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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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Cantalapiedra-Hijar G, Martinez-Fernandez G, Forano E, Denman SE, Morgavi D, McSweeney CS. The extent of nitrogen isotopic fractionation in rumen bacteria is associated with changes in rumen nitrogen metabolism. PLoS One 2023; 18:e0291243. [PMID: 37703250 PMCID: PMC10499230 DOI: 10.1371/journal.pone.0291243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 08/25/2023] [Indexed: 09/15/2023] Open
Abstract
Nitrogen use efficiency is an important index in ruminants and can be indirectly evaluated through the N isotopic discrimination between the animal and its diet (Δ15Nanimal-diet). The concentration and source of N may determine both the extent of the N isotopic discrimination in bacteria and N use efficiency. We hypothesised that the uptake and release of ammonia by rumen bacteria will affect the natural 15N enrichment of the bacterial biomass over their substrates (Δ15Nbacteria-substrate) and thereby further impacting Δ15Nanimal-diet. To test this hypothesis, two independent in vitro experiments were conducted using two contrasting N sources (organic vs inorganic) at different levels either in pure rumen bacteria culture incubations (Experiment #1) or in mixed rumen cultures (Experiment #2). In Experiment #1, tryptone casein or ammonium chloride were tested at low (1 mM N) and high (11.5 mM N) concentrations on three rumen bacterial strains (Fibrobacter succinogenes, Eubacterium limosum and Xylanibacter ruminicola) incubated in triplicate in anaerobic batch monocultures during 48h. In Experiment #2 mixed rumen cultures were incubated during 120 h with peptone or ammonium chloride at five different levels of N (1.5, 3, 4.5, 6 and 12-mM). In experiment #1, Δ15Nbacteria-substrate was lowest when the ammonia-consumer bacterium Fibrobacter succinogenes was grown on ammonium chloride, and highest when the proteolytic bacterial strain Xylanibacter ruminicola was grown on tryptone. In experiment #2, Δ15Nbacteria-substrate was lower with inorganic (ammonium chloride) vs organic (peptone) N source. A strong negative correlation between Δ15Nbacteria-substrate and Rikenellaceae_RC9_gut_group, a potential fibrolytic rumen bacterium, was detected. Together, our results showed that Δ15Nbacteria-substrate may change according to the balance between synthesis of microbial protein from ammonia versus non-ammonia N sources and confirm the key role of rumen bacteria as modulators of Δ15Nanimal-diet.
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Affiliation(s)
| | | | - Evelyne Forano
- INRAE, Université Clermont Auvergne, UMR 454 MEDIS, Saint-Genès-Champanelle, France
| | | | - Diego Morgavi
- INRAE, Université Clermont Auvergne, Vetagro Sup, UMRH, Saint-Genes-Champanelle, France
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Martinez-Fernandez G, Jiao J, Padmanabha J, Denman SE, McSweeney CS. Correction: Martinez-Fernandez et al. Seasonal and Nutrient Supplement Responses in Rumen Microbiota Structure and Metabolites of Tropical Rangeland Cattle. Microorganisms 2020, 8, 1550. Microorganisms 2021; 9:microorganisms9051053. [PMID: 34068449 PMCID: PMC8153255 DOI: 10.3390/microorganisms9051053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 11/29/2022] Open
Affiliation(s)
| | - Jinzhen Jiao
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China;
| | - Jagadish Padmanabha
- Agriculture and Food, CSIRO, St Lucia, QLD 4067, Australia; (G.M.-F.); (J.P.); (S.E.D.)
| | - Stuart E. Denman
- Agriculture and Food, CSIRO, St Lucia, QLD 4067, Australia; (G.M.-F.); (J.P.); (S.E.D.)
| | - Christopher S. McSweeney
- Agriculture and Food, CSIRO, St Lucia, QLD 4067, Australia; (G.M.-F.); (J.P.); (S.E.D.)
- Correspondence:
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Martinez-Fernandez G, Jiao J, Padmanabha J, Denman SE, McSweeney CS. Seasonal and Nutrient Supplement Responses in Rumen Microbiota Structure and Metabolites of Tropical Rangeland Cattle. Microorganisms 2020; 8:E1550. [PMID: 33049981 PMCID: PMC7600044 DOI: 10.3390/microorganisms8101550] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/29/2020] [Accepted: 10/05/2020] [Indexed: 01/31/2023] Open
Abstract
This study aimed to characterize the rumen microbiota structure of cattle grazing in tropical rangelands throughout seasons and their responses in rumen ecology and productivity to a N-based supplement during the dry season. Twenty pregnant heifers grazing during the dry season of northern Australia were allocated to either N-supplemented or un-supplemented diets and monitored through the seasons. Rumen fluid, blood, and feces were analyzed before supplementation (mid-dry season), after two months supplementation (late-dry season), and post supplementation (wet season). Supplementation increased average daily weight gain (ADWG), rumen NH3-N, branched fatty acids, butyrate and acetic:propionic ratio, and decreased plasma δ15N. The supplement promoted bacterial populations involved in hemicellulose and pectin degradation and ammonia assimilation: Bacteroidales BS11, Cyanobacteria, and Prevotella spp. During the dry season, fibrolytic populations were promoted: the bacteria Fibrobacter, Cyanobacteria and Kiritimatiellaeota groups; the fungi Cyllamyces; and the protozoa Ostracodinium. The wet season increased the abundances of rumen protozoa and fungi populations, with increases of bacterial families Lachnospiraceae, Ruminococcaceae, and Muribaculaceae; the protozoa Entodinium and Eudiplodinium; the fungi Pecoramyces; and the archaea Methanosphera. In conclusion, the rumen microbiota of cattle grazing in a tropical grassland is distinctive from published studies that mainly describe ruminants consuming better quality diets.
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Affiliation(s)
| | - Jinzhen Jiao
- CAS Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China;
| | - Jagadish Padmanabha
- Agriculture and Food, CSIRO, St Lucia, QLD 4067, Australia; (G.M.-F.); (J.P.); (S.E.D.)
| | - Stuart E. Denman
- Agriculture and Food, CSIRO, St Lucia, QLD 4067, Australia; (G.M.-F.); (J.P.); (S.E.D.)
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Abstract
The standardization of collection and processing methods for rumen samples is crucial to reduce the level of errors that may affect the analysis and interpretation of the data. The aim of this study was to compare two processing methods and their impacts on the microbial community composition analysis, from material that was either immediately frozen or samples that were stored as cell pellets after removing the supernatant prior to freezing. Eight rumen-fistulated Brahman steers received chloroform as an antimethanogenic compound for 21 days. Rumen fluid samples (60 mL per animal) were collected using a probe covered with two layers of cheesecloth at 3 h post feeding at day 0 prior-treatment (control period) and day 21 of treatment. One sub-set of samples were placed in dry ice and stored at −80°C (Method 1) for subsequent DNA extraction, while a second subset of samples was centrifuged, the supernatant removed and the microbial pellet and rumen contents placed in dry ice and stored at −80°C (Method 2) prior to DNA extractions. Phylogenetic based methods (Illumina Miseq) targeting the 16S rRNA gene were used to characterize the bacterial and archaeal communities from both collection methods for the control and treatment periods. The results from this study showed that the chloroform treatment was significantly different for all beta diversity measures regardless of the processing method used. Significant differences in the relative abundances of some bacteria and archaea, such as Elusimicrobia, Fibrobacteres, Lentisphaerae, Spirochaetes, and Verrucomicrobia and Methanomassiliicoccaceae, were observed at higher levels in the Method 2. These microbial populations are known to have fragile cell wall structures and are susceptible to cell lysis. Regardless of the processing method used, both identified the key microbial groups and can be used to compare the relative shifts in the rumen microbiome between treatments. However, immediately freezing samples might alter the abundance of material from species that are more readily lysed and will not be suitable for studies that aim to assign absolute abundance values to these species within the rumen.
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Affiliation(s)
- Gonzalo Martinez-Fernandez
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, St Lucia, QLD, Australia
| | - Stuart E Denman
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, St Lucia, QLD, Australia
| | - Christopher S McSweeney
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, St Lucia, QLD, Australia
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Martinez-Fernandez G, Duval S, Kindermann M, Schirra HJ, Denman SE, McSweeney CS. 3-NOP vs. Halogenated Compound: Methane Production, Ruminal Fermentation and Microbial Community Response in Forage Fed Cattle. Front Microbiol 2018; 9:1582. [PMID: 30131771 PMCID: PMC6090035 DOI: 10.3389/fmicb.2018.01582] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/25/2018] [Indexed: 12/17/2022] Open
Abstract
The aim of this study was to investigate the effects of 3-nitrooxypropanol (3-NOP) and chloroform on methane (CH4) and H2 production, ruminal metabolites and microbial community structure in cattle fed a tropical forage diet. Eight rumen-fistulated steers were fed a roughage hay diet (Rhodes grass; Chloris gayana) for 31 days (control period). Four animals received the antimethanogenic compound chloroform (1.6 g chloroform-cyclodextrin/100 kg live weight (LW)) while the other four received 3-NOP (2.5 g 3-NOP/animal/day) for 21 days. Methane decrease compared with control period was similar for both treatments (30-38%) with no differences for expelled H2 between controls and treatments. Daily weight gain (DWG) was significantly increased when animals were treated with 3-NOP compared with chloroform and control. Regarding the ruminal fermentation parameters increases in ammonia, acetate and branched chain fatty acids were observed with both compounds compared with the controls. Also, methylamines, alcohols and dimethyl sulfone (DMSO2) concentrations were significantly increased with the treatments compared with control, being greater with 3-NOP. The rumen microbial analyses revealed a similar profile for both treatments, with a shift in operational taxonomic units (OTUs) assigned to the Prevotellaceae and Campylobacteraceae family. Moreover, major archaeal OTUs associated with Methanobrevibacter and Methanosphaera were significantly affected to varying extents based on the inhibitory treatments compared to the control. The abundance of the Methanobrevibacter spp. was decreased by 3-NOP and chloroform, while the Methanomassiliicoccaceae family was inhibited only by 3-NOP. The results suggest that despite the specific mode of action of 3-NOP on methanogens, inhibition of methanogenesis by both compounds resulted in similar responses in metabolism and microbial community structure in the rumen. We hypothesized that these changes were driven by the redirection of metabolic hydrogen ([H]) by both treatments. Therefore results from previous publications using chloroform as an inhibitor of methanogenesis may be useful in predicting ruminal microbiota and fermentation responses to 3-NOP.
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Affiliation(s)
| | - Stephane Duval
- Research Centre for Animal Nutrition and Health, DSM Nutritional Products, Saint-Louis, France
| | - Maik Kindermann
- Animal Nutrition and Health, DSM Nutritional Products, Basel, Switzerland
| | - Horst J Schirra
- The University of Queensland, Centre for Advanced Imaging, Brisbane, QLD, Australia
| | - Stuart E Denman
- CSIRO, Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD, Australia
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Martinez-Fernandez G, Denman SE, Cheung J, McSweeney CS. Phloroglucinol Degradation in the Rumen Promotes the Capture of Excess Hydrogen Generated from Methanogenesis Inhibition. Front Microbiol 2017; 8:1871. [PMID: 29051749 PMCID: PMC5633678 DOI: 10.3389/fmicb.2017.01871] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 09/13/2017] [Indexed: 11/21/2022] Open
Abstract
Strategies to manage metabolic hydrogen ([H]) in the rumen should be considered when reducing ruminant methane (CH4) emissions. However, little is known about the use of dietary treatments to stimulate rumen microorganisms capable of capturing the [H] available when CH4 is inhibited in vivo. The effects of the phenolic compound phloroglucinol on CH4 production, [H] flows and subsequent responses in rumen fermentation and microbial community composition when methanogenesis is inhibited were investigated in cattle. Eight rumen fistulated Brahman steers were randomly allocated in two groups receiving chloroform as an antimethanogenic compound for 21 days. Following that period one group received chloroform + phloroglucinol for another 16 days, whilst the other group received only chloroform during the same period. The chloroform treatment resulted in a decrease in CH4 production and an increase in H2 expelled with a shift in rumen fermentation toward higher levels of propionate and formate and lower levels of acetate at day 21 of treatment. Bacterial operational taxonomic units (OTUs) assigned to Prevotella were promoted whilst Archaea and Synergistetes OTUs were decreased with the chloroform treatment as expected. The shift toward formate coincided with increases in Ruminococcus flavefaciens, Butyrivibrio fibrisolvens, and Methanobrevibacter ruminantium species. The addition of chloroform + phloroglucinol in the rumen resulted in a decrease of H2 expelled (g) per kg of DMI and moles of H2 expelled per mol of CH4 decreased compared with the chloroform only treated animals. A shift toward acetate and a decrease in formate were observed for the chloroform + phloroglucinol-treated animals at day 37. These changes in the rumen fermentation profile were accompanied by a relative increase of OTUs assigned to Coprococcus spp., which could suggest this genus is a significant contributor to the metabolism of this phenolic compound in the rumen. This study demonstrates for the first time in vivo that under methanogenesis inhibition, H2 gas accumulation can be decreased by redirecting [H] toward alternative sinks through the nutritional stimulation of specific microbial groups. This results in the generation of metabolites of value for the host while also helping to maintain a low H2 partial pressure in the methane-inhibited rumen.
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Affiliation(s)
- Gonzalo Martinez-Fernandez
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Queensland Bioscience Precinct, St Lucia, QLD, Australia
| | - Stuart E Denman
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Queensland Bioscience Precinct, St Lucia, QLD, Australia
| | - Jane Cheung
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Queensland Bioscience Precinct, St Lucia, QLD, Australia
| | - Christopher S McSweeney
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Queensland Bioscience Precinct, St Lucia, QLD, Australia
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Martinez-Fernandez G, Denman SE, Yang C, Cheung J, Mitsumori M, McSweeney CS. Methane Inhibition Alters the Microbial Community, Hydrogen Flow, and Fermentation Response in the Rumen of Cattle. Front Microbiol 2016; 7:1122. [PMID: 27486452 PMCID: PMC4949212 DOI: 10.3389/fmicb.2016.01122] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/06/2016] [Indexed: 11/13/2022] Open
Abstract
Management of metabolic hydrogen ([H]) in the rumen has been identified as an important consideration when reducing ruminant CH4 emissions. However, little is known about hydrogen flux and microbial rumen population responses to CH4 inhibition when animals are fed with slowly degradable diets. The effects of the anti-methanogenic compound, chloroform, on rumen fermentation, microbial ecology, and H2/CH4 production were investigated in vivo. Eight rumen fistulated Brahman steers were fed a roughage hay diet (Rhode grass hay) or roughage hay:concentrate diet (60:40) with increasing levels (low, mid, and high) of chloroform in a cyclodextrin matrix. The increasing levels of chloroform resulted in an increase in H2 expelled as CH4 production decreased with no effect on dry matter intakes. The amount of expelled H2 per mole of decreased methane, was lower for the hay diet suggesting a more efficient redirection of hydrogen into other microbial products compared with hay:concentrate diet. A shift in rumen fermentation toward propionate and branched-chain fatty acids was observed for both diets. Animals fed with the hay:concentrate diet had both higher formate concentration and H2 expelled than those fed only roughage hay. Metabolomic analyses revealed an increase in the concentration of amino acids, organic, and nucleic acids in the fluid phase for both diets when methanogenesis was inhibited. These changes in the rumen metabolism were accompanied by a shift in the microbiota with an increase in Bacteroidetes:Firmicutes ratio and a decrease in Archaea and Synergistetes for both diets. Within the Bacteroidetes family, some OTUs assigned to Prevotella were promoted under chloroform treatment. These bacteria may be partly responsible for the increase in amino acids and propionate in the rumen. No significant changes were observed for abundance of fibrolytic bacteria, protozoa, and fungi, which suggests that fiber degradation was not impaired. The observed 30% decrease in methanogenesis did not adversely affect rumen metabolism and the rumen microbiota was able to adapt and redirect [H] into other microbial end-products for both diets. However, it is also required dietary supplements or microbial treatments to capture the additional H2 expelled by the animal to further improve rumen digestive efficiency.
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Affiliation(s)
| | - Stuart E Denman
- CSIRO, Agriculture and Food, Queensland Bioscience Precinct St Lucia, QLD, Australia
| | - Chunlei Yang
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University Hangzhou, China
| | - Jane Cheung
- CSIRO, Agriculture and Food, Queensland Bioscience Precinct St Lucia, QLD, Australia
| | - Makoto Mitsumori
- NARO Institute of Livestock and Grassland Science Tsukuba, Japan
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Gallego-Valcarce E, Ortega-Cerrato A, Llamas-Fuentes F, Martinez-Fernandez G, Perez-Martinez J, Gomez-Roldan C. Conversion to Tacrolimus Extended-Release Formulation: Short-term Clinical Results. Transplant Proc 2009; 41:2326-7. [DOI: 10.1016/j.transproceed.2009.06.070] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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