Abstract
Executive summary:
It is estimated that over 11.7 percent of humans do not have access to sufficient food and hence suffer fromnutrient deficiencies and conditions such as anaemia and stunting. Moreover, it is predicted that the world’s population will reach 10.4 billion in the 2080s. Ruminant products are high in protein and micronutrients; however, ruminant production is a major source of methane (CH4), a greenhouse gas (GHG) that hasbetween 27 and 30 times the global warming potential (GWP) of carbon dioxide (CO2).
Ruminant productivity and CH4 emissions are mainly a consequence of the biochemical processes that occur within the rumen (the main compartment of the forestomach of ruminant animals) when dietary carbohydrates are broken down by rumen microbes. The process results in the production of volatile fatty acids (VFAs), which provide a source of energy for the animal, but also involves the generation of hydrogen that is used by methanogenic rumen microbes to convert CO2 into CH4. The production of certain VFAs can result in more hydrogen being used up and thus directed away from methanogenesis. The need to understand the rumen microbiome has consequently never been greater.
The rumen is a complex, dynamic ecosystem composed of anaerobic bacteria, protozoa, anaerobic fungi, methanogenic archaea and the very understudied bacteriophages. The scientist Robert Hungate is considered the “father of rumen microbiology”. His research resulted in many of the culture technologies for anaerobic bacteria and archaea used today and revealed that the rumen bacteria contain the most abundant and diverse group of rumen microorganisms. The rumen bacteria have a multitude of functions. For example, they can be amylolytic (have the capacity to break down starch), cellulolytic (have the capacity to break down cellulose), proteolytic (have the capacity to break down protein) and lipolytic (have the capacity to breakdown lipids/fats). Many are considered to be generalists, i.e. to have a broad range of functions, and others as more specialist.
While the rumen bacteria are the most numerous rumen microorganisms, the rumen protozoa occupy the most space within the rumen (up to 50 percent). However, they remain understudied. This is also the case for the rumen fungi, although they have received more attention in recent years, with a total of 18 genera now identified. Together, the rumen protozoa and fungi are termed the “eukaryotome” or “eukaryome”. Certain rumen protozoa (e.g. Entodinium and Epidinium spp.) are fibrolytic, while others (e.g. Dastrychia and Isotrichia spp.) utilize “simple carbohydrates”, thus aiding forage breakdown and increasing the availability of nutrients to the host. Likewise, anaerobic rumen fungi are potent fibre degraders thanks to their extensive repertoire of carbohydrate-degrading enzymes. Rumen protozoa are, however, linked to methanogenesis. Defaunated ruminants (animals that have had the protozoa chemically removed from their rumens) have been found to have on average 11 percent lower CH4 emissions than their non-defaunated counterparts. Defaunated ruminants are also more productive in terms of average daily weight gain or milk production.
Methane is produced mainly via the hydrogenotrophic pathway, which results in CH4 being produced from hydrogen and CO2, although a small amount can be produced through utilization of methyl groups (methylotrophic pathway) or, even less commonly, from acetate (the acetoclastic pathway). Hydrogenotrophic methanogens include the genus Methanobrevibacter (Mbb.), which is subdivided into the SMT clade (Mbb. smithii, Mbb. gottschalki, Mbb. millerae and Mbb. thaurei) and the RO clade (Mbb. ruminantium and Mbb. olleyae), which are the most abundant rumen methanogens.Methylotrophic methanogens are less abundant and include Methanosarcinales, Methanosphaera and Methanomassiliicoccaceae. The Methanosarcinales can alsoproduce methane via the acetoclastic pathway.It is estimated that over 11.7 percent of humans do not have access to sufficient food and hence suffer from nutrient deficiencies and conditions such as anaemia and stunting. Moreover, it is predicted that the world’spopulation will reach 10.4 billion in the 2080s.Ruminant products are high in protein and micronutrients; however, ruminant production is a major source of methane (CH4), a greenhouse gas (GHG) that hasbetween 27 and 30 times the global warming potential (GWP) of carbon dioxide (CO2).gottschalkii and Mbb. ruminantium clades have been confirmed as the two largest groups and account for Specifically, the Mbb. 74 percent of all rumen archaea globally.
It has been shown that the rumen contains a core microbial community, the diversity of which is driven primarily by diet but is also influenced by the species and breed of host. Recent work has also demonstrated the potential to breed for specific host-selected microbiomes, especially in the context of reducing GHG emissions. Minor groups of rumen organisms appear to be geographically specific, probably driven by climate-specific changes in the plant material consumed or linked to local breeds of ruminants. While some rumen microorganisms may be opportunistic, evidence suggests that the majority play a role in the health and efficiency of the host and have been linked to milk production traits, feed efficiency and methane emissions.
The increasing focus on efficiency and reduction of emissions in the livestock sector is linked to a reduction in rumen microbial diversity. This underlines the need to capture and catalogue the natural communities of rumen bacteria, archaea, fungi, protozoa and viruses, as there is a danger they will be lost. Respondents to a survey of members of the Global Research’s Alliance’s (GRA’s) Rumen Microbial Genomics (RMG) network conducted for the present study mentioned this risk of losing microbial diversity. However, they indicated that their expectations for the health of the diversity of the rumen microbiome over the next decade were positive, primarily because of advances in knowledge generation and the promise offered by initiatives in the field of culturing and cataloguing the microbiome.
Effective management of the rumen microbiome can result in mitigation of CH4 emissions from ruminants. An “optimum” rumen microbiome can be achieved through breeding or dietary interventions. Efforts to breed ruminants with such an “optimum” microbiome are well underway globally, with a lot of data having been generated. Making this a commercially feasible option will require more data from more animals. However, early predictions suggest that breeding efforts could result in reductions of up to 30 percent in CH4 emissions. Dietary interventions can be broadly grouped into the following categories: plant-based strategies (e.g. feeding plants that are high in secondary compounds, such as tannins), targeted CH4 inhibitors (such as 3- NOP, which is commercially known as Bovaer), oils and oilseeds, and hydrogen sinks (e.g. chemicals or microbes that utilize hydrogen so that there is less available for methanogenesis). Forage-based strategies can decrease CH4 emissions by up to 18 percent based on emission intensity for milk produced(g CH4/kg of milk), and forage management interventions (as opposed to using different forages) such as feeding less mature forages can increase average daily weight gain or milk production by up to 13 percent based on CH4 emission intensity for a given amount of milk produced (g CH4/kg milk). CH4 inhibitors, especially 3-NOP, can achieve CH4 reductions of 35 percent based on methane intensity and daily CH4 measurements. However, they do not result in any production gains.More recently developed dietary interventions to reduce CH4 emissions include feeding macroalgae. The red seaweed macroalgae Asparagopsis taxiformis inhibits methanogens and consequently methanogenesis, and so can be considered a CH4 inhibitor. It has been shown to reduce CH4 intensity and daily CH4 emissions by up to 80 percent in both dairy and beef animals, which is the largest reduction achieved to date. Potential future strategies, supported by a growing wealth of data, include the use of hydrogen sinks and the of use of novel direct-fed microbes. The expert survey respondents noted enhance knowledge of rumen microbes and management strategies promoting livestock productionthe need to further efficiency. The interconnectedness of microbes across the human–animal–environmental axis has been demonstrated by many researchers, and the implications of this need to be considered, especially with respect to One Health challenges such as the spread of antimicrobial resistance (AMR). It has been shown that rumen bacteria possess antimicrobial resistance genes on integrative elements that are easily transferred to other bacteria, illustrating the importance of rumen bacteria to the spread of AMR genes. Rumen microbes also offer novel bioactive compounds, which can be used to enhance planetary health (e.g. therapeutic development of novel antimicrobials). Current policies affecting the management of microorganisms of relevance to ruminant nutrition include those related to climate change and those, such as the Nagoya Protocol, related to access and benefit- sharing. Climate policies are increasingly influencing the allocation of research funding, with many funders focusing calls on optimizing the rumen microbiome to achieve reductions in CH4 emissions. Climate policies have also influenced innovation, leading to more effort being put into the development of practical innovative solutions that improve understanding of “optimal” rumen microbiomes and how to achieve them. However, regulatory frameworks also act as a barrier to the use of such technologies because of the amount of time needed to obtain approval. For example, 3-NOP is currently approved as a dietary additive for dairy cows in many countries, including Australia, Brazil, Chile and the countries of the European Union. However, the approval process took approximately ten years, and a large body of research was needed in order to provide the required evidence of the product’s efficacy and safety. Feeding dietary additives has a cost to the farmer, and uptake will be constrained unless these costs can be borne by the consumer or through a governmental payment scheme under an emissions-reduction policy. 56 CGRFA/WG-AnGR-12/23/6/Inf.1 The cost implications of feeding dietary additives are also a barrier to their use in developing countries. Thealternatives for these countries may be land management-based ones such as utilizing more dietarylegumes. However, these will not reduce CH4 emissions to the same extent as using additives such as 3-NOP. The expert survey respondents noted that there was insufficient funding to study and implementmethane mitigation technologies, especially in low- and middle-income countries.With regard to the sharing of rumen microbial genetic resources, it should be noted that the paperwork associated with the need to comply with the Nagoya Protocol acts as a barrier to exchange. While the ethos of the protocol is admirable, there is a need to simplify these requirements in order to ensure the conservation of rumen microbial genetic resources globally. Likewise, lack of open access to rumen microbial cultures is a major hurdle, with many cultures remaining in laboratory freezers across the world, and therefore in danger of being lost. Most funding agencies and journals have an open-access policy that requires that all data must be publicly available when articles are submitted for review. However, this is not the case for research on novel microbial isolates, and this results in poor access to such isolates for continued research and societal benefit. This is a major challenge and requires changes. However, it must also be noted that such changes will require enhanced infrastructure for existing culture collections to enable them to maintain and make available the increased number of isolates.The expert survey respondents indicated that they believed that there was currently no activity on the development of policies, legislation and institutional arrangements for the management of microorganisms of relevance to ruminant digestion in their respective jurisdictions and that they believed that progress in this area is essential if the sector is to move forward in terms of addressing challenges it currently faces.Based on a review of the available scientific data, current policies and regulations and the opinions expressed by experts, the authors recommend the following potential ways in which the Commission and its Members could contribute to addressing gaps and weaknesses in the sustainable use and conservation of microorganisms of relevance to ruminant digestion:• establishing a global expert group to work on the prioritization of activities related to the management of microorganisms of relevance to ruminant digestion and on the identification of threats to the sustainable use and conservation of these organisms;• ensuring adequate resourcing global research initiatives for the culture, cataloguing and management of rumen microbes;• promoting open-access policies ensuring that all pure culture microbial isolates must be deposited in culture collections before publication of any data related to the respective organism(s);• enhancing the capacity of global culture collections to deal with the increased demand that having an open policy requiring isolate deposition in a culture collection would bring;• promoting the funding of research on innovations in the management of the rumen microbiome, particularly with respect to ruminant breeding and dietary innovations;• instigating a change to the Nagoya Protocol to enable ease of sample/microbial exchange globally; and• providing stimulus to encourage global collaboration, especially collaboration involving low- andmiddle-income countries.
It is estimated that over 11.7 percent of humans do not have access to sufficient food and hence suffer fromnutrient deficiencies and conditions such as anaemia and stunting. Moreover, it is predicted that the world’s population will reach 10.4 billion in the 2080s. Ruminant products are high in protein and micronutrients; however, ruminant production is a major source of methane (CH4), a greenhouse gas (GHG) that hasbetween 27 and 30 times the global warming potential (GWP) of carbon dioxide (CO2).
Ruminant productivity and CH4 emissions are mainly a consequence of the biochemical processes that occur within the rumen (the main compartment of the forestomach of ruminant animals) when dietary carbohydrates are broken down by rumen microbes. The process results in the production of volatile fatty acids (VFAs), which provide a source of energy for the animal, but also involves the generation of hydrogen that is used by methanogenic rumen microbes to convert CO2 into CH4. The production of certain VFAs can result in more hydrogen being used up and thus directed away from methanogenesis. The need to understand the rumen microbiome has consequently never been greater.
The rumen is a complex, dynamic ecosystem composed of anaerobic bacteria, protozoa, anaerobic fungi, methanogenic archaea and the very understudied bacteriophages. The scientist Robert Hungate is considered the “father of rumen microbiology”. His research resulted in many of the culture technologies for anaerobic bacteria and archaea used today and revealed that the rumen bacteria contain the most abundant and diverse group of rumen microorganisms. The rumen bacteria have a multitude of functions. For example, they can be amylolytic (have the capacity to break down starch), cellulolytic (have the capacity to break down cellulose), proteolytic (have the capacity to break down protein) and lipolytic (have the capacity to breakdown lipids/fats). Many are considered to be generalists, i.e. to have a broad range of functions, and others as more specialist.
While the rumen bacteria are the most numerous rumen microorganisms, the rumen protozoa occupy the most space within the rumen (up to 50 percent). However, they remain understudied. This is also the case for the rumen fungi, although they have received more attention in recent years, with a total of 18 genera now identified. Together, the rumen protozoa and fungi are termed the “eukaryotome” or “eukaryome”. Certain rumen protozoa (e.g. Entodinium and Epidinium spp.) are fibrolytic, while others (e.g. Dastrychia and Isotrichia spp.) utilize “simple carbohydrates”, thus aiding forage breakdown and increasing the availability of nutrients to the host. Likewise, anaerobic rumen fungi are potent fibre degraders thanks to their extensive repertoire of carbohydrate-degrading enzymes. Rumen protozoa are, however, linked to methanogenesis. Defaunated ruminants (animals that have had the protozoa chemically removed from their rumens) have been found to have on average 11 percent lower CH4 emissions than their non-defaunated counterparts. Defaunated ruminants are also more productive in terms of average daily weight gain or milk production.
Methane is produced mainly via the hydrogenotrophic pathway, which results in CH4 being produced from hydrogen and CO2, although a small amount can be produced through utilization of methyl groups (methylotrophic pathway) or, even less commonly, from acetate (the acetoclastic pathway). Hydrogenotrophic methanogens include the genus Methanobrevibacter (Mbb.), which is subdivided into the SMT clade (Mbb. smithii, Mbb. gottschalki, Mbb. millerae and Mbb. thaurei) and the RO clade (Mbb. ruminantium and Mbb. olleyae), which are the most abundant rumen methanogens.Methylotrophic methanogens are less abundant and include Methanosarcinales, Methanosphaera and Methanomassiliicoccaceae. The Methanosarcinales can alsoproduce methane via the acetoclastic pathway.It is estimated that over 11.7 percent of humans do not have access to sufficient food and hence suffer from nutrient deficiencies and conditions such as anaemia and stunting. Moreover, it is predicted that the world’spopulation will reach 10.4 billion in the 2080s.Ruminant products are high in protein and micronutrients; however, ruminant production is a major source of methane (CH4), a greenhouse gas (GHG) that hasbetween 27 and 30 times the global warming potential (GWP) of carbon dioxide (CO2).gottschalkii and Mbb. ruminantium clades have been confirmed as the two largest groups and account for Specifically, the Mbb. 74 percent of all rumen archaea globally.
It has been shown that the rumen contains a core microbial community, the diversity of which is driven primarily by diet but is also influenced by the species and breed of host. Recent work has also demonstrated the potential to breed for specific host-selected microbiomes, especially in the context of reducing GHG emissions. Minor groups of rumen organisms appear to be geographically specific, probably driven by climate-specific changes in the plant material consumed or linked to local breeds of ruminants. While some rumen microorganisms may be opportunistic, evidence suggests that the majority play a role in the health and efficiency of the host and have been linked to milk production traits, feed efficiency and methane emissions.
The increasing focus on efficiency and reduction of emissions in the livestock sector is linked to a reduction in rumen microbial diversity. This underlines the need to capture and catalogue the natural communities of rumen bacteria, archaea, fungi, protozoa and viruses, as there is a danger they will be lost. Respondents to a survey of members of the Global Research’s Alliance’s (GRA’s) Rumen Microbial Genomics (RMG) network conducted for the present study mentioned this risk of losing microbial diversity. However, they indicated that their expectations for the health of the diversity of the rumen microbiome over the next decade were positive, primarily because of advances in knowledge generation and the promise offered by initiatives in the field of culturing and cataloguing the microbiome.
Effective management of the rumen microbiome can result in mitigation of CH4 emissions from ruminants. An “optimum” rumen microbiome can be achieved through breeding or dietary interventions. Efforts to breed ruminants with such an “optimum” microbiome are well underway globally, with a lot of data having been generated. Making this a commercially feasible option will require more data from more animals. However, early predictions suggest that breeding efforts could result in reductions of up to 30 percent in CH4 emissions. Dietary interventions can be broadly grouped into the following categories: plant-based strategies (e.g. feeding plants that are high in secondary compounds, such as tannins), targeted CH4 inhibitors (such as 3- NOP, which is commercially known as Bovaer), oils and oilseeds, and hydrogen sinks (e.g. chemicals or microbes that utilize hydrogen so that there is less available for methanogenesis). Forage-based strategies can decrease CH4 emissions by up to 18 percent based on emission intensity for milk produced(g CH4/kg of milk), and forage management interventions (as opposed to using different forages) such as feeding less mature forages can increase average daily weight gain or milk production by up to 13 percent based on CH4 emission intensity for a given amount of milk produced (g CH4/kg milk). CH4 inhibitors, especially 3-NOP, can achieve CH4 reductions of 35 percent based on methane intensity and daily CH4 measurements. However, they do not result in any production gains.More recently developed dietary interventions to reduce CH4 emissions include feeding macroalgae. The red seaweed macroalgae Asparagopsis taxiformis inhibits methanogens and consequently methanogenesis, and so can be considered a CH4 inhibitor. It has been shown to reduce CH4 intensity and daily CH4 emissions by up to 80 percent in both dairy and beef animals, which is the largest reduction achieved to date. Potential future strategies, supported by a growing wealth of data, include the use of hydrogen sinks and the of use of novel direct-fed microbes. The expert survey respondents noted enhance knowledge of rumen microbes and management strategies promoting livestock productionthe need to further efficiency. The interconnectedness of microbes across the human–animal–environmental axis has been demonstrated by many researchers, and the implications of this need to be considered, especially with respect to One Health challenges such as the spread of antimicrobial resistance (AMR). It has been shown that rumen bacteria possess antimicrobial resistance genes on integrative elements that are easily transferred to other bacteria, illustrating the importance of rumen bacteria to the spread of AMR genes. Rumen microbes also offer novel bioactive compounds, which can be used to enhance planetary health (e.g. therapeutic development of novel antimicrobials). Current policies affecting the management of microorganisms of relevance to ruminant nutrition include those related to climate change and those, such as the Nagoya Protocol, related to access and benefit- sharing. Climate policies are increasingly influencing the allocation of research funding, with many funders focusing calls on optimizing the rumen microbiome to achieve reductions in CH4 emissions. Climate policies have also influenced innovation, leading to more effort being put into the development of practical innovative solutions that improve understanding of “optimal” rumen microbiomes and how to achieve them. However, regulatory frameworks also act as a barrier to the use of such technologies because of the amount of time needed to obtain approval. For example, 3-NOP is currently approved as a dietary additive for dairy cows in many countries, including Australia, Brazil, Chile and the countries of the European Union. However, the approval process took approximately ten years, and a large body of research was needed in order to provide the required evidence of the product’s efficacy and safety. Feeding dietary additives has a cost to the farmer, and uptake will be constrained unless these costs can be borne by the consumer or through a governmental payment scheme under an emissions-reduction policy. 56 CGRFA/WG-AnGR-12/23/6/Inf.1 The cost implications of feeding dietary additives are also a barrier to their use in developing countries. Thealternatives for these countries may be land management-based ones such as utilizing more dietarylegumes. However, these will not reduce CH4 emissions to the same extent as using additives such as 3-NOP. The expert survey respondents noted that there was insufficient funding to study and implementmethane mitigation technologies, especially in low- and middle-income countries.With regard to the sharing of rumen microbial genetic resources, it should be noted that the paperwork associated with the need to comply with the Nagoya Protocol acts as a barrier to exchange. While the ethos of the protocol is admirable, there is a need to simplify these requirements in order to ensure the conservation of rumen microbial genetic resources globally. Likewise, lack of open access to rumen microbial cultures is a major hurdle, with many cultures remaining in laboratory freezers across the world, and therefore in danger of being lost. Most funding agencies and journals have an open-access policy that requires that all data must be publicly available when articles are submitted for review. However, this is not the case for research on novel microbial isolates, and this results in poor access to such isolates for continued research and societal benefit. This is a major challenge and requires changes. However, it must also be noted that such changes will require enhanced infrastructure for existing culture collections to enable them to maintain and make available the increased number of isolates.The expert survey respondents indicated that they believed that there was currently no activity on the development of policies, legislation and institutional arrangements for the management of microorganisms of relevance to ruminant digestion in their respective jurisdictions and that they believed that progress in this area is essential if the sector is to move forward in terms of addressing challenges it currently faces.Based on a review of the available scientific data, current policies and regulations and the opinions expressed by experts, the authors recommend the following potential ways in which the Commission and its Members could contribute to addressing gaps and weaknesses in the sustainable use and conservation of microorganisms of relevance to ruminant digestion:• establishing a global expert group to work on the prioritization of activities related to the management of microorganisms of relevance to ruminant digestion and on the identification of threats to the sustainable use and conservation of these organisms;• ensuring adequate resourcing global research initiatives for the culture, cataloguing and management of rumen microbes;• promoting open-access policies ensuring that all pure culture microbial isolates must be deposited in culture collections before publication of any data related to the respective organism(s);• enhancing the capacity of global culture collections to deal with the increased demand that having an open policy requiring isolate deposition in a culture collection would bring;• promoting the funding of research on innovations in the management of the rumen microbiome, particularly with respect to ruminant breeding and dietary innovations;• instigating a change to the Nagoya Protocol to enable ease of sample/microbial exchange globally; and• providing stimulus to encourage global collaboration, especially collaboration involving low- andmiddle-income countries.
| Original language | English |
|---|---|
| Type | FAO policy document |
| Media of output | |
| Publisher | Food and Agriculture Organization of the United Nations |
| Number of pages | 48 |
| Publication status | Published - 01 Nov 2022 |
