1
|
Zhao Y, Tan J, Fang L, Jiang L. Harnessing meta-omics to unveil and mitigate methane emissions in ruminants: Integrative approaches and future directions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175732. [PMID: 39182764 DOI: 10.1016/j.scitotenv.2024.175732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 08/17/2024] [Accepted: 08/21/2024] [Indexed: 08/27/2024]
Abstract
Methane emissions from enteric fermentation present a dual challenge globally: they not only contribute significantly to atmospheric greenhouse gases but also represent a considerable energy loss for ruminant animals. Utilizing high-throughput omics technologies to analyze rumen microbiome samples (meta-omics, i.e., metagenomics, metatranscriptomics, metaproteomics, metabolomics) holds vast potential for uncovering the intricate interplay between diet, microbiota, and methane emissions in these animals. The primary obstacle is the effective integration of diverse meta-omic approaches and their broader application across different ruminant species. Genetic variability significantly impacts methane production in ruminants, suggesting that genomic selection could be a viable strategy to reduce emissions. While substantial research has been conducted on the microbiological aspects of methane production, there remains a critical need to delineate the specific genetic interactions between the host and its microbiome. Advancements in meta-omics technologies are poised to shed light on these interactions, enhancing our understanding of the genetic factors that govern methane output. This review explores the potential of meta-omics to accelerate genetic advancements that could lead to reduced methane emissions in ruminants. By employing a systems biology approach, the integration of various omics technologies allows for the identification of key genomic regions and genetic markers linked to methane production. These markers can then be leveraged in selective breeding programs to cultivate traits associated with lower emissions. Moreover, the review addresses current challenges in applying genomic selection for this purpose and discusses how omics technologies can overcome these obstacles. The systematic integration and analysis of diverse biological data provide deeper insights into the genetic underpinnings and overall biology of methane production traits in ruminants. Ultimately, this comprehensive approach not only aids in reducing the environmental impact of agriculture but also contributes to the sustainability and efficiency of livestock management.
Collapse
Affiliation(s)
- Yuchao Zhao
- Beijing Key Laboratory of Dairy Cow Nutrition, College of Animal Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Jian Tan
- Beijing Key Laboratory of Dairy Cow Nutrition, College of Animal Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Luoyun Fang
- Beijing Key Laboratory of Dairy Cow Nutrition, College of Animal Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Linshu Jiang
- Beijing Key Laboratory of Dairy Cow Nutrition, College of Animal Science and Technology, Beijing University of Agriculture, Beijing 102206, China.
| |
Collapse
|
2
|
Fregulia P, Campos MM, Dhakal R, Dias RJP, Neves ALA. Feed efficiency and enteric methane emissions indices are inconsistent with the outcomes of the rumen microbiome composition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:175263. [PMID: 39102957 DOI: 10.1016/j.scitotenv.2024.175263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/23/2024] [Accepted: 08/01/2024] [Indexed: 08/07/2024]
Abstract
The correlation between enteric methane emissions (eME) and feed efficiency (FE) in cattle is linked to the anaerobic fermentation of feedstuffs that occurs in the rumen. Several mathematical indices have been developed to predict feed efficiency and identify low methane emitters in herds. To investigate this, the current study aimed to evaluate the rumen microbial composition in the same group of animals ranked according to six different indices (three indices for FE and three for eME). Thirty-three heifers were ranked into three groups, each consisting of 11 animals, based on FE (feed conversion efficiency - FCE, residual weight gain - RG, and residual feed intake - RFI) and eME indices (production, yield, and intensity). Rumen fluids were collected using a stomach tube and analyzed using 16S rRNA and 18S rRNA, targeting rumen bacteria, archaea, and protozoa. The sequencing analysis revealed that the presence of unique microbial species in the rumen varies across animals ranked by the FE and eME indices. The High RG group harbored 17 unique prokaryotic taxa, while the High FCE group contained only seven. Significant differences existed in the microbial profiles of the animals based on the FE and eME indices. For instance, Raoultibacter was more abundant in the Intermediate RFI group but less so in the Intermediate RG and Intermediate FCE groups. The abundance of Entodinium was higher while Diplodinium was lower in the High FCE group, in contrast to the High RG and High RFI groups. Methanobrevibacter exhibited similar abundances across eME indices. However, the heifers did not demonstrate the same production, yield, and intensity of eME. The present findings underscore the importance of standardizing the FE and eME indices. This standardization is crucial for ensuring consistent and reliable assessments of the composition and function of the rumen microbiome across different herds.
Collapse
Affiliation(s)
- Priscila Fregulia
- Laboratório de Protozoologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, 36036-900 Juiz de Fora, Minas Gerais, Brazil; Programa de Pós-graduação em Biodiversidade e Conservação da Natureza, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - Mariana Magalhães Campos
- Brazilian Agricultural Research Corporation (Empresa Brasileira de Pesquisa Agropecuária, EMBRAPA), National Center for Research on Dairy Cattle, Juiz de Fora, Brazil
| | - Rajan Dhakal
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark
| | - Roberto Júnio Pedroso Dias
- Laboratório de Protozoologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, 36036-900 Juiz de Fora, Minas Gerais, Brazil; Programa de Pós-graduação em Biodiversidade e Conservação da Natureza, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - André Luis Alves Neves
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark.
| |
Collapse
|
3
|
Worku D. Unraveling the genetic basis of methane emission in dairy cattle: a comprehensive exploration and breeding approach to lower methane emissions. Anim Biotechnol 2024; 35:2362677. [PMID: 38860914 DOI: 10.1080/10495398.2024.2362677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Ruminant animals, such as dairy cattle, produce CH4, which contributes to global warming emissions and reduces dietary energy for the cows. While the carbon foot print of milk production varies based on production systems, milk yield and farm management practices, enteric fermentation, and manure management are major contributors togreenhouse gas emissions from dairy cattle. Recent emerging evidence has revealed the existence of genetic variation for CH4 emission traits among dairy cattle, suggests their potential inclusion in breeding goals and genetic selection programs. Advancements in high-throughput sequencing technologies and analytical techniques have enabled the identification of potential metabolic biomarkers, candidate genes, and SNPs linked to methane emissions. Indeed, this review critically examines our current understanding of carbon foot print in milk production, major emission sources, rumen microbial community and enteric fermentation, and the genetic architecture of methane emission traits in dairy cattle. It also emphasizes important implications for breeding strategies aimed at halting methane emissions through selective breeding, microbiome driven breeding, breeding for feed efficiency, and breeding by gene editing.
Collapse
Affiliation(s)
- Destaw Worku
- Department of Animal Science, College of Agriculture, Food and Climate Science, Injibara University, Injibara, Ethiopia
| |
Collapse
|
4
|
Yergaliyev T, Künzel S, Hanauska A, Rees A, Wild KJ, Pétursdóttir ÁH, Gunnlaugsdóttir H, Reynolds CK, Humphries DJ, Rodehutscord M, Camarinha-Silva A. The effect of Asparagopsis taxiformis, Ascophyllum nodosum, and Fucus vesiculosus on ruminal methanogenesis and metagenomic functional profiles in vitro. Microbiol Spectr 2024:e0394223. [PMID: 39347544 DOI: 10.1128/spectrum.03942-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 07/08/2024] [Indexed: 10/01/2024] Open
Abstract
The ruminant-microorganism symbiosis is unique by providing high-quality food from fibrous materials but also contributes to the production of one of the most potent greenhouse gases-methane. Mitigating methanogenesis in ruminants has been a focus of interest in the past decades. One of the promising strategies to combat methane production is the use of feed supplements, such as seaweeds, that might mitigate methanogenesis via microbiome modulation and direct chemical inhibition. We conducted in vitro investigations of the effect of three seaweeds (Ascophyllum nodosum, Asparagopsis taxiformis, and Fucus vesiculosus) harvested at different locations (Iceland, Scotland, and Portugal) on methane production. We applied metataxonomics (16S rRNA gene amplicons) and metagenomics (shotgun) methods to uncover the interplay between the microbiome's taxonomical and functional states, methanogenesis rates, and seaweed supplementations. Methane concentration was reduced by A. nodosum and F. vesiculosus, both harvested in Scotland and A. taxiformis, with the greatest effect of the latter. A. taxiformis acted through the reduction of archaea-to-bacteria ratios but not eukaryotes-to-bacteria. Moreover, A. taxiformis application was accompanied by shifts in both taxonomic and functional profiles of the microbial communities, decreasing not only archaeal ratios but also abundances of methanogenesis-associated functions. Methanobrevibacter "SGMT" (M. smithii, M. gottschalkii, M. millerae or M. thaueri; high methane yield) to "RO" (M. ruminantium and M. olleyae; low methane yield) clades ratios were also decreased, indicating that A. taxiformis application favored Methanobrevibacter species that produce less methane. Most of the functions directly involved in methanogenesis were less abundant, while the abundances of the small subset of functions that participate in methane assimilation were increased. IMPORTANCE The application of A. taxiformis significantly reduced methane production in vitro. We showed that this reduction was linked to changes in microbial function profiles, the decline in the overall archaeal community counts, and shifts in ratios of Methanobrevibacter "SGMT" and "RO" clades. A. nodosum and F. vesiculosus, obtained from Scotland, also decreased methane concentration in the total gas, while the same seaweed species from Iceland did not.
Collapse
Affiliation(s)
- Timur Yergaliyev
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
| | - Susanne Künzel
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
| | - Anna Hanauska
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Antonia Rees
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Katharina J Wild
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | | | | | - Christopher K Reynolds
- School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
| | - David J Humphries
- School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
| | - Markus Rodehutscord
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
| | - Amélia Camarinha-Silva
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
| |
Collapse
|
5
|
Plata G, Srinivasan K, Krishnamurthy M, Herron L, Dixit P. Designing host-associated microbiomes using the consumer/resource model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.28.538625. [PMID: 37162888 PMCID: PMC10168316 DOI: 10.1101/2023.04.28.538625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
A key step towards rational microbiome engineering is in silico sampling of realistic microbial communities that correspond to desired host phenotypes, and vice versa. This remains challenging due to a lack of generative models that simultaneously capture compositions of host-associated microbiomes and host phenotypes. To that end, we present a generative model based on the mechanistic consumer/resource (C/R) framework. In the model, variation in microbial ecosystem composition arises due to differences in the availability of effective resources (inferred latent variables) while species' resource preferences remain conserved. The same latent variables are used to model phenotypic states of hosts. In silico microbiomes generated by our model accurately reproduce universal and dataset-specific statistics of bacterial communities. The model allows us to address three salient questions in host-associated microbial ecologies: (1) which host phenotypes maximally constrain the composition of the host-associated microbiomes? (2) how context-specific are phenotype/microbiome associations, and (3) what are plausible microbiome compositions that correspond to desired host phenotypes? Our approach aids the analysis and design of microbial communities associated with host phenotypes of interest.
Collapse
|
6
|
Stothart MR, McLoughlin PD, Medill SA, Greuel RJ, Wilson AJ, Poissant J. Methanogenic patterns in the gut microbiome are associated with survival in a population of feral horses. Nat Commun 2024; 15:6012. [PMID: 39039075 PMCID: PMC11263349 DOI: 10.1038/s41467-024-49963-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 06/21/2024] [Indexed: 07/24/2024] Open
Abstract
Gut microbiomes are widely hypothesised to influence host fitness and have been experimentally shown to affect host health and phenotypes under laboratory conditions. However, the extent to which they do so in free-living animal populations and the proximate mechanisms involved remain open questions. In this study, using long-term, individual-based life history and shallow shotgun metagenomic sequencing data (2394 fecal samples from 794 individuals collected between 2013-2019), we quantify relationships between gut microbiome variation and survival in a feral population of horses under natural food limitation (Sable Island, Canada), and test metagenome-derived predictions using short-chain fatty acid data. We report detailed evidence that variation in the gut microbiome is associated with a host fitness proxy in nature and outline hypotheses of pathogenesis and methanogenesis as key causal mechanisms which may underlie such patterns in feral horses, and perhaps, wild herbivores more generally.
Collapse
Affiliation(s)
- Mason R Stothart
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada.
- Department of Biology, University of Oxford, Oxford, United Kingdom.
| | - Philip D McLoughlin
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Sarah A Medill
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ruth J Greuel
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Alastair J Wilson
- Centre for Ecology and Conservation, University of Exeter, Penryn, United Kingdom
| | - Jocelyn Poissant
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada.
| |
Collapse
|
7
|
Mohapatra A, Trivedi S, Kolte AP, Tejpal CS, Elavarasan K, Vaswani S, Malik PK, Ravishankar CN, Bhatta R. Effect of Padina gymnospora biowaste inclusion on in vitro methane production, feed fermentation, and microbial diversity. Front Microbiol 2024; 15:1431131. [PMID: 39027100 PMCID: PMC11254855 DOI: 10.3389/fmicb.2024.1431131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 06/19/2024] [Indexed: 07/20/2024] Open
Abstract
In vitro studies were undertaken aiming to study the methane (CH4) mitigation potential of biowaste (BW) of Padina gymnospora at the graded inclusion of 0% (C), 2% (A2), 5% (A5), and 10% (A10) of the diet composed of straw and concentrate in 40:60 ratio. The chemical composition analysis revealed that the BW contained higher crude protein (CP), neutral detergent fiber (NDF), acid detergent fiber (ADF), and ether extract (EE) than the PF (fresh seaweed, P. gymnospora). The concentration of cinnamic acid, sinapic acid, kaempferol, fisetin p-coumaric acid, ellagic acid, and luteolin in BW was 1.5-6-folds less than the PF. Inclusion of BW decreased (P < 0.0001) CH4 production by 34%, 38%, and 45% in A2, A5, and A10 treatments, respectively. A decrease (P < 0.0001) of 7.5%-8% in dry matter (DM) and organic matter (OM) digestibility was also recorded with the BW supplementation. The BW inclusion also decreased the numbers of total (P = 0.007), Entodinomorphs (P = 0.011), and Holotrichs (P = 0.004) protozoa. Metagenome data revealed the dominance of Bacteroidetes, Proteobacteria, Firmicutes, Actinobacteria, and Fibrobacter microbial phyla. At the phylum level, Euryarchaeota dominated the archaeal community, whereas Methanobrevibacter was most abundant at the genus level. It can be concluded that the inclusion of BW in straw and concentrate based diet by affecting rumen fermentation, protozoal numbers, and compositional shift in the archaeal community significantly decreased CH4 production. Utilization of biowaste of P. gymnospora as a CH4 mitigating agent will ensure its efficient utilization rather than dumping, which shall cause environmental pollution and health hazards.
Collapse
Affiliation(s)
- Archit Mohapatra
- Indian Council of Agricultural Research (ICAR)-National Institute of Animal Nutrition and Physiology, Bengaluru, India
- School of Sciences, JAIN (Deemed-to-be-University), Bengaluru, India
| | - Shraddha Trivedi
- Indian Council of Agricultural Research (ICAR)-National Institute of Animal Nutrition and Physiology, Bengaluru, India
| | - Atul P. Kolte
- Indian Council of Agricultural Research (ICAR)-National Institute of Animal Nutrition and Physiology, Bengaluru, India
| | - Chaluvanahalli S. Tejpal
- Indian Council of Agricultural Research (ICAR)-Central Institute of Fisheries Technology, Kochi, India
| | - Krishnamoorthy Elavarasan
- Indian Council of Agricultural Research (ICAR)-Central Institute of Fisheries Technology, Kochi, India
| | - Shalini Vaswani
- Uttar Pradesh Pandit Deen Dayal Upadhyaya Pashu Chikitsa Vigyan Vishwavidyalaya Evam Go-Anusandhan Sansthan, Mathura, India
| | - Pradeep Kumar Malik
- Indian Council of Agricultural Research (ICAR)-National Institute of Animal Nutrition and Physiology, Bengaluru, India
| | | | | |
Collapse
|
8
|
Giagnoni G, Friggens NC, Johansen M, Maigaard M, Wang W, Lund P, Weisbjerg MR. How much can performance measures explain of the between-cow variation in enteric methane? J Dairy Sci 2024; 107:4658-4669. [PMID: 38310957 DOI: 10.3168/jds.2023-24094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 12/29/2023] [Indexed: 02/06/2024]
Abstract
Enteric CH4 produced from dairy cows contributes to the emission of greenhouse gases from anthropogenic sources. Recent studies have shown that the selection of lower CH4-emitting cows is possible, but doing so would be simpler if performance measures already recorded on farm could be used, instead of measuring gas emissions from individual cows. These performance measures could be used for selection of low emitting cows. The aim of this analysis was to quantify how much of the between-cow variation in CH4 production can be explained by variation in performance measures. A dataset with 3 experiments and a total of 149 lactating dairy cows with repeated measures was used to estimate the between-cow variation (the variation between cow estimates) for performance and gas measures from GreenFeed (C-Lock, Rapid City, SD). The cow estimates were obtained with a linear mixed model with the diet within period effect as a fixed effect and the cow within experiment as a random effect. The cow estimates for CH4 production were first regressed on the performance and gas measures individually, and then performance and CO2 production measures were grouped in 3 subsets for principal component analysis and principal component regression. The variables that explained most of the between-cow variation in CH4 production were DMI (R2 = 0.44), among the performance measures, and CO2 production (R2 = 0.61), among gas measures. Grouping the measures increased the R2 to 0.53 when only performance measures were used, and to 0.66 when CO2 production was added to the significant performance measures. We found the marginal improvement to be insufficient to justify the use of grouped measures rather than an individual measure because the latter simplifies the model and avoids over-fitting. Investigation of other measures that can be explored to increase explanatory power of between-cow variation in CH4 production is briefly discussed. Finally, the use of residual CH4 as a measure for CH4 efficiency could be considered by using either DMI or CO2 production as the sole predicting variables.
Collapse
Affiliation(s)
- Giulio Giagnoni
- Department of Animal and Veterinary Sciences, AU Viborg Research Centre Foulum, Aarhus University, DK 8830 Tjele, Denmark.
| | - Nicolas C Friggens
- Université Paris Saclay, INRAE, AgroParisTech, UMR 0791 MoSAR, 91120 Palaiseau, France
| | - Marianne Johansen
- Department of Animal and Veterinary Sciences, AU Viborg Research Centre Foulum, Aarhus University, DK 8830 Tjele, Denmark
| | - Morten Maigaard
- Department of Animal and Veterinary Sciences, AU Viborg Research Centre Foulum, Aarhus University, DK 8830 Tjele, Denmark
| | - Wenji Wang
- Department of Animal and Veterinary Sciences, AU Viborg Research Centre Foulum, Aarhus University, DK 8830 Tjele, Denmark
| | - Peter Lund
- Department of Animal and Veterinary Sciences, AU Viborg Research Centre Foulum, Aarhus University, DK 8830 Tjele, Denmark
| | - Martin R Weisbjerg
- Department of Animal and Veterinary Sciences, AU Viborg Research Centre Foulum, Aarhus University, DK 8830 Tjele, Denmark.
| |
Collapse
|
9
|
Wu F, Ji P, Yang H, Zhu X, Wu X. Interpretation of the effects of rumen acidosis on the gut microbiota and serum metabolites in calves based on 16S rDNA sequencing and non-target metabolomics. Front Cell Infect Microbiol 2024; 14:1427763. [PMID: 39006744 PMCID: PMC11239342 DOI: 10.3389/fcimb.2024.1427763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 06/12/2024] [Indexed: 07/16/2024] Open
Abstract
Introduction Rumen acidosis is one of the most common diseases in beef cattle. It severely affects the normal development of calves and poses a significant threat to the farming industry. However, the influence of rumen acidosis on the gut microbiota and serum metabolites of calves is currently unclear. Objective The aim of this study is to investigate the changes in the gut microbiota and serum metabolites in calves after rumen acidosis and analyse the correlation. Methods Eight calves were selected as the rumen acidosis group, and eight health calves were selected as the healthy group. The faecal gut microbiota and serum metabolites of calves were detected respectively using 16S rDNA high-throughput sequencing and non-target metabolomics. The correlation between gut microbiota and serum metabolites was analyzed by Spearman correlation analysis. Results Differential analysis of the diversity and composition of gut microbiota between eight male healthy (Health) and eight male rumen acidosis (Disease) calves revealed that rumen acidosis increased the abundance of the gut microbiota in calves. At the phylum level, compared to the Healthy group, the relative abundance of Proteobacteria in the Disease group significantly decreased (P<0.05), while the relative abundance of Desulfobacterota significantly increased in the Disease group (P<0.05). At the genus level, compared to the Disease group, the relative abundance of Alloprevotella, Muribaculaceae, Succinivibrio, Prevotella, Agathobacter and Parabacteroides significantly increased in the Healthy group (P<0.05), while the relative abundance of Christensenellaceae_R-7 and Monoglobus significantly decreased in the Healthy group (P<0.05). Differential analysis results showed the Healthy group had 23 genera with higher abundance, while the Disease group had 47 genera with higher abundance. Serum metabolomics results revealed the differential metabolites associated with rumen acidosis, including nicotinamide, niacin, L-glutamic acid and carnosine, were mainly enriched in the nicotinate and nicotinamide pathway and the histidine pathway. Conclusion The occurrence of rumen acidosis can induce changes in the gut microbiota of calves, with a significant increase of the Christensenellaceae_R-7 genus and a significant decrease of Prevotella and Succinivibrio genera. In addition, the occurrence of rumen acidosis can also induce changes in serum metabolites including niacin, niacinamide, L-glutamine, and carnosine, which may serve as the diagnostic biomarkers of rumen acidosis of calves.
Collapse
Affiliation(s)
- Fanlin Wu
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Peng Ji
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | - Haochi Yang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | - Xiaopeng Zhu
- Zhangye Wanhe Grass Livestock Industry Science and Technology Development Co., Ltd, Zhangye, China
| | - Xiaohu Wu
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, China
| |
Collapse
|
10
|
Shinkai T, Takizawa S, Enishi O, Higuchi K, Ohmori H, Mitsumori M. Characteristics of rumen microbiota and Prevotella isolates found in high propionate and low methane-producing dairy cows. Front Microbiol 2024; 15:1404991. [PMID: 38887715 PMCID: PMC11180796 DOI: 10.3389/fmicb.2024.1404991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 05/21/2024] [Indexed: 06/20/2024] Open
Abstract
Ruminal methane production is the main sink for metabolic hydrogen generated during rumen fermentation, and is a major contributor to greenhouse gas (GHG) emission. Individual ruminants exhibit varying methane production efficiency; therefore, understanding the microbial characteristics of low-methane-emitting animals could offer opportunities for mitigating enteric methane. Here, we investigated the association between rumen fermentation and rumen microbiota, focusing on methane production, and elucidated the physiological characteristics of bacteria found in low methane-producing cows. Thirteen Holstein cows in the late lactation stage were fed a corn silage-based total mixed ration (TMR), and feed digestion, milk production, rumen fermentation products, methane production, and rumen microbial composition were examined. Cows were classified into two ruminal fermentation groups using Principal component analysis: low and high methane-producing cows (36.9 vs. 43.2 L/DMI digested) with different ruminal short chain fatty acid ratio [(C2+C4)/C3] (3.54 vs. 5.03) and dry matter (DM) digestibility (67.7% vs. 65.3%). However, there were no significant differences in dry matter intake (DMI) and milk production between both groups. Additionally, there were differences in the abundance of OTUs assigned to uncultured Prevotella sp., Succinivibrio, and other 12 bacterial phylotypes between both groups. Specifically, a previously uncultured novel Prevotella sp. with lactate-producing phenotype was detected, with higher abundance in low methane-producing cows. These findings provide evidence that Prevotella may be associated with low methane and high propionate production. However, further research is required to improve the understanding of microbial relationships and metabolic processes involved in the mitigation of enteric methane.
Collapse
Affiliation(s)
- Takumi Shinkai
- Division of Dairy Cattle Feeding and Breeding Research, Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | | | | | | | | | | |
Collapse
|
11
|
Ncho CM, Kim SH, Rang SA, Lee SS. A meta-analysis of probiotic interventions to mitigate ruminal methane emissions in cattle: implications for sustainable livestock farming. Animal 2024; 18:101180. [PMID: 38823282 DOI: 10.1016/j.animal.2024.101180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 04/27/2024] [Accepted: 04/30/2024] [Indexed: 06/03/2024] Open
Abstract
In recent years, the significant impact of ruminants on methane emissions has garnered international attention. While dietary strategies have been implemented to solve this issue, probiotics gained the attention of researchers due to their sustainability. However, it is challenging to ascertain their effectiveness as an extensive range of strains and doses have been reported in the literature. Hence, the objective of this experiment was to perform a meta-analysis of probiotic interventions aiming to reduce ruminal methane emissions from cattle. From 362 articles retrieved from scientific databases, 85 articles were assessed independently by two reviewers, and 20 articles representing 49 comparisons were found eligible for meta-analysis. In each study, data such as mean, SD, and sample sizes of both the control and probiotic intervention groups were extracted. The outcomes of interest were methane emission, methane yield, and methane intensity. For the meta-analysis, effect sizes were pooled using a fixed effect or a random effect model depending on the heterogeneity. Afterward, sensitivity analyses were conducted to confirm the robustness of the findings. Overall pooled standardized mean differences (SMDs) with their confidence intervals (CIs) did not detect significant differences in methane emission (SMD = -0.04; 95% CI = -0.18-0.11; P = 0.632), methane yield (SMD = -0.08; 95% CI = -0.24-0.07; P = 0.291), and methane intensity (SMD = -0.22; 95% CI = -0.50-0.07; P = 0.129) between cattle supplemented with probiotics and the control group. However, subgroup analyses revealed that multiple-strain bacterial probiotics (SMD = -0.36; 95% CI = -0.62 to -0.11; P = 0.005), specifically the combination of bacteria involved in reductive acetogenesis and propionate production (SMD = -0.71; 95% CI = -1.04 to -0.36; P = 0.001), emerged as better interventions. Likewise, crossbreeds (SMD = -0.48; 95% CI = -0.78 to -0.18; P = 0.001) exhibited a more favorable response to the treatments. Furthermore, meta-regression demonstrated that longer periods of supplementation led to significant reductions in methane emissions (P = 0.001), yield (P = 0.032), and intensity (P = 0.012) effect sizes. Overall, the results of the current study suggest that cattle responses to probiotic interventions are highly dependent on the probiotic category. Therefore, extended trials performed with probiotics containing multiple bacterial strains are showing the most promising results. Ideally, further trials focusing on the use of probiotics to reduce ruminal methane in cattle should be conducted to complete the available literature.
Collapse
Affiliation(s)
- C M Ncho
- Ruminant Nutrition and Anaerobe Laboratory, Department of Animal Science and Technology, Sunchon National University, Suncheon, South Korea
| | - S-H Kim
- Ruminant Nutrition and Anaerobe Laboratory, Department of Animal Science and Technology, Sunchon National University, Suncheon, South Korea
| | - S A Rang
- Ruminant Nutrition and Anaerobe Laboratory, Department of Animal Science and Technology, Sunchon National University, Suncheon, South Korea
| | - S S Lee
- Ruminant Nutrition and Anaerobe Laboratory, Department of Animal Science and Technology, Sunchon National University, Suncheon, South Korea.
| |
Collapse
|
12
|
Zhang C, Jiang X, Wu S, Zhang J, Wang Y, Li Z, Yao J. Dietary fat and carbohydrate-balancing the lactation performance and methane emissions in the dairy cow industry: A meta-analysis. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2024; 17:347-357. [PMID: 38800741 PMCID: PMC11127094 DOI: 10.1016/j.aninu.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 01/11/2024] [Accepted: 02/20/2024] [Indexed: 05/29/2024]
Abstract
For the agroecosystems of the dairy cow industry, dietary carbohydrate (starch, neutral detergent fiber [NDF]) and fat could directly affect rumen methane emissions and host energy utilization. However, the relationships among diet, lactation performance, and methane emissions need to be further determined to assist dairy farms to adjust diet formulations and feeding strategies for environmental and production management. A meta-analysis was conducted in the current study to explore quantitative patterns of dietary fat and carbohydrate at different levels in balancing lactation performance and environment sustainability of dairy cows, and to establish a methane emission prediction model using the artificial neural network (ANN) model. The results showed that the regression relationship between dietary fat, carbohydrate and methane emissions could be shown by the following models: methane = 106.78 + (14.86 × DMI), R2 = 0.80; methane = 443.17 - (46.41 × starch/NDF), R2 = 0.76; and methane = 388.91 + (31.40 × fat) - (5.42 × fat2), R2 = 0.80. The regression relationships between dietary fat, carbohydrate and lactation performance could be shown by the following models: milk fat yield = 1.08 + (0.43 × starch/NDF) - [0.34 × (starch/NDF)2], R2 = 0.79; milk protein yield = 0.68 + (0.15 × fat) - (0.016 × fat2), R2 = 0.82. In the structural equation model, we found that when formulating dietary carbohydrates and fats, it was necessary to balance the relationship between methane emissions and lactation performance. Specifically, dietary starch/NDF was lower than 0.63 (extremum point) and dietary fat was between 2.89% and 4.69% (extremum point), it could ensure that the aim of methane emission reduction (methane emissions decrease with increasing dietary starch/NDF and fat) was achieved without losing lactation performance of dairy cows (lactation performance increase with increasing dietary starch/NDF and fat). Finally, we established the ANN model to predict methane emissions (training set: R2 = 0.62; validation set: R2 = 0.61).
Collapse
Affiliation(s)
| | | | - Shengru Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jun Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yue Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Zongjun Li
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Junhu Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| |
Collapse
|
13
|
Vadroňová M, Šťovíček A, Výborná A, Tyrolová Y, Tichá D, Joch M. Insights into Effects of Combined Capric and Lauric Acid on Rumen Bacterial Composition. Microorganisms 2024; 12:1085. [PMID: 38930467 PMCID: PMC11206137 DOI: 10.3390/microorganisms12061085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 05/22/2024] [Accepted: 05/25/2024] [Indexed: 06/28/2024] Open
Abstract
This study used next-generation sequencing to assess the impact of combined capric acid (C10) and lauric acid (C12) on the ruminal bacterial composition. Eight Holstein cows were randomly assigned to two groups using a cross-over design. The cows were fed two silage-based diets with the addition of either 100 g of stearic acid per cow per day (control), or 50 g of capric acid and 50 g of lauric acid per cow per day (C10 + C12). On day 18, 250 mL of rumen fluid was collected from each cow, and DNA was isolated, amplified, and sequenced. Treatment did not alter bacterial diversity indices, the relative abundance of archaea, nor the fiber-degrading microorganisms, except for a decrease in Fibrobacter (from 2.9% to 0.7%; p = 0.04). The relative abundance of Prevotellaceae decreased (from 39.9% to 29.6%; p = 0.009), which is notable because some members help to efficiently utilize ammonia by releasing it slowly into the rumen. Furthermore, the relative abundance of Clostridia increased (from 28.4% to 41.5%; p = 0.008), which may have aided the increased ammonia-nitrogen levels in the rumen, as this class contains hyperammonia-producing members. Our study reveals alterations in bacterial abundances with implications for rumen ammonia levels, offering insights into potential strategies for modulating rumen fermentation processes and methane production in ruminant livestock.
Collapse
Affiliation(s)
- Mariana Vadroňová
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, 165 00 Prague, Czech Republic; (M.V.); (A.Š.); (D.T.)
- Department of Nutrition and Feeding of Farm Animals, Institute of Animal Science, Přátelství 815, 104 00 Prague, Czech Republic; (A.V.); (Y.T.)
| | - Adam Šťovíček
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, 165 00 Prague, Czech Republic; (M.V.); (A.Š.); (D.T.)
| | - Alena Výborná
- Department of Nutrition and Feeding of Farm Animals, Institute of Animal Science, Přátelství 815, 104 00 Prague, Czech Republic; (A.V.); (Y.T.)
| | - Yvona Tyrolová
- Department of Nutrition and Feeding of Farm Animals, Institute of Animal Science, Přátelství 815, 104 00 Prague, Czech Republic; (A.V.); (Y.T.)
| | - Denisa Tichá
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, 165 00 Prague, Czech Republic; (M.V.); (A.Š.); (D.T.)
- Department of Nutrition and Feeding of Farm Animals, Institute of Animal Science, Přátelství 815, 104 00 Prague, Czech Republic; (A.V.); (Y.T.)
| | - Miroslav Joch
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, 165 00 Prague, Czech Republic; (M.V.); (A.Š.); (D.T.)
- Department of Nutrition and Feeding of Farm Animals, Institute of Animal Science, Přátelství 815, 104 00 Prague, Czech Republic; (A.V.); (Y.T.)
| |
Collapse
|
14
|
Li K, Du H, Guo W, Na M, Na R. Alfalfa supplementation timing changes the rumen archaeal and fungal community composition and colonization in pre-weaning lambs. Front Microbiol 2024; 15:1380322. [PMID: 38784814 PMCID: PMC11112515 DOI: 10.3389/fmicb.2024.1380322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
The establishment of the rumen microbiota plays an important role in the rumen development. However, little is known about the effects of alfalfa supplementation time on rumen microbiota establishment. Here, a total of 42 Hu lambs, seven-day-old, were chosen for the study. After a week of adjustment, six lambs were sacrificed to establish a baseline. The remaining 36 lambs were randomly split into two groups: one receiving alfalfa hay at 14 days (EAF), the other at 42 days (LAF), both groups received milk replacer and starter pellets. Introducing alfalfa at 14 days of age significantly improved total dry matter intake between 28 and 42 days (p = 0.04) and average daily gain from both 14 to 28 days (p = 0.04) and 28 to 42 days (p < 0.01), but this effect disappears from 56 to 70 days (p > 0.05). At 42 days, the abundances of Naganishia, Ascochyta, and Neosetophoma in the EAF group were significantly higher (p < 0.05) than those in the LAF group (17.8% vs. 3.97, 10.89% vs. 1.77, and 1.27% vs. 0.09%, respectively). At 56 days, the abundances of Ascochyta, Wallemia, and Aspergillus in the EAF group were significantly lower (p < 0.05) than in the LAF group (3.53% vs. 16.40, 8.78% vs. 18.89, and 2.14% vs. 4.69%). At 70 days, Aspergillus abundance in the EAF group was significantly higher (p < 0.05) than in the LAF group (2.69% vs. 0.85%). The LEfSe analysis showed that Methanobrevibacter_smithii was the archaeal biomarker at 14 days in both groups. Methanobrevibacter_sp_AbM4 was enriched at 56 days in the LAF group. Compared to the LAF group, the specific fungal biomarkers in the EAF group included Sporobolomyces and Bullera at 14 days, Naganishia, Didymella, Cleistothelebolus, and Alloleptosphaeria at 42 days, Ascochyta, Neoascochyta, and Alfaria at 70 days. Correlation analysis results showed strong patterns of association both within and between archaea and fungi, which were influenced by alfalfa supplementation time. In summary, alfalfa supplementation at 14 days of age promotes the growth performance of lambs before weaning, and alfalfa supplementation timing significantly affects rumen archaeal and fungal communities and dynamical changes.
Collapse
Affiliation(s)
| | | | | | | | - Renhua Na
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| |
Collapse
|
15
|
Kotsou K, Chatzimitakos T, Athanasiadis V, Bozinou E, Lalas SI. Exploiting Agri-Food Waste as Feed for Tenebrio molitor Larvae Rearing: A Review. Foods 2024; 13:1027. [PMID: 38611333 PMCID: PMC11011778 DOI: 10.3390/foods13071027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/20/2024] [Accepted: 03/24/2024] [Indexed: 04/14/2024] Open
Abstract
The agri-food industry generates substantial amounts of waste, including by-products and residues. The increasing demand for sustainable and eco-friendly practices in the agri-food sector has sparked an interest in finding alternative uses for such waste materials. One promising approach is the utilization of waste from the agri-food industry as feed for the rearing of mealworms (Tenebrio molitor). Since agri-food waste is rich in proteins, carbohydrates, lipids, and vitamins, as well as other bioactive compounds, all of which are essential for insect growth and development, incorporating such waste into the diet of mealworms promotes sustainable insect production, reducing the economic and environmental problems associated with waste disposal. This practice can also be beneficial for the rearing of mealworms since their nutritional value can also be enhanced. To this end, various waste materials, such as fruit and vegetable peels, spent grains, and food processing residues, have been investigated as potential feed sources, leading to increased mass production, lower cost, and enhanced nutritional value. This review aims to highlight the potential of agri-food waste as a feed source for mealworms, as well as their potential to enhance their nutritional value. Furthermore, the potential applications of mealworms reared on agri-food waste are highlighted, including their potential as a sustainable protein source for human consumption and as feed ingredients in the livestock and aquaculture sectors.
Collapse
Affiliation(s)
- Konstantina Kotsou
- Department of Food Science and Nutrition, University of Thessaly, Terma N. Temponera Str., 43100 Karditsa, Greece; (T.C.); (V.A.); (E.B.); (S.I.L.)
| | | | | | | | | |
Collapse
|
16
|
Lester RE, Macqueen A, Armstrong EK, Dodemaide DT, Dwyer GK, Mock TS, Payne S, Smith M, Storen M, Webb L. Can freshwater plants and algae act as an effective feed supplement to reduce methane emissions from ruminant livestock? THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169296. [PMID: 38104811 DOI: 10.1016/j.scitotenv.2023.169296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/08/2023] [Accepted: 12/09/2023] [Indexed: 12/19/2023]
Abstract
Methane production by livestock is a substantial component of greenhouse gas emissions worldwide. The marine red algae, Asparagopsis taxiformis, has been identified as a possible supplement in livestock feeds due to its potent inhibition of methane production but currently is unable to be produced at scale. Finding additional taxa that inhibit methane production is therefore desirable. Here we provide foundational evidence of methanogenesis-inhibiting properties in Australian freshwater plants and algae, reviewing candidate species and testing species' chemical composition and efficacy in vitro. Candidate plant species and naturally-occurring algal mixes were collected and assessed for ability to reduce methane in batch testing and characterised for biochemical composition, lipids and fatty acids, minerals and DNA. We identified three algal mixes and one plant (Montia australasica) with potential to reduce methane yield in in vitro batch assay trials. All three algal mixes contained Spirogyra, although additional testing would be needed to confirm this alga was responsible for the observed activity. For the two samples that underwent multiple dose testing, Algal mix 1 (predominantly Spirogyra maxima) and M. australasica, there seems to be an optimum dose but sources, harvesting and storage conditions potentially determine their methanogenesis-inhibiting activity. Based on their compositions, fatty acids are likely to be acting to reduce methane in Algal mix 1 while M. australasica likely contains substantial amounts of the flavonoids apigenin and kaempferol, which are associated with methane reduction. Based on their mineral composition, the samples tested would be safe for livestock consumption at an inclusion rate of 20%. Thus, we identified multiple Australian species that have potential to be used as a feed supplement to reduce methane yield in livestock which may be suitable for individual farmers to grow and feed, reducing complexities of supply associated with marine alternatives and suggesting avenues for investigation for similar species elsewhere.
Collapse
Affiliation(s)
- Rebecca E Lester
- Centre for Regional and Rural Futures, Deakin University, Locked Bag 20000, Geelong, Victoria 3220, Australia.
| | - Ashley Macqueen
- Centre for Regional and Rural Futures, Deakin University, Locked Bag 20000, Geelong, Victoria 3220, Australia
| | - Emily K Armstrong
- Centre for Regional and Rural Futures, Deakin University, Locked Bag 20000, Geelong, Victoria 3220, Australia
| | - David T Dodemaide
- Centre for Regional and Rural Futures, Deakin University, Locked Bag 20000, Geelong, Victoria 3220, Australia
| | - Georgia K Dwyer
- Centre for Regional and Rural Futures, Deakin University, Locked Bag 20000, Geelong, Victoria 3220, Australia
| | - Thomas S Mock
- Nutrition and Seafood Laboratory, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3220, Australia
| | - Stephanie Payne
- School of Agriculture and Environment, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Michael Smith
- Centre for Regional and Rural Futures, Deakin University, Locked Bag 20000, Geelong, Victoria 3220, Australia
| | - Michaela Storen
- School of Life and Environmental Sciences, Deakin University, Locked Bag 20000, Geelong, Victoria 3220, Australia
| | - Lawrence Webb
- School of Life and Environmental Sciences, Deakin University, Locked Bag 20000, Geelong, Victoria 3220, Australia
| |
Collapse
|
17
|
Keum GB, Pandey S, Kim ES, Doo H, Kwak J, Ryu S, Choi Y, Kang J, Kim S, Kim HB. Understanding the Diversity and Roles of the Ruminal Microbiome. J Microbiol 2024; 62:217-230. [PMID: 38662310 DOI: 10.1007/s12275-024-00121-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 04/26/2024]
Abstract
The importance of ruminal microbiota in ruminants is emphasized, not only as a special symbiotic relationship with ruminants but also as an interactive and dynamic ecosystem established by the metabolites of various rumen microorganisms. Rumen microbial community is essential for life maintenance and production as they help decompose and utilize fiber that is difficult to digest, supplying about 70% of the energy needed by the host and 60-85% of the amino acids that reach the small intestine. Bacteria are the most abundant in the rumen, but protozoa, which are relatively large, account for 40-50% of the total microorganisms. However, the composition of these ruminal microbiota is not conserved or constant throughout life and is greatly influenced by the host. It is known that the initial colonization of calves immediately after birth is mainly influenced by the mother, and later changes depending on various factors such as diet, age, gender and breed. The initial rumen microbial community contains aerobic and facultative anaerobic bacteria due to the presence of oxygen, but as age increases, a hypoxic environment is created inside the rumen, and anaerobic bacteria become dominant in the rumen microbial community. As calves grow, taxonomic diversity increases, especially as they begin to consume solid food. Understanding the factors affecting the rumen microbial community and their effects and changes can lead to the early development and stabilization of the microbial community through the control of rumen microorganisms, and is expected to ultimately help improve host productivity and efficiency.
Collapse
Affiliation(s)
- Gi Beom Keum
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Sriniwas Pandey
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Eun Sol Kim
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Hyunok Doo
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Jinok Kwak
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Sumin Ryu
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Yejin Choi
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Juyoun Kang
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Sheena Kim
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea.
| | - Hyeun Bum Kim
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea.
| |
Collapse
|
18
|
Omondi VO, Bosire GO, Onyari JM, Kibet C, Mwasya S, Onyonyi VN, Getahun MN. Multi-omics analyses reveal rumen microbes and secondary metabolites that are unique to livestock species. mSystems 2024; 9:e0122823. [PMID: 38294243 PMCID: PMC10878066 DOI: 10.1128/msystems.01228-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 12/21/2023] [Indexed: 02/01/2024] Open
Abstract
Ruminant livestock, including cattle, sheep, goats, and camels, possess a distinctive digestive system with complex microbiota communities critical for feed conversion and secondary metabolite production, including greenhouse gases. Yet, there is limited knowledge regarding the diversity of rumen microbes and metabolites benefiting livestock physiology, productivity, climate impact, and defense mechanisms across ruminant species. In this study, we utilized metataxonomics and metabolomics data from four evolutionarily distinct livestock species, which had fed on diverse plant materials like grass, shrubs, and acacia trees, to uncover the unique signature microbes and secondary metabolites. We established the presence of a distinctive anaerobic fungus called Oontomyces in camels, while cattle exhibited a higher prevalence of unique microbes like Psychrobacter, Anaeromyces, Cyllamyces, and Orpinomyces. Goats hosted Cleistothelebolus, and Liebetanzomyces was unique to sheep. Furthermore, we identified a set of conserved core microbes, including Prevotella, Rickenellaceae, Cladosporium, and Pecoramyces, present in all the ruminants, irrespective of host genetics and dietary composition. This underscores their indispensable role in maintaining crucial physiological functions. Regarding secondary metabolites, camel's rumen is rich in organic acids, goat's rumen is rich in alcohols and hydrocarbons, sheep's rumen is rich in indoles, and cattle's rumen is rich in sesquiterpenes. Additionally, linalool propionate and terpinolene were uniquely found in sheep rumen, while valencene was exclusive to cattle. This may suggest the existence of species-specific microbes and metabolites that require host rumen-microbes' environment balance. These results have implications for manipulating the rumen environment to target specific microbes and secondary metabolite networks, thereby enhancing livestock productivity, resilience, reducing susceptibility to vectors, and environmentally preferred livestock husbandry.IMPORTANCERumen fermentation, which depends on feed components and rumen microbes, plays a crucial role in feed conversion and the production of various metabolites important for the physiological functions, health, and environmental smartness of ruminant livestock, in addition to providing food for humans. However, given the complexity and variation of the rumen ecosystem and feed of these various livestock species, combined with inter-individual differences between gut microbial communities, how they influence the rumen secondary metabolites remains elusive. Using metagenomics and metabolomics approaches, we show that each livestock species has a signature microbe(s) and secondary metabolites. These findings may contribute toward understanding the rumen ecosystem, microbiome and metabolite networks, which may provide a gateway to manipulating rumen ecosystem pathways toward making livestock production efficient, sustainable, and environmentally friendly.
Collapse
Affiliation(s)
- Victor O. Omondi
- Animal Health Theme and Behavioural and Chemical Ecology Unit, International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
- Department of Chemistry, University of Nairobi (U.o.N), Nairobi, Kenya
| | | | - John M. Onyari
- Department of Chemistry, University of Nairobi (U.o.N), Nairobi, Kenya
| | - Caleb Kibet
- Animal Health Theme and Behavioural and Chemical Ecology Unit, International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
| | - Samuel Mwasya
- Animal Health Theme and Behavioural and Chemical Ecology Unit, International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
| | - Vanessa N. Onyonyi
- Animal Health Theme and Behavioural and Chemical Ecology Unit, International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
| | - Merid N. Getahun
- Animal Health Theme and Behavioural and Chemical Ecology Unit, International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
| |
Collapse
|
19
|
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] [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.
Collapse
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; , ,
| |
Collapse
|
20
|
Abdillah AE, Sarah D, Ardian AA, Anas MA, Aprianto MA, Hanim C, Kurniawati A, Muhlisin, Yusiati LM. Effect of nutmeg essential oil (Myristica fragrans Houtt.) on methane production, rumen fermentation, and nutrient digestibility in vitro. Sci Rep 2024; 14:3554. [PMID: 38347010 PMCID: PMC10861442 DOI: 10.1038/s41598-024-52532-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 01/19/2024] [Indexed: 02/15/2024] Open
Abstract
The study evaluated the effect of adding of nutmeg (Myristica fragrans Houtt.) essential oil (NEO) as a feed additive on methane production, rumen fermentation parameters, rumen enzyme activity, and nutrient digestibility in vitro. This study was divided into three treatments based on the level of NEO addition, which included 0 µL/L (T0), 100 µL/L (T1), and 200 µL/L (T2). The feed substrate composition consisted of king grass as forage and concentrate in a 60:40 ratio. Feed fermentation was conducted using the Menke and Steingass gas production and two-step Tilley and Terry in-vitro digestibility technique. The data obtained from the study were analyzed using one-way ANOVA and if there were differences between means, they were further assessed using DMRT. The results showed that T2 treatment significantly decreased (P < 0.05) ammonia (NH3) levels, total VFA, acetate, propionate, butyrate, and microbial protein (P < 0.05). Methane production and the activity of rumen protease enzyme significantly decreased (P < 0.05) at T1 and T2 treatment. The T2 treatment significantly reduced (P < 0.05) protein digestibility (IVCPD) at 48 h, while IVCPD at 96 h significantly increased (P < 0.05). On the other hand, the addition of nutmeg essential oil did not effect the activity of the amylase, carboxymethyl cellulase, and β-glucosidase enzymes, as well as the in-vitro digestibility of dry matter (IVDMD), crude fiber (IVCFD), and organic matter (IVOMD). The conclusion drawn from this study is that the optimum level for NEO is 200 µL/L, which can reduce methane production and increase crude protein digestibility at 96 h without any negative effect on rumen fermentation and nutrient digestibility.
Collapse
Affiliation(s)
- Achmad Ezar Abdillah
- Laboratory of Nutritional Biochemistry, Faculty of Animal Science, Universitas Gadjah Mada, Sleman Regency, Daerah Istimewa Yogyakarta, 55281, Indonesia
| | - Dewi Sarah
- Laboratory of Nutritional Biochemistry, Faculty of Animal Science, Universitas Gadjah Mada, Sleman Regency, Daerah Istimewa Yogyakarta, 55281, Indonesia
| | - Aziz Aji Ardian
- Laboratory of Nutritional Biochemistry, Faculty of Animal Science, Universitas Gadjah Mada, Sleman Regency, Daerah Istimewa Yogyakarta, 55281, Indonesia
| | - Muhsin Al Anas
- Laboratory of Nutritional Biochemistry, Faculty of Animal Science, Universitas Gadjah Mada, Sleman Regency, Daerah Istimewa Yogyakarta, 55281, Indonesia
| | - Muhammad Anang Aprianto
- Laboratory of Nutritional Biochemistry, Faculty of Animal Science, Universitas Gadjah Mada, Sleman Regency, Daerah Istimewa Yogyakarta, 55281, Indonesia
| | - Chusnul Hanim
- Laboratory of Nutritional Biochemistry, Faculty of Animal Science, Universitas Gadjah Mada, Sleman Regency, Daerah Istimewa Yogyakarta, 55281, Indonesia
| | - Asih Kurniawati
- Laboratory of Nutritional Biochemistry, Faculty of Animal Science, Universitas Gadjah Mada, Sleman Regency, Daerah Istimewa Yogyakarta, 55281, Indonesia
| | - Muhlisin
- Laboratory of Nutritional Biochemistry, Faculty of Animal Science, Universitas Gadjah Mada, Sleman Regency, Daerah Istimewa Yogyakarta, 55281, Indonesia
| | - Lies Mira Yusiati
- Laboratory of Nutritional Biochemistry, Faculty of Animal Science, Universitas Gadjah Mada, Sleman Regency, Daerah Istimewa Yogyakarta, 55281, Indonesia.
| |
Collapse
|
21
|
Shinkai T, Takizawa S, Fujimori M, Mitsumori M. - Invited Review - The role of rumen microbiota in enteric methane mitigation for sustainable ruminant production. Anim Biosci 2024; 37:360-369. [PMID: 37946422 PMCID: PMC10838666 DOI: 10.5713/ab.23.0301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/13/2023] [Accepted: 10/11/2023] [Indexed: 11/12/2023] Open
Abstract
Ruminal methane production functions as the main sink for metabolic hydrogen generated through rumen fermentation and is recognized as a considerable source of greenhouse gas emissions. Methane production is a complex trait affected by dry matter intake, feed composition, rumen microbiota and their fermentation, lactation stage, host genetics, and environmental factors. Various mitigation approaches have been proposed. Because individual ruminants exhibit different methane conversion efficiencies, the microbial characteristics of low-methane-emitting animals can be essential for successful rumen manipulation and environment-friendly methane mitigation. Several bacterial species, including Sharpea, uncharacterized Succinivibrionaceae, and certain Prevotella phylotypes have been listed as key players in low-methane-emitting sheep and cows. The functional characteristics of the unclassified bacteria remain unclear, as they are yet to be cultured. Here, we review ruminal methane production and mitigation strategies, focusing on rumen fermentation and the functional role of rumen microbiota, and describe the phylogenetic and physiological characteristics of a novel Prevotella species recently isolated from low methane-emitting and high propionate-producing cows. This review may help to provide a better understanding of the ruminal digestion process and rumen function to identify holistic and environmentally friendly methane mitigation approaches for sustainable ruminant production.
Collapse
Affiliation(s)
- Takumi Shinkai
- NARO Institute of Livestock and Grassland Science, Ibaraki 305-0901,
Japan
| | - Shuhei Takizawa
- NARO Institute of Livestock and Grassland Science, Ibaraki 305-0901,
Japan
| | - Miho Fujimori
- NARO Institute of Livestock and Grassland Science, Ibaraki 305-0901,
Japan
| | - Makoto Mitsumori
- NARO Institute of Livestock and Grassland Science, Ibaraki 305-0901,
Japan
| |
Collapse
|
22
|
Rabee AE, Mohamed M Ghandour M, Sallam A, Elwakeel EA, Mohammed RS, Sabra EA, Abdel-Wahed AM, Mourad DM, Hamed AA, Hafez OR. Rumen fermentation and microbiota in Shami goats fed on condensed tannins or herbal mixture. BMC Vet Res 2024; 20:35. [PMID: 38297287 PMCID: PMC10829277 DOI: 10.1186/s12917-024-03887-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 01/17/2024] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Phytochemical compounds can modify the rumen microbiome and improve rumen fermentation. This study evaluated the impact of supplementation with tannin and an herbal mixture containing ginger (Zingiber officinale), garlic (Allium sativum), Artemisia (Artemisia vulgaris), and turmeric (Curcuma longa) on the rumen fermentation and microbiota, and histology of rumen tissue of goats. Eighteen Shami male goats were divided into three groups (n = 6): non-supplemented animals fed the basal diet (C, control); animals fed basal diet and supplemented with condensed tannin (T); and animals fed basal diet and supplemented with herbal mixture (HM). Each animal received a basal diet composed of Alfalfa hay and a concentrate feed mixture. RESULTS Group HM revealed higher (P < 0.05) rumen pH, total volatile fatty acids (VFA), acetic, propionic, isobutyric, butyric, isovaleric, and valeric. Principal Co-ordinate analysis (PCoA) showed that rumen microbial communities in the control group and supplemented groups were distinct. The supplementation increased (P < 0.05) the relative abundances of phylum Bacteroidota and Proteobacteria and declined (P < 0.05) Firmicutes and Fibrobacterota. Additionally, the dominant genus Prevotella and Rikenellaceae RC9 gut group were increased (P < 0.05) and the family Ruminococcaceae was declined (P < 0.05) due to the supplementation. The supplementation decreased (P < 0.05) the archaeal genus Methanobrevibacter and increased (P < 0.05) Candidatus Methanomethylophilus. Tannin supplementation in T group shortened the rumen papillae. CONCLUSIONS The results revealed that the herbal mixture might be used to alter the rumen microbiota to improve rumen fermentation.
Collapse
Affiliation(s)
- Alaa Emara Rabee
- Animal and Poultry Nutrition Department, Desert Research Center, Ministry of Agriculture and Land Reclamation, Cairo, Egypt.
| | - Moustafa Mohamed M Ghandour
- Animal and Poultry Nutrition Department, Desert Research Center, Ministry of Agriculture and Land Reclamation, Cairo, Egypt
| | - Ahmed Sallam
- Animal and Poultry Breeding Department, Desert Research Center, Cairo, Egypt
| | - Eman A Elwakeel
- Department of Animal and Fish production, Faculty of Agriculture, Alexandria University, Alexandria, Egypt
| | - Rasha S Mohammed
- Animal and Poultry Health Department, Desert Research Center, Ministry of Agriculture and Land Reclamation, Cairo, Egypt
| | - Ebrahim A Sabra
- Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Egypt
| | - Adel M Abdel-Wahed
- Animal and Poultry Nutrition Department, Desert Research Center, Ministry of Agriculture and Land Reclamation, Cairo, Egypt
| | - Disouky Mohamed Mourad
- Animal and Poultry Health Department, Desert Research Center, Ministry of Agriculture and Land Reclamation, Cairo, Egypt
| | - Amal Amin Hamed
- Botany and Microbiology Department, Faculty of science, Cairo University, Cairo, Egypt
| | - Osama Raef Hafez
- Animal and Poultry Nutrition Department, Desert Research Center, Ministry of Agriculture and Land Reclamation, Cairo, Egypt
| |
Collapse
|
23
|
Zeng X, Chen Y, Li W, Liu S. Application of fenugreek in ruminant feed: implications for methane emissions and productivity. PeerJ 2024; 12:e16842. [PMID: 38313019 PMCID: PMC10838068 DOI: 10.7717/peerj.16842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/05/2024] [Indexed: 02/06/2024] Open
Abstract
Background Human demand for meat and dairy products will increase as a result of economic development and population growth, and the farming of ruminants, such as cattle and sheep, will also increase. Methane (CH4) emission from the enteric fermentation of ruminant livestock is a major source of greenhouse gas emissions and a significant contributor to global warming. Meanwhile, growth performance is often limited and animals are more vulnerable to diseases in high-density, intensive farming, greatly reducing livestock productivity, so developing ways to reduce CH4 emissions and improve ruminant productivity has become a research hotspot. Studies have reported that fenugreek (Trigonella foenum-graecum L.) as feed additives have the potential to reduce ruminant methane and improve the productivity. However, systematic reviews of such studies are lacking. Methodology In this review, databases of Google Scholar, Web of Science, PubMed, Scopus and Science Direct were used for the literature search. The initial keywords search was fenugreek or Trigonella foenum-graecum L. For more focused search, we added terms such as methane, rumen fermentation, growth, milk production and antioxidants. All were done for ruminants. The literature that conforms to the theme of this article is selected, summarized, and finally completed this article. Results By regulating the rumen microbiome (suppressing protozoans, methanogenic bacteria, and fungi), fenugreek can lower CH4 emissions according to many in vitro anaerobic fermentation experiments. Fenugreek secondary metabolites (saponins and tannins) are responsible for this impact, but it is still unclear exactly how they work. Therefore, more long-term in vivo experiments are needed to verify its efficacy. Fenugreek is also rich in alkaloids, amino acids, flavonoids, saponins and phenolic acids. These compounds have been shown to have beneficial effects on ruminant growth, lactation, and total antioxidant capacity. Therefore, fenugreek has a great opportunity to develop into a new green feed additive. Conclusions This review provides a summary of the effect of fenugreek and its bioactive compounds on rumen fermentation, CH4 emissions and production performance by ruminants. In addition, based on the available data, the possible biochemical pathway of fenugreek to reduce CH4 emissions in ruminants was described. Overall, the livestock feed industry has the opportunity to develop natural, environmentally-friendly feed additives based on fenugreek.
Collapse
Affiliation(s)
- Xiangbiao Zeng
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Yiwen Chen
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Wenjuan Li
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Shijun Liu
- Shanghai Mugao Biotechnology Co., Ltd, Shanghai, China
| |
Collapse
|
24
|
Wang W, Dong Y, Guo W, Zhang X, Degen AA, Bi S, Ding L, Chen X, Long R. Linkages between rumen microbiome, host, and environment in yaks, and their implications for understanding animal production and management. Front Microbiol 2024; 15:1301258. [PMID: 38348184 PMCID: PMC10860762 DOI: 10.3389/fmicb.2024.1301258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 01/03/2024] [Indexed: 02/15/2024] Open
Abstract
Livestock on the Qinghai-Tibetan Plateau is of great importance for the livelihood of the local inhabitants and the ecosystem of the plateau. The natural, harsh environment has shaped the adaptations of local livestock while providing them with requisite eco-services. Over time, unique genes and metabolic mechanisms (nitrogen and energy) have evolved which enabled the yaks to adapt morphologically and physiologically to the Qinghai-Tibetan Plateau. The rumen microbiota has also co-evolved with the host and contributed to the host's adaptation to the environment. Understanding the complex linkages between the rumen microbiota, the host, and the environment is essential to optimizing the rumen function to meet the growing demands for animal products while minimizing the environmental impact of ruminant production. However, little is known about the mechanisms of host-rumen microbiome-environment linkages and how they ultimately benefit the animal in adapting to the environment. In this review, we pieced together the yak's adaptation to the Qinghai-Tibetan Plateau ecosystem by summarizing the natural selection and nutritional features of yaks and integrating the key aspects of its rumen microbiome with the host metabolic efficiency and homeostasis. We found that this homeostasis results in higher feed digestibility, higher rumen microbial protein production, higher short-chain fatty acid (SCFA) concentrations, and lower methane emissions in yaks when compared with other low-altitude ruminants. The rumen microbiome forms a multi-synergistic relationship among the rumen microbiota services, their communities, genes, and enzymes. The rumen microbial proteins and SCFAs act as precursors that directly impact the milk composition or adipose accumulation, improving the milk or meat quality, resulting in a higher protein and fat content in yak milk and a higher percentage of protein and abundant fatty acids in yak meat when compared to dairy cow or cattle. The hierarchical interactions between the climate, forage, rumen microorganisms, and host genes have reshaped the animal's survival and performance. In this review, an integrating and interactive understanding of the host-rumen microbiome environment was established. The understanding of these concepts is valuable for agriculture and our environment. It also contributes to a better understanding of microbial ecology and evolution in anaerobic ecosystems and the host-environment linkages to improve animal production.
Collapse
Affiliation(s)
- Weiwei Wang
- Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang, Guizhou, China
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Yuntao Dong
- Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang, Guizhou, China
| | - Wei Guo
- Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang, Guizhou, China
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xiao Zhang
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - A. Allan Degen
- Desert Animal Adaptations and Husbandry, Wyler Department of Dryland Agriculture, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Sisi Bi
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Luming Ding
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xiang Chen
- Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang, Guizhou, China
| | - Ruijun Long
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| |
Collapse
|
25
|
Hartinger T, Castillo-Lopez E, Reisinger N, Zebeli Q. Elucidating the factors and consequences of the severity of rumen acidosis in first-lactation Holstein cows during transition and early lactation. J Anim Sci 2024; 102:skae041. [PMID: 38364366 PMCID: PMC10946224 DOI: 10.1093/jas/skae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/08/2024] [Indexed: 02/18/2024] Open
Abstract
First-lactation cows are particularly prone to subacute ruminal acidosis (SARA) during transition. Besides common risk factors of SARA, such as feeding of starch-rich diets, an individual severity of SARA in cows has been recently evidenced. Yet, the factors that play a role in SARA severity have not been elucidated. The main goal of this research was to evaluate the factors of SARA severity in first-lactation cows during transition and early lactation, which go beyond high-grain feeding, and to explore their impact on behavior, health, and fermentation in the rumen and hindgut. Twenty-four first-lactation Holstein cows with the same feeding regime were used starting from 3 wk before the expected calving day until 10 wk postpartum. Cows received a close-up diet (32% concentrate) until calving and were then transitioned to a lactation diet (60% concentrate) within 1 week. The SARA severity was assessed by cluster analysis of several rumen pH metrics, which revealed exceptionally longer and more severe SARA in cows denominated as high (n = 9), as compared to moderate (n = 9) and low (n = 6) SARA severity cows (P < 0.01). The logistic analysis showed that the length of close-up feeding, age at parturition, and the level of dry matter intake (DMI) were the main factors that influenced the cows' odds for high SARA severity (each P ≤ 0.01). Moreover, the ANOVA hinted differences in the metabolic activity of the ruminal microbiome to promote SARA severity, as indicated by highest ruminal propionate proportions (P = 0.05) in high SARA severity cows, also with similar DMI. The distinct SARA severity was marginally reflected in behavior and there were no effects of SARA severity or high-grain feeding on blood inflammation markers, which peaked at parturition regardless of SARA severity (P < 0.01). Still, ongoing high-grain feeding increased liver enzyme concentrations from 6 wk postpartum on, compared to weeks before (P < 0.01), yet irrespectively of SARA severity. In conclusion, first-lactation cows differed in SARA severity under the same feeding regime, which was ascribed to management factors and differences in ruminal fermentation. Further research is warranted to validate these findings and to understand the mechanisms behind differences in the metabolic function of rumen microbiome, in particular in terms of evaluating markers for various SARA severity, as well as to evaluate potential long-term effects on health, performance, fertility, and longevity of dairy cows.
Collapse
Affiliation(s)
- Thomas Hartinger
- Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, 1210 Vienna, Austria
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, 1210 Vienna, Austria
| | - Ezequias Castillo-Lopez
- Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, 1210 Vienna, Austria
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, 1210 Vienna, Austria
| | | | - Qendrim Zebeli
- Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, 1210 Vienna, Austria
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, 1210 Vienna, Austria
| |
Collapse
|
26
|
Woodmartin S, Smith PE, Creighton P, Boland TM, Dunne E, McGovern FM. Sward type alters enteric methane emissions, nitrogen output and the relative abundance of the rumen microbial ecosystem in sheep. J Anim Sci 2024; 102:skae256. [PMID: 39252598 PMCID: PMC11439154 DOI: 10.1093/jas/skae256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 09/18/2024] [Indexed: 09/11/2024] Open
Abstract
Observed improvements in animal and sward performance, coupled with a desire for more sustainable pasture-based feeding systems, has triggered a surge in the implementation of more botanically diverse pastures. However, thus far, there has been limited research investigating the effects of botanically diverse sward types on enteric methane (CH4) or nitrogen (N) excretion, alongside the ruminal microbiota and fermentation profile, in sheep. Hence, this study investigates the effect of sward type on CH4 production and N excretion, in addition to assessing the rumen microbiome, volatile fatty acid proportions, and ammonia nitrogen (NH3-N) concentration in sheep. A 5 × 5 Latin square design experiment was implemented to investigate 5 dietary treatments; perennial ryegrass (Lolium perenne L.; PRG) only or PRG plus white clover (Trifolium repens L.; PRG + WC), red clover (Trifolium pratense L.; PRG + RC), chicory (Chicorium intybus L.; PRG + Chic) or plantain (Plantago lanceolata L.; PRG + Plan). Diets were mixed at a ratio of 75% PRG and 25% of the respective companion forage and 100% PRG for the PRG treatment, on a dry matter basis. Twenty castrated male sheep were housed in metabolism crates across 5 feeding periods. Methane measurements were acquired utilizing portable accumulation chambers. Rumen fluid was harvested using a transoesophageal sampling device. Microbial rumen DNA was extracted and subjected to 16S rRNA amplicon sequencing and fermentation analysis. Data were analyzed using PROC MIXED in SAS. Results show that animals consuming PRG + WC ranked lower for CH4 production (g/d) than sheep offered PRG, PRG + Chic or PRG + Plan (P < 0.01) while the addition of any companion forage ranked CH4 yield (g/kg dry matter intake (DMI)) lower (P < 0.001) than PRG. There was a moderate positive correlation between DMI and CH4 (g/d; r = 0.51). Ruminal NH3-N was lowest in animals consuming the PRG diet (P < 0.01). There was a greater abundance of Methanobrevibacter and reduced abundance of Methanosphaera (P < 0.001) in sheep offered PRG, compared with any binary sward. On average, herb diets (PRG + Chic or PRG + Plan) reduced the urinary nitrogen concentration of sheep by 34% in comparison to legume diets (PRG + WC or PRG + RC) and 13% relative to the PRG diet (P < 0.001). Sheep offered PRG + Chic had a greater dietary nitrogen use efficiency than PRG + RC (P < 0.05). This study demonstrates the potential for sward type to influence rumen function and the microbial community, along with CH4 and N output from sheep.
Collapse
Affiliation(s)
- Sarah Woodmartin
- Teagasc, Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Mellows Campus, Athenry, Co. Galway, Ireland
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Paul E Smith
- Teagasc, Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland
| | - Philip Creighton
- Teagasc, Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Mellows Campus, Athenry, Co. Galway, Ireland
| | - Tommy M Boland
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Eoin Dunne
- Teagasc, Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Mellows Campus, Athenry, Co. Galway, Ireland
| | - Fiona M McGovern
- Teagasc, Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Mellows Campus, Athenry, Co. Galway, Ireland
| |
Collapse
|
27
|
Conteville LC, da Silva JV, Andrade BGN, Cardoso TF, Bruscadin JJ, de Oliveira PSN, Mourão GB, Coutinho LL, Palhares JCP, Berndt A, de Medeiros SR, Regitano LCDA. Rumen and fecal microbiomes are related to diet and production traits in Bos indicus beef cattle. Front Microbiol 2023; 14:1282851. [PMID: 38163076 PMCID: PMC10754987 DOI: 10.3389/fmicb.2023.1282851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/22/2023] [Indexed: 01/03/2024] Open
Abstract
Background Ruminants harbor a complex microbial community within their gastrointestinal tract, which plays major roles in their health and physiology. Brazil is one of the largest producers of beef in the world and more than 90% of the beef cattle herds are composed of pure and crossbred Nelore (Bos indicus). Despite its importance to the Brazilian economy and human feeding, few studies have characterized the Nelore microbiome. Therefore, using shotgun metagenomics, we investigated the impact of diet on the composition and functionality of the Nelore microbiome, and explored the associations between specific microbial taxa and their functionality with feed efficiency and methane emission. Results The ruminal microbiome exhibited significantly higher microbial diversity, distinctive taxonomic profile and variations in microbial functionality compared to the fecal microbiome, highlighting the distinct contributions of the microbiomes of these environments. Animals subjected to different dietary treatments exhibited significant differences in their microbiomes' archaeal diversity and in the abundance of 89 genera, as well as in the functions associated with the metabolism of components of each diet. Moreover, depending on the diet, feed-efficient animals and low methane emitters displayed higher microbial diversity in their fecal microbiome. Multiple genera were associated with an increase or decrease of the phenotypes. Upon analyzing the functions attributed to these taxa, we observed significant differences on the ruminal taxa associated with feed efficient and inefficient cattle. The ruminal taxa that characterized feed efficient cattle stood out for having significantly more functions related to carbohydrate metabolism, such as monosaccharides, di-/oligosaccharides and amino acids. The taxa associated with methane emission had functions associated with methanogenesis and the production of substrates that may influence methane production, such as hydrogen and formate. Conclusion Our findings highlight the significant role of diet in shaping Nelore microbiomes and how its composition and functionality may affect production traits such as feed efficiency and methane emission. These insights provide valuable support for the implementation of novel feeding and biotechnological strategies.
Collapse
Affiliation(s)
| | - Juliana Virginio da Silva
- Embrapa Southeast Livestock, São Carlos, Brazil
- Department of Genetics and Evolution, Federal University of São Carlos (UFSCar), São Carlos, Brazil
| | | | | | - Jennifer Jessica Bruscadin
- Embrapa Southeast Livestock, São Carlos, Brazil
- Department of Genetics and Evolution, Federal University of São Carlos (UFSCar), São Carlos, Brazil
| | - Priscila Silva Neubern de Oliveira
- Embrapa Southeast Livestock, São Carlos, Brazil
- Department of Genetics and Evolution, Federal University of São Carlos (UFSCar), São Carlos, Brazil
| | - Gerson Barreto Mourão
- Department of Animal Science, Center for Functional Genomics, University of São Paulo/ESALQ, Piracicaba, Brazil
| | - Luiz Lehmann Coutinho
- Department of Animal Science, Center for Functional Genomics, University of São Paulo/ESALQ, Piracicaba, Brazil
| | | | | | | | | |
Collapse
|
28
|
Dawson B, Drewer J, Roberts T, Levy P, Heal M, Cowan N. Measurements of methane and nitrous oxide in human breath and the development of UK scale emissions. PLoS One 2023; 18:e0295157. [PMID: 38091323 PMCID: PMC10718453 DOI: 10.1371/journal.pone.0295157] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023] Open
Abstract
Exhaled human breath can contain small, elevated concentrations of methane (CH4) and nitrous oxide (N2O), both of which contribute to global warming. These emissions from humans are not well understood and are rarely quantified in global greenhouse gas inventories. This study investigated emissions of CH4 and N2O in human breath from 104 volunteers in the UK population, to better understand what drives these emissions and to quantify national-scale estimates. A total of 328 breath samples were collected, and age, sex, dietary preference, and smoking habits were recorded for every participant. The percentage of methane producers (MPs) identified in this study was 31%. The percentage of MPs was higher in older age groups with 25% of people under the age of 30 classified as MPs compared to 40% in the 30+ age group. Females (38%) were more likely to be MPs than males (25%), though overall concentrations emitted from both MP groups were similar. All participants were found to emit N2O in breath, though none of the factors investigated explained the differences in emissions. Dietary preference was not found to affect CH4 or N2O emissions from breath in this study. We estimate a total emission of 1.04 (0.86-1.40) Gg of CH4 and 0.069 (0.066-0.072) Gg of N2O in human breath annually in the UK, the equivalent of 53.9 (47.8-60.0) Gg of CO2. In terms of magnitude, these values are approximately 0.05% and 0.1% of the total emissions of CH4 and N2O reported in the UK national greenhouse gas inventories.
Collapse
Affiliation(s)
- Ben Dawson
- UK Centre for Ecology and Hydrology, Bush Estate, Midlothian, United Kingdom
- The University of Edinburgh, School of Chemistry, Edinburgh, United Kingdom
| | - Julia Drewer
- UK Centre for Ecology and Hydrology, Bush Estate, Midlothian, United Kingdom
| | - Toby Roberts
- UK Centre for Ecology and Hydrology, Bush Estate, Midlothian, United Kingdom
| | - Peter Levy
- UK Centre for Ecology and Hydrology, Bush Estate, Midlothian, United Kingdom
| | - Mathew Heal
- The University of Edinburgh, School of Chemistry, Edinburgh, United Kingdom
| | - Nicholas Cowan
- UK Centre for Ecology and Hydrology, Bush Estate, Midlothian, United Kingdom
| |
Collapse
|
29
|
Rabee AE, Askar AR. Composition of the rumen archaeal community of growing camels fed different concentrate levels. Int Microbiol 2023:10.1007/s10123-023-00459-6. [PMID: 38057458 DOI: 10.1007/s10123-023-00459-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 12/08/2023]
Abstract
Understanding the rumen fermentation and methanogenic community in camels fed intensively is critical for optimizing rumen fermentation, improving feed efficiency, and lowering methane emissions. Using Illumina MiSeq sequencing, quantitative real-time PCR, and high-performance liquid chromatography, this study evaluates the influence of different concentrate supplement levels in the diet on rumen fermentation as well as the diversity and structure of the rumen methanogenic community for growing dromedary camels. Twelve growing camels were divided into three groups and given three levels of concentrate supplement, 0.7% (C1), 1% (C2), and 1.3% (C3) based on their body weight. All animals were fed alfalfa hay ad libitum. The levels of total volatile fatty acid, rumen ammonia, and methanogen copy number were unaffected by the supplementation level. Increasing the concentrate supplement level increased the proportion of propionic acid while decreasing the proportion of acetic acid. Increasing the level of concentrate in the diet had no effect on alpha diversity metrics or beta diversity of rumen methanogens. Methanobrevibacter and Methanosphaera predominated the methanogenic community and were declined as concentrate supplement level increased. This study sheds new light on the effect of concentrate supplement level in growing camels' diet on rumen fermentation and methanogenic community, which could help in the development of a strategy that aimed to reduce methane emissions and enhance feed efficiency.
Collapse
Affiliation(s)
- Alaa Emara Rabee
- Animal and Poultry Nutrition Department, Desert Research Center, Ministry of Agriculture and Land Reclamation, Cairo, Egypt.
| | - Ahmed R Askar
- Animal and Poultry Nutrition Department, Desert Research Center, Ministry of Agriculture and Land Reclamation, Cairo, Egypt
| |
Collapse
|
30
|
McGurrin A, Maguire J, Tiwari BK, Garcia-Vaquero M. Anti-methanogenic potential of seaweeds and seaweed-derived compounds in ruminant feed: current perspectives, risks and future prospects. J Anim Sci Biotechnol 2023; 14:145. [PMID: 38041152 PMCID: PMC10693045 DOI: 10.1186/s40104-023-00946-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/06/2023] [Indexed: 12/03/2023] Open
Abstract
With methane emissions from ruminant agriculture contributing 17% of total methane emissions worldwide, there is increasing urgency to develop strategies to reduce greenhouse gas emissions in this sector. One of the proposed strategies is ruminant feed intervention studies focused on the inclusion of anti-methanogenic compounds which are those capable of interacting with the rumen microbiome, reducing the capacity of ruminal microorganisms to produce methane. Recently, seaweeds have been investigated for their ability to reduce methane in ruminants in vitro and in vivo, with the greatest methane abatement reported when using the red seaweed Asparagopsis taxiformis (attributed to the bromoform content of this species). From the literature analysis in this study, levels of up to 99% reduction in ruminant methane emissions have been reported from inclusion of this seaweed in animal feed, although further in vivo and microbiome studies are required to confirm these results as other reports showed no effect on methane emission resulting from the inclusion of seaweed to basal feed. This review explores the current state of research aiming to integrate seaweeds as anti-methanogenic feed additives, as well as examining the specific bioactive compounds within seaweeds that are likely to be related to these effects. The effects of the inclusion of seaweeds on the ruminal microbiome are also reviewed, as well as the future challenges when considering the large-scale inclusion of seaweeds into ruminant diets as anti-methanogenic agents.
Collapse
Affiliation(s)
- Ailbhe McGurrin
- Section of Food and Nutrition, School of Agriculture and Food Science, University College Dublin, Dublin 4, Belfield, Ireland
- TEAGASC, Food Research Centre, Dublin 15, Ashtown, Ireland
| | - Julie Maguire
- Bantry Marine Research Station Ltd, Bantry, Co. Cork, P75 AX07, Gearhies, Ireland
| | | | - Marco Garcia-Vaquero
- Section of Food and Nutrition, School of Agriculture and Food Science, University College Dublin, Dublin 4, Belfield, Ireland.
| |
Collapse
|
31
|
Zhang B, Lin S, Moraes L, Firkins J, Hristov AN, Kebreab E, Janssen PH, Bannink A, Bayat AR, Crompton LA, Dijkstra J, Eugène MA, Kreuzer M, McGee M, Reynolds CK, Schwarm A, Yáñez-Ruiz DR, Yu Z. Methane prediction equations including genera of rumen bacteria as predictor variables improve prediction accuracy. Sci Rep 2023; 13:21305. [PMID: 38042941 PMCID: PMC10693554 DOI: 10.1038/s41598-023-48449-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 11/27/2023] [Indexed: 12/04/2023] Open
Abstract
Methane (CH4) emissions from ruminants are of a significant environmental concern, necessitating accurate prediction for emission inventories. Existing models rely solely on dietary and host animal-related data, ignoring the predicting power of rumen microbiota, the source of CH4. To address this limitation, we developed novel CH4 prediction models incorporating rumen microbes as predictors, alongside animal- and feed-related predictors using four statistical/machine learning (ML) methods. These include random forest combined with boosting (RF-B), least absolute shrinkage and selection operator (LASSO), generalized linear mixed model with LASSO (glmmLasso), and smoothly clipped absolute deviation (SCAD) implemented on linear mixed models. With a sheep dataset (218 observations) of both animal data and rumen microbiota data (relative sequence abundance of 330 genera of rumen bacteria, archaea, protozoa, and fungi), we developed linear mixed models to predict CH4 production (g CH4/animal·d, ANIM-B models) and CH4 yield (g CH4/kg of dry matter intake, DMI-B models). We also developed models solely based on animal-related data. Prediction performance was evaluated 200 times with random data splits, while fitting performance was assessed without data splitting. The inclusion of microbial predictors improved the models, as indicated by decreased root mean square prediction error (RMSPE) and mean absolute error (MAE), and increased Lin's concordance correlation coefficient (CCC). Both glmmLasso and SCAD reduced the Akaike information criterion (AIC) and Bayesian information criterion (BIC) for both the ANIM-B and the DMI-B models, while the other two ML methods had mixed outcomes. By balancing prediction performance and fitting performance, we obtained one ANIM-B model (containing 10 genera of bacteria and 3 animal data) fitted using glmmLasso and one DMI-B model (5 genera of bacteria and 1 animal datum) fitted using SCAD. This study highlights the importance of incorporating rumen microbiota data in CH4 prediction models to enhance accuracy and robustness. Additionally, ML methods facilitate the selection of microbial predictors from high-dimensional metataxonomic data of the rumen microbiota without overfitting. Moreover, the identified microbial predictors can serve as biomarkers of CH4 emissions from sheep, providing valuable insights for future research and mitigation strategies.
Collapse
Affiliation(s)
- Boyang Zhang
- Department of Animal Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Shili Lin
- Department of Statistics, The Ohio State University, 2029 Fyffe Road, Columbus, OH, 43210, USA.
| | - Luis Moraes
- Department of Animal Sciences, The Ohio State University, Columbus, OH, 43210, USA
- Consultoria, Piracicaba, SP, Brazil
| | - Jeffrey Firkins
- Department of Animal Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Alexander N Hristov
- Department of Animal Science, The Pennsylvania State University, University Park, PA, USA
| | - Ermias Kebreab
- Department of Animal Science, University of California, Davis, CA, USA
| | - Peter H Janssen
- AgResearch Limited, Grasslands Research Centre, Palmerston North, 4442, New Zealand
| | - André Bannink
- Wageningen Livestock Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Alireza R Bayat
- Milk Production, Production Systems, Natural Resources Institute Finland (Luke), 31600, Jokioinen, Finland
| | - Les A Crompton
- School of Agriculture, Policy, and Development, University of Reading, Reading, UK
| | - Jan Dijkstra
- Animal Nutrition Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Maguy A Eugène
- INRAE UMR Herbivores, VetAgro Sup, Université Clermont Auvergne, Saint-Genès-Champanelle, France
| | - Michael Kreuzer
- Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Mark McGee
- Teagasc, AGRIC, Grange, Dunsany., CO., Meath, Ireland
| | | | - Angela Schwarm
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
| | | | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State University, Columbus, OH, 43210, USA.
| |
Collapse
|
32
|
Diaz GR, Gaire TN, Ferm P, Case L, Caixeta LS, Goldsmith TJ, Armstrong J, Noyes NR. Effect of castration timing and weaning strategy on the taxonomic and functional profile of ruminal bacteria and archaea of beef calves. Anim Microbiome 2023; 5:61. [PMID: 38041127 PMCID: PMC10691087 DOI: 10.1186/s42523-023-00284-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/28/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Beef cattle experience several management challenges across their lifecycle. Castration and weaning, two major interventions in the early life of beef cattle, can have a substantial impact on animal performance. Despite the key role of the rumen microbiome on productive traits of beef cattle, the effect of castration timing and weaning strategy on this microbial community has not been formally described. We assessed the effect of four castration time windows (at birth, turnout, pre-weaning and weaning) and two weaning strategies (fence-line and truck transportation) on the rumen microbiome in a randomized controlled study with 32 male calves across 3 collection days (i.e., time points). Ruminal fluid samples were submitted to shotgun metagenomic sequencing and changes in the taxonomic (microbiota) and functional profile (metagenome) of the rumen microbiome were described. RESULTS Using a comprehensive yet stringent taxonomic classification approach, we identified 10,238 unique taxa classified under 40 bacterial and 7 archaeal phyla across all samples. Castration timing had a limited long-term impact on the rumen microbiota and was not associated with changes in alpha and beta diversity. The interaction of collection day and weaning strategy was associated with changes in the rumen microbiota, which experienced a significant decrease in alpha diversity and shifts in beta diversity within 48 h post-weaning, especially in calves abruptly weaned by truck transportation. Calves weaned using a fence-line weaning strategy had lower relative abundance of Bacteroides, Lachnospira, Fibrobacter and Ruminococcus genera compared to calves weaned by truck transportation. Some genes involved in the hydrogenotrophic methanogenesis pathway (fwdB and fwdF) had higher relative abundance in fence-line-weaned calves post-weaning. The antimicrobial resistance gene tetW consistently represented more than 50% of the resistome across time, weaning and castration groups, without significant changes in relative abundance. CONCLUSIONS Within the context of this study, castration timing had limited long-term effects on the rumen microbiota, while weaning strategy had short-term effects on the rumen microbiota and methane-associated metagenome, but not on the rumen resistome.
Collapse
Affiliation(s)
- Gerardo R Diaz
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Tara N Gaire
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Peter Ferm
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Lacey Case
- North Central Research and Outreach Center, Department of Animal Science, University of Minnesota, St. Paul, MN, 55108, USA
| | - Luciano S Caixeta
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Timothy J Goldsmith
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Joe Armstrong
- Agricultural and Natural Resource Systems, University of Minnesota Extension, University of Minnesota, St. Paul, MN, 55108, USA
| | - Noelle R Noyes
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA.
| |
Collapse
|
33
|
Alayón-Gamboa JA, Albores-Moreno S, Jiménez-Ferrer G, Alarcón-Zúñiga B, Miranda-Romero LA, Pérez-Luna EJ, Canul-Solís J. Tropical tree foliage supplementation in ruminants improves rumen fermentation and the bacterial profile and decreases methane production. Anim Biotechnol 2023; 34:4510-4522. [PMID: 36639141 DOI: 10.1080/10495398.2023.2165935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The main of this study was to evaluate the effect of supplementation of tropical tree foliage in ruminant diets on the in vitro fermentation, bacterial population, volatile fatty acids (VFAs), and enteric CH4 production. Seven experimental diets were evaluated: a control treatment of Pennisetum purpureum (T7) and six treatments of P. purpureum supplemented (30%) with the foliage of Neomillspaughia emargiata (T1), Tabernaemontana amygdalifolia (T2), Caesalpinia gaumeri (T3), Piscidia piscipula (T4), Leucaena leucocephala (T5), and Havardia albicans (T6). The T2, T7, and T5 treatments had the highest (p < 0.05) digestibility of dry matter. Overall, supplementation increased (p < 0.05) the concentrations of propionic and butyric acid and decreased acetic acid. Methanogenic bacteria decreased (p < 0.05) in T1, T2, T5, and T6. Ruminococcus albus decreased in T1, T2, T3, and T5 and Selenomonas ruminiantum increased in T3. Fibrobacter succinogenes increased, except in T5. Methane production decreased (p < 0.05) in T1, T4, T5, and T6. The supplementation with Leucaena leucocephala, Tabernaemontana amygdalifolia, Neomillspaughia emargiata, Piscidia piscipula, Havardia albicans, and Caesalpinia gaumeri is a potential alternative nutritional strategy for ruminants that results in positive changes in VFAs profile, a decrease on CH4 production and methanogenic bacteria, and changes on fibrolytic and non-fibrolytic bacteria composition.HIGHLIGHTSTropical tree foliage supplementation increased propionic and butyric acid and decreased acetic acid concentrations.Fibrolytic, non-fibrolytic, and Methanogenic bacteria were selectively modulated with the supplementation of tropical tree foliage.The enteric methane (CH4) production decreased with the supplementation of tree foliage.The supplementation of Tabernaemontana amygdalifolia and Leucaena leucocephala had the highest digestibility and is a potential alternative nutritional strategy for ruminants.
Collapse
Affiliation(s)
| | | | | | - B Alarcón-Zúñiga
- Graduate Department of Animal Production, Autonomous University of Chapingo, Chapingo, Mexico
| | - L A Miranda-Romero
- Graduate Department of Animal Production, Autonomous University of Chapingo, Chapingo, Mexico
| | - E J Pérez-Luna
- Faculty of Agronomic Sciences C-V, Autonomous University of Chiapas, Villaflores, Chiapas, Mexico
| | - J Canul-Solís
- National Technological Institute of Mexico, Technological Institute of Tizimín, Tizimín, Mexico
| |
Collapse
|
34
|
Aryee G, Luecke SM, Dahlen CR, Swanson KC, Amat S. Holistic View and Novel Perspective on Ruminal and Extra-Gastrointestinal Methanogens in Cattle. Microorganisms 2023; 11:2746. [PMID: 38004757 PMCID: PMC10673468 DOI: 10.3390/microorganisms11112746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Despite the extensive research conducted on ruminal methanogens and anti-methanogenic intervention strategies over the last 50 years, most of the currently researched enteric methane (CH4) abatement approaches have shown limited efficacy. This is largely because of the complex nature of animal production and the ruminal environment, host genetic variability of CH4 production, and an incomplete understanding of the role of the ruminal microbiome in enteric CH4 emissions. Recent sequencing-based studies suggest the presence of methanogenic archaea in extra-gastrointestinal tract tissues, including respiratory and reproductive tracts of cattle. While these sequencing data require further verification via culture-dependent methods, the consistent identification of methanogens with relatively greater frequency in the airway and urogenital tract of cattle, as well as increasing appreciation of the microbiome-gut-organ axis together highlight the potential interactions between ruminal and extra-gastrointestinal methanogenic communities. Thus, a traditional singular focus on ruminal methanogens may not be sufficient, and a holistic approach which takes into consideration of the transfer of methanogens between ruminal, extra-gastrointestinal, and environmental microbial communities is of necessity to develop more efficient and long-term ruminal CH4 mitigation strategies. In the present review, we provide a holistic survey of the methanogenic archaea present in different anatomical sites of cattle and discuss potential seeding sources of the ruminal methanogens.
Collapse
Affiliation(s)
- Godson Aryee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58108, USA; (G.A.); (S.M.L.)
| | - Sarah M. Luecke
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58108, USA; (G.A.); (S.M.L.)
| | - Carl R. Dahlen
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND 58102, USA; (C.R.D.); (K.C.S.)
| | - Kendall C. Swanson
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND 58102, USA; (C.R.D.); (K.C.S.)
| | - Samat Amat
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58108, USA; (G.A.); (S.M.L.)
| |
Collapse
|
35
|
Qiu Q, Wei X, Zhang L, Li Y, Qu M, Ouyang K. Effect of dietary inclusion of tea residue and tea leaves on ruminal fermentation characteristics and methane production. Anim Biotechnol 2023; 34:825-834. [PMID: 34730482 DOI: 10.1080/10495398.2021.1998092] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The aim of this study was to compare the differences of dietary tea leaves (TL) and tea residue (TR) inclusion on rumen fermentation characteristics and to explore whether TR could be an alternative feedstuff of ruminants. For these purposes, seven treatments consisted of two inclusion types (TL vs. TR) and three inclusion levels (g/g of dry matter basis) of 10% (TL10/TR10), 20% (TL20/TR20), and 30% (TL30/TR30) in each inclusion type, plus control group with inclusion of 0% (CON) were designed, with four replicates in each group, to conduct an in vitro ruminal fermentation test. Results showed that the contents of crude protein, neutral detergent fiber, and acid detergent fiber were higher in TR than TL, while TL contained more ether extract and crude ash than TR. Interaction effects between inclusion type and inclusion level were observed in concentrations of isobutyrate and microbial crude protein (MCP), as well as in gas production and digestibility of organic matter. Fermentation characteristics were significantly influenced by TL and TR depending on the inclusion level, except for the concentration of total branched-chain volatile fatty acid. These significant differences of fermentation characteristics due to inclusion level mainly focused on CON and tea inclusion, with higher values in CON than TR or TL groups. The total gas production during the 48-h incubation showed no differences among CON, TL10, and TR10. The inclusion of TR and TL decreased the production of methane. The concentration of MCP in CON, TR10 and TR30 was lower than TR20 and all TL groups. In conclusion, dietary inclusion of TR and TL possessed equivalent effect on rumen fermentation characteristics and methane production, substituting diet with TR or TL for over 10% would inhibit rumen fermentation despite positive effects in TR20 and all TL groups regarding more MCP and less methane production. This study indicates that special attention should be paid to the inclusion level of TR and TL when considering them as alternative feedstuffs of ruminants. Further in vivo study is needed to evaluate the applicability of tea residue as a feedstuff for production of ruminants.
Collapse
Affiliation(s)
- Qinghua Qiu
- Animal Nutrition and Feed Safety Innovation Team, Jiangxi Agricultural University, Nanchang, China
- Jiangxi Province Key Laboratory of Animal Nutrition/Engineering Research Center of Feed Development, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Xiao Wei
- Jiangxi Province Key Laboratory of Animal Nutrition/Engineering Research Center of Feed Development, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Li Zhang
- Jiangxi Province Key Laboratory of Animal Nutrition/Engineering Research Center of Feed Development, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yanjiao Li
- Animal Nutrition and Feed Safety Innovation Team, Jiangxi Agricultural University, Nanchang, China
- Jiangxi Province Key Laboratory of Animal Nutrition/Engineering Research Center of Feed Development, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Mingren Qu
- Jiangxi Province Key Laboratory of Animal Nutrition/Engineering Research Center of Feed Development, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Kehui Ouyang
- Animal Nutrition and Feed Safety Innovation Team, Jiangxi Agricultural University, Nanchang, China
- Jiangxi Province Key Laboratory of Animal Nutrition/Engineering Research Center of Feed Development, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| |
Collapse
|
36
|
Lazzari G, Münger A, Eggerschwiler L, Borda-Molina D, Seifert J, Camarinha-Silva A, Schrade S, Zähner M, Zeyer K, Kreuzer M, Dohme-Meier F. Effects of Acacia mearnsii added to silages differing in nutrient composition and condensed tannins on ruminal and manure-derived methane emissions of dairy cows. J Dairy Sci 2023; 106:6816-6833. [PMID: 37500448 DOI: 10.3168/jds.2022-22901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 03/23/2023] [Indexed: 07/29/2023]
Abstract
This study investigated the effects of acacia (extract of Acacia mearnsii) and sainfoin (Onobrychis viciifolia) as condensed tannin (CT)-rich sources on ruminal and manure methane (CH4) emissions in comparison with non-CT silages characterized by different contents of the cell wall and water-soluble carbohydrates. In a 3 × 6 incomplete Latin square design, 30 Holstein cows (63 ± 23 d in milk; mean ± SD; 33.8 ± 7.6 kg of milk per day, body weight 642 ± 81 kg) were provided with ad libitum access to 1 of 6 total mixed rations comprising 790 g of silage and 210 g of concentrate per kilogram of dry matter (DM). The silages were either rich in sainfoin [neutral detergent fiber (NDF): 349 g/kg of DM], perennial ryegrass (NDF: 420 g/kg of DM), or red clover (NDF: 357 g/kg of DM). Each silage was supplemented with 20 g/kg (of total diet DM) of acacia or straw meal. Feed intake and milk yield were recorded daily. Milk composition and ruminal fluid characteristics and microbiota were analyzed. The individual ruminal CH4 production was determined using the GreenFeed system, and CH4 emissions from the manure of cows fed the same diets were measured in a parallel experiment over 30 d at 25°C using a dynamic flux chamber. The CT sources did not reduce CH4 yield or emission intensity. Acacia reduced milk production (from 26.3 to 23.2 kg/d) and DM intake (from 19.7 to 16.7 kg/d) when supplemented with ryegrass, and both CT sources reduced the milk protein content and yield. Acacia supplementation and ryegrass silage reduced the ruminal acetate:propionate ratio. Furthermore, during acacia treatment, the abundance of Methanobrevibacter archaea tended to be lower and that of Thermoplasmata was higher. Acacia reduced the CH4 emissions from manure for the ryegrass group by 17% but not for the sainfoin and clover groups. Feeding sainfoin silage resulted in the lowest manure-derived CH4 emissions (-47% compared with ryegrass). In conclusion, acacia reduced ruminal CH4 production by 10%, but not emission intensity, and the mitigation effect of sainfoin depended on the silage to which it was compared. Because mitigation was partially associated with animal productivity losses, careful evaluation is required before the implementation of tanniferous feeds in farm practice.
Collapse
Affiliation(s)
- G Lazzari
- Ruminant Nutrition and Emissions, Agroscope, 1725 Posieux and 8356 Ettenhausen, Switzerland; ETH Zurich, Institute of Agricultural Sciences, 8315 Lindau, Switzerland
| | - A Münger
- Ruminant Nutrition and Emissions, Agroscope, 1725 Posieux and 8356 Ettenhausen, Switzerland
| | - L Eggerschwiler
- Research Contracts Animals, Agroscope, 1725 Posieux, Switzerland
| | - D Borda-Molina
- Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, 70599 Stuttgart, Germany; Institute of Animal Science, University of Hohenheim, 70599 Stuttgart, Germany
| | - J Seifert
- Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, 70599 Stuttgart, Germany; Institute of Animal Science, University of Hohenheim, 70599 Stuttgart, Germany
| | - A Camarinha-Silva
- Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, 70599 Stuttgart, Germany; Institute of Animal Science, University of Hohenheim, 70599 Stuttgart, Germany
| | - S Schrade
- Ruminant Nutrition and Emissions, Agroscope, 1725 Posieux and 8356 Ettenhausen, Switzerland
| | - M Zähner
- Ruminant Nutrition and Emissions, Agroscope, 1725 Posieux and 8356 Ettenhausen, Switzerland
| | - K Zeyer
- Empa, Laboratory for Air Pollution/Environmental Technology, 8600 Duebendorf, Switzerland
| | - M Kreuzer
- ETH Zurich, Institute of Agricultural Sciences, 8315 Lindau, Switzerland
| | - F Dohme-Meier
- Ruminant Nutrition and Emissions, Agroscope, 1725 Posieux and 8356 Ettenhausen, Switzerland.
| |
Collapse
|
37
|
Mao Y, Wang F, Kong W, Wang R, Liu X, Ding H, Ma Y, Guo Y. Dynamic changes of rumen bacteria and their fermentative ability in high-producing dairy cows during the late perinatal period. Front Microbiol 2023; 14:1269123. [PMID: 37817752 PMCID: PMC10560760 DOI: 10.3389/fmicb.2023.1269123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 08/31/2023] [Indexed: 10/12/2023] Open
Abstract
Background High-producing dairy cows face varying degrees of metabolic stress and challenges during the late perinatal period, resulting in ruminal bacteria abundance and their fermentative ability occurring as a series of changes. However, the dynamic changes are still not clear. Aims/methods Ten healthy, high-producing Holstein dairy cows with similar body conditions and the same parity were selected, and ruminal fluid from the dairy cows at postpartum 0, 7, 14, and 21 d was collected before morning feeding. 16S rRNA high-throughput sequencing, GC-MS/MS targeted metabolomics, and UPLC-MS/MS untargeted metabolomics were applied in the study to investigate the dynamic changes within 21 d postpartum. Results The results displayed that the structures of ruminal bacteria were significantly altered from 0 to 7 d postpartum (R = 0.486, P = 0.002), reflecting the significantly declining abundances of Euryarchaeota and Chloroflexi phyla and Christensenellaceae, Methanobrevibacter, and Flexilinea genera (P < 0.05) and the obviously ascending abundances of Ruminococcaceae, Moryella, Pseudobutyrivibrio, and Prevotellaceae genera at 7 d postpartum (P < 0.05). The structures of ruminal bacteria also varied significantly from 7 to 14 d postpartum (R = 0.125, P = 0.022), reflecting the reducing abundances of Christensenellaceae, Ruminococcaceae, and Moryella genera (P < 0.05), and the elevating abundances of Sharpea and Olsenella genera at 14 d postpartum (P < 0.05). The metabolic profiles of ruminal SCFAs were obviously varied from 0 to 7 d postpartum, resulting in higher levels of propionic acid, butyric acid, and valeric acid at 7 d postpartum (P < 0.05); the metabolic profiles of other ruminal metabolites were significantly shifted from 0 to 7 d postpartum, with 27 significantly elevated metabolites and 35 apparently reduced metabolites (P < 0.05). The correlation analysis indicated that propionic acid was positively correlated with Prevotellaceae and Ruminococcaceae (P < 0.05), negatively correlated with Methanobrevibacter (P < 0.01); butyric acid was positively associated with Prevotellaceae, Ruminococcaceae, and Pseudobutyrivibrio (P < 0.05), negatively associated with Christensenellaceae (P < 0.01); valeric acid was positively linked with Prevotellaceae and Ruminococcaceae (P < 0.05); pyridoxal was positively correlated with Flexilinea and Methanobrevibacter (P < 0.05) and negatively correlated with Ruminococcaceae (P < 0.01); tyramine was negatively linked with Ruminococcaceae (P < 0.01). Conclusion The findings contribute to the decision of nutritional management and prevention of metabolic diseases in high-producing dairy cows during the late perinatal period.
Collapse
Affiliation(s)
- Yongxia Mao
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Feifei Wang
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Weiyi Kong
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Ruiling Wang
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Xin Liu
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Hui Ding
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Yun Ma
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Yansheng Guo
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan, China
| |
Collapse
|
38
|
Stepanchenko N, Stefenoni H, Hennessy M, Nagaraju I, Wasson DE, Cueva SF, Räisänen SE, Dechow CD, Pitta DW, Hristov AN. Microbial composition, rumen fermentation parameters, enteric methane emissions, and lactational performance of phenotypically high and low methane-emitting dairy cows. J Dairy Sci 2023; 106:6146-6170. [PMID: 37479584 DOI: 10.3168/jds.2022-23190] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/05/2023] [Indexed: 07/23/2023]
Abstract
This experiment was designed to investigate the relation of high and low methane-yield phenotypes with body weight (BW), dry matter intake (DMI), lactation performance, enteric CH4 emissions, and rumen fermentation parameters in lactating dairy cows. A total of 130 multi- and primiparous Holstein cows were screened for enteric CH4 emissions using the GreenFeed system (C-Lock Inc.). Out of these 130 cows, 5 were identified as phenotypically high (HM) and 5 as phenotypically low (LM) CH4 emitters. Cows in the LM group had lower daily enteric CH4 emissions than cows in the HM group (on average 346 vs. 439 g/d, respectively), lower CH4 yield (15.5 vs. 20.4 g of CH4/kg of DMI), and CH4 intensity (13.2 vs. 17.0 g of CH4/ kg of energy-corrected milk yield). Enteric emissions of CO2 and H2 did not differ between HM and LM cows. These 10 cows were blocked by parity, days in milk, and milk production, and were used in a 5-wk randomized complete block design experiment. Milk composition, production, and BW were also not different between LM and HM cows. The concentration of total volatile fatty acids in ruminal contents did not differ between CH4 phenotypes, but LM cows had a lower molar proportion of acetate (57 vs. 62.1%), a higher proportion of propionate (27.5 vs. 21.6%, respectively), and therefore a lower acetate-to-propionate ratio than HM cows. Consistently, the 16S cDNA analysis revealed the abundance of Succinivibrionaceae and unclassified Veillonellaceae to be higher in LM cows compared with HM cows, bacteria that were positively correlated with ruminal propionate concentration. Notably, Succinivibrionaceae trigger the formation of propionate via oxaloacetate pathway from phosphoenolpyruvate via Enzyme Commission: 4.1.1.49, which showed a trend to be higher in LM cows compared with HM cows. Additionally, LM cows possessed fewer transcripts of a gene encoding for methyl-CoM reductase enzyme compared with HM. In this study, low and high CH4-yield cows have similar production performance and milk composition, but total-tract apparent digestibility of organic matter and fiber fractions was lower in the former group of animals.
Collapse
Affiliation(s)
- N Stepanchenko
- Department of Animal Science, The Pennsylvania State University, University Park 16802
| | - H Stefenoni
- Department of Animal Science, The Pennsylvania State University, University Park 16802
| | - M Hennessy
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, New Bolton Center, Kennett Square 193482
| | - I Nagaraju
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, New Bolton Center, Kennett Square 193482
| | - D E Wasson
- Department of Animal Science, The Pennsylvania State University, University Park 16802
| | - S F Cueva
- Department of Animal Science, The Pennsylvania State University, University Park 16802
| | - S E Räisänen
- Department of Animal Science, The Pennsylvania State University, University Park 16802; Department of Agricultural Sciences, University of Helsinki, P.O. Box 28, FI-00014 University of Helsinki, Finland
| | - C D Dechow
- Department of Animal Science, The Pennsylvania State University, University Park 16802
| | - D W Pitta
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, New Bolton Center, Kennett Square 193482.
| | - A N Hristov
- Department of Animal Science, The Pennsylvania State University, University Park 16802.
| |
Collapse
|
39
|
Palmer MA, Garland MJ, Stewart LD, Helyar SJ, O'Connell NE. Variations in the Physical Properties and Microbial Community of Dairy Cow Manure-Implications for Testing and Efficacy of Footbathing Products. Animals (Basel) 2023; 13:2386. [PMID: 37508163 PMCID: PMC10376490 DOI: 10.3390/ani13142386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/03/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Footbaths containing disinfectants are used on dairy farms to reduce the spread of digital dermatitis; however, they commonly become contaminated with manure. This trial investigated the physical properties and microbial composition of dairy cow manure from two production systems and examined whether the source of manure impacted the efficacy of footbathing disinfectants. Manure was collected from eighteen dairy cows, nine housed and fed grass silage (HOUSED) and nine at pasture (PASTURE). The pH and dry matter content was determined, total DNA was extracted and the region v3-v4 of the 16s rRNA gene sequenced. The efficacy of formalin and two trial products (TP1: peracetic acid and hydrogen peroxide; TP2: chlorocresol and triamine) was evaluated when mixed with manure from the two production systems. Production system differences were found in manure dry matter content, bacterial microbiome and the efficacy of both trial footbathing products but not formalin. The properties of manure affected the results of laboratory testing and therefore have the potential to influence footbathing disinfectant efficacy when footbaths are contaminated with manure. Further research into the impact of organic contaminants on the efficacy of disinfectants could facilitate the development of improved testing programmes and disinfectant products.
Collapse
Affiliation(s)
- Maeve A Palmer
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 5DL, UK
| | - Martin J Garland
- Functional Chemical Research Centre, Kersia Group UK and Ireland Ltd., Belfast BT36 4TY, UK
| | - Linda D Stewart
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 5DL, UK
| | - Sarah J Helyar
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 5DL, UK
| | - Niamh E O'Connell
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 5DL, UK
| |
Collapse
|
40
|
Khurana R, Brand T, Tapio I, Bayat AR. Effect of a garlic and citrus extract supplement on performance, rumen fermentation, methane production, and rumen microbiome of dairy cows. J Dairy Sci 2023:S0022-0302(23)00273-4. [PMID: 37225588 DOI: 10.3168/jds.2022-22838] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 01/23/2023] [Indexed: 05/26/2023]
Abstract
The aim of this trial was to determine the effect of a garlic and citrus extract supplement (GCE) on the performance, rumen fermentation, methane emissions, and rumen microbiome of dairy cows. Fourteen multiparous Nordic Red cows in mid-lactation from the research herd of Luke (Jokioinen, Finland) were allocated to 7 blocks in a complete randomized block design based on body weight, days in milk, dry matter intake (DMI), and milk yield. Animals within each block were randomly allocated to a diet with or without GCE. The experimental period for each block of cows (one for each of the control and GCE groups) consisted of 14 d of adaptation followed by 4 d of methane measurements inside the open circuit respiration chambers, with the first day being considered as acclimatization. Data were analyzed using the GLM procedure of SAS (SAS Institute Inc.). Methane production (g/d) and methane intensity (g/kg of energy-corrected milk) were lower by 10.3 and 11.7%, respectively, and methane yield (g/kg of DMI) tended to be lower by 9.7% in cows fed GCE compared with the control. Dry matter intake, milk production, and milk composition were similar between treatments. Rumen pH and total volatile fatty acid concentrations in rumen fluid were similar, whereas GCE tended to increase molar propionate concentration and decrease the molar ratio of acetate to propionate. Supplementation with GCE resulted in greater abundance of Succinivibrionaceae, which was associated with reduced methane. The relative abundance of the strict anaerobic Methanobrevibacter genus was reduced by GCE. The change in microbial community and rumen propionate proportion may explain the decrease in enteric methane emissions. In conclusion, feeding GCE to dairy cows for 18 d modified rumen fermentation and microbiota, leading to reduced methane production and intensity without compromising DMI or milk production in dairy cows. This could be an effective strategy for enteric methane mitigation of dairy cows.
Collapse
Affiliation(s)
| | | | - Ilma Tapio
- Production Systems, Natural Resources Institute Finland (Luke), Jokioinen 31600, Finland
| | - Ali-Reza Bayat
- Production Systems, Natural Resources Institute Finland (Luke), Jokioinen 31600, Finland
| |
Collapse
|
41
|
Forwood DL, Innes DJ, Parra MC, Stark T, de Souza DP, Chaves AV, Meale SJ. Feeding an unsalable carrot total-mixed ration altered bacterial amino acid degradation in the rumen of lambs. Sci Rep 2023; 13:6942. [PMID: 37117259 PMCID: PMC10147942 DOI: 10.1038/s41598-023-34181-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 04/25/2023] [Indexed: 04/30/2023] Open
Abstract
The objective of this study was to determine the influence of a total-mixed ration including unsalable carrots at 45% DM on the rumen microbiome; and the plasma, rumen and liver metabolomes. Carrots discarded at processing were investigated as an energy-dense substitute for barley grain in a conventional feedlot diet, and improved feed conversion efficiency by 25%. Here, rumen fluid was collected from 34 Merino lambs at slaughter (n = 16 control; n = 18 carrot) after a feeding period of 11-weeks. The V4 region of the 16S rRNA gene was sequenced to profile archaeal and bacterial microbe communities. Further, a comprehensive, targeted profile of known metabolites was constructed for blood plasma, rumen fluid and biopsied liver metabolites using a gas chromatography mass spectrometry (GC-MS) metabolomics approach. An in vitro batch culture was used to characterise ruminal fermentation including gas and methane (CH4) production. In vivo rumen microbial community structure of carrot fed lambs was dissimilar (P < 0.01; PERMANOVA), and all measures of alpha diversity were greater (P < 0.01), compared to those fed the control diet. Unclassified genera in Bacteroidales (15.9 ± 6.74% relative abundance; RA) were more abundant (P < 0.01) in the rumen fluid of carrot-fed lambs, while unclassified taxa in the Succinivibrionaceae family (11.1 ± 3.85% RA) were greater (P < 0.01) in the control. The carrot diet improved in vitro ruminal fermentation evidenced as an 8% increase (P < 0.01) in DM digestibility and a 13.8% reduction (P = 0.01) in CH4 on a mg/ g DM basis, while the control diet increased (P = 0.04) percentage of propionate within total VFA by 20%. Fourteen rumen fluid metabolites and 27 liver metabolites were influenced (P ≤ 0.05) by diet, while no effect (P ≥ 0.05) was observed in plasma metabolites. The carrot diet enriched (impact value = 0.13; P = 0.01) the tyrosine metabolism pathway (acetoacetic acid, dopamine and pyruvate), while the control diet enriched (impact value = 0.42; P ≤ 0.02) starch and sucrose metabolism (trehalose and glucose) in rumen fluid. This study demonstrated that feeding 45% DM unsalable carrots diversified bacterial communities in the rumen. These dietary changes influenced pathways of tyrosine degradation, such that previous improvements in feed conversion efficiency in lambs could be explained.
Collapse
Affiliation(s)
- Daniel L Forwood
- School of Agriculture and Food Sciences, Faculty of Science, The University of Queensland, Gatton, Australia
| | - David J Innes
- School of Agriculture and Food Sciences, Faculty of Science, The University of Queensland, Gatton, Australia
| | - Mariano C Parra
- School of Agriculture and Food Sciences, Faculty of Science, The University of Queensland, Gatton, Australia
| | - Terra Stark
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
| | - David P de Souza
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Parkville, Australia
| | - Alex V Chaves
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camperdown, Australia
| | - Sarah J Meale
- School of Agriculture and Food Sciences, Faculty of Science, The University of Queensland, Gatton, Australia.
| |
Collapse
|
42
|
Tapio M, Fischer D, Mäntysaari P, Tapio I. Rumen Microbiota Predicts Feed Efficiency of Primiparous Nordic Red Dairy Cows. Microorganisms 2023; 11:1116. [PMID: 37317090 DOI: 10.3390/microorganisms11051116] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/17/2023] [Accepted: 04/23/2023] [Indexed: 06/16/2023] Open
Abstract
Efficient feed utilization in dairy cows is crucial for economic and environmental reasons. The rumen microbiota plays a significant role in feed efficiency, but studies utilizing microbial data to predict host phenotype are limited. In this study, 87 primiparous Nordic Red dairy cows were ranked for feed efficiency during their early lactation based on residual energy intake, and the rumen liquid microbial ecosystem was subsequently evaluated using 16S rRNA amplicon and metagenome sequencing. The study used amplicon data to build an extreme gradient boosting model, demonstrating that taxonomic microbial variation can predict efficiency (rtest = 0.55). Prediction interpreters and microbial network revealed that predictions were based on microbial consortia and the efficient animals had more of the highly interacting microbes and consortia. Rumen metagenome data was used to evaluate carbohydrate-active enzymes and metabolic pathway differences between efficiency phenotypes. The study showed that an efficient rumen had a higher abundance of glycoside hydrolases, while an inefficient rumen had more glycosyl transferases. Enrichment of metabolic pathways was observed in the inefficient group, while efficient animals emphasized bacterial environmental sensing and motility over microbial growth. The results suggest that inter-kingdom interactions should be further analyzed to understand their association with the feed efficiency of animals.
Collapse
Affiliation(s)
- Miika Tapio
- Genomics and Breeding, Production Systems, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland
| | - Daniel Fischer
- Applied Statistical Methods, Natural Resources, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland
| | - Päivi Mäntysaari
- Animal Nutrition, Production Systems, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland
| | - Ilma Tapio
- Genomics and Breeding, Production Systems, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland
| |
Collapse
|
43
|
Firkins JL, Mitchell KE. Invited review: Rumen modifiers in today's dairy rations. J Dairy Sci 2023; 106:3053-3071. [PMID: 36935236 DOI: 10.3168/jds.2022-22644] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/23/2022] [Indexed: 03/19/2023]
Abstract
Our aim was to review feed additives that have a potential ruminal mechanism of action when fed to dairy cattle. We discuss how additives can influence ruminal fermentation stoichiometry through electron transfer mechanisms, particularly the production and usage of dihydrogen. Lactate accumulation should be avoided, especially when acidogenic conditions suppress ruminal neutral detergent fiber digestibility or lead to subclinical acidosis. Yeast products and other probiotics are purported to influence lactate uptake, but growing evidence also supports that yeast products influence expression of gut epithelial genes promoting barrier function and resulting inflammatory responses by the host to various stresses. We also have summarized methane-suppressing additives for potential usage in dairy rations. We focused on those with potential to decrease methane production without decreasing fiber digestibility or milk production. We identified some mitigating factors that need to be addressed more fully in future research. Growth factors such as branched-chain volatile fatty acids also are part of crucial cross-feeding among groups of microbes, particularly to optimize fiber digestibility in the rumen. Our developments of mechanisms of action for various rumen-active modifiers should help nutrition advisors anticipate when a benefit in field conditions is more likely.
Collapse
Affiliation(s)
- J L Firkins
- Department of Animal Sciences, The Ohio State University, Columbus 43210.
| | - K E Mitchell
- Department of Animal Sciences, The Ohio State University, Columbus 43210
| |
Collapse
|
44
|
Dietary biochar as a feed additive for increasing livestock performance: A meta-analysis of in vitro and in vivo experiment. CZECH JOURNAL OF ANIMAL SCIENCE 2023. [DOI: 10.17221/124/2022-cjas] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
|
45
|
Effect of Spirulina Dietary Supplementation in Modifying the Rumen Microbiota of Ewes. Animals (Basel) 2023; 13:ani13040740. [PMID: 36830527 PMCID: PMC9952741 DOI: 10.3390/ani13040740] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/01/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Supplementing ruminant diets with microalgae, may prove an effective nutritional strategy to manipulate rumen microbiota. Forty-eight ewes were divided into four homogenous groups (n = 12) according to their fat-corrected milk yield (6%), body weight, age, and days in milk, and were fed individually with concentrate, alfalfa hay, and wheat straw. The concentrate of the control group (CON) had no Spirulina supplementation, while in the treated groups 5 (SP5), 10 (SP10), and 15 g (SP15) of Spirulina were supplemented as an additive in the concentrate. An initial screening using metagenomic next-generation sequencing technology was followed by RT-qPCR analysis for the targeting of specific microbes, which unveiled the main alterations of the rumen microbiota under the Spirulina supplementation levels. The relative abundance of Eubacterium ruminantium and Fibrobacter succinogenes in rumen fluid, as well as Ruminococcus albus in rumen solid fraction, were significantly increased in the SP15 group. Furthermore, the relative abundance of Prevotella brevis was significantly increased in the rumen fluid of the SP5 and SP10 groups. In contrast, the relative abundance of Ruminobacter amylophilus was significantly decreased in the rumen fluid of the SP10 compared to the CON group, while in the solid fraction it was significantly decreased in the SP groups. Moreover, the relative abundance of Selenomonas ruminantium was significantly decreased in the SP5 and SP15 groups, while the relative abundance of Streptococcus bovis was significantly decreased in the SP groups. Consequently, supplementing 15 g Spirulina/ewe/day increased the relative abundance of key cellulolytic species in the rumen, while amylolytic species were reduced only in the solid fraction.
Collapse
|
46
|
Effect of Energy Provision Strategy on Rumen Fermentation Characteristics, Bacterial Diversity and Community Composition. Bioengineering (Basel) 2023; 10:bioengineering10010107. [PMID: 36671679 PMCID: PMC9854636 DOI: 10.3390/bioengineering10010107] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 12/29/2022] [Accepted: 01/04/2023] [Indexed: 01/15/2023] Open
Abstract
This study was conducted to explore the rumen fermentation characteristics, bacterial diversity, and community composition of Hu sheep under four energy provision strategies. Ninety-six Hu sheep (body weight: 17.78 ± 1.24 kg) were equally assigned to four energy provision strategies: (1) low-energy diet for the whole finishing stage (LL); (2) high-energy diet for the whole finishing stage (HH); (3) low-energy diet in the early finishing stage and high-energy diet in the late finishing stage (LH); (4) high-energy diet in the early finishing stage and low-energy diet in the late finishing stage (HL). The results showed that the proportion of acetate was lower in the HH group than that in the HL group, whereas the opposite result was observed for the butyrate proportion (p < 0.05). The Chao 1, observed species, PD whole tree, and Shannon index of the rumen bacteria were higher in the LL group than that in the HH group (p < 0.05). The taxonomic annotations revealed that the Patescibacteria, Rikenellaceae RC9 gut group, Christensenellaceae R-7 group, and Anaeroplasma abundances were higher in the HL group than that in the HH group, and the opposite results were observed regarding the relative abundances of Selenomonas and Anaerovibrio (p < 0.05). The relative abundances of Spirochaetota and Treponema were higher in the LH group than that in the HH group (p < 0.05). Moreover, the analysis of similarity (ANOSIM) showed significant differences between groups (R = 0.6792 and p = 0.001). This study indicates that the energy provision strategy had little impact on the rumen fermentation characteristics, while it heavily affected the rumen bacterial diversity and community composition. This study may provide insight into the rumen fermentation characteristics and bacterial community under routine finishing models and contribute to the optimization of energy provision strategies of Hu sheep.
Collapse
|
47
|
Schwarz C, Mathieu J, Gomez JL, Miller MR, Tikhonova M, Nagaraja T, Alvarez PJJ. Unexpected finding of Fusobacterium varium as the dominant Fusobacterium species in cattle rumen: potential implications for liver abscess etiology and interventions. J Anim Sci 2023; 101:skad130. [PMID: 37104065 PMCID: PMC10195197 DOI: 10.1093/jas/skad130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/25/2023] [Indexed: 04/28/2023] Open
Abstract
Fusobacterium varium has been generally overlooked in cattle rumen microbiome studies relative to the presumably more abundant liver abscess-causing Fusobacterium necrophorum. However, F. varium was found to be more abundant in the rumen fluid of cattle and under culture conditions tailored to enrich F. necrophorum. Using near-full length 16S ribosomal ribonucleic acid sequencing, we demonstrate that F. varium grows under restrictive conditions commonly used to enumerate F. necrophorum, suggesting that previous F. necrophorum abundance assessment may have been inaccurate and that F. varium may be an underestimated member of the ruminal bacterial community. Fusobacterium varium were not as susceptible as F. necrophorum to in-feed antibiotics conventionally used in feedlots. Exposure to tylosin, the current gold standard for liver abscess reduction strategies in cattle, consistently hindered growth of the F. necrophorum strains tested by over 67% (P < 0.05) relative to the unexposed control. In contrast, F. varium strains were totally or highly resistant (0%-13% reduction in maximum yield, P < 0.05). Monensin, an ionophore antibiotic, had greater inhibitory activity against F. necrophorum than F. varium. Finally, preliminary genomic analysis of two F. varium isolates from the rumen revealed the presence of virulence genes related to those of pathogenic human F. varium isolates associated with active invasion of mammalian cells. The data presented here encourage further investigation into the ecological role of F. varium within the bovine rumen and potential role in liver abscess development, and proactive interventions.
Collapse
Affiliation(s)
- Cory Schwarz
- Department of Civil and Environmental Engineering, Rice University, Houston, TX 77005, USA
- Sentinel Environmental Group, LLC, Houston, TX 77082, USA
| | - Jacques Mathieu
- Department of Civil and Environmental Engineering, Rice University, Houston, TX 77005, USA
- Sentinel Environmental Group, LLC, Houston, TX 77082, USA
| | | | - Megan R Miller
- Department of Civil and Environmental Engineering, Rice University, Houston, TX 77005, USA
| | | | - Tiruvoor.G Nagaraja
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, TX 77005, USA
- Sentinel Environmental Group, LLC, Houston, TX 77082, USA
| |
Collapse
|
48
|
Santos Torres RDN, Coelho LM, Ghedini CP, Neto ORM, Chardulo LAL, Torrecilhas JA, de Lima Valença R, Baldassini WA, Almeida MTC. Potential of Nutritional Strategies to Reduce Enteric Methane Emission in Feedlot Sheep: A Meta-analysis and Multivariate Analysis. Small Rumin Res 2023. [DOI: 10.1016/j.smallrumres.2023.106919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
|
49
|
Rodríguez-González S, González-Dávalos L, Robles-Rodríguez C, Lozano-Flores C, Varela-Echavarría A, Shimada A, Mora-Izaguirre O. Isolation of bacterial consortia with probiotic potential from the rumen of tropical calves. J Anim Physiol Anim Nutr (Berl) 2023; 107:62-76. [PMID: 35253270 PMCID: PMC10078749 DOI: 10.1111/jpn.13699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 01/10/2022] [Accepted: 02/06/2022] [Indexed: 01/10/2023]
Abstract
Probiotics are live microorganisms that confer health benefits to their animal host by balancing the composition of its gastrointestinal microbiota and modulating its immune response. In this work, we studied bacterial consortia isolated from the rumen of 28- and 42-day-old calves to select those showing probiotic capacity. Consortia were characterized and their growth dynamics were determined in several growth media. The number of viable bacteria was larger in the Man, Rogosa and Sharpe broth (MRS) than in nutritive medium A (MNA) and the largest was for A3D42. Antibiotic susceptibility of bacterial consortia in MRS was higher than in MNA and the most susceptible samples were A1D28 and A3D42. In turn, A3D42 showed the highest tolerance to bile salts in MRS and MNA. Moreover, all bacterial consortia showed optimal growth at pH 5, 5.5, 6 and 7 in both media, while their temperature tolerance was higher in MRS. The antagonistic activity of bacterial consortia in MNA was higher than in MRS with A2D42 showing the best antagonistic activity for Pseudomona aureginosa (ATCC 9027) and Staphylococcus aureus (ATCC 6538) in MNA. Additionally, A1D42 and A2D42 in MRS and A3D42 in MNA had significant adhesion to mucins, and A1D42 in MRS had the highest. Regarding their species composition, all bacterial consortia in MRS belonged to the phylum Firmicutes, and the class Bacilli and bacterial consortia in MNA belonged to three phyla; Proteobacteria, Firmicutes, and Bacteroidetes. Lactobacillus casei, Lactobacillus rhamnosus, Lactobacillus fermentum, and Lactobacillus johnsonii were identified in all bacterial consortia in MRS broth. Based on these results, A1D42 and A3D42 grown in MRS showed the best potential as probiotics for calves, which could result in health benefits and improve their production.
Collapse
Affiliation(s)
- Sarahí Rodríguez-González
- Laboratorio de Rumiología y Metabolismo Nutricional, Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Laura González-Dávalos
- Laboratorio de Rumiología y Metabolismo Nutricional, Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Carolina Robles-Rodríguez
- Laboratorio de Rumiología y Metabolismo Nutricional, Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Carlos Lozano-Flores
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | | | - Armando Shimada
- Laboratorio de Rumiología y Metabolismo Nutricional, Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Ofelia Mora-Izaguirre
- Laboratorio de Rumiología y Metabolismo Nutricional, Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Querétaro, Mexico
| |
Collapse
|
50
|
Miller GA, Auffret MD, Roehe R, Nisbet H, Martínez-Álvaro M. Different microbial genera drive methane emissions in beef cattle fed with two extreme diets. Front Microbiol 2023; 14:1102400. [PMID: 37125186 PMCID: PMC10133469 DOI: 10.3389/fmicb.2023.1102400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/29/2023] [Indexed: 05/02/2023] Open
Abstract
The ratio of forage to concentrate in cattle feeding has a major influence on the composition of the microbiota in the rumen and on the mass of methane produced. Using methane measurements and microbiota data from 26 cattle we aimed to investigate the relationships between microbial relative abundances and methane emissions, and identify potential biomarkers, in animals fed two extreme diets - a poor quality fresh cut grass diet (GRASS) or a high concentrate total mixed ration (TMR). Direct comparisons of the effects of such extreme diets on the composition of rumen microbiota have rarely been studied. Data were analyzed considering their multivariate and compositional nature. Diet had a relevant effect on methane yield of +10.6 g of methane/kg of dry matter intake for GRASS with respect to TMR, and on the centered log-ratio transformed abundance of 22 microbial genera. When predicting methane yield based on the abundance of 28 and 25 selected microbial genera in GRASS and TMR, respectively, we achieved cross-validation prediction accuracies of 66.5 ± 9% and 85 ± 8%. Only the abundance of Fibrobacter had a consistent negative association with methane yield in both diets, whereas most microbial genera were associated with methane yield in only one of the two diets. This study highlights the stark contrast in the microbiota controlling methane yield between animals fed a high concentrate diet, such as that found on intensive finishing units, and a low-quality grass forage that is often found in extensive grazing systems. This contrast must be taken into consideration when developing strategies to reduce methane emissions by manipulation of the rumen microbial composition.
Collapse
Affiliation(s)
- Gemma A. Miller
- Scotland’s Rural College (SRUC), Edinburgh, United Kingdom
- Gemma A. Miller,
| | | | - Rainer Roehe
- Scotland’s Rural College (SRUC), Edinburgh, United Kingdom
| | - Holly Nisbet
- Scotland’s Rural College (SRUC), Edinburgh, United Kingdom
| | - Marina Martínez-Álvaro
- Institute for Animal Science and Technology, Universitat Politècnica de València, Valencia, Spain
- *Correspondence: Marina Martínez-Álvaro,
| |
Collapse
|