites, a thorough examination of available sample preparation protocols for milk has not been reported yet. We evaluated the performance of eight milk preparation methods namely (1) raw milk without any processing; (2) skimmed milk; (3) ultrafiltered milk; (4) skimming followed by ultrafiltration; (5) ultracentrifuged milk; (6) methanol; (7) dichloromethane; and (8) methanol/dichloromethane, in terms of spectra quality, repeatability, signal-to-noise ratio, extraction efficiency and yield criteria. A pooled sample of milk was used for all protocols. Skimming, ultracentrifugation and unprocessed milk protocols showed poor NMR spectra quality. Protocols involving multiple steps, namely methanol/dichloromethane extraction, and skimming followed by ultrafiltration produced inadequate results for signal-to-noise ratio parameter. Methanol and skimming associated to ultrafiltration provided good repeatability results compared to the other protocols. Chemical-based sample preparation protocols, particularly methanol, showed more efficient metabolite extraction compared to physical preparation methods. When considering all evaluation parameters, the methanol extraction protocol proved to be the best method. As a proof of utility, methanol protocol was then applied to milk samples from dairy cows fed a diet with or without a feed additive, showing a clear separation between the two groups of cows.
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Affiliation(s)
- Bénédict Yanibada
- Université Clermont Auvergne, INRA, VetAgro Sup, UMR Herbivores, F-63122, Saint-Genès-Champanelle, France
| | - Hamid Boudra
- Université Clermont Auvergne, INRA, VetAgro Sup, UMR Herbivores, F-63122, Saint-Genès-Champanelle, France
| | - Laurent Debrauwer
- Toxalim, Research Centre in Food Toxicology, Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, F-31027, Toulouse, France.,Axiom Platform, MetaToul-MetaboHUB, National Infrastructure for Metabolomics and Fluxomics, F-31027, Toulouse, France
| | - Cécile Martin
- Université Clermont Auvergne, INRA, VetAgro Sup, UMR Herbivores, F-63122, Saint-Genès-Champanelle, France
| | - Diego P Morgavi
- Université Clermont Auvergne, INRA, VetAgro Sup, UMR Herbivores, F-63122, Saint-Genès-Champanelle, France
| | - Cécile Canlet
- Toxalim, Research Centre in Food Toxicology, Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, F-31027, Toulouse, France.,Axiom Platform, MetaToul-MetaboHUB, National Infrastructure for Metabolomics and Fluxomics, F-31027, Toulouse, France
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26
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Huws SA, Creevey CJ, Oyama LB, Mizrahi I, Denman SE, Popova M, Muñoz-Tamayo R, Forano E, Waters SM, Hess M, Tapio I, Smidt H, Krizsan SJ, Yáñez-Ruiz DR, Belanche A, Guan L, Gruninger RJ, McAllister TA, Newbold CJ, Roehe R, Dewhurst RJ, Snelling TJ, Watson M, Suen G, Hart EH, Kingston-Smith AH, Scollan ND, do Prado RM, Pilau EJ, Mantovani HC, Attwood GT, Edwards JE, McEwan NR, Morrisson S, Mayorga OL, Elliott C, Morgavi DP. Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future. Front Microbiol 2018; 9:2161. [PMID: 30319557 PMCID: PMC6167468 DOI: 10.3389/fmicb.2018.02161] [Citation(s) in RCA: 170] [Impact Index Per Article: 28.3] [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: 05/31/2018] [Accepted: 08/23/2018] [Indexed: 12/24/2022] Open
Abstract
The rumen is a complex ecosystem composed of anaerobic bacteria, protozoa, fungi, methanogenic archaea and phages. These microbes interact closely to breakdown plant material that cannot be digested by humans, whilst providing metabolic energy to the host and, in the case of archaea, producing methane. Consequently, ruminants produce meat and milk, which are rich in high-quality protein, vitamins and minerals, and therefore contribute to food security. As the world population is predicted to reach approximately 9.7 billion by 2050, an increase in ruminant production to satisfy global protein demand is necessary, despite limited land availability, and whilst ensuring environmental impact is minimized. Although challenging, these goals can be met, but depend on our understanding of the rumen microbiome. Attempts to manipulate the rumen microbiome to benefit global agricultural challenges have been ongoing for decades with limited success, mostly due to the lack of a detailed understanding of this microbiome and our limited ability to culture most of these microbes outside the rumen. The potential to manipulate the rumen microbiome and meet global livestock challenges through animal breeding and introduction of dietary interventions during early life have recently emerged as promising new technologies. Our inability to phenotype ruminants in a high-throughput manner has also hampered progress, although the recent increase in “omic” data may allow further development of mathematical models and rumen microbial gene biomarkers as proxies. Advances in computational tools, high-throughput sequencing technologies and cultivation-independent “omics” approaches continue to revolutionize our understanding of the rumen microbiome. This will ultimately provide the knowledge framework needed to solve current and future ruminant livestock challenges.
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Affiliation(s)
- Sharon A Huws
- Institute for Global Food Security, Queen's University of Belfast, Belfast, United Kingdom
| | - Christopher J Creevey
- Institute for Global Food Security, Queen's University of Belfast, Belfast, United Kingdom
| | - Linda B Oyama
- Institute for Global Food Security, Queen's University of Belfast, Belfast, United Kingdom
| | - Itzhak Mizrahi
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Stuart E Denman
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Queensland Bioscience Precinct, St Lucia, QLD, Australia
| | - Milka Popova
- Institute National de la Recherche Agronomique, UMR1213 Herbivores, Clermont Université, VetAgro Sup, UMR Herbivores, Clermont-Ferrand, France
| | - Rafael Muñoz-Tamayo
- UMR Modélisation Systémique Appliquée aux Ruminants, INRA, AgroParisTech, Université Paris-Saclay, Paris, France
| | - Evelyne Forano
- UMR 454 MEDIS, INRA, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Sinead M Waters
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Grange, Ireland
| | - Matthias Hess
- College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA, United States
| | - Ilma Tapio
- Natural Resources Institute Finland, Jokioinen, Finland
| | - Hauke Smidt
- Department of Agrotechnology and Food Sciences, Wageningen, Netherlands
| | - Sophie J Krizsan
- Department of Agricultural Research for Northern Sweden, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - David R Yáñez-Ruiz
- Estacion Experimental del Zaidin, Consejo Superior de Investigaciones Cientificas, Granada, Spain
| | - Alejandro Belanche
- Estacion Experimental del Zaidin, Consejo Superior de Investigaciones Cientificas, Granada, Spain
| | - Leluo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Robert J Gruninger
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Tim A McAllister
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | | | - Rainer Roehe
- Scotland's Rural College, Edinburgh, United Kingdom
| | | | - Tim J Snelling
- The Rowett Institute, University of Aberdeen, Aberdeen, United Kingdom
| | - Mick Watson
- The Roslin Institute and the Royal (Dick) School of Veterinary Studies (R(D)SVS), University of Edinburgh, Edinburgh, United Kingdom
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Elizabeth H Hart
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Alison H Kingston-Smith
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Nigel D Scollan
- Institute for Global Food Security, Queen's University of Belfast, Belfast, United Kingdom
| | - Rodolpho M do Prado
- Laboratório de Biomoléculas e Espectrometria de Massas-Labiomass, Departamento de Química, Universidade Estadual de Maringá, Maringá, Brazil
| | - Eduardo J Pilau
- Laboratório de Biomoléculas e Espectrometria de Massas-Labiomass, Departamento de Química, Universidade Estadual de Maringá, Maringá, Brazil
| | | | - Graeme T Attwood
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Joan E Edwards
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Neil R McEwan
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen, United Kingdom
| | - Steven Morrisson
- Sustainable Livestock, Agri-Food and Bio-Sciences Institute, Hillsborough, United Kingdom
| | - Olga L Mayorga
- Colombian Agricultural Research Corporation, Mosquera, Colombia
| | - Christopher Elliott
- Institute for Global Food Security, Queen's University of Belfast, Belfast, United Kingdom
| | - Diego P Morgavi
- Institute National de la Recherche Agronomique, UMR1213 Herbivores, Clermont Université, VetAgro Sup, UMR Herbivores, Clermont-Ferrand, France
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27
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Saro C, Hohenester UM, Bernard M, Lagrée M, Martin C, Doreau M, Boudra H, Popova M, Morgavi DP. Effectiveness of Interventions to Modulate the Rumen Microbiota Composition and Function in Pre-ruminant and Ruminant Lambs. Front Microbiol 2018; 9:1273. [PMID: 29967596 PMCID: PMC6015893 DOI: 10.3389/fmicb.2018.01273] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [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: 03/26/2018] [Accepted: 05/24/2018] [Indexed: 11/24/2022] Open
Abstract
Modulating the assembly of the ruminal microbiota might have practical implications in production. We tested how an early-life dietary intervention in lambs influences the diversity and function of the ruminal microbiota during and after the intervention. Microbiota resilience during a repeated dietary intervention was also tested. The treatment, aiming to mitigate enteric methane emissions, combined garlic essential oil and linseed oil. Fifty-six lambs and their dams were allocated to two groups and treatment (T1) or placebo (C1) was drenched from birth until 10 weeks of life. Lambs were weaned at 8 weeks. From 16 to 20 weeks, lambs in each group were divided in two subgroups that received (T1–T2 and C1–T2) or not (T1–C2 and C1–C2) the same treatment. Measurements were done at 8, 14, and 20 weeks. Average daily gain was similar between groups. Methane production was reduced by treatment at 8 and 20 weeks but at 14 weeks it was similar between C1 and T1. Interestingly, early-life treated lambs displayed a numerical increase (P = 0.12) in methane emissions at 20 weeks compared with non-treated lambs. Concentration of VFA was not affected by the intervention at 8 or 14 weeks but a lower concentration was observed in T2 lambs compared with C2 at week 20. Metataxonomics (rRNA gene) revealed differences in archaeal communities between groups of lambs when treatment was applied (weeks 8 and 20); whereas, in accord with methane emissions, these differences disappeared when treatment was discontinued (week 14). Protozoal community structure was not affected by treatment. In contrast, bacterial community structure differed between treated and non-treated lambs during and after the intervention. Rumen and urine LC-MS and NMR metabolomics at week 20 separated C2 from T2 lambs and correlation analysis highlighted interactions between microbes and metabolites, notably that of methylated compounds and Methanomassiliicocceae methanogens. This study demonstrates that a long-term early-life intervention induced modifications in the composition of the rumen bacterial community that persisted after the intervention ceased with little or no effect on archaeal and protozoal communities. However, there was no persistency of the early-life intervention on methanogenesis indicating resilience for this function.
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Affiliation(s)
- Cristina Saro
- Université Clermont Auvergne, INRA, VetAgro Sup, UMR Herbivores, Saint-Genès-Champanelle, France
| | - Ulli M Hohenester
- Université Clermont Auvergne, INRA, VetAgro Sup, UMR Herbivores, Saint-Genès-Champanelle, France
| | | | - Marie Lagrée
- Université Clermont Auvergne - CNRS - SIGMA-Clermont, Institut de Chimie de Clermont-Ferrand, Clermont-Ferrand, France.,Université Clermont Auvergne - INRA, MetaboHUB/Plateforme d'Exploration du Métabolisme, Clermont-Ferrand, France
| | - Cécile Martin
- Université Clermont Auvergne, INRA, VetAgro Sup, UMR Herbivores, Saint-Genès-Champanelle, France
| | - Michel Doreau
- Université Clermont Auvergne, INRA, VetAgro Sup, UMR Herbivores, Saint-Genès-Champanelle, France
| | - Hamid Boudra
- Université Clermont Auvergne, INRA, VetAgro Sup, UMR Herbivores, Saint-Genès-Champanelle, France
| | - Milka Popova
- Université Clermont Auvergne, INRA, VetAgro Sup, UMR Herbivores, Saint-Genès-Champanelle, France
| | - Diego P Morgavi
- Université Clermont Auvergne, INRA, VetAgro Sup, UMR Herbivores, Saint-Genès-Champanelle, France
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28
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Ufarté L, Potocki-Veronese G, Cecchini D, Tauzin AS, Rizzo A, Morgavi DP, Cathala B, Moreau C, Cleret M, Robe P, Klopp C, Laville E. Highly Promiscuous Oxidases Discovered in the Bovine Rumen Microbiome. Front Microbiol 2018; 9:861. [PMID: 29780372 PMCID: PMC5945886 DOI: 10.3389/fmicb.2018.00861] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 09/30/2017] [Accepted: 04/13/2018] [Indexed: 11/17/2022] Open
Abstract
The bovine rumen hosts a diverse microbiota, which is highly specialized in the degradation of lignocellulose. Ruminal bacteria, in particular, are well equipped to deconstruct plant cell wall polysaccharides. Nevertheless, their potential role in the breakdown of the lignin network has never been investigated. In this study, we used functional metagenomics to identify bacterial redox enzymes acting on polyaromatic compounds. A new methodology was developed to explore the potential of uncultured microbes to degrade lignin derivatives, namely kraft lignin and lignosulfonate. From a fosmid library covering 0.7 Gb of metagenomic DNA, three hit clones were identified, producing enzymes able to oxidize a wide variety of polyaromatic compounds without the need for the addition of copper, manganese, or mediators. These promiscuous redox enzymes could thus be of potential interest both in plant biomass refining and dye remediation. The enzymes were derived from uncultured Clostridia, and belong to complex gene clusters involving proteins of different functional types, including hemicellulases, which likely work in synergy to produce substrate degradation.
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Affiliation(s)
- Lisa Ufarté
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Institut National des Sciences Appliquées de Toulouse, Université de Toulouse, Toulouse, France
| | - Gabrielle Potocki-Veronese
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Institut National des Sciences Appliquées de Toulouse, Université de Toulouse, Toulouse, France
| | - Davide Cecchini
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Institut National des Sciences Appliquées de Toulouse, Université de Toulouse, Toulouse, France
| | - Alexandra S Tauzin
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Institut National des Sciences Appliquées de Toulouse, Université de Toulouse, Toulouse, France
| | - Angeline Rizzo
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Institut National des Sciences Appliquées de Toulouse, Université de Toulouse, Toulouse, France
| | | | - Bernard Cathala
- UR1268 Biopolymères Interactions Assemblages, INRA, Nantes, France
| | - Céline Moreau
- UR1268 Biopolymères Interactions Assemblages, INRA, Nantes, France
| | - Megane Cleret
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Institut National des Sciences Appliquées de Toulouse, Université de Toulouse, Toulouse, France
| | | | - Christophe Klopp
- Plateforme Bio-informatique Toulouse Genopole, UBIA INRA, BP 52627, Castanet-Tolosan, France
| | - Elisabeth Laville
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Institut National des Sciences Appliquées de Toulouse, Université de Toulouse, Toulouse, France
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29
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Meale SJ, Morgavi DP, Cassar-Malek I, Andueza D, Ortigues-Marty I, Robins RJ, Schiphorst AM, Migné C, Pétéra M, Laverroux S, Graulet B, Boudra H, Cantalapiedra-Hijar G. Correction to Exploration of Biological Markers of Feed Efficiency in Young Bulls. J Agric Food Chem 2018; 66:4580. [PMID: 29682965 DOI: 10.1021/acs.jafc.8b01910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- Sarah J Meale
- Université Clermont Auvergne , INRA, VetAgro Sup, UMR Herbivores , F-63122 Saint-Genès-Champanelle , France
| | - Diego P Morgavi
- Université Clermont Auvergne , INRA, VetAgro Sup, UMR Herbivores , F-63122 Saint-Genès-Champanelle , France
| | - Isabelle Cassar-Malek
- Université Clermont Auvergne , INRA, VetAgro Sup, UMR Herbivores , F-63122 Saint-Genès-Champanelle , France
| | - Donato Andueza
- Université Clermont Auvergne , INRA, VetAgro Sup, UMR Herbivores , F-63122 Saint-Genès-Champanelle , France
| | - Isabelle Ortigues-Marty
- Université Clermont Auvergne , INRA, VetAgro Sup, UMR Herbivores , F-63122 Saint-Genès-Champanelle , France
| | - Richard J Robins
- Elucidation of Biosynthesis by Isotopic Spectrometry Group, CEISAM , CNRS-University of Nantes UMR6230 , B.P. 92208, F-44322 Nantes , France
| | - Anne-Marie Schiphorst
- Elucidation of Biosynthesis by Isotopic Spectrometry Group, CEISAM , CNRS-University of Nantes UMR6230 , B.P. 92208, F-44322 Nantes , France
| | - Carole Migné
- Université Clermont Auvergne , INRA, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont , F-63000 Clermont-Ferrand , France
| | - Mélanie Pétéra
- Université Clermont Auvergne , INRA, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont , F-63000 Clermont-Ferrand , France
| | - Sophie Laverroux
- Université Clermont Auvergne , INRA, VetAgro Sup, UMR Herbivores , F-63122 Saint-Genès-Champanelle , France
| | - Benoit Graulet
- Université Clermont Auvergne , INRA, VetAgro Sup, UMR Herbivores , F-63122 Saint-Genès-Champanelle , France
| | - Hamid Boudra
- Université Clermont Auvergne , INRA, VetAgro Sup, UMR Herbivores , F-63122 Saint-Genès-Champanelle , France
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30
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Meale SJ, Auffret MD, Watson M, Morgavi DP, Cantalapiedra-Hijar G, Duthie CA, Roehe R, Dewhurst RJ. Fat accretion measurements strengthen the relationship between feed conversion efficiency and Nitrogen isotopic discrimination while rumen microbial genes contribute little. Sci Rep 2018; 8:3854. [PMID: 29497066 PMCID: PMC5832862 DOI: 10.1038/s41598-018-22103-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [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: 10/04/2017] [Accepted: 02/16/2018] [Indexed: 01/20/2023] Open
Abstract
The use of biomarkers for feed conversion efficiency (FCE), such as Nitrogen isotopic discrimination (Δ15N), facilitates easier measurement and may be useful in breeding strategies. However, we need to better understand the relationship between FCE and Δ15N, particularly the effects of differences in the composition of liveweight gain and rumen N metabolism. Alongside measurements of FCE and Δ15N, we estimated changes in body composition and used dietary treatments with and without nitrates, and rumen metagenomics to explore these effects. Nitrate fed steers had reduced FCE and higher Δ15N in plasma compared to steers offered non-nitrate containing diets. The negative relationship between FCE and Δ15N was strengthened with the inclusion of fat depth change at the 3rd lumbar vertebrae, but not with average daily gain. We identified 1,700 microbial genes with a relative abundance >0.01% of which, 26 were associated with Δ15N. These genes explained 69% of variation in Δ15N and showed clustering in two distinct functional networks. However, there was no clear relationship between their relative abundances and Δ15N, suggesting that rumen microbial genes contribute little to Δ15N. Conversely, we show that changes in the composition of gain (fat accretion) provide additional strength to the relationship between FCE and Δ15N.
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Affiliation(s)
- Sarah J Meale
- Université Clermont Auvergne, INRA, VetAgro Sup, UMR Herbivores, F-63122, Saint-Genès-Champanelle, France
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD 4343, Australia
| | - Marc D Auffret
- SRUC, West Mains Road, Edinburgh, EH9 3JG, United Kingdom
| | - Mick Watson
- Division of Genetics and Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, EH25 9RG, United Kingdom
- Edinburgh Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, EH25 9RG, United Kingdom
| | - Diego P Morgavi
- Université Clermont Auvergne, INRA, VetAgro Sup, UMR Herbivores, F-63122, Saint-Genès-Champanelle, France
| | | | | | - Rainer Roehe
- SRUC, West Mains Road, Edinburgh, EH9 3JG, United Kingdom
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31
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Meale SJ, Morgavi DP, Cassar-Malek I, Andueza D, Ortigues-Marty I, Robins RJ, Schiphorst AM, Migné C, Pétéra M, Laverroux S, Graulet B, Boudra H, Cantalapiedra-Hijar G. Exploration of Biological Markers of Feed Efficiency in Young Bulls. J Agric Food Chem 2017; 65:9817-9827. [PMID: 29058420 DOI: 10.1021/acs.jafc.7b03503] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The efficiency with which ruminants convert feed to desirable products is difficult to measure under normal commercial settings. We explored the use of potential biological markers from easily obtainable samples, that is, blood, hair, and feces, to characterize potential causes of divergent efficiency when considered as residual feed intake (RFI) or feed conversion efficiency (FCE). A total of 54 Charolais bulls, 20 in period 1 and 34 in period 2, were examined for individual dry matter intake (DMI) and growth. Bulls were offered a diet of 70:30 wrapped grass silage to concentrate for 99 d. At the conclusion of the test period, blood samples were collected for the determination of vitamins B2 and B6, and plasma used for the determination of metabolites, natural isotopic 15N abundance (15N NIA, expressed as δ15N ‰) and fractionation (Δ15Nplasma proteins-diet and Δ13Cplasma proteins-diet) and near-infrared spectroscopy (NIRS). Feces were analyzed by NIRS. Bulls were slaughtered at 15-17 months of age and carcass characteristics determined. Bulls were ranked according to RFI with extremes (SD ± 0.5; n = 31) classified as either efficient (Neg-RFI) or inefficient (Pos-RFI). Extreme bulls were then classified for FCE (high vs low FCE), changing the groups. Pos-RFI bulls consumed 14% more feed than Neg-RFI bulls for the same level of weight gain. Low FCE bulls tended to eat more, but had lower weight gains than high FCE bulls. No differences were detected in carcass conformation, fat scores, hot carcass weight, or dressing percentage. Yet, heart and bladder weights were heavier in Pos-RFI, and rumen weight tended to be heavier in Pos-RFI bulls. RFI did not affect bulk 15N or 13C fractionation. A negative correlation was observed between FCE and Δ15Nplasma proteins-diet. Inefficient bulls (Pos-RFI) had higher δ15N in glycine compared to Neg-RFI bulls. Similarly, metabolomic analysis showed a tendency for concentrations of glycine and sarcosine to be elevated in Pos-RFI bulls, whereas aspartic acid and carnosine tended to be elevated, and serine tended to be lower in High FCE. Among vitamins, only flavin adenine dinucleotide concentration was higher in the blood of bulls with High FCE. These results suggest that the two feed efficiency metrics differ in the underlying mechanisms of metabolism, where RFI is driven by differences in the energetic requirements of visceral organs and the extent of AA catabolism.
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Affiliation(s)
- Sarah J Meale
- Université Clermont Auvergne, INRA , VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - Diego P Morgavi
- Université Clermont Auvergne, INRA , VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - Isabelle Cassar-Malek
- Université Clermont Auvergne, INRA , VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - Donato Andueza
- Université Clermont Auvergne, INRA , VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - Isabelle Ortigues-Marty
- Université Clermont Auvergne, INRA , VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - Richard J Robins
- Elucidation of Biosynthesis by Isotopic Spectrometry Group, CEISAM, CNRS-University of Nantes UMR6230 , B.P. 92208, F-44322 Nantes, France
| | - Anne-Marie Schiphorst
- Elucidation of Biosynthesis by Isotopic Spectrometry Group, CEISAM, CNRS-University of Nantes UMR6230 , B.P. 92208, F-44322 Nantes, France
| | | | | | - Sophie Laverroux
- Université Clermont Auvergne, INRA , VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - Benoit Graulet
- Université Clermont Auvergne, INRA , VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - Hamid Boudra
- Université Clermont Auvergne, INRA , VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
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Popova M, McGovern E, McCabe MS, Martin C, Doreau M, Arbre M, Meale SJ, Morgavi DP, Waters SM. The Structural and Functional Capacity of Ruminal and Cecal Microbiota in Growing Cattle Was Unaffected by Dietary Supplementation of Linseed Oil and Nitrate. Front Microbiol 2017; 8:937. [PMID: 28596764 PMCID: PMC5442214 DOI: 10.3389/fmicb.2017.00937] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [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: 02/28/2017] [Accepted: 05/09/2017] [Indexed: 01/13/2023] Open
Abstract
Microorganisms in the digestive tract of ruminants differ in their functionality and ability to use feed constituents. While cecal microbiota play an important role in post-rumen fermentation of residual substrates undigested in the rumen, limited knowledge exists regarding its structure and function. In this trial we investigated the effect of dietary supplementation with linseed oil and nitrate on methane emissions and on the structure of ruminal and cecal microbiota of growing bulls. Animals were allocated to either a CTL (control) or LINNIT (CTL supplemented with 1.9% linseed and 1.0% nitrates) diet. Methane emissions were measured using the GreenFeed system. Microbial diversity was assessed using amplicon sequencing of microbial genomic DNA. Additionally, total RNA was extracted from ruminal contents and functional mcrA and mtt genes were targeted in amplicon sequencing approach to explore the diversity of functional gene expression in methanogens. LINNIT had no effect on methane yield (g/kg DMI) even though it decreased methane production by 9% (g/day; P < 0.05). Methanobrevibacter- and Methanomassiliicoccaceae-related OTUs were more abundant in cecum (72 and 24%) compared to rumen (60 and 11%) irrespective of the diet (P < 0.05). Feeding LINNIT reduced the relative abundance of Methanomassiliicoccaceae mcrA cDNA reads in the rumen. Principal component analysis revealed significant differences in taxonomic composition and abundance of bacterial communities between rumen and cecum. Treatment decreased the relative abundance of a few Ruminococcaceae genera, without affecting global bacterial community structure. Our research confirms a high level of heterogeneity in species composition of microbial consortia in the main gastrointestinal compartments where feed is fermented in ruminants. There was a parallel between the lack of effect of LINNIT on ruminal and cecal microbial community structure and functions on one side and methane emission changes on the other. These results suggest that the sequencing strategy used here to study microbial diversity and function accurately reflected the absence of effect on methane phenotypes in bulls treated with linseed plus nitrate.
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Affiliation(s)
- Milka Popova
- UMR1213 Herbivores, Institut National de la Recherche Agronomique, VetAgro Sup, Clermont Université, Université de LyonSaint Genès-Champanelle, France
| | - Emily McGovern
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, TeagascDunsany, County Meath, Ireland
| | - Matthew S McCabe
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, TeagascDunsany, County Meath, Ireland
| | - Cécile Martin
- UMR1213 Herbivores, Institut National de la Recherche Agronomique, VetAgro Sup, Clermont Université, Université de LyonSaint Genès-Champanelle, France
| | - Michel Doreau
- UMR1213 Herbivores, Institut National de la Recherche Agronomique, VetAgro Sup, Clermont Université, Université de LyonSaint Genès-Champanelle, France
| | - Marie Arbre
- UMR1213 Herbivores, Institut National de la Recherche Agronomique, VetAgro Sup, Clermont Université, Université de LyonSaint Genès-Champanelle, France
| | - Sarah J Meale
- UMR1213 Herbivores, Institut National de la Recherche Agronomique, VetAgro Sup, Clermont Université, Université de LyonSaint Genès-Champanelle, France
| | - Diego P Morgavi
- UMR1213 Herbivores, Institut National de la Recherche Agronomique, VetAgro Sup, Clermont Université, Université de LyonSaint Genès-Champanelle, France
| | - Sinéad M Waters
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, TeagascDunsany, County Meath, Ireland
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Guyader J, Eugène M, Doreau M, Morgavi DP, Gérard C, Martin C. Tea saponin reduced methanogenesis in vitro but increased methane yield in lactating dairy cows. J Dairy Sci 2017; 100:1845-1855. [PMID: 28109588 DOI: 10.3168/jds.2016-11644] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 11/22/2016] [Indexed: 11/19/2022]
Abstract
The effect of tea saponin supplementation in the ruminant diet on methane emissions, rumen fermentation, and digestive processes is still under debate. The objective of this study was to assess the effect of this plant extract on methanogenesis, total-tract digestibility, and lactating performances of dairy cows. The work included 2 independent and successive experiments. First, the effect of 7 tea saponin doses (from 0 to 0.50 g/L) on methane emissions and protozoa concentrations was tested in 2 repeated in vitro batch culture incubations using bovine rumen contents as inoculum and a cereal mixture as substrate. After 18 h of incubation, total gas production and composition as well as rumen fermentation parameters and protozoa concentration were analyzed. Increasing dosage of the plant extract reduced methane production and protozoa concentration, with a maximum reduction of 29% for CH4 (mL/g of substrate) and 51% for protozoa (105/mL). Tea saponin did not affect volatile fatty acids concentration, but marginally decreased total gas production by 5% at the highest dose. Second, a 2-period crossover design experiment was carried out with 8 lactating dairy cows fed a basal diet (54% corn silage, 6% hay, and 40% pelleted concentrates on a dry matter basis) without (control) or with 0.52% tea saponin (TSP). Each experimental period lasted 5 wk. Animals were fed ad libitum during the first 3 wk of the period (wk 1, 2, and 3) and restricted (95% of ad libitum intake) during the last 2 wk (wk 4 and 5). Intake and milk production were recorded daily. Methane emissions were quantified using open chambers (2 d, wk 4). Total-tract digestibility and nitrogen balance were determined from total feces and urine collected separately (5 d, wk 5). Rumen fermentation parameters and protozoa concentration were analyzed from samples taken after morning feeding (1 d, wk 5). Milk production, dry matter intake, and feed efficiency were reduced with TSP (-18, -12, and -8%, respectively). As daily methane production (g/d) was not affected, methane emissions (g/kg of dry matter intake) increased by 14% with TSP. Total-tract digestibility and nitrogen balance were similar between diets, except for acid detergent fiber digestibility, which tended to be improved with TSP (+4 percentage units). Rumen fermentation parameters and protozoa concentration were relatively unchanged by diets. Under the conditions of this experiment, tea saponin is not efficient to reduce methane emissions from dairy cows.
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Affiliation(s)
- J Guyader
- UMR1213 Herbivores, INRA, VetAgro Sup, Clermont Université, Université de Lyon, F-63122 Saint-Genès-Champanelle, France
| | - M Eugène
- UMR1213 Herbivores, INRA, VetAgro Sup, Clermont Université, Université de Lyon, F-63122 Saint-Genès-Champanelle, France
| | - M Doreau
- UMR1213 Herbivores, INRA, VetAgro Sup, Clermont Université, Université de Lyon, F-63122 Saint-Genès-Champanelle, France
| | - D P Morgavi
- UMR1213 Herbivores, INRA, VetAgro Sup, Clermont Université, Université de Lyon, F-63122 Saint-Genès-Champanelle, France
| | - C Gérard
- NEOVIA by InVivo, Talhouët, F-56250 Saint-Nolff, France
| | - C Martin
- UMR1213 Herbivores, INRA, VetAgro Sup, Clermont Université, Université de Lyon, F-63122 Saint-Genès-Champanelle, France.
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Pantaya D, Morgavi DP, Silberberg M, Chaucheyras-Durand F, Martin C, Suryahadi, Wiryawan KG, Boudra H. Bioavailability of aflatoxin B 1 and ochratoxin A, but not fumonisin B 1 or deoxynivalenol, is increased in starch-induced low ruminal pH in nonlactating dairy cows. J Dairy Sci 2016; 99:9759-9767. [PMID: 27771083 DOI: 10.3168/jds.2016-11421] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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: 05/09/2016] [Accepted: 08/24/2016] [Indexed: 11/19/2022]
Abstract
High-production dairy and beef systems require diets rich in starch. This practice may induce ruminal acidosis and also increase exposure to mycotoxins because starches in starch-rich diets are the main vehicles of mycotoxin contamination. The aim of this study was to investigate the effects of low ruminal pH on the bioavailability of 4 major mycotoxins [i.e., aflatoxin B1 (AFB1), ochratoxin A (OTA), deoxynivalenol (DON), and fumonisin B1 (FB1)]. Eight nonlactating dairy cows fitted with rumen cannulas were used in a double crossover experiment. The trial was divided into 4 periods with 2 periods per crossover. Cows were divided into 2 groups receiving a low (15% dry matter basis) and high-starch diet (30.8%) with and without live yeast supplementation (1×1010 cfu per cow) in the first and second crossover, respectively. At the end of each period, cows received a single dose of mycotoxin-contaminated feed containing 0.05, 0.2, 0.24, and 0.56mg of AFB1, OTA, DON, and FB1 per kg of feed, respectively. The fecal and urinary excretion of mycotoxins and their metabolites was monitored for up to 48h postdosing. As expected, ruminal pH decreased in cows fed the high-starch diet. The high-starch diet increased the bioavailability of OTA and AFB1. Urinary excretion of OTA 24h after mycotoxin administration increased 3-fold in the high-starch diet, correlated with lower fecal excretion. Similarly, a decrease in fecal excretion of AFB1 was accompanied by an increase in urinary excretion of its major metabolite, aflatoxin M1, 48h after mycotoxin administration. In contrast to AFB1 and OTA, the bioavailability of DON and FB1 remained unchanged. Yeast supplementation had no effect on the excretion balance of these 2 mycotoxins. In conclusion, these results show that high-starch diets increased the bioavailability of OTA and AFB1, most probably through the lowering effect on ruminal pH. This greater bioavailability potentially increases the toxic effects of these mycotoxins.
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Affiliation(s)
- D Pantaya
- UMRH, INRA, Vetagro Sup, 63122 Saint-Genès-Champanelle, France; Department of Animal Science, State Polytechnic Jember, Jember, Indonesia, 68121
| | - D P Morgavi
- UMRH, INRA, Vetagro Sup, 63122 Saint-Genès-Champanelle, France
| | - M Silberberg
- UMRH, INRA, Vetagro Sup, 63122 Saint-Genès-Champanelle, France
| | - F Chaucheyras-Durand
- Lallemand Animal Nutrition, 31702 Blagnac Cedex, France; Unité de Microbiologie, INRA, 63122 Saint-Genès-Champanelle, France
| | - C Martin
- UMRH, INRA, Vetagro Sup, 63122 Saint-Genès-Champanelle, France
| | - Suryahadi
- Faculty of Animal Science, Bogor Agricultural University, Bogor, Indonesia, 16680
| | - K G Wiryawan
- Faculty of Animal Science, Bogor Agricultural University, Bogor, Indonesia, 16680
| | - H Boudra
- UMRH, INRA, Vetagro Sup, 63122 Saint-Genès-Champanelle, France.
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Guyader J, Eugène M, Meunier B, Doreau M, Morgavi DP, Silberberg M, Rochette Y, Gerard C, Loncke C, Martin C. Additive methane-mitigating effect between linseed oil and nitrate fed to cattle. J Anim Sci 2016; 93:3564-77. [PMID: 26440025 DOI: 10.2527/jas.2014-8196] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The objective of this study was to test the effect of linseed oil and nitrate fed alone or in combination on methane (CH4) emissions and diet digestibility in cows. The experiment was conducted as a 2 × 2 factorial design using 4 multiparous nonlactating Holstein cows (initial BW 656 ± 31 kg). Each experimental period lasted 5 wk, with measures performed in the final 3 wk (wk 3 to 5). Diets given on a DM basis were 1) control (CON; 50% natural grassland hay and 50% concentrate), 2) CON with 4% linseed oil (LIN), 3) CON with 3% calcium nitrate (NIT), and 4) CON with 4% linseed oil plus 3% calcium nitrate (LIN+NIT). Diets were offered twice daily and were formulated to deliver similar amounts (DM basis) of CP (12.2%), starch (25.5%), and NDF (39.5%). Feed offer was restricted to 90% of voluntary intake (12.4 kg DMI/d). Total tract digestibility and N balance were determined from total feces and urine collected separately for 6 d during wk 4. Daily CH4 emissions were quantified using open chambers for 4 d during wk 5. Rumen fermentation and microbial parameters were analyzed from samples taken before and 3 h after the morning feeding. Rumen concentrations of dissolved hydrogen (H2) were measured continuously up to 6 h after feeding using a H2 sensor. Compared with the CON diet linseed oil and nitrate decreased (P < 0.01) CH4 emissions (g/kg DMI) by 17 and 22%, respectively, when fed alone and by 32% when combined. The LIN diet reduced CH4 production throughout the day, increased (P = 0.02) propionate proportion, and decreased (P = 0.03) ruminal protozoa concentration compared with CON diet. The NIT diet strongly reduced CH4 production 3 h after feeding, with a simultaneous increase in rumen dissolved H2 concentration, suggesting that nitrate does not act only as an electron acceptor. As a combined effect, linseed plus nitrate also increased H2 concentrations in the rumen. Diets had no effect (P > 0.05) on total tract digestibility of nutrients, except linseed oil, which tended to reduce (P < 0.10) fiber digestibility. Nitrogen balance (% of N intake) was positive for all diets but retention was less (P = 0.03) with linseed oil. This study demonstrates an additive effect between nitrate and linseed oil for reducing methanogenesis in cows without altering diet digestibility.
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Rira M, Morgavi DP, Archimède H, Marie-Magdeleine C, Popova M, Bousseboua H, Doreau M. Potential of tannin-rich plants for modulating ruminal microbes and ruminal fermentation in sheep. J Anim Sci 2015; 93:334-47. [PMID: 25568379 DOI: 10.2527/jas.2014-7961] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The objective of this work was to study nutritional strategies for decreasing methane production by ruminants fed tropical diets, combining in vitro and in vivo methods. The in vitro approach was used to evaluate the dose effect of condensed tannins (CT) contained in leaves of Gliricidia sepium, Leucaena leucocephala, and Manihot esculenta (39, 75, and 92 g CT/kg DM, respectively) on methane production and ruminal fermentation characteristics. Tannin-rich plants (TRP) were incubated for 24 h alone or mixed with a natural grassland hay based on Dichanthium spp. (control plant), so that proportions of TRP were 0, 0.25, 0.5, 0.75, and 1.0. Methane production, VFA concentration, and fermented OM decreased with increased proportions of TRP. Numerical differences on methane production and VFA concentration among TRP sources may be due to differences in their CT content, with greater effects for L. leucocephala and M. esculenta than for G. sepium. Independently of TRP, the response to increasing doses of CT was linear for methane production but quadratic for VFA concentration. As a result, at moderate tannin dose, methane decreased more than VFA. The in vivo trial was conducted to investigate the effect of TRP on different ruminal microbial populations. To this end, 8 rumen-cannulated sheep from 2 breeds (Texel and Blackbelly) were used in two 4 × 4 Latin square designs. Diets were fed ad libitum and were composed of the same feeds used for the in vitro trial: control plant alone or combined with pellets made from TRP leaves at 44% of the diet DM. Compared to TRP, concentration of Ruminococcus flavefaciens was greater for the control diet and concentration of Ruminococcus albus was least for the control diet. The methanogen population was greater for Texel than for Blackbelly. By contrast, TRP-containing diets did not affect protozoa or Fibrobacter succinogenes numbers. Hence, TRP showed potential for mitigating methane production by ruminants. These findings suggest that TRP fed as pellets could be used to decrease methane production.
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Affiliation(s)
- M Rira
- INRA, UMR 1213 Herbivores, 63122 Saint-Genès Champanelle, France
| | - D P Morgavi
- INRA, UMR 1213 Herbivores, 63122 Saint-Genès Champanelle, France
| | - H Archimède
- INRA, Unité de Recherches Zootechniques, 97170 Petit-Bourg, Guadeloupe, France
| | - C Marie-Magdeleine
- INRA, Unité de Recherches Zootechniques, 97170 Petit-Bourg, Guadeloupe, France
| | - M Popova
- INRA, UMR 1213 Herbivores, 63122 Saint-Genès Champanelle, France
| | - H Bousseboua
- Ecole Nationale Supérieure des Biotechnologies, Ali Mendjli, BP E66. 25100 Constantine, Algeria
| | - M Doreau
- INRA, UMR 1213 Herbivores, 63122 Saint-Genès Champanelle, France
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Archimède H, Rira M, Barde DJ, Labirin F, Marie-Magdeleine C, Calif B, Periacarpin F, Fleury J, Rochette Y, Morgavi DP, Doreau M. Potential of tannin-rich plants, Leucaena leucocephala, Glyricidia sepium and Manihot esculenta, to reduce enteric methane emissions in sheep. J Anim Physiol Anim Nutr (Berl) 2015; 100:1149-1158. [PMID: 27870287 DOI: 10.1111/jpn.12423] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [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: 06/14/2015] [Accepted: 09/15/2015] [Indexed: 11/29/2022]
Abstract
An in vivo trial was conducted in sheep to investigate the effect of three tropical tannin-rich plants (TRP) on methane emission, intake and digestibility. The TRP used were leaves of Glyricidia sepium, Leucaena leucocephala and Manihot esculenta that contained, respectively, 39, 75 and 92 g condensed tannins/kg DM. Methane was determined with the sulphur hexafluoride tracer technique. Eight rumen-cannulated sheep of two breeds (four Texel, four Blackbelly) were used in two 4 × 4 Latin square designs. Four experimental diets were tested. They consisted in a tropical natural grassland hay based on Dichanthium spp. fed alone (C) or in association with G. sepium (G), L. leucocephala (L) or M. esculenta (M) given as pellets at 44% of the daily ration. Daily organic matter intake was higher in TRP diets (686, 984, 1054 and 1186 g/day for C, G, L and M respectively; p < 0.05) while apparent organic matter total tract digestibility was not affected (69.9%, 62.8%, 65.3% and 64.7% for C, G, L and M respectively; p > 0.05). Methane emission was 47.1, 44.9, 33.3 and 33.5 g/kg digestible organic matter intake for C, G, L and M, respectively, and was significantly lower (p < 0.05) for L and M than for G and C. Our results confirm the potential of some TRP to reduce methane production. The strong decrease in methane and the increase in intake with TRPs may be due to their presentation as pellets.
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Affiliation(s)
- H Archimède
- INRA, UR143, Unité de Recherches Zootechnique, Guadeloupe, French West Indies
| | - M Rira
- INRA, UMR 1213, Unité de Recherches sur les Herbivores, Saint-Genès Champanelle, France
| | - D J Barde
- INRA, UR143, Unité de Recherches Zootechnique, Guadeloupe, French West Indies
| | - F Labirin
- INRA UE1284, Plateforme Tropicale d'Expérimentation sur l'Animal, Guadeloupe, French West Indies
| | - C Marie-Magdeleine
- INRA, UR143, Unité de Recherches Zootechnique, Guadeloupe, French West Indies
| | - B Calif
- INRA, UR143, Unité de Recherches Zootechnique, Guadeloupe, French West Indies
| | - F Periacarpin
- INRA UE1284, Plateforme Tropicale d'Expérimentation sur l'Animal, Guadeloupe, French West Indies
| | - J Fleury
- INRA UE1284, Plateforme Tropicale d'Expérimentation sur l'Animal, Guadeloupe, French West Indies
| | | | - D P Morgavi
- INRA, UMR 1213, Unité de Recherches sur les Herbivores, Saint-Genès Champanelle, France
| | - M Doreau
- INRA, UMR 1213, Unité de Recherches sur les Herbivores, Saint-Genès Champanelle, France
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Colin PY, Kintses B, Gielen F, Miton CM, Fischer G, Mohamed MF, Hyvönen M, Morgavi DP, Janssen DB, Hollfelder F. Ultrahigh-throughput discovery of promiscuous enzymes by picodroplet functional metagenomics. Nat Commun 2015; 6:10008. [PMID: 26639611 PMCID: PMC4686663 DOI: 10.1038/ncomms10008] [Citation(s) in RCA: 178] [Impact Index Per Article: 19.8] [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: 06/30/2015] [Accepted: 10/25/2015] [Indexed: 12/25/2022] Open
Abstract
Unculturable bacterial communities provide a rich source of biocatalysts, but their experimental discovery by functional metagenomics is difficult, because the odds are stacked against the experimentor. Here we demonstrate functional screening of a million-membered metagenomic library in microfluidic picolitre droplet compartments. Using bait substrates, new hydrolases for sulfate monoesters and phosphotriesters were identified, mostly based on promiscuous activities presumed not to be under selection pressure. Spanning three protein superfamilies, these break new ground in sequence space: promiscuity now connects enzymes with only distantly related sequences. Most hits could not have been predicted by sequence analysis, because the desired activities have never been ascribed to similar sequences, showing how this approach complements bioinformatic harvesting of metagenomic sequencing data. Functional screening of a library of unprecedented size with excellent assay sensitivity has been instrumental in identifying rare genes constituting catalytically versatile hubs in sequence space as potential starting points for the acquisition of new functions.
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Affiliation(s)
- Pierre-Yves Colin
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Balint Kintses
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Fabrice Gielen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Charlotte M Miton
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Gerhard Fischer
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Mark F Mohamed
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Diego P Morgavi
- INRA, UMR1213 Herbivores, F-63122 Saint-Genès-Champanelle, France.,Clermont Université, VetAgro Sup, UMR Herbivores, BP 10448, F-63000 Clermont-Ferrand, France
| | - Dick B Janssen
- Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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Lazuka A, Auer L, Bozonnet S, Morgavi DP, O'Donohue M, Hernandez-Raquet G. Efficient anaerobic transformation of raw wheat straw by a robust cow rumen-derived microbial consortium. Bioresour Technol 2015; 196:241-9. [PMID: 26247975 DOI: 10.1016/j.biortech.2015.07.084] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/23/2015] [Accepted: 07/24/2015] [Indexed: 05/15/2023]
Abstract
A rumen-derived microbial consortium was enriched on raw wheat straw as sole carbon source in a sequential batch-reactor (SBR) process under strict mesophilic anaerobic conditions. After five cycles of enrichment the procedure enabled to select a stable and efficient lignocellulolytic microbial consortium, mainly constituted by members of Firmicutes and Bacteroidetes phyla. The enriched community, designed rumen-wheat straw-derived consortium (RWS) efficiently hydrolyzed lignocellulosic biomass, degrading 55.5% w/w of raw wheat straw over 15days at 35°C and accumulating carboxylates as main products. Cellulolytic and hemicellulolytic activities, mainly detected on the cell bound fraction, were produced in the earlier steps of degradation, their production being correlated with the maximal lignocellulose degradation rates. Overall, these results demonstrate the potential of RWS to convert unpretreated lignocellulosic substrates into useful chemicals.
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Affiliation(s)
- Adèle Lazuka
- Université de Toulouse, INSA, UPS, LISBP, 135 Avenue de Rangueil, F-31077 Toulouse Cedex 4, France; INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France; CNRS, UMR5504, F-31400 Toulouse, France
| | - Lucas Auer
- Université de Toulouse, INSA, UPS, LISBP, 135 Avenue de Rangueil, F-31077 Toulouse Cedex 4, France; INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France; CNRS, UMR5504, F-31400 Toulouse, France
| | - Sophie Bozonnet
- Université de Toulouse, INSA, UPS, LISBP, 135 Avenue de Rangueil, F-31077 Toulouse Cedex 4, France; INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France; CNRS, UMR5504, F-31400 Toulouse, France
| | - Diego P Morgavi
- INRA, UR1213 Herbivores, Centre de Theix, F-63122 St-Genès-Champanelle, France
| | - Michael O'Donohue
- Université de Toulouse, INSA, UPS, LISBP, 135 Avenue de Rangueil, F-31077 Toulouse Cedex 4, France; INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France; CNRS, UMR5504, F-31400 Toulouse, France
| | - Guillermina Hernandez-Raquet
- Université de Toulouse, INSA, UPS, LISBP, 135 Avenue de Rangueil, F-31077 Toulouse Cedex 4, France; INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France; CNRS, UMR5504, F-31400 Toulouse, France.
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Morgavi DP, Rathahao-Paris E, Popova M, Boccard J, Nielsen KF, Boudra H. Rumen microbial communities influence metabolic phenotypes in lambs. Front Microbiol 2015; 6:1060. [PMID: 26528248 PMCID: PMC4601264 DOI: 10.3389/fmicb.2015.01060] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [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: 07/30/2015] [Accepted: 09/14/2015] [Indexed: 12/15/2022] Open
Abstract
The rumen microbiota is an essential part of ruminants shaping their nutrition and health. Despite its importance, it is not fully understood how various groups of rumen microbes affect host-microbe relationships and functions. The aim of the study was to simultaneously explore the rumen microbiota and the metabolic phenotype of lambs for identifying host-microbe associations and potential biomarkers of digestive functions. Twin lambs, separated in two groups after birth were exposed to practices (isolation and gavage with rumen fluid with protozoa or protozoa-depleted) that differentially restricted the acquisition of microbes. Rumen microbiota, fermentation parameters, digestibility and growth were monitored for up to 31 weeks of age. Microbiota assembled in isolation from other ruminants lacked protozoa and had low bacterial and archaeal diversity whereas digestibility was not affected. Exposure to adult sheep microbiota increased bacterial and archaeal diversity independently of protozoa presence. For archaea, Methanomassiliicoccales displaced Methanosphaera. Notwithstanding, protozoa induced differences in functional traits such as digestibility and significantly shaped bacterial community structure, notably Ruminococcaceae and Lachnospiraceae lower up to 6 folds, Prevotellaceae lower by ~40%, and Clostridiaceae and Veillonellaceae higher up to 10 folds compared to microbiota without protozoa. An orthogonal partial least squares-discriminant analysis of urinary metabolome matched differences in microbiota structure. Discriminant metabolites were mainly involved in amino acids and protein metabolic pathways while a negative interaction was observed between methylotrophic methanogens Methanomassiliicoccales and trimethylamine N-oxide. These results stress the influence of gut microbes on animal phenotype and show the potential of metabolomics for monitoring rumen microbial functions.
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Affiliation(s)
- Diego P Morgavi
- Institute National de la Recherche Agronomique, UMR1213 Herbivores, Clermont Université, VetAgro Sup, UMR Herbivores Clermont-Ferrand, France
| | - Estelle Rathahao-Paris
- Institute National de la Recherche Agronomique, UMR 1145 Ingénierie Procédés Aliments Paris, France ; Agroparistech, UMR 1145 Ingénierie Procédés Aliments Paris, France
| | - Milka Popova
- Institute National de la Recherche Agronomique, UMR1213 Herbivores, Clermont Université, VetAgro Sup, UMR Herbivores Clermont-Ferrand, France
| | - Julien Boccard
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne Geneva, Switzerland
| | - Kristian F Nielsen
- Department of Systems Biology, Technical University of Denmark Kgs. Lyngby, Denmark
| | - Hamid Boudra
- Institute National de la Recherche Agronomique, UMR1213 Herbivores, Clermont Université, VetAgro Sup, UMR Herbivores Clermont-Ferrand, France
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41
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Redouane-Salah S, Morgavi DP, Arhab R, Messaï A, Boudra H. Presence of aflatoxin M1 in raw, reconstituted, and powdered milk samples collected in Algeria. Environ Monit Assess 2015; 187:375. [PMID: 26009161 DOI: 10.1007/s10661-015-4627-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 05/19/2015] [Indexed: 06/04/2023]
Abstract
Aflatoxins are potent toxic metabolites produced by Aspergillus spp. Aflatoxin M1 (AFM1) is a metabolite of aflatoxin B1 that can be present in milk, and it is a public health concern. There is scarce information on the incidence of aflatoxin M1 contamination in milk consumed in Algeria. The presence of AFM1 was investigated in raw milk samples collected between February and October 2011 from 11 dairy farms representative of Algerian production conditions and that were located around Constantine city. Reconstituted and powdered milk samples were purchased from local supermarkets. The analysis was performed by liquid chromatography-fluorescence detection after immunoaffinity purification. AFM1 was detected in 5 out of 47 samples (11 %) at levels ranging from 9 to 103 ng/L, with one sample exceeding the limit of 50 ng/L set by European regulations. Traces of AFM1 (less than 8 ng/L) were also found in 11 other samples. The incidence of AFM1 contamination was higher in imported powdered milk (29 %) than in raw milk (5 %). Although the concentration of AFM1 in contaminated samples was low, the relatively considerable prevalence found in this exploratory study justifies more detailed and continuous monitoring to reduce consumers' exposure to AFM1.
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Affiliation(s)
- S Redouane-Salah
- Department of Agricultural Sciences, University of Biskra, BP 145 RP, 07000, Biskra, Algeria
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Boudra H, Saivin S, Buffiere C, Morgavi DP. Short communication: Toxicokinetics of ochratoxin A in dairy ewes and carryover to milk following a single or long-term ingestion of contaminated feed. J Dairy Sci 2013; 96:6690-6. [PMID: 23972496 DOI: 10.3168/jds.2013-6707] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [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: 02/18/2013] [Accepted: 07/04/2013] [Indexed: 11/19/2022]
Abstract
Ruminal microbes have the capacity to inactivate ochratoxins, rendering ruminants less sensitive to this fungal contaminant found in cereal feeds. However, ochratoxin A has been reported in milk surveys. The objective of this study was to assess the toxicokinetics, excretion, and transmission into milk of ochratoxin A using doses similar to those of naturally occurring field contaminations. Six Lacaune dairy ewes in late lactation were separated into 2 groups that received a single dose of contaminated wheat containing 5 or 30 μg of ochratoxin A/kg of body weight. After administration, toxicokinetics and excretion were monitored for 48 h. Subsequently, ewes were administered the corresponding toxin dose daily for 24 d followed by a second toxicokinetics and excretion monitoring period for this long-term exposure. The doses used did not affect production or health of ewes. After a single dose, ochratoxin A and its main metabolite, ochratoxin α, were found in blood 1h postexposure. The maximum blood concentrations of ochratoxin A and α, respectively, were dose dependent and were observed, on average, 6 and 8h after exposure. Long-term exposure increased the maximum concentration of ochratoxin A detected in blood, whereas ochratoxin α was not affected. In contrast, the time to reach the maximum concentration was reduced to 3h for both molecules. Ochratoxins, essentially ochratoxin α, were mainly excreted in feces. Ochratoxin A and α were detected in milk at concentrations that were dose dependent but with a low carryover rate (<0.02%). Chronic administration did not increase the concentration of toxin in milk. Even though ochratoxin A can escape ruminal degradation and traces were found in milk of experimentally exposed ewes, the low carryover of ochratoxin A in milk minimizes the risk to consumers.
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Affiliation(s)
- H Boudra
- INRA, UMR1213 Herbivores, F-63122 Saint-Genès-Champanelle and Clermont Université, VetAgro Sup, UMR Herbivores, BP 10448, F-63000, Clermont-Ferrand, France
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Denonfoux J, Parisot N, Dugat-Bony E, Biderre-Petit C, Boucher D, Morgavi DP, Le Paslier D, Peyretaillade E, Peyret P. Gene capture coupled to high-throughput sequencing as a strategy for targeted metagenome exploration. DNA Res 2013; 20:185-96. [PMID: 23364577 PMCID: PMC3628448 DOI: 10.1093/dnares/dst001] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [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] [Indexed: 01/15/2023] Open
Abstract
Next-generation sequencing (NGS) allows faster acquisition of metagenomic data, but complete exploration of complex ecosystems is hindered by the extraordinary diversity of microorganisms. To reduce the environmental complexity, we created an innovative solution hybrid selection (SHS) method that is combined with NGS to characterize large DNA fragments harbouring biomarkers of interest. The quality of enrichment was evaluated after fragments containing the methyl coenzyme M reductase subunit A gene (mcrA), the biomarker of methanogenesis, were captured from a Methanosarcina strain and a metagenomic sample from a meromictic lake. The methanogen diversity was compared with direct metagenome and mcrA-based amplicon pyrosequencing strategies. The SHS approach resulted in the capture of DNA fragments up to 2.5 kb with an enrichment efficiency between 41 and 100%, depending on the sample complexity. Compared with direct metagenome and amplicons sequencing, SHS detected broader mcrA diversity, and it allowed efficient sampling of the rare biosphere and unknown sequences. In contrast to amplicon-based strategies, SHS is less biased and GC independent, and it recovered complete biomarker sequences in addition to conserved regions. Because this method can also isolate the regions flanking the target sequences, it could facilitate operon reconstructions.
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Affiliation(s)
- Jérémie Denonfoux
- Centre de Recherche en Nutrition Humaine Auvergne, Clermont Université, Université d'Auvergne, EA 4678, Conception, Ingénierie et Développement de l'Aliment et du Médicament, BP 10448, Clermont-Ferrand 63000, France
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El Marnissi B, Belkhou R, Morgavi DP, Bennani L, Boudra H. Occurrence of aflatoxin M1 in raw milk collected from traditional dairies in Morocco. Food Chem Toxicol 2012; 50:2819-21. [DOI: 10.1016/j.fct.2012.05.031] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Revised: 05/14/2012] [Accepted: 05/15/2012] [Indexed: 11/30/2022]
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Lettat A, Nozière P, Silberberg M, Morgavi DP, Berger C, Martin C. Rumen microbial and fermentation characteristics are affected differently by bacterial probiotic supplementation during induced lactic and subacute acidosis in sheep. BMC Microbiol 2012; 12:142. [PMID: 22812531 PMCID: PMC3438074 DOI: 10.1186/1471-2180-12-142] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [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: 02/20/2012] [Accepted: 06/21/2012] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Ruminal disbiosis induced by feeding is the cause of ruminal acidosis, a digestive disorder prevalent in high-producing ruminants. Because probiotic microorganisms can modulate the gastrointestinal microbiota, propionibacteria- and lactobacilli-based probiotics were tested for their effectiveness in preventing different forms of acidosis. RESULTS Lactic acidosis, butyric and propionic subacute ruminal acidosis (SARA) were induced by feed chalenges in three groups of four wethers intraruminally dosed with wheat, corn or beet pulp. In each group, wethers were either not supplemented (C) or supplemented with Propionibacterium P63 alone (P) or combined with L. plantarum (Lp + P) or L. rhamnosus (Lr + P). Compared with C, all the probiotics stimulated lactobacilli proliferation, which reached up to 25% of total bacteria during wheat-induced lactic acidosis. This induced a large increase in lactate concentration, which decreased ruminal pH. During the corn-induced butyric SARA, Lp + P decreased Prevotella spp. proportion with a concomitant decrease in microbial amylase activity and total volatile fatty acids concentration, and an increase in xylanase activity and pH. Relative to the beet pulp-induced propionic SARA, P and Lr + P improved ruminal pH without affecting the microbial or fermentation characteristics. Regardless of acidosis type, denaturing gradient gel electrophoresis revealed that probiotic supplementations modified the bacterial community structure. CONCLUSION This work showed that the effectiveness of the bacterial probiotics tested depended on the acidosis type. Although these probiotics were ineffective in lactic acidosis because of a deeply disturbed rumen microbiota, some of the probiotics tested may be useful to minimize the occurrence of butyric and propionic SARA in sheep. However, their modes of action need to be further investigated.
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Affiliation(s)
- Abderzak Lettat
- INRA, UR1213 Herbivores, Centre de Recherches de Clermont-Ferrand/Theix, F-63122 Saint Genès, Champanelle, France
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Firmin S, Gandia P, Morgavi DP, Houin G, Jouany JP, Bertin G, Boudra H. Modification of aflatoxin B1 and ochratoxin A toxicokinetics in rats administered a yeast cell wall preparation. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2010; 27:1153-60. [PMID: 20512710 DOI: 10.1080/19440041003801174] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The cell wall of Saccharomyces cerevisiae can bind mycotoxins in vitro, but there is scarce information on whether this property decreases the absorption of mycotoxins in vivo. The effect of a yeast cell wall preparation (YCW) on toxicokinetics and balance excretion (urine and faeces) of aflatoxin B(1) (AFB1) and ochratoxin A (OTA) was tested in rats after oral administration of each toxin. The (3)H-labelled mycotoxins were used at low doses. Co-administration of YCW with AFB1 decreased the extent, but not the rate, of absorption. Concurrently, radioactivity excreted in faeces increased by up to 55% when compared with controls, whilst the excretion in urine decreased (p < 0.05). The effect of YCW on OTA was less marked, although it increased radioactivity excretion in faeces (up to 16%; p < 0.05) it did not result in changes in urine and toxicokinetic parameters. The in vivo effect is in agreement with the reported in vitro binding ability for these toxins (AFB1 > OTA). In conclusion, these results indicate that YCW could be used to protect monogastric animals against exposure to low dietary levels of selected mycotoxins.
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Affiliation(s)
- S Firmin
- INRA, UR1213 Herbivores, Site de Theix, F-63122 Saint Genès-Champanelle, France
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Popova M, Martin C, Morgavi DP. Improved protocol for high-quality co-extraction of DNA and RNA from rumen digesta. Folia Microbiol (Praha) 2010; 55:368-72. [PMID: 20680573 DOI: 10.1007/s12223-010-0060-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Revised: 04/14/2010] [Indexed: 10/19/2022]
Abstract
We report an improved method for total nucleic acids extraction from rumen content samples. The method employs bead beating, and phenol-chloroform extraction followed by saline-alcohol precipitation. Total nucleic acids and RNA yield and purity were assessed by spectrophotometric measurements; RNA integrity was estimated using Agilent RNA 6000 Nano Kit on an Agilent 2100 Bioanalyzer. The method provided total nucleic acids and RNA extracts of good quantity and quality. The extraction is not time consuming and it is valuable for ecological studies of rumen microbial community structure and gene expression.
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Affiliation(s)
- M Popova
- INRA Clermont-Ferrand-Theix, 63122, Saint Gènes Champanelle, France
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de la Fuente G, Fondevila M, Morgavi DP. Predation of Salmonella enterica serovar Typhimurium by the rumen protozoon Entodinium caudatum studied in vitro by fluorescence emission. Eur J Protistol 2010; 46:189-95. [DOI: 10.1016/j.ejop.2010.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Revised: 03/10/2010] [Accepted: 03/23/2010] [Indexed: 11/28/2022]
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Abstract
Under unfavorable climatic conditions, Fusarium spp. can contaminate corn plants in the field and produce toxins that are present at the time of ensiling. The stability of deoxynivalenol, fumonisins B1 and B2, and zearalenone in corn silage was tested over two consecutive years. Variables studied were corn dry matter (DM) and storage length and temperature. The concentration of all Fusarium toxins decreased upon ensiling ( P < 0.001). Increasing the length of storage and ensiling with low DM resulted in a higher rate of toxin disappearance, particularly for the water soluble toxins deoxynivalenol and fumonisin B1. Toxin disappearance ranged from 50% for zearalenone to 100% for deoxynivalenol. In contrast, temperature did not have any effect on stability ( P > 0.05). These results indicate that low DM at ensiling as well as a prolonged storage could be a practical way to reduce or eliminate some Fusarium toxins in contaminated silages.
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Affiliation(s)
- Hamid Boudra
- INRA, UR1213 Herbivores, Site de Theix, F-63122 Saint Genès-Champanelle, France.
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Abstract
Mycotoxins in milk are a public health concern and have to be regularly monitored. A survey on the presence of aflatoxin M1 (AFM1) and ochratoxin A (OTA) in raw bulk milk was conducted in 2003 in the northwest of France, the main French milk-producing basin. Randomly selected farms (n = 132) were characterized by a diet based on corn silage and containing a large proportion of on-farm produced cereals, feeding sources that are frequently contaminated by mycotoxins. Farms were surveyed twice in winter and in summer. At each sampling time, a trained surveyor completed a questionnaire recording farm management procedures and production traits. The AFM1 was found in 3 out of 264 samples but at levels (26 ng/L or less) that are below the European legislation limit of 50 ng/L. Traces of AFM1 (less than 8 ng/L) were also found in 6 other samples. The OTA was detected in 3 samples also at low levels, 5 to 8 ng/L. Farms that tested positive to the presence of mycotoxins, 12 in total including 6 farms that had traces of AFM1, differed from negative farms by a more extensive use of total mixed rations, 58 vs. 27%. In addition, the positive farms tended to have lower milk yields. Although the incidence of milk contamination with AFM1 and OTA at the farm level was low during the period studied, production and management data from the surveyed farms suggest a link between feeding management practices and mycotoxin contamination.
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Affiliation(s)
- H Boudra
- UR1213 Herbivores, Institut National de la Recherche Agronomique, Site de Theix, F-63122 Saint Genès-Champanelle, France.
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