1
|
Harakawa K, Kawarai S, Kryukov K, Nakagawa S, Moriya S, Imakawa K. Buccal Swab Samples from Japanese Brown Cattle Fed with Limonite Reveal Altered Rumen Microbiome. Animals (Basel) 2024; 14:1968. [PMID: 38998081 DOI: 10.3390/ani14131968] [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: 06/12/2024] [Revised: 06/27/2024] [Accepted: 07/01/2024] [Indexed: 07/14/2024] Open
Abstract
The areas of the Mount Aso grasslands in Kumamoto, Japan, are the primary location for the breeding of the Kumamoto strain of Japanese Brown cattle (JBRK). Although Aso limonite, deposited by volcanic ash and magma, has been commonly fed to pregnant JBRK in this area, the mechanisms of its salutary effects on pregnant JBRK have not yet been elucidated. Approximately 100 days before the expected day of calf delivery, seven JBRK (four supplemented with limonite and three controls without limonite) were assigned to this study, from which a buccal swab was collected at the highest rumination every 30 days for 90 days. DNA extracted from these swabs was then analyzed using a 16S rRNA gene amplicon sequence analysis. Statistically significant differences between the two groups were discovered through beta-diversity analysis, though results from alpha-diversity analysis were inconclusive. The microbiota identified were classified into six clusters, and three of the main clusters were core-rumen bacteria, primarily cellulose digestion in cluster 1, oral bacteria in cluster 2, and non-core-rumen bacteria in cluster 3. In the limonite group, core-rumen bacteria decreased while non-core-rumen bacteria increased, suggesting that limonite feeding alters rumen microbiota, particularly activation of non-core-rumen microbiota.
Collapse
Affiliation(s)
- Kentaro Harakawa
- Research Institute of Agriculture, Tokai University, Kumamoto 862-8652, Kumamoto, Japan
| | - Shinpei Kawarai
- Research Institute of Agriculture, Tokai University, Kumamoto 862-8652, Kumamoto, Japan
| | - Kirill Kryukov
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima 411-8540, Shizuoka, Japan
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima 411-8540, Shizuoka, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara 259-1193, Kanagawa, Japan
- Micro/Nano Technology Center, Tokai University, Hiratsuka 259-1292, Kanagawa, Japan
- Institute of Medical Sciences, Tokai University, Isehara 259-1193, Kanagawa, Japan
| | - Shigeharu Moriya
- Photonics Control Technology Team, Riken Center for Advanced Photonics, Numazu 410-8601, Shizuoka, Japan
| | - Kazuhiko Imakawa
- Research Institute of Agriculture, Tokai University, Kumamoto 862-8652, Kumamoto, Japan
| |
Collapse
|
2
|
Liu Y, Li X, Diao Q, Ma T, Tu Y. In-Silico and in vitro Studies Revealed that Rosmarinic Acid Inhibited Methanogenesis via Regulating Composition and Function of Rumen Microbiota. J Dairy Sci 2024:S0022-0302(24)00905-6. [PMID: 38851580 DOI: 10.3168/jds.2024-24970] [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: 03/28/2024] [Accepted: 05/11/2024] [Indexed: 06/10/2024]
Abstract
Inhibition of methyl-coenzyme M reductase can suppress the activity of ruminal methanogens, thereby reducing enteric methane emissions of ruminants. However, developing specific and environmentally friendly inhibitors is a challenging endeavor. To identify a natural and effective methane inhibitor that specifically targets methyl-coenzyme M reductase, molecular docking technology was employed to screen a library of phytogenic compounds. A total of 52 candidate compounds were obtained through molecular docking technique. Rosmarinic acid (RA) was one of the compounds that could traverse a narrow channel and bind to the active sites of methyl-coenzyme M reductase, with a calculated binding free energy of -9.355 kcal/mol. Furthermore, the effects of rosmarinic acid supplementation on methane production, rumen fermentation, and the microorganism's community in dairy cows were investigated through in vitro rumen fermentation simulations according to a random design. Supplementation of RA resulted in a 15% decrease in methane production compared with the control. In addition, RA increased the molar proportion of acetate and propionate, whereas the sum of acetate and butyrate divided by propionate was decreased. At the bacterial level, the relative abundance of Rikenellaceae RC9 gut group, Christensenellaceae R7 group, Candidatus Saccharimonas, Desulfovibrio, and Lachnospiraceae FE2018 group decreased with RA supplementation. Conversely, the addition of RA significantly increased the relative abundance of DNF00809 (a genus from Eggerthellaceae), Denitrobacterium, an unclassified genus from Eggerthellaceae, an unclassified genus from Bacteroidales, and an unclassified genus from Atopobiaceae. At the archaeal level, the relative abundance of Methanobrevibacter decreased, while that of Methanosphaera increased with the RA supplementation. These findings suggested that RA has the potential to be used as a novel natural additive for inhibiting ruminal methane production.
Collapse
Affiliation(s)
- Yunlong Liu
- Beijing Key Laboratory for Dairy Cow Nutrition, Beijing, Institute of Feed Research of Chinese Academy of Agricultural Sciences, 100081, P.R. China
| | - Xiaopeng Li
- Beijing Key Laboratory of Dairy Cow Nutrition, College of Animal Science and Technology, Beijing University of Agriculture, Beijing, 102206, P.R. China
| | - Qiyu Diao
- Beijing Key Laboratory for Dairy Cow Nutrition, Beijing, Institute of Feed Research of Chinese Academy of Agricultural Sciences, 100081, P.R. China
| | - Tao Ma
- Beijing Key Laboratory for Dairy Cow Nutrition, Beijing, Institute of Feed Research of Chinese Academy of Agricultural Sciences, 100081, P.R. China.
| | - Yan Tu
- Beijing Key Laboratory for Dairy Cow Nutrition, Beijing, Institute of Feed Research of Chinese Academy of Agricultural Sciences, 100081, P.R. China.
| |
Collapse
|
3
|
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
|
4
|
Zhang F, Zhang Y, He T, Ji Q, Hou S, Gui L. Changes in Rumen Microbiology and Metabolism of Tibetan Sheep with Different Lys/Met Ratios in Low-Protein Diets. Animals (Basel) 2024; 14:1533. [PMID: 38891581 PMCID: PMC11171176 DOI: 10.3390/ani14111533] [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: 04/19/2024] [Revised: 05/14/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024] Open
Abstract
In ruminants, supplementing appropriate amounts of amino acids improves growth, feed utilization efficiency, and productivity. This study aimed to assess the effects of different Lys/Met ratios on the ruminal microbial community and the metabolic profiling in Tibetan sheep using 16S rDNA sequencing and non-target metabolomics. Ninety-two-month-old Tibetan rams (initial weight = 15.37 ± 0.92 kg) were divided into three groups and fed lysine/methionine (Lys/Met) of 1:1 (LP-L), 2:1 (LP-M), and 3:1 (LP-H) in low-protein diet, respectively. Results: The T-AOC, GSH-Px, and SOD were significantly higher in the LP-L group than in LP-H and LP-M groups (p < 0.05). Cellulase activity was significantly higher in the LP-L group than in the LP-H group (p < 0.05). In the fermentation parameters, acetic acid concentration was significantly higher in the LP-L group than in the LP-H group (p < 0.05). Microbial sequencing analysis showed that Ace and Chao1 indicators were significantly higher in LP-L than in LP-H and LP-M (p < 0.05). At the genus level, the abundance of Rikenellaceae RC9 gut group flora and Succiniclasticum were significantly higher in LP-L than in LP-M group (p < 0.05). Non-target metabolomics analyses revealed that the levels of phosphoric acid, pyrocatechol, hydrocinnamic acid, banzamide, l-gulono-1,4-lactone, cis-jasmone, Val-Asp-Arg, and tropinone content were higher in LP-L. However, l-citrulline and purine levels were lower in the LP-L group than in the LP-M and LP-H groups. Banzamide, cis-jasmone, and Val-Asp-Arg contents were positively correlated with the phenotypic contents, including T-AOC, SOD, and cellulase. Phosphoric acid content was positively correlated with cellulase and lipase activities. In conclusion, the Met/Lys ratio of 1:1 in low-protein diets showed superior antioxidant status and cellulase activity in the rumen by modulating the microbiota and metabolism of Tibetan sheep.
Collapse
Affiliation(s)
| | | | | | | | | | - Linsheng Gui
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810000, China; (F.Z.); (Y.Z.); (Q.J.); (S.H.)
| |
Collapse
|
5
|
Kang R, Lee H, Seon H, Park C, Song J, Park JK, Kim YK, Kim M, Park T. Effects of diets for three growing stages by rumen inocula donors on in vitro rumen fermentation and microbiome. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2024; 66:523-542. [PMID: 38975572 PMCID: PMC11222118 DOI: 10.5187/jast.2023.e109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/25/2023] [Accepted: 10/10/2023] [Indexed: 07/09/2024]
Abstract
Hanwoo and Jeju Black cattle (Jeju Black) are native breeds of Korean cattle. Jeju Black cattle are recognized as natural monuments and are known to exhibit slower growth rates compared to Hanwoo. While several studies have analyzed the genetic characteristics of these cattle, there has been limited research on the differences in their microbiome. In this study, rumen fluid was obtained from three Hanwoo steers and three Jeju Black steers, and three different diets (total mixed rations [TMRs] for growing, early fattening, and late fattening periods) were used as substrates for in vitro fermentation. The in vitro incubation was conducted for 3 h and 24 h following a 2 × 3 factorial arrangement. After both incubation periods, fermentation characteristics were analyzed, and ruminal microbiome analysis was performed using 16S rRNA gene sequencing, employing both QIIME2 and PICRUSt2. The results revealed significant differences in the ruminal microbiota due to the inoculum effect. At the phylum level, Patescibacteria and Synergistota were found to be enriched in the Jeju Black inoculum-treated group. Additionally, using different inocula also affected the relative abundance of major taxa, including Ruminococcus, Pseudoramibacter, Ruminococcaceae CAG-352, and the [Eubacterium] ruminantium group. These microbial differences induced by the inoculum may have originated from varying levels of domestication between the two subspecies of donor animals, which mainly influenced the fermentation and microbiome features in the early incubation stages, although this was only partially offset afterward. Furthermore, predicted commission numbers of microbial enzymes, some of which are involved in the biosynthesis of secondary metabolites, fatty acids, and alpha amylase, differed based on the inoculum effect. However, these differences may account for only a small proportion of the overall metabolic pathway. Conversely, diets were found to affect protein biosynthesis and its related metabolism, which showed differential abundance in the growing diet and were potentially linked to the growth-promoting effects in beef cattle during the growing period. In conclusion, this study demonstrated that using different inocula significantly affected in vitro fermentation characteristics and microbiome features, mainly in the early stages of incubation, with some effects persisting up to 24 h of incubation.
Collapse
Affiliation(s)
- Ryukseok Kang
- Department of Animal Science and
Technology, Chung-Ang University, Anseong 17546, Korea
| | - Huseong Lee
- Division of Animal Science, Chonnam
National University, Gwangju 61186, Korea
- Graduate School of Agricultural Science,
Tohoku University, Sendai 980-0845, Japan
| | - Hyeonsu Seon
- Division of Animal Science, Chonnam
National University, Gwangju 61186, Korea
| | - Cheolju Park
- Division of Animal Science, Chonnam
National University, Gwangju 61186, Korea
| | | | | | | | - Minseok Kim
- Division of Animal Science, Chonnam
National University, Gwangju 61186, Korea
| | - Tansol Park
- Department of Animal Science and
Technology, Chung-Ang University, Anseong 17546, Korea
| |
Collapse
|
6
|
Guo J, Shi W, Li X, Yang B, Qin C, Su L. Comparative Analysis of Gut Microbiomes in Laboratory Chinchillas, Ferrets, and Marmots: Implications for Pathogen Infection Research. Microorganisms 2024; 12:646. [PMID: 38674591 PMCID: PMC11051751 DOI: 10.3390/microorganisms12040646] [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: 02/20/2024] [Revised: 03/17/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
Gut microbes play a vital role in the health and disease of animals, especially in relation to pathogen infections. Chinchillas, ferrets, and marmots are commonly used as important laboratory animals for infectious disease research. Here, we studied the bacterial and fungal microbiota and discovered that chinchillas had higher alpha diversity and a higher abundance of bacteria compared to marmots and ferrets by using the metabarcoding of 16S rRNA genes and ITS2, coupled with co-occurrence network analysis. The dominant microbes varied significantly among the three animal species, particularly in the gut mycobiota. In the ferrets, the feces were dominated by yeast such as Rhodotorula and Kurtzmaniella, while in the chinchillas, we found Teunomyces and Penicillium dominating, and Acaulium, Piromyces, and Kernia in the marmots. Nevertheless, the dominant bacterial genera shared some similarities, such as Clostridium and Pseudomonas across the three animal species. However, there were significant differences observed, such as Vagococcus and Ignatzschineria in the ferrets, Acinetobacter and Bacteroides in the chinchillas, and Bacteroides and Cellvibrio in the marmots. Additionally, our differential analysis revealed significant differences in classification levels among the three different animal species, as well as variations in feeding habitats that resulted in distinct contributions from the host microbiome. Therefore, our data are valuable for monitoring and evaluating the impacts of the microbiome, as well as considering potential applications.
Collapse
Affiliation(s)
| | | | | | | | | | - Lei Su
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Comparative Medicine Center, Peking Union Medical College (PUMC), Beijing 100021, China; (J.G.); (W.S.); (X.L.); (B.Y.); (C.Q.)
| |
Collapse
|
7
|
Ungerfeld EM, Cancino-Padilla N, Vera-Aguilera N, Scorcione MC, Saldivia M, Lagos-Pailla L, Vera M, Cerda C, Muñoz C, Urrutia N, Martínez ED. Effects of type of substrate and dilution rate on fermentation in serial rumen mixed cultures. Front Microbiol 2024; 15:1356966. [PMID: 38389534 PMCID: PMC10883771 DOI: 10.3389/fmicb.2024.1356966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 01/18/2024] [Indexed: 02/24/2024] Open
Abstract
Forages and concentrates have consistently distinct patterns of fermentation in the rumen, with forages producing more methane (CH4) per unit of digested organic matter (OM) and higher acetate to propionate ratio than concentrates. A mechanism based on the Monod function of microbial growth has been proposed to explain the distinct fermentation pattern of forages and concentrates, where greater dilution rates and lower pH associated with concentrate feeding increase dihydrogen (H2) concentration through increasing methanogens growth rate and decreasing methanogens theoretically maximal growth rate, respectively. Increased H2 concentration would in turn inhibit H2 production, decreasing methanogenesis, inhibit H2-producing pathways such as acetate production via pyruvate oxidative decarboxylation, and stimulate H2-incorporating pathways such as propionate production. We examined the hypothesis that equalizing dilution rates in serial rumen cultures would result in a similar fermentation profile of a high forage and a high concentrate substrate. Under a 2 × 3 factorial arrangement, a high forage and a high concentrate substrate were incubated at dilution rates of 0.14, 0.28, or 0.56 h-1 in eight transfers of serial rumen cultures. Each treatment was replicated thrice, and the experiment repeated in two different months. The high concentrate substrate accumulated considerably more H2 and formate and produced less CH4 than the high forage substrate. Methanogens were nearly washed-out with high concentrate and increased their initial numbers with high forage. The effect of dilution rate was minor in comparison to the effect of the type of substrate. Accumulation of H2 and formate with high concentrate inhibited acetate and probably H2 and formate production, and stimulated butyrate, rather than propionate, as an electron sink alternative to CH4. All three dilution rates are considered high and selected for rapidly growing bacteria. The archaeal community composition varied widely and inconsistently. Lactate accumulated with both substrates, likely favored by microbial growth kinetics rather than by H2 accumulation thermodynamically stimulating electron disposal from NADH into pyruvate reduction. In this study, the type of substrate had a major effect on rumen fermentation largely independent of dilution rate and pH.
Collapse
Affiliation(s)
- Emilio M Ungerfeld
- Centro Regional de Investigación Carillanca, Instituto de Investigaciones Agropecuarias, Vilcún, Chile
| | - Nathaly Cancino-Padilla
- Centro Regional de Investigación Carillanca, Instituto de Investigaciones Agropecuarias, Vilcún, Chile
| | - Nelson Vera-Aguilera
- Centro Regional de Investigación Carillanca, Instituto de Investigaciones Agropecuarias, Vilcún, Chile
| | | | - Marcelo Saldivia
- Instituto de Ciencia Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
| | - Lorena Lagos-Pailla
- Instituto de Ingeniería Agraria y Suelos, Facultad de Ciencias Agrarias y Alimentarias, Universidad Austral de Chile, Valdivia, Chile
- Centro de Investigación de Suelos Volcánicos, Universidad Austral de Chile, Valdivia, Chile
- Centro de Humedales Río Cruces, Valdivia, Chile
| | - Milena Vera
- Instituto de Ingeniería Agraria y Suelos, Facultad de Ciencias Agrarias y Alimentarias, Universidad Austral de Chile, Valdivia, Chile
| | - Cristián Cerda
- Departamento de Procesos Industriales, Universidad Católica de Temuco, Temuco, Chile
| | - Camila Muñoz
- Centro Regional de Investigación Remehue, Instituto de Investigaciones Agropecuarias, Osorno, Chile
| | - Natalie Urrutia
- Centro Regional de Investigación Remehue, Instituto de Investigaciones Agropecuarias, Osorno, Chile
| | - Emilio D Martínez
- Instituto de Ciencia Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
| |
Collapse
|
8
|
Mackie RI, Kim H, Kim NK, Cann I. - Invited Review - Hydrogen production and hydrogen utilization in the rumen: key to mitigating enteric methane production. Anim Biosci 2024; 37:323-336. [PMID: 38186257 PMCID: PMC10838669 DOI: 10.5713/ab.23.0294] [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: 08/11/2023] [Revised: 10/13/2023] [Accepted: 11/08/2023] [Indexed: 01/09/2024] Open
Abstract
Molecular hydrogen (H2) and formate (HCOO-) are metabolic end products of many primary fermenters in the rumen ecosystem. Both play a vital role in fermentation where they are electron sinks for individual microbes in an anaerobic environment that lacks external electron acceptors. If H2 and/or formate accumulate within the rumen, the ability of primary fermenters to regenerate electron carriers may be inhibited and microbial metabolism and growth disrupted. Consequently, H2- and/or formate-consuming microbes such as methanogens and possibly homoacetogens play a key role in maintaining the metabolic efficiency of primary fermenters. There is increasing interest in identifying approaches to manipulate the rumen ecosystem for the benefit of the host and the environment. As H2 and formate are important mediators of interspecies interactions, an understanding of their production and utilization could be a significant starting point for the development of successful interventions aimed at redirecting electron flow and reducing methane emissions. We conclude by discussing in brief ruminant methane mitigation approaches as a model to help understand the fate of H2 and formate in the rumen ecosystem.
Collapse
Affiliation(s)
- Roderick I. Mackie
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801,
USA
- Carle R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801,
USA
| | - Hyewon Kim
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801,
USA
| | - Na Kyung Kim
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801,
USA
| | - Isaac Cann
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801,
USA
- Carle R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801,
USA
- Department of Microbiology, University of Illinois, Urbana, IL 61801,
USA
| |
Collapse
|
9
|
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
|
10
|
Li Q, Ma Z, Huo J, Zhang X, Wang R, Zhang S, Jiao J, Dong X, Janssen PH, Ungerfeld EM, Greening C, Tan Z, Wang M. Distinct microbial hydrogen and reductant disposal pathways explain interbreed variations in ruminant methane yield. THE ISME JOURNAL 2024; 18:wrad016. [PMID: 38365243 PMCID: PMC10811737 DOI: 10.1093/ismejo/wrad016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 02/18/2024]
Abstract
Ruminants are essential for global food security, but these are major sources of the greenhouse gas methane. Methane yield is controlled by the cycling of molecular hydrogen (H2), which is produced during carbohydrate fermentation and is consumed by methanogenic, acetogenic, and respiratory microorganisms. However, we lack a holistic understanding of the mediators and pathways of H2 metabolism and how this varies between ruminants with different methane-emitting phenotypes. Here, we used metagenomic, metatranscriptomic, metabolomics, and biochemical approaches to compare H2 cycling and reductant disposal pathways between low-methane-emitting Holstein and high-methane-emitting Jersey dairy cattle. The Holstein rumen microbiota had a greater capacity for reductant disposal via electron transfer for amino acid synthesis and propionate production, catalyzed by enzymes such as glutamate synthase and lactate dehydrogenase, and expressed uptake [NiFe]-hydrogenases to use H2 to support sulfate and nitrate respiration, leading to enhanced coupling of H2 cycling with less expelled methane. The Jersey rumen microbiome had a greater proportion of reductant disposal via H2 production catalyzed by fermentative hydrogenases encoded by Clostridia, with H2 mainly taken up through methanogenesis via methanogenic [NiFe]-hydrogenases and acetogenesis via [FeFe]-hydrogenases, resulting in enhanced methane and acetate production. Such enhancement of electron incorporation for metabolite synthesis with reduced methanogenesis was further supported by two in vitro measurements of microbiome activities, metabolites, and public global microbiome data of low- and high-methane-emitting beef cattle and sheep. Overall, this study highlights the importance of promoting alternative H2 consumption and reductant disposal pathways for synthesizing host-beneficial metabolites and reducing methane production in ruminants.
Collapse
Affiliation(s)
- Qiushuang Li
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiyuan Ma
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
| | - Jiabin Huo
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
| | - Xiumin Zhang
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
| | - Rong Wang
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
| | - Shizhe Zhang
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
| | - Jinzhen Jiao
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
| | - Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Peter H Janssen
- AgResearch Limited, Grasslands Research Centre, Palmerston North, Private Bag 11008, New Zealand
| | - Emilio M Ungerfeld
- Centro Regional de Investigación Carillanca, Instituto de Investigaciones Agropecuarias (INIA), Temuco, Vilcún 4880000, Chile
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Zhiliang Tan
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Wang
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
11
|
Sarmikasoglou E, Sumadong P, Roesch LF, Halima S, Hikita C, Watanabe T, Faciola A. Effects of monensin and cashew nut-shell extract on bacterial community composition in a dual-flow continuous culture system. Transl Anim Sci 2023; 8:txad148. [PMID: 38221956 PMCID: PMC10787353 DOI: 10.1093/tas/txad148] [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: 10/31/2023] [Accepted: 12/20/2023] [Indexed: 01/16/2024] Open
Abstract
The objective of this study was to evaluate the effects of including monensin and two doses of CNSE in a high producing dairy cow diet on ruminal bacterial communities. A dual-flow continuous culture system was used in a replicated 4 × 4 Latin Square design. A basal diet was formulated to meet the requirements of a cow producing 45 kg of milk per d (17% crude protein and 27% starch). There were four experimental treatments: the basal diet without any feed additive (CON), 2.5 μM monensin (MON), 100 ppm CNSE granule (CNSE100), and 200 ppm CNSE granule (CNSE200). Samples were collected from the fluid and solid effluents at 3, 6, and 9 h after feeding; a composite of all time points was made for each fermenter within their respective fractions. Bacterial community composition was analyzed by sequencing the V4 region of the 16S rRNA gene using the Illumina MiSeq platform. Treatment responses for bacterial community structure were analyzed with the PERMANOVA test run with the R Vegan package. Treatment responses for correlations were analyzed with the CORR procedure of SAS. Orthogonal contrasts were used to test the effects of (1) ADD (CON vs. MON, CNSE100, and CNSE200); (2) MCN (MON vs. CNSE100 and CNSE200); and (3) DOSE (CNSE100 vs. CNSE200). Significance was declared at P ≤ 0.05. We observed that the relative abundance of Sharpea (P < 0.01), Mailhella (P = 0.05), Ruminococcus (P = 0.03), Eubacterium (P = 0.01), and Coprococcus (P < 0.01) from the liquid fraction and the relative abundance of Ruminococcus (P = 0.03) and Catonella (P = 0.02) from the solid fraction decreased, while the relative abundance of Syntrophococcus (P = 0.02) increased in response to MON when compared to CNSE treatments. Our results demonstrate that CNSE and monensin have similar effects on the major ruminal bacterial genera, while some differences were observed in some minor genera. Overall, the tested additives would affect the ruminal fermentation in a similar pattern.
Collapse
Affiliation(s)
- Efstathios Sarmikasoglou
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
- Department of Animal Sciences, University of Florida, Gainesville, 32611 FL, USA
| | - Phussorn Sumadong
- Department of Animal Sciences, University of Florida, Gainesville, 32611 FL, USA
- Department of Animal Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Luiz Fernando Roesch
- Department of Microbiology and Cell Science, University of Florida, Gainesville, 32603 FL, USA
| | - Sultana Halima
- Department of Animal Sciences, University of Florida, Gainesville, 32611 FL, USA
| | - Chie Hikita
- Product Development Department, SDS Biotech K.K., Tokyo 101-0022, Japan
| | - Tomonori Watanabe
- Product Development Department, SDS Biotech K.K., Tokyo 101-0022, Japan
| | - Antonio P Faciola
- Department of Animal Sciences, University of Florida, Gainesville, 32611 FL, USA
| |
Collapse
|
12
|
Vadroňová M, Šťovíček A, Jochová K, Výborná A, Tyrolová Y, Tichá D, Homolka P, Joch M. Combined effects of nitrate and medium-chain fatty acids on methane production, rumen fermentation, and rumen bacterial populations in vitro. Sci Rep 2023; 13:21961. [PMID: 38081855 PMCID: PMC10713576 DOI: 10.1038/s41598-023-49138-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 12/05/2023] [Indexed: 12/18/2023] Open
Abstract
This study investigated the combined effects of nitrate (NT) and medium-chain fatty acids (MCFA), including C8, C10, C12, and C14, on methane (CH4) production, rumen fermentation characteristics, and rumen bacteria using a 24 h batch incubation technique. Four types of treatments were used: control (no nitrate, no MCFA), NT (nitrate at 3.65 mM), NT + MCFA (nitrate at 3.65 mM + one of the four MCFA at 500 mg/L), and NT + MCFA/MCFA (nitrate at 3.65 mM + a binary combination of MCFA at 250 and 250 mg/L). All treatments decreased (P < 0.001) methanogenesis (mL/g dry matter incubated) compared with the control, but their efficiency was dependent on the MCFA type. The most efficient CH4 inhibitor was the NT + C10 treatment (- 40%). The combinations containing C10 and C12 had the greatest effect on bacterial alpha and beta diversity and relative microbial abundance (P < 0.001). Next-generation sequencing showed that the family Succinivibrionaceae was favored in treatments with the greatest CH4 inhibition at the expense of Prevotella and Ruminococcaceae. Furthermore, the relative abundance of Archaea decreased (P < 0.05) in the NT + C10 and NT + C10/C12 treatments. These results confirm that the combination of NT with MCFA (C10 and C12 in particular) may effectively reduce CH4 production.
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
- Department of Nutrition and Feeding of Farm Animals, Institute of Animal Science, Přátelství 815, 104 00, Prague, Czech Republic
| | - 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
| | - Kateřina Jochová
- 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
- Department of Nutrition and Feeding of Farm Animals, Institute of Animal Science, Přátelství 815, 104 00, Prague, Czech Republic
| | - Alena Výborná
- Department of Nutrition and Feeding of Farm Animals, Institute of Animal Science, Přátelství 815, 104 00, Prague, Czech Republic
| | - Yvona Tyrolová
- Department of Nutrition and Feeding of Farm Animals, Institute of Animal Science, Přátelství 815, 104 00, Prague, Czech Republic
| | - 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
- Department of Nutrition and Feeding of Farm Animals, Institute of Animal Science, Přátelství 815, 104 00, Prague, Czech Republic
| | - Petr Homolka
- 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
- Department of Nutrition and Feeding of Farm Animals, Institute of Animal Science, Přátelství 815, 104 00, Prague, Czech Republic
| | - 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.
- Department of Nutrition and Feeding of Farm Animals, Institute of Animal Science, Přátelství 815, 104 00, Prague, Czech Republic.
| |
Collapse
|
13
|
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
|
14
|
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
|
15
|
Khairunisa BH, Heryakusuma C, Ike K, Mukhopadhyay B, Susanti D. Evolving understanding of rumen methanogen ecophysiology. Front Microbiol 2023; 14:1296008. [PMID: 38029083 PMCID: PMC10658910 DOI: 10.3389/fmicb.2023.1296008] [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: 09/17/2023] [Accepted: 10/12/2023] [Indexed: 12/01/2023] Open
Abstract
Production of methane by methanogenic archaea, or methanogens, in the rumen of ruminants is a thermodynamic necessity for microbial conversion of feed to volatile fatty acids, which are essential nutrients for the animals. On the other hand, methane is a greenhouse gas and its production causes energy loss for the animal. Accordingly, there are ongoing efforts toward developing effective strategies for mitigating methane emissions from ruminant livestock that require a detailed understanding of the diversity and ecophysiology of rumen methanogens. Rumen methanogens evolved from free-living autotrophic ancestors through genome streamlining involving gene loss and acquisition. The process yielded an oligotrophic lifestyle, and metabolically efficient and ecologically adapted descendants. This specialization poses serious challenges to the efforts of obtaining axenic cultures of rumen methanogens, and consequently, the information on their physiological properties remains in most part inferred from those of their non-rumen representatives. This review presents the current knowledge of rumen methanogens and their metabolic contributions to enteric methane production. It also identifies the respective critical gaps that need to be filled for aiding the efforts to mitigate methane emission from livestock operations and at the same time increasing the productivity in this critical agriculture sector.
Collapse
Affiliation(s)
| | - Christian Heryakusuma
- Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, United States
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States
| | - Kelechi Ike
- Department of Biology, North Carolina Agricultural and Technical State University, Greensboro, NC, United States
| | - Biswarup Mukhopadhyay
- Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, United States
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States
- Virginia Tech Carilion School of Medicine, Virginia Tech, Blacksburg, VA, United States
| | - Dwi Susanti
- Microbial Discovery Research, BiomEdit, Greenfield, IN, United States
| |
Collapse
|
16
|
Hess MK, Hodgkinson HE, Hess AS, Zetouni L, Budel JCC, Henry H, Donaldson A, Bilton TP, van Stijn TC, Kirk MR, Dodds KG, Brauning R, McCulloch AF, Hickey SM, Johnson PL, Jonker A, Morton N, Hendy S, Oddy VH, Janssen PH, McEwan JC, Rowe SJ. Large-scale analysis of sheep rumen metagenome profiles captured by reduced representation sequencing reveals individual profiles are influenced by the environment and genetics of the host. BMC Genomics 2023; 24:551. [PMID: 37723422 PMCID: PMC10506323 DOI: 10.1186/s12864-023-09660-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 09/07/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND Producing animal protein while reducing the animal's impact on the environment, e.g., through improved feed efficiency and lowered methane emissions, has gained interest in recent years. Genetic selection is one possible path to reduce the environmental impact of livestock production, but these traits are difficult and expensive to measure on many animals. The rumen microbiome may serve as a proxy for these traits due to its role in feed digestion. Restriction enzyme-reduced representation sequencing (RE-RRS) is a high-throughput and cost-effective approach to rumen metagenome profiling, but the systematic (e.g., sequencing) and biological factors influencing the resulting reference based (RB) and reference free (RF) profiles need to be explored before widespread industry adoption is possible. RESULTS Metagenome profiles were generated by RE-RRS of 4,479 rumen samples collected from 1,708 sheep, and assigned to eight groups based on diet, age, time off feed, and country (New Zealand or Australia) at the time of sample collection. Systematic effects were found to have minimal influence on metagenome profiles. Diet was a major driver of differences between samples, followed by time off feed, then age of the sheep. The RF approach resulted in more reads being assigned per sample and afforded greater resolution when distinguishing between groups than the RB approach. Normalizing relative abundances within the sampling Cohort abolished structures related to age, diet, and time off feed, allowing a clear signal based on methane emissions to be elucidated. Genus-level abundances of rumen microbes showed low-to-moderate heritability and repeatability and were consistent between diets. CONCLUSIONS Variation in rumen metagenomic profiles was influenced by diet, age, time off feed and genetics. Not accounting for environmental factors may limit the ability to associate the profile with traits of interest. However, these differences can be accounted for by adjusting for Cohort effects, revealing robust biological signals. The abundances of some genera were consistently heritable and repeatable across different environments, suggesting that metagenomic profiles could be used to predict an individual's future performance, or performance of its offspring, in a range of environments. These results highlight the potential of using rumen metagenomic profiles for selection purposes in a practical, agricultural setting.
Collapse
Affiliation(s)
- Melanie K Hess
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand.
| | - Hannah E Hodgkinson
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Andrew S Hess
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
- Agriculture, Veterinary & Rangeland Sciences, University of Nevada-Reno, 1664 N. Virginia St. Mail stop 202, Reno, NV, 89557, USA
| | - Larissa Zetouni
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
- Wageningen University & Research, P.O. Box 338, 6700, AH, Wageningen, The Netherlands
| | - Juliana C C Budel
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
- Graduate Program in Animal Science, Universidade Federal do Pará (UFPa), Castanhal, Brazil
| | - Hannah Henry
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Alistair Donaldson
- NSW Department of Primary Industries, University of New England, Armidale, 2351, Australia
| | - Timothy P Bilton
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Tracey C van Stijn
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Michelle R Kirk
- AgResearch Ltd., Grasslands Research Centre, Private Bag 11,008, Palmerston North, 4410, New Zealand
| | - Ken G Dodds
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Rudiger Brauning
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Alan F McCulloch
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Sharon M Hickey
- AgResearch Ltd., Ruakura Research Centre, Private Bag 3115, Hamilton, 3214, New Zealand
| | - Patricia L Johnson
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Arjan Jonker
- AgResearch Ltd., Grasslands Research Centre, Private Bag 11,008, Palmerston North, 4410, New Zealand
| | - Nickolas Morton
- Te Pūnaha Matatini, University of Auckland, Auckland, 1010, New Zealand
| | - Shaun Hendy
- Te Pūnaha Matatini, University of Auckland, Auckland, 1010, New Zealand
| | - V Hutton Oddy
- NSW Department of Primary Industries, University of New England, Armidale, 2351, Australia
| | - Peter H Janssen
- AgResearch Ltd., Grasslands Research Centre, Private Bag 11,008, Palmerston North, 4410, New Zealand
| | - John C McEwan
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Suzanne J Rowe
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| |
Collapse
|
17
|
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
|
18
|
Huaiquipán R, Quiñones J, Díaz R, Velásquez C, Sepúlveda G, Velázquez L, Paz EA, Tapia D, Cancino D, Sepúlveda N. Review: Effect of Experimental Diets on the Microbiome of Productive Animals. Microorganisms 2023; 11:2219. [PMID: 37764062 PMCID: PMC10536378 DOI: 10.3390/microorganisms11092219] [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: 05/04/2023] [Revised: 07/14/2023] [Accepted: 07/24/2023] [Indexed: 09/29/2023] Open
Abstract
The microorganisms that inhabit the gastrointestinal tract are responsible for multiple chains of reactions that affect their environment and modify the internal metabolism, their study receives the name of microbiome, which has become more relevant in recent years. In the near future, the challenges related to feeding are anticipated to escalate, encompassing the nutritional needs to sustain an overpopulated world. Therefore, it is expected that a better understanding of the interactions between microorganisms within the digestive tract will allow their modulation in order to provide an improvement in the immune system, feed efficiency or the promotion of nutritional characteristics in production animals, among others. In the present study, the main effects of experimental diets in production animals were described, emphasizing the diversity of the bacterial populations found in response to the diets, ordering them between polygastric and monogastric animals, and then describing the experimental diets used and their effect on the microorganisms. It is hoped that this study will help as a first general approach to the study of the role of the microbiome in production animals under different diets.
Collapse
Affiliation(s)
- Rodrigo Huaiquipán
- Programa de Doctorado en Ciencias Agroalimentarias y Medioambiente, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de la Frontera, Temuco 4780000, Chile; (R.H.); (C.V.); (G.S.); (L.V.); (D.T.)
| | - John Quiñones
- Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de la Frontera, Temuco 4780000, Chile; (R.D.); (D.C.)
- Centro de Tecnología e Innovación de la Carne, Universidad de La Frontera, Temuco 4780000, Chile
| | - Rommy Díaz
- Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de la Frontera, Temuco 4780000, Chile; (R.D.); (D.C.)
- Centro de Tecnología e Innovación de la Carne, Universidad de La Frontera, Temuco 4780000, Chile
| | - Carla Velásquez
- Programa de Doctorado en Ciencias Agroalimentarias y Medioambiente, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de la Frontera, Temuco 4780000, Chile; (R.H.); (C.V.); (G.S.); (L.V.); (D.T.)
| | - Gastón Sepúlveda
- Programa de Doctorado en Ciencias Agroalimentarias y Medioambiente, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de la Frontera, Temuco 4780000, Chile; (R.H.); (C.V.); (G.S.); (L.V.); (D.T.)
| | - Lidiana Velázquez
- Programa de Doctorado en Ciencias Agroalimentarias y Medioambiente, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de la Frontera, Temuco 4780000, Chile; (R.H.); (C.V.); (G.S.); (L.V.); (D.T.)
| | - Erwin A. Paz
- UWA Institute of Agriculture, The University of Western Australia, Perth 6009, Australia;
| | - Daniela Tapia
- Programa de Doctorado en Ciencias Agroalimentarias y Medioambiente, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de la Frontera, Temuco 4780000, Chile; (R.H.); (C.V.); (G.S.); (L.V.); (D.T.)
| | - David Cancino
- Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de la Frontera, Temuco 4780000, Chile; (R.D.); (D.C.)
- Centro de Tecnología e Innovación de la Carne, Universidad de La Frontera, Temuco 4780000, Chile
| | - Néstor Sepúlveda
- Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de la Frontera, Temuco 4780000, Chile; (R.D.); (D.C.)
- Centro de Tecnología e Innovación de la Carne, Universidad de La Frontera, Temuco 4780000, Chile
| |
Collapse
|
19
|
Hess MK, Zetouni L, Hess AS, Budel J, Dodds KG, Henry HM, Brauning R, McCulloch AF, Hickey SM, Johnson PL, Elmes S, Wing J, Bryson B, Knowler K, Hyndman D, Baird H, McRae KM, Jonker A, Janssen PH, McEwan JC, Rowe SJ. Combining host and rumen metagenome profiling for selection in sheep: prediction of methane, feed efficiency, production, and health traits. Genet Sel Evol 2023; 55:53. [PMID: 37491204 PMCID: PMC10367317 DOI: 10.1186/s12711-023-00822-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 07/03/2023] [Indexed: 07/27/2023] Open
Abstract
BACKGROUND Rumen microbes break down complex dietary carbohydrates into energy sources for the host and are increasingly shown to be a key aspect of animal performance. Host genotypes can be combined with microbial DNA sequencing to predict performance traits or traits related to environmental impact, such as enteric methane emissions. Metagenome profiles were generated from 3139 rumen samples, collected from 1200 dual purpose ewes, using restriction enzyme-reduced representation sequencing (RE-RRS). Phenotypes were available for methane (CH4) and carbon dioxide (CO2) emissions, the ratio of CH4 to CH4 plus CO2 (CH4Ratio), feed efficiency (residual feed intake: RFI), liveweight at the time of methane collection (LW), liveweight at 8 months (LW8), fleece weight at 12 months (FW12) and parasite resistance measured by faecal egg count (FEC1). We estimated the proportion of phenotypic variance explained by host genetics and the rumen microbiome, as well as prediction accuracies for each of these traits. RESULTS Incorporating metagenome profiles increased the variance explained and prediction accuracy compared to fitting only genomics for all traits except for CO2 emissions when animals were on a grass diet. Combining the metagenome profile with host genotype from lambs explained more than 70% of the variation in methane emissions and residual feed intake. Predictions were generally more accurate when incorporating metagenome profiles compared to genetics alone, even when considering profiles collected at different ages (lamb vs adult), or on different feeds (grass vs lucerne pellet). A reference-free approach to metagenome profiling performed better than metagenome profiles that were restricted to capturing genera from a reference database. We hypothesise that our reference-free approach is likely to outperform other reference-based approaches such as 16S rRNA gene sequencing for use in prediction of individual animal performance. CONCLUSIONS This paper shows the potential of using RE-RRS as a low-cost, high-throughput approach for generating metagenome profiles on thousands of animals for improved prediction of economically and environmentally important traits. A reference-free approach using a microbial relationship matrix from log10 proportions of each tag normalized within cohort (i.e., the group of animals sampled at the same time) is recommended for future predictions using RE-RRS metagenome profiles.
Collapse
Affiliation(s)
- Melanie K Hess
- University Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand.
- University of Nebraska-Lincoln, Institute of Agriculture and Natural Resources, 300 Agricultural Hall, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA.
| | - Larissa Zetouni
- University Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
- Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
| | - Andrew S Hess
- University Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
- University of Nevada, Reno, Agriculture, Veterinary & Rangeland Sciences, 1664 N. Virginia St., Mail Stop 202, Reno, NV, 89557, USA
| | - Juliana Budel
- University Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
- Graduate Program in Animal Science, Universidade Federal do Pará (UFPa), Castanhal, Brazil
| | - Ken G Dodds
- University Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Hannah M Henry
- University Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Rudiger Brauning
- University Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Alan F McCulloch
- University Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Sharon M Hickey
- Ruakura Research Centre, AgResearch Ltd., Private Bag 3115, Hamilton, 3240, New Zealand
| | - Patricia L Johnson
- University Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Sara Elmes
- Deer Industry New Zealand, PO Box 10702, Wellington, 6140, New Zealand
| | - Janine Wing
- Pāmu, Landcorp Farming Ltd, PO Box 5349, Wellington, 6011, New Zealand
| | - Brooke Bryson
- Woodlands Research Farm, AgResearch Ltd., 204 Woodlands-Morton Mains Road, Woodlands, 9871, New Zealand
| | - Kevin Knowler
- University Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Dianne Hyndman
- University Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Hayley Baird
- University Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Kathryn M McRae
- University Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Arjan Jonker
- Grasslands Research Centre, AgResearch Ltd., Private Bag 11008, Palmerston North, 4410, New Zealand
| | - Peter H Janssen
- Grasslands Research Centre, AgResearch Ltd., Private Bag 11008, Palmerston North, 4410, New Zealand
| | - John C McEwan
- University Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Suzanne J Rowe
- University Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
| |
Collapse
|
20
|
Burnham CM, McKenney EA, van Heugten KA, Minter LJ, Trivedi S. Effects of age, seasonality, and reproductive status on the gut microbiome of Southern White Rhinoceros (Ceratotherium simum simum) at the North Carolina zoo. Anim Microbiome 2023; 5:27. [PMID: 37147724 PMCID: PMC10163733 DOI: 10.1186/s42523-023-00249-5] [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: 07/19/2022] [Accepted: 04/22/2023] [Indexed: 05/07/2023] Open
Abstract
BACKGROUND Managed southern white rhinoceros (Ceratotherium simum simum) serve as assurance populations for wild conspecifics threatened by poaching and other anthropocentric effects, though many managed populations experience subfertility and reproductive failure. Gut microbiome and host health are inextricably linked, and reproductive outcomes in managed southern white rhinoceros may be mediated in part by their diet and gut microbial diversity. Thus, understanding microbial dynamics within managed populations may help improve conservation efforts. We characterized the taxonomic composition of the gut microbiome in the managed population of female southern white rhinoceros (n = 8) at the North Carolina Zoo and investigated the effects of seasonality (summer vs. winter) and age classes (juveniles (n = 2; 0-2 years), subadults (n = 2; 3-7 years), and adults (n = 4; >7 years)) on microbial richness and community structure. Collection of a fecal sample was attempted for each individual once per month from July-September 2020 and January-March 2021 resulting in a total of 41 samples analyzed. Microbial DNA was extracted and sequenced using the V3-V4 region of the 16S rRNA bacterial gene. Total operational taxonomic units (OTUs), alpha diversity (species richness, Shannon diversity), and beta diversity (Bray-Curtis dissimilarity, linear discriminant analysis effect size) indices were examined, and differentially enriched taxa were identified. RESULTS There were differences (p < 0.05) in alpha and beta diversity indices across individuals, age groups, and sampling months. Subadult females had higher levels of Shannon diversity (Wilcoxon, p < 0.05) compared to adult females and harbored a community cluster distinct from both juveniles and adults. Samples collected during winter months (January-March 2021) possessed higher species richness and statistically distinct communities compared to summer months (July-September 2020) (PERMANOVA, p < 0.05). Reproductively active (n = 2) and currently nonreproductive adult females (n = 2) harbored differentially enriched taxa, with the gut microbiome of nonreproductive females significantly enriched (p = 0.001) in unclassified members of Mobiluncus, a genus which possesses species associated with poor reproductive outcomes in other animal species when identified in the cervicovaginal microbiome. CONCLUSION Together, our results increase the understanding of age and season related microbial variation in southern white rhinoceros at the North Carolina Zoo and have identified a potential microbial biomarker for reproductive concern within managed female southern white rhinoceros.
Collapse
Affiliation(s)
- Christina M Burnham
- Department of Animal Science, North Carolina State University, 120 W Broughton Dr, Raleigh, NC, 27607, USA
| | - Erin A McKenney
- Department of Applied Ecology, North Carolina State University, 100 Brooks Ave, Raleigh, NC, 27607, USA
| | - Kimberly Ange- van Heugten
- Department of Animal Science, North Carolina State University, 120 W Broughton Dr, Raleigh, NC, 27607, USA
| | - Larry J Minter
- North Carolina Zoo, 4401 Zoo Parkway, Asheboro, NC, 27205, USA
| | - Shweta Trivedi
- Department of Animal Science, North Carolina State University, 120 W Broughton Dr, Raleigh, NC, 27607, USA.
| |
Collapse
|
21
|
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
|
22
|
Teobaldo RW, Granja-Salcedo YT, Cardoso ADS, Constancio MTL, Brito TR, Romanzini EP, Reis RA. The Impact of Mineral and Energy Supplementation and Phytogenic Compounds on Rumen Microbial Diversity and Nitrogen Utilization in Grazing Beef Cattle. Microorganisms 2023; 11:microorganisms11030810. [PMID: 36985382 PMCID: PMC10051884 DOI: 10.3390/microorganisms11030810] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/11/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
The objective of this study was to evaluate the effect of the addition of a phytogenic compound blend (PHA) containing hydrolyzable tannins, carvacrol, and cinnamaldehyde oil to mineral salt or energy supplementation on the rumen microbiota and nitrogen metabolism of grazing Nellore cattle. Eight castrated Nellore steers were distributed in a double-Latin-square 4 × 4 design, with a 2 × 2 factorial arrangement (two types of supplements with or without the addition of the PHA), as follows: energy supplement without the PHA addition (EW); energy supplement with the PHA addition (EPHA); mineral supplement without the addition of the PHA (MW); mineral supplement with the PHA addition (MPHA). Steers that received supplements with the PHA have a lower ruminal proportion of valerate (with the PHA, 1.06%; without the PHA, 1.15%), a lower ruminal abundance of Verrucomicrobia, and a tendency for lower DM digestibility (with the PHA, 62.8%; without the PHA, 64.8%). Energy supplements allowed for higher ammonia concentrations (+2.28 mg of NH3-N/dL), increased the propionate proportion (+0.29% of total VFA), and had a higher ruminal abundance of Proteobacteria and Spirochaetae phyla in the rumen. The PHA addition in the supplement did not improve nitrogen retention, reduced the ruminal proportion of valerate, and had a negative impact on both the total dry-matter digestibility and the abundance of several ruminal bacterial groups belonging to the Firmicutes and Verrucomicrobia phyla.
Collapse
Affiliation(s)
- Ronyatta Weich Teobaldo
- Department of Animal Science, São Paulo State University "Júlio de Mesquita Filho" (UNESP), Jaboticabal 14887-900, Brazil
| | - Yury Tatiana Granja-Salcedo
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Centro de Investigación El Nus, San Roque 053030, Colombia
| | | | | | - Thais Ribeiro Brito
- Department of Animal Science, São Paulo State University "Júlio de Mesquita Filho" (UNESP), Jaboticabal 14887-900, Brazil
| | - Eliéder Prates Romanzini
- Department of Animal Science, São Paulo State University "Júlio de Mesquita Filho" (UNESP), Jaboticabal 14887-900, Brazil
| | - Ricardo Andrade Reis
- Department of Animal Science, São Paulo State University "Júlio de Mesquita Filho" (UNESP), Jaboticabal 14887-900, Brazil
| |
Collapse
|
23
|
Cui X, Wang Z, Guo P, Li F, Chang S, Yan T, Zheng H, Hou F. Shift of Feeding Strategies from Grazing to Different Forage Feeds Reshapes the Rumen Microbiota To Improve the Ability of Tibetan Sheep (Ovis aries) To Adapt to the Cold Season. Microbiol Spectr 2023; 11:e0281622. [PMID: 36809032 PMCID: PMC10100778 DOI: 10.1128/spectrum.02816-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 01/22/2023] [Indexed: 02/23/2023] Open
Abstract
The dynamics of ruminant-rumen microbiome symbiosis associated with feeding strategies in the cold season were examined. Twelve pure-grazing adult Tibetan sheep (Ovis aries) (18 months old; body weight, 40 ± 0.23 kg) were transferred from natural pasture to two indoor feedlots and fed either a native-pasture diet (NPF group) or an oat hay diet (OHF group) (n = 6 per treatment), and then the flexibility of rumen microbiomes to adapt to these compositionally different feeding strategies was examined. Principal-coordinate analysis and similarity analysis indicated that the rumen bacterial composition correlated with altered feeding strategies. Microbial diversity was higher in the grazing group than in those fed with native pasture and an oat hay diet (P < 0.05). The dominant microbial phyla were Bacteroidetes and Firmicutes, and the core bacterial taxa comprised mostly (42.49% of shared operational taxonomic units [OTUs]) Ruminococcaceae (408 taxa), Lachnospiraceae (333 taxa), and Prevotellaceae (195 taxa), which were relatively stable across different treatments. Greater relative abundances of Tenericutes at the phylum level, Pseudomonadales at the order level, Mollicutes at the class level, and Pseudomonas at the genus level were observed in a grazing period than in the other two treatments (NPF and OHF) (P < 0.05). In the OHF group, due to the high nutritional quality of the forage, Tibetan sheep can produce high concentrations of short-chain fatty acids (SCFAs) and NH3-N by increasing the relative abundances of key bacteria in the rumen, such as Lentisphaerae, Negativicutes, Selenomonadales, Veillonellaceae, Ruminococcus 2, Quinella, Bacteroidales RF16 group, and Prevotella 1, to aid in nutrients degradation and energy utilization. The levels of beneficial bacteria were increased by the oat hay diet; these microbiotas are likely to help improve and maintain host health and metabolic ability in Tibetan sheep to adapt to cold environments. The rumen fermentation parameters were significantly influenced by feeding strategy in the cold season (P < 0.05). Overall, the results of this study demonstrate the strong effect of feeding strategies on the rumen microbiota of Tibetan sheep, which provided a new idea for the nutrition regulation of Tibetan sheep grazing in the cold season on the Qinghai-Tibetan Plateau. IMPORTANCE During the cold season, like other high-altitude mammals, Tibetan sheep have to adapt their physiological and nutritional strategies, as well as the structure and function of their rumen microbial community, to the seasonal variation of lower food availability and quality. This study focused on the changes and adaptability in the rumen microbiota of Tibetan sheep when they adapted from grazing to a high-efficiency feeding strategy during the cold season by analyzing the rumen microbiota of Tibetan sheep raised under the different management systems, and it shows the linkages among the rumen core and pan-bacteriomes, nutrient utilization, and rumen short-chain fatty acids. The findings from this study suggest that the feeding strategies potentially contribute to variations in the pan-rumen bacteriome, together with the core bacteriome. Fundamental knowledge on the rumen microbiomes and their roles in nutrient utilization furthers our understanding of how rumen microbial adaptation to harsh environments may function in hosts. The facts obtained from the present trial clarified the possible mechanisms of the positive effects of feeding strategy on nutrient utilization and rumen fermentation in harsh environments.
Collapse
Affiliation(s)
- Xiongxiong Cui
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Zhaofeng Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Penghui Guo
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Fuhou Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Shenghua Chang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Tianhai Yan
- Livestock Production Science Branch, Agri-Food and Biosciences Institute, Hillsborough, County Down, United Kingdom
| | - Huiru Zheng
- School of Computing, University of Ulster, Belfast, United Kingdom
| | - Fujiang Hou
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| |
Collapse
|
24
|
Breed and ruminal fraction effects on bacterial and archaeal community composition in sheep. Sci Rep 2023; 13:3336. [PMID: 36849493 PMCID: PMC9971215 DOI: 10.1038/s41598-023-28909-1] [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: 11/22/2021] [Accepted: 01/27/2023] [Indexed: 03/01/2023] Open
Abstract
While the breed of cattle can impact on the composition and structure of microbial communities in the rumen, breed-specific effects on rumen microbial communities have rarely been examined in sheep. In addition, rumen microbial composition can differ between ruminal fractions, and be associated with ruminant feed efficiency and methane emissions. In this study, 16S rRNA amplicon sequencing was used to investigate the effects of breed and ruminal fraction on bacterial and archaeal communities in sheep. Solid, liquid and epithelial rumen samples were obtained from a total of 36 lambs, across 4 different sheep breeds (Cheviot (n = 10), Connemara (n = 6), Lanark (n = 10) and Perth (n = 10)), undergoing detailed measurements of feed efficiency, who were offered a nut based cereal diet ad-libitum supplemented with grass silage. Our results demonstrate that the feed conversion ratio (FCR) was lowest for the Cheviot (most efficient), and highest for the Connemara breed (least efficient). In the solid fraction, bacterial community richness was lowest in the Cheviot breed, while Sharpea azabuensis was most abundant in the Perth breed. Lanark, Cheviot and Perth breeds exhibited a significantly higher abundance of epithelial associated Succiniclasticum compared to the Connemara breed. When comparing ruminal fractions, Campylobacter, Family XIII, Mogibacterium, and Lachnospiraceae UCG-008 were most abundant in the epithelial fraction. Our findings indicate that breed can impact the abundance of specific bacterial taxa in sheep while having little effect on the overall composition of the microbial community. This finding has implications for genetic selection breeding programs aimed at improving feed conversion efficiency of sheep. Furthermore, the variations in the distribution of bacterial species identified between ruminal fractions, notably between solid and epithelial fractions, reveals a rumen fraction bias, which has implications for sheep rumen sampling techniques.
Collapse
|
25
|
Grandi G, Chiappa G, Ullman K, Lindgren PE, Olivieri E, Sassera D, Östlund E, Omazic A, Perissinotto D, Söderlund R. Characterization of the bacterial microbiome of Swedish ticks through 16S rRNA amplicon sequencing of whole ticks and of individual tick organs. Parasit Vectors 2023; 16:39. [PMID: 36717919 PMCID: PMC9885626 DOI: 10.1186/s13071-022-05638-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 12/24/2022] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND The composition of the microbial flora associated with ixodid ticks has been studied in several species, revealing the importance of geographical origin, developmental stage(s) and feeding status of the tick, as well as substantial differences between tissues and organs. Studying the microbiome in the correct context and scale is therefore necessary for understanding the interactions between tick-borne pathogens and other microorganisms as well as other aspects of tick biology. METHODS In the present study the microbial flora of whole Ixodes ricinus, I. persulcatus and I. trianguliceps ticks were analyzed with 16S rRNA amplicon sequencing. Additionally, tick organs (midguts, Malpighian tubules, ovaries, salivary glands) from flat and engorged I. ricinus female ticks were examined with the same methodology. RESULTS The most abundant bacteria belonged to the group of Proteobacteria (Cand. Midichloria mitochondrii and Cand. Lariskella). 16S amplicon sequencing of dissected tick organs provided more information on the diversity of I. ricinus-associated microbial flora, especially when organs were collected from engorged ticks. Bacterial genera significantly associated with tick feeding status as well as genera associated with the presence of tick-borne pathogens were identified. CONCLUSIONS These results contribute to the knowledge of microbial flora associated with ixodid ticks in their northernmost distribution limit in Europe and opens new perspectives for other investigations on the function of these bacteria, including those using other approaches like in vitro cultivation and in vitro models.
Collapse
Affiliation(s)
- Giulio Grandi
- grid.419788.b0000 0001 2166 9211Department of Microbiology, National Veterinary Institute (SVA), 751 89 Uppsala, Sweden ,grid.6341.00000 0000 8578 2742Department of Biomedical Sciences and Veterinary Public Health (BVF), Swedish University of Agricultural Sciences (SLU), Ulls Väg 26, 750 07 Uppsala, Sweden
| | - Giulia Chiappa
- grid.419788.b0000 0001 2166 9211Department of Microbiology, National Veterinary Institute (SVA), 751 89 Uppsala, Sweden
| | - Karin Ullman
- grid.419788.b0000 0001 2166 9211Department of Microbiology, National Veterinary Institute (SVA), 751 89 Uppsala, Sweden
| | - Per-Eric Lindgren
- grid.5640.70000 0001 2162 9922Department of Biomedical and Clinical Sciences, Division of Inflammation and Infection, Linköping University, 581 85 Linköping, Sweden ,grid.413253.2Department of Clinical Microbiology, County Hospital Ryhov, 551 85 Jönköping, Sweden
| | - Emanuela Olivieri
- grid.419583.20000 0004 1757 1598Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Strada Campeggi, 59/61, 27100 Pavia, Italy
| | - Davide Sassera
- grid.8982.b0000 0004 1762 5736Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Emma Östlund
- grid.419788.b0000 0001 2166 9211Department of Microbiology, National Veterinary Institute (SVA), 751 89 Uppsala, Sweden
| | - Anna Omazic
- grid.419788.b0000 0001 2166 9211Department of Chemistry, Environment, and Feed Hygiene, National Veterinary Institute (SVA), 751 89 Uppsala, Sweden
| | - Debora Perissinotto
- grid.419788.b0000 0001 2166 9211Department of Microbiology, National Veterinary Institute (SVA), 751 89 Uppsala, Sweden
| | - Robert Söderlund
- grid.419788.b0000 0001 2166 9211Department of Microbiology, National Veterinary Institute (SVA), 751 89 Uppsala, Sweden
| |
Collapse
|
26
|
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
|
27
|
Smith PE, Kelly AK, Kenny DA, Waters SM. Enteric methane research and mitigation strategies for pastoral-based beef cattle production systems. Front Vet Sci 2022; 9:958340. [PMID: 36619952 PMCID: PMC9817038 DOI: 10.3389/fvets.2022.958340] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 11/09/2022] [Indexed: 12/25/2022] Open
Abstract
Ruminant livestock play a key role in global society through the conversion of lignocellulolytic plant matter into high-quality sources of protein for human consumption. However, as a consequence of the digestive physiology of ruminant species, methane (CH4), which originates as a byproduct of enteric fermentation, is accountable for 40% of global agriculture's carbon footprint and ~6% of global greenhouse gas (GHG) emissions. Therefore, meeting the increasing demand for animal protein associated with a growing global population while reducing the GHG intensity of ruminant production will be a challenge for both the livestock industry and the research community. In recent decades, numerous strategies have been identified as having the potential to reduce the methanogenic output of livestock. Dietary supplementation with antimethanogenic compounds, targeting members of the rumen methanogen community and/or suppressing the availability of methanogenesis substrates (mainly H2 and CO2), may have the potential to reduce the methanogenic output of housed livestock. However, reducing the environmental impact of pasture-based beef cattle may be a challenge, but it can be achieved by enhancing the nutritional quality of grazed forage in an effort to improve animal growth rates and ultimately reduce lifetime emissions. In addition, the genetic selection of low-CH4-emitting and/or faster-growing animals will likely benefit all beef cattle production systems by reducing the methanogenic potential of future generations of livestock. Similarly, the development of other mitigation technologies requiring minimal intervention and labor for their application, such as anti-methanogen vaccines, would likely appeal to livestock producers, with high uptake among farmers if proven effective. Therefore, the objective of this review is to give a detailed overview of the CH4 mitigation solutions, both currently available and under development, for temperate pasture-based beef cattle production systems. A description of ruminal methanogenesis and the technologies used to estimate enteric emissions at pastures are also presented.
Collapse
Affiliation(s)
- Paul E. Smith
- Teagasc, Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Dunsany, Ireland,*Correspondence: Paul E. Smith
| | - Alan K. Kelly
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - David A. Kenny
- Teagasc, Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Dunsany, Ireland
| | - Sinéad M. Waters
- Teagasc, Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Dunsany, Ireland
| |
Collapse
|
28
|
Liu Z, Wang K, Nan X, Yang L, Wang Y, Zhang F, Cai M, Zhao Y, Xiong B. Effects of combined addition of 3-nitrooxypropanol and vitamin B12 on methane and propionate production in dairy cows by in vitro-simulated fermentation. J Dairy Sci 2022; 106:219-232. [DOI: 10.3168/jds.2022-22207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/13/2022] [Indexed: 11/09/2022]
|
29
|
Genomic insights into the physiology of Quinella, an iconic uncultured rumen bacterium. Nat Commun 2022; 13:6240. [PMID: 36266280 PMCID: PMC9585023 DOI: 10.1038/s41467-022-34013-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 10/11/2022] [Indexed: 12/25/2022] Open
Abstract
Quinella is a genus of iconic rumen bacteria first reported in 1913. There are no cultures of these bacteria, and information on their physiology is scarce and contradictory. Increased abundance of Quinella was previously found in the rumens of some sheep that emit low amounts of methane (CH4) relative to their feed intake, but whether Quinella contributes to low CH4 emissions is not known. Here, we concentrate Quinella cells from sheep rumen contents, extract and sequence DNA, and reconstruct Quinella genomes that are >90% complete with as little as 0.20% contamination. Bioinformatic analyses of the encoded proteins indicate that lactate and propionate formation are major fermentation pathways. The presence of a gene encoding a potential uptake hydrogenase suggests that Quinella might be able to use free hydrogen (H2). None of the inferred metabolic pathways is predicted to produce H2, a major precursor of CH4, which is consistent with the lower CH4 emissions from those sheep with high abundances of this bacterium.
Collapse
|
30
|
Liu X, Gao J, Liu S, Cheng Y, Hao L, Liu S, Zhu W. The uniqueness and superiority of energy utilization in yaks compared with cattle in the highlands: A review. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2022; 12:138-144. [PMID: 36683881 PMCID: PMC9841238 DOI: 10.1016/j.aninu.2022.09.011] [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: 10/08/2021] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 11/05/2022]
Abstract
Yaks living on the Qinghai-Tibetan Plateau for a long time have evolved a series of mechanisms to adapt to the unique geographical environment and climate characteristics of the plateau. Compared with other ruminants, yaks have higher energy utilization and metabolic efficiency. This paper presents possible mechanisms responsible for the efficient energy utilization, absorption and metabolism resulting from the unique evolutionary process of yaks. It is hoped that the information discussed in this review will give a better insight into the uniqueness and superiority of yaks in regards to energy metabolism and utilization compared with cattle and open new avenues for the targeted regulation of energy utilization pathways of other ruminants.
Collapse
Affiliation(s)
- Xiaojing Liu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Jian Gao
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Suozhu Liu
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, China
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China,Corresponding authors.
| | - Lizhuang Hao
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Plateau Yak Research Center, Qinghai Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining 810016, China,Corresponding authors.
| | - Shujie Liu
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Plateau Yak Research Center, Qinghai Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining 810016, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|
31
|
Bačėninaitė D, Džermeikaitė K, Antanaitis R. Global Warming and Dairy Cattle: How to Control and Reduce Methane Emission. Animals (Basel) 2022; 12:2687. [PMID: 36230428 PMCID: PMC9559257 DOI: 10.3390/ani12192687] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/19/2022] [Accepted: 10/03/2022] [Indexed: 11/27/2022] Open
Abstract
Agriculture produces greenhouse gases. Methane is a result of manure degradation and microbial fermentation in the rumen. Reduced CH4 emissions will slow climate change and reduce greenhouse gas concentrations. This review compiled studies to evaluate the best ways to decrease methane emissions. Longer rumination times reduce methane emissions and milk methane. Other studies have not found this. Increasing propionate and reducing acetate and butyrate in the rumen can reduce hydrogen equivalents that would otherwise be transferred to methanogenesis. Diet can reduce methane emissions. Grain lowers rumen pH, increases propionate production, and decreases CH4 yield. Methane generation per unit of energy-corrected milk yield reduces with a higher-energy diet. Bioactive bromoform discovered in the red seaweed Asparagopsis taxiformis reduces livestock intestinal methane output by inhibiting its production. Essential oils, tannins, saponins, and flavonoids are anti-methanogenic. While it is true that plant extracts can assist in reducing methane emissions, it is crucial to remember to source and produce plants in a sustainable manner. Minimal lipid supplementation can reduce methane output by 20%, increasing energy density and animal productivity. Selecting low- CH4 cows may lower GHG emissions. These findings can lead to additional research to completely understand the impacts of methanogenesis suppression on rumen fermentation and post-absorptive metabolism, which could improve animal productivity and efficiency.
Collapse
Affiliation(s)
- Dovilė Bačėninaitė
- Large Animal Clinic, Veterinary Academy, Lithuanian University of Health Sciences, LT-47181 Kaunas, Lithuania
| | | | | |
Collapse
|
32
|
Hickey SM, Bain WE, Bilton TP, Greer GJ, Elmes S, Bryson B, Pinares-Patiño CS, Wing J, Jonker A, Young EA, Knowler K, Pickering NK, Dodds KG, Janssen PH, McEwan JC, Rowe SJ. Impact of breeding for reduced methane emissions in New Zealand sheep on maternal and health traits. Front Genet 2022; 13:910413. [PMID: 36246641 PMCID: PMC9561099 DOI: 10.3389/fgene.2022.910413] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/21/2022] [Indexed: 11/13/2022] Open
Abstract
Enteric methane emissions from ruminants account for ∼35% of New Zealand’s greenhouse gas emissions. This poses a significant threat to the pastoral sector. Breeding has been shown to successfully lower methane emissions, and genomic prediction for lowered methane emissions has been introduced at the national level. The long-term genetic impacts of including low methane in ruminant breeding programs, however, are unknown. The success of the New Zealand sheep industry is currently heavily reliant on the prolificacy, fecundity and survival of adult ewes. The objective of this study was to determine genetic and phenotypic correlations between adult maternal ewe traits (live weight, body condition score, number of lambs born, litter survival to weaning, pregnancy scanning and fleece weight), faecal and Nematodirus egg counts and measures of methane in respiration chambers. More than 9,000 records for methane from over 2,200 sheep measured in respiration chambers were collected over 10 years. Sheep were fed on a restricted diet calculated as approximately twice the maintenance. Methane measures were converted to absolute daily emissions of methane measured in g per day (CH4/day). Two measures of methane yield were recorded: the ratio of CH4 to dry matter intake (g CH4/kg DMI; CH4/DMI) and the ratio of CH4 to total gas emissions (CH4/(CH4 + CO2)). Ewes were maintained in the flocks for at least two parities. Non-methane trait data from over 8,000 female relatives were collated to estimate genetic correlations. Results suggest that breeding for low CH4/DMI is unlikely to negatively affect faecal egg counts, adult ewe fertility and litter survival traits, with no evidence for significant genetic correlations. Fleece weight was unfavourably (favourably) correlated with CH4/DMI (rg = −0.21 ± 0.09). Live weight (rg = 0.3 ± 0.1) and body condition score (rg = 0.2 ± 0.1) were positively correlated with methane yield. Comparing the two estimates of methane yield, CH4/DMI had lower heritability and repeatability. However, correlations of both measures with adult ewe traits were similar. This suggests that breeding is a suitable mitigation strategy for lowering methane yield, but wool, live weight and fat deposition traits may be affected over time and should be monitored.
Collapse
Affiliation(s)
| | - Wendy E. Bain
- Invermay Agricultural Centre, AgResearch Ltd., Mosgiel, New Zealand
| | | | - Gordon J. Greer
- Invermay Agricultural Centre, AgResearch Ltd., Mosgiel, New Zealand
| | - Sara Elmes
- Invermay Agricultural Centre, AgResearch Ltd., Mosgiel, New Zealand
| | - Brooke Bryson
- Invermay Agricultural Centre, AgResearch Ltd., Mosgiel, New Zealand
| | | | - Janine Wing
- Invermay Agricultural Centre, AgResearch Ltd., Mosgiel, New Zealand
| | - Arjan Jonker
- Grasslands Research Centre, AgResearch Ltd., Palmerston North, New Zealand
| | - Emily A. Young
- Invermay Agricultural Centre, AgResearch Ltd., Mosgiel, New Zealand
| | - Kevin Knowler
- Invermay Agricultural Centre, AgResearch Ltd., Mosgiel, New Zealand
| | | | - Ken G. Dodds
- Invermay Agricultural Centre, AgResearch Ltd., Mosgiel, New Zealand
| | - Peter H. Janssen
- Grasslands Research Centre, AgResearch Ltd., Palmerston North, New Zealand
| | - John C. McEwan
- Invermay Agricultural Centre, AgResearch Ltd., Mosgiel, New Zealand
| | - Suzanne J. Rowe
- Invermay Agricultural Centre, AgResearch Ltd., Mosgiel, New Zealand
- *Correspondence: Suzanne J. Rowe,
| |
Collapse
|
33
|
Luo T, Li Y, Zhang W, Liu J, Shi H. Rumen and fecal microbiota profiles associated with immunity of young and adult goats. Front Immunol 2022; 13:978402. [PMID: 36177023 PMCID: PMC9513485 DOI: 10.3389/fimmu.2022.978402] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
Low immunity at birth increases risk of disease of young livestock, such as goat kids. Microbiomes change as animals mature, and a healthy microbiome is related to decreased risk of disease. The relationship between microbiota profiles and immunity at different developmental stages remains unclear. Young (female, n = 12, 30 d) and adult (female, n = 12, 2 yrs. old) Saanen dairy goats were used to investigate changes in rumen microbiomes, fecal microbiomes, and their correlations to circulating immune factors. Serum IgG (P = 0.02) and IgM (P < 0.01) were higher at 2 years than 30 d of age, but there were no differences in IgA (P = 0.34), IL-2 (P = 0.05), IL-4 (P = 0.37) and IL-6 (P = 0.73) between ages. Amplicon sequencing analysis revealed young goats had a higher diversity of bacterial communities in rumen and lower diversity in feces compared with adult goats. Ten genera in rumen and 14 genera in feces were positively correlated with serum IgM concentration across both ages. Olsenella, Methanosphaera, Quinella, Candidatus_Saccharimonas, and Methanobrevibacter in rumen and Ruminobacter, Treponema, Rikenelaceae_ RC9_ gut_ Group in feces were positively correlated with the concentration of IgG. The correlation analysis using weighted gene co-expression network analysis showed the MEblue module was positively associated with the IgG and IgM. These data provide novel insight into the association between rumen-feces microbiota and immune response. Further experiments are needed to investigate whether inoculating young livestock with immune-related bacteria identified can improve the immune status. Our data suggest a possible strategy to improve the immunity of the kids by alterative microbiota profiles.
Collapse
Affiliation(s)
- Tao Luo
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yongtao Li
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Wenying Zhang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Jianxin Liu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Hengbo Shi
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, China
- *Correspondence: Hengbo Shi,
| |
Collapse
|
34
|
Costa-Roura S, Villalba D, Balcells J, De la Fuente G. First Steps into Ruminal Microbiota Robustness. Animals (Basel) 2022; 12:2366. [PMID: 36139226 PMCID: PMC9495070 DOI: 10.3390/ani12182366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/01/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Despite its central role in ruminant nutrition, little is known about ruminal microbiota robustness, which is understood as the ability of the microbiota to cope with disturbances. The aim of the present review is to offer a comprehensive description of microbial robustness, as well as its potential drivers, with special focus on ruminal microbiota. First, we provide a briefing on the current knowledge about ruminal microbiota. Second, we define the concept of disturbance (any discrete event that disrupts the structure of a community and changes either the resource availability or the physical environment). Third, we discuss community resistance (the ability to remain unchanged in the face of a disturbance), resilience (the ability to return to the initial structure following a disturbance) and functional redundancy (the ability to maintain or recover initial function despite compositional changes), all of which are considered to be key properties of robust microbial communities. Then, we provide an overview of the currently available methodologies to assess community robustness, as well as its drivers (microbial diversity and network complexity) and its potential modulation through diet. Finally, we propose future lines of research on ruminal microbiota robustness.
Collapse
|
35
|
Liu H, Li Z, Pei C, Degen A, Hao L, Cao X, Liu H, Zhou J, Long R. A comparison between yaks and Qaidam cattle in in vitro rumen fermentation, methane emission, and bacterial community composition with poor quality substrate. Anim Feed Sci Technol 2022. [DOI: 10.1016/j.anifeedsci.2022.115395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
36
|
Responses of Fermentation Characteristics and Microbial Communities to Vitamin B12 Supplementation in In Vitro Ruminal Cultures. FERMENTATION 2022. [DOI: 10.3390/fermentation8080406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Vitamin B12, an important cofactor involved in propionate formation, is synthesized exclusively by bacteria and archaebacteria. Humans need to intake vitamin B12 through food, and dairy products are generally the best source of vitamin B12. In the present study, the effects of vitamin B12 supplementation in diets on in vitro ruminal fermentation characteristics and microbial communities were investigated to provide a reference for increasing the vitamin B12 content in milk by dietary supplementation. A completely randomized design was carried out using the in vitro rumen culture technique, and 5 vitamin B12 dose levels (0, 0.5, 1.0, 2.0, and 4 mg/g of dry matter) were used. The results showed that vitamin B12 supplementation in diets decreased acetate: propionate ratio and butyrate concentration. The change in the acetate: propionate ratio can be attributed to the increased relative abundances of the Proteobacteria phylum and the Negativicutes class, both of which are involved in propionate metabolism. The decrease in butyrate concentration can likely be attributed to a reduction in relative abundance of species belonging to the Clostridia class, which are known as the predominant butyrate producers in the mammalian intestine. In addition, vitamin B12 supplementation in diets reduced the CH4 production by altering the species composition of the archaeal community. In conclusion, dietary supplementation of vitamin B12 resulted in rumen perturbation. In vivo studies should be conducted cautiously when evaluating the effects of vitamin B12 supplementation on the synthesis and absorption of it, as well as its content in milk.
Collapse
|
37
|
Response of Phytogenic Additives on Enteric Methane Emissions and Animal Performance of Nellore Bulls Raised in Grassland. SUSTAINABILITY 2022. [DOI: 10.3390/su14159395] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The objective of this study was to evaluate the intake and digestibility of nutrients, emission of enteric CH4, and productive performance of Nellore bulls grazing Urochloa brizantha cv. Marandu palisade grass pastures during the rainy season, receiving an energy supplement or mineral supplement, with or without the inclusion of phytogenic additives. Forty-eight Nellore bulls were treated with: (1) energy supplement without the inclusion of phytogenic additives; (2) energy supplement with the inclusion of phytogenic additives; (3) mineral supplement without the inclusion of phytogenic additives; and (4) mineral supplement with the inclusion of phytogenic additives. Consumption of total dry matter (DM), crude protein (CP), apNDF, and energy; digestibility of DM, CP, and energy; average daily gain; stocking rate; and gain per area were higher in animals consuming energy supplements than those consuming mineral supplements. Digestibility of DM, NDF, and energy levels were lower in animals that consumed phytogenic additives. Compared with mineral supplements, the supply of energy supplements provides higher nutrient intake, increases enteric CH4 emission, and improves nutrient digestibility, providing a greater productive performance. The inclusion of phytogenic additives negatively affected nutrient intake and digestibility, did not reduce enteric CH4 emission, and influenced productive performance.
Collapse
|
38
|
Ross EM, Hayes BJ. Metagenomic Predictions: A Review 10 years on. Front Genet 2022; 13:865765. [PMID: 35938022 PMCID: PMC9348756 DOI: 10.3389/fgene.2022.865765] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
Metagenomic predictions use variation in the metagenome (microbiome profile) to predict the unknown phenotype of the associated host. Metagenomic predictions were first developed 10 years ago, where they were used to predict which cattle would produce high or low levels of enteric methane. Since then, the approach has been applied to several traits and species including residual feed intake in cattle, and carcass traits, body mass index and disease state in pigs. Additionally, the method has been extended to include predictions based on other multi-dimensional data such as the metabolome, as well to combine genomic and metagenomic information. While there is still substantial optimisation required, the use of metagenomic predictions is expanding as DNA sequencing costs continue to fall and shows great promise particularly for traits heavily influenced by the microbiome such as feed efficiency and methane emissions.
Collapse
|
39
|
Sun X, Cheng L, Jonker A, Munidasa S, Pacheco D. A Review: Plant Carbohydrate Types—The Potential Impact on Ruminant Methane Emissions. Front Vet Sci 2022; 9:880115. [PMID: 35782553 PMCID: PMC9249355 DOI: 10.3389/fvets.2022.880115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/16/2022] [Indexed: 11/25/2022] Open
Abstract
Carbohydrates are the major component of most ruminant feeds. The digestion of carbohydrates in the rumen provides energy to the ruminants but also contributes to enteric methane (CH4) emissions. Fresh forage is the main feed for grazing ruminants in temperate regions. Therefore, this review explored how dietary carbohydrate type and digestion affect ruminant CH4 emissions, with a focus on fresh forage grown in temperate regions. Carbohydrates include monosaccharides, disaccharides, oligosaccharides, and polysaccharides. Rhamnose is the only monosaccharide that results in low CH4 emissions. However, rhamnose is a minor component in most plants. Among polysaccharides, pectic polysaccharides lead to greater CH4 production due to the conversion of methyl groups to methanol and finally to CH4. Thus, the degree of methyl esterification of pectic polysaccharides is an important structural characteristic to better understand CH4 emissions. Apart from pectic polysaccharides, the chemical structure of other polysaccharides per se does not seem to affect CH4 formation. However, rumen physiological parameters and fermentation types resulting from digestion in the rumen of polysaccharides differing in the rate and extent of degradation do affect CH4 emissions. For example, low rumen pH resulting from the rapid degradation of readily fermentable carbohydrates decreases and inhibits the activities of methanogens and further reduces CH4 emissions. When a large quantity of starch is supplemented or the rate of starch degradation is low, some starch may escape from the rumen and the escaped starch will not yield CH4. Similar bypass from rumen digestion applies to other polysaccharides and needs to be quantified to facilitate the interpretation of animal experiments in which CH4 emissions are measured. Rumen bypass carbohydrates may occur in ruminants fed fresh forage, especially when the passage rate is high, which could be a result of high feed intake or high water intake. The type of carbohydrates affects the concentration of dissolved hydrogen, which consequently alters fermentation pathways and finally results in differences in CH4 emissions. We recommend that the degree of methyl esterification of pectic polysaccharides is needed for pectin-rich forage. The fermentation type of carbohydrates and rumen bypass carbohydrates should be determined in the assessment of mitigation potential.
Collapse
Affiliation(s)
- Xuezhao Sun
- The Innovation Centre of Ruminant Precision Nutrition and Smart and Ecological Farming, Jilin Agricultural Science and Technology University, Jilin, China
- Jilin Inter-Regional Cooperation Centre for the Scientific and Technological Innovation of Ruminant Precision Nutrition and Smart and Ecological Farming, Jilin, China
- Grasslands Research Centre, AgResearch Limited, Palmerston North, New Zealand
- *Correspondence: Xuezhao Sun
| | - Long Cheng
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Arjan Jonker
- Grasslands Research Centre, AgResearch Limited, Palmerston North, New Zealand
| | - Sineka Munidasa
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
| | - David Pacheco
- Grasslands Research Centre, AgResearch Limited, Palmerston North, New Zealand
- David Pacheco
| |
Collapse
|
40
|
Budel JCC, Hess MK, Bilton TP, Henry H, Dodds KG, Janssen PH, McEwan JC, Rowe SJ. Low-cost sample preservation methods for high-throughput processing of rumen microbiomes. Anim Microbiome 2022; 4:39. [PMID: 35668514 PMCID: PMC9171989 DOI: 10.1186/s42523-022-00190-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 05/30/2022] [Indexed: 11/10/2022] Open
Abstract
Background The use of rumen microbial community (RMC) profiles to predict methane emissions has driven interest in ruminal DNA preservation and extraction protocols that can be processed cheaply while also maintaining or improving DNA quality for RMC profiling. Our standard approach for preserving rumen samples, as defined in the Global Rumen Census (GRC), requires time-consuming pre-processing steps of freeze drying and grinding prior to international transportation and DNA extraction. This impedes researchers unable to access sufficient funding or infrastructure. To circumvent these pre-processing steps, we investigated three methods of preserving rumen samples for subsequent DNA extraction, based on existing lysis buffers Tris-NaCl-EDTA-SDS (TNx2) and guanidine hydrochloride (GHx2), or 100% ethanol. Results Rumen samples were collected via stomach intubation from 151 sheep at two time-points 2 weeks apart. Each sample was separated into four subsamples and preserved using the three preservation methods and the GRC method (n = 4 × 302). DNA was extracted and sequenced using Restriction Enzyme-Reduced Representation Sequencing to generate RMC profiles. Differences in DNA yield, quality and integrity, and sequencing metrics were observed across the methods (p < 0.0001). Ethanol exhibited poorer quality DNA (A260/A230 < 2) and more failed samples compared to the other methods. Samples preserved using the GRC method had smaller relative abundances in gram-negative genera Anaerovibrio, Bacteroides, Prevotella, Selenomonas, and Succiniclasticum, but larger relative abundances in the majority of 56 additional genera compared to TNx2 and GHx2. However, log10 relative abundances across all genera and time-points for TNx2 and GHx2 were on average consistent (R2 > 0.99) but slightly more variable compared to the GRC method. Relative abundances were moderately to highly correlated (0.68 ± 0.13) between methods for samples collected within a time-point, which was greater than the average correlation (0.17 ± 0.11) between time-points within a preservation method. Conclusions The two modified lysis buffers solutions (TNx2 and GHx2) proposed in this study were shown to be viable alternatives to the GRC method for RMC profiling in sheep. Use of these preservative solutions reduces cost and improves throughput associated with processing and sequencing ruminal samples. This development could significantly advance implementation of RMC profiles as a tool for breeding ruminant livestock. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-022-00190-z.
Collapse
Affiliation(s)
- Juliana C C Budel
- Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand.,Graduate Program in Animal Science, Federal University of Pará, UFPA, Castanhal, 68740-970, Brazil
| | - Melanie K Hess
- Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Timothy P Bilton
- Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand.
| | - Hannah Henry
- Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Ken G Dodds
- Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Peter H Janssen
- Grasslands Research Centre, AgResearch Ltd., Private Bag 11008, Palmerston North, 4410, New Zealand
| | - John C McEwan
- Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Suzanne J Rowe
- Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
| |
Collapse
|
41
|
Dietary Cysteamine Supplementation Remarkably Increased Feed Efficiency and Shifted Rumen Fermentation toward Glucogenic Propionate Production via Enrichment of Prevotella in Feedlot Lambs. Microorganisms 2022; 10:microorganisms10061105. [PMID: 35744623 PMCID: PMC9227252 DOI: 10.3390/microorganisms10061105] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/24/2022] [Accepted: 05/24/2022] [Indexed: 12/23/2022] Open
Abstract
Cysteamine (CS) is an essential nutritional regulator that improves the productive performance of animals by regulating somatotropic hormone secretion. To investigate the fattening potential and effects of CS on rumen microbial fermentation, 48 feedlot lambs were randomly assigned to four groups and fed diets supplemented with different CS concentrations (0, 20, 40, and 60 mg/kg BW). An increase in dietary CS concentrations linearly increased the average daily gain (ADG) and dry matter intake (p < 0.05) but decreased the feed-to-gain ratio (p < 0.01). For the serum hormone, increasing the dietary CS concentration linearly decreased somatostatin and leptin concentration (p < 0.01) but linearly increased the concentration of growth hormone and insulin-like growth factor 1 (p < 0.01). Regarding rumen fermentation, ruminal pH, ammonia-N, and butyrate content did not differ among the four treatments, although dietary CS supplementation linearly increased microbial protein and propionate and decreased the amount of acetate (p < 0.05). Furthermore, an increase in dietary CS concentrations quadratically decreased the estimated methane production and methane production per kg ADG (p < 0.05). High-throughput sequencing revealed that increased dietary CS concentrations quadratically increased Prevotella (p < 0.05), and Prevotella and norank_f__norank_o__Clostridia_UCG-014 were positively correlated with growth performance and rumen fermentation in a Spearman correlation analysis (r > 0.55, p < 0.05). Overall, a CS concentration higher than 20 mg/kg BW produced growth-promoting effects by inhibiting somatostatin concentrations and shifting the rumen toward glucogenic propionate fermentation by enriching Prevotella. In addition, Prevotella and norank_f__norank_o__Clostridia_UCG-014 were positively correlated with growth performance in lambs.
Collapse
|
42
|
Smith PE, Kelly AK, Kenny DA, Waters SM. Differences in the Composition of the Rumen Microbiota of Finishing Beef Cattle Divergently Ranked for Residual Methane Emissions. Front Microbiol 2022; 13:855565. [PMID: 35572638 PMCID: PMC9099143 DOI: 10.3389/fmicb.2022.855565] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 03/10/2022] [Indexed: 11/13/2022] Open
Abstract
With the advent of high throughput technology, it is now feasible to study the complex relationship of the rumen microbiota with methanogenesis in large populations of ruminant livestock divergently ranked for enteric emissions. Recently, the residual methane emissions (RME) concept has been identified as the optimal phenotype for assessing the methanogenic potential of ruminant livestock due to the trait's independence from animal productivity but strong correlation with daily methane emissions. However, there is currently a dearth of data available on the bacterial and archaeal microbial communities residing in the rumens of animals divergently ranked for RME. Therefore, the objective of this study was to investigate the relationship between the rumen microbiota and RME in a population of finishing beef cattle. Methane emissions were estimated from individual animals using the GreenFeed Emissions Monitoring system for 21 days over a mean feed intake measurement period of 91 days. Residual methane emissions were calculated for 282 crossbred finishing beef cattle, following which a ∼30% difference in all expressions of methane emissions was observed between high and low RME ranked animals. Rumen fluid samples were successfully obtained from 268 animals during the final week of the methane measurement period using a trans-oesophageal sampling device. Rumen microbial DNA was extracted and subjected to 16S rRNA amplicon sequencing. Animals ranked as low RME had the highest relative abundances (P < 0.05) of lactic-acid-producing bacteria (Intestinibaculum, Sharpea, and Olsenella) and Selenomonas, and the lowest (P < 0.05) proportions of Pseudobutyrivibrio, Butyrivibrio, and Mogibacterium. Within the rumen methanogen community, an increased abundance (P < 0.05) of the genus Methanosphaera and Methanobrevibacter RO clade was observed in low RME animals. The relative abundances of both Intestinibaculum and Olsenella were negatively correlated (P < 0.05) with RME and positively correlated with ruminal propionate. A similar relationship was observed for the abundance of Methanosphaera and the Methanobrevibacter RO clade. Findings from this study highlight the ruminal abundance of bacterial genera associated with the synthesis of propionate via the acrylate pathway, as well as the methanogens Methanosphaera and members of the Methanobrevibacter RO clade as potential microbial biomarkers of the methanogenic potential of beef cattle.
Collapse
Affiliation(s)
- Paul E. Smith
- Teagasc, Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Meath, Ireland
- UCD School of Agricultural and Food Science, University College Dublin, Dublin, Ireland
| | - Alan K. Kelly
- UCD School of Agricultural and Food Science, University College Dublin, Dublin, Ireland
| | - David A. Kenny
- Teagasc, Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Meath, Ireland
| | - Sinéad M. Waters
- Teagasc, Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Meath, Ireland
| |
Collapse
|
43
|
Dai X, Chen L, Liu M, Liu Y, Jiang S, Xu T, Wang A, Yang S, Wei W. Effect of 6-Methoxybenzoxazolinone on the Cecal Microbiota of Adult Male Brandt's Vole. Front Microbiol 2022; 13:847073. [PMID: 35422782 PMCID: PMC9002351 DOI: 10.3389/fmicb.2022.847073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 02/28/2022] [Indexed: 11/28/2022] Open
Abstract
The anti-microbial effects of plant secondary metabolite (PSM) 6-methoxybenzoxazolinone (6-MBOA) have been overlooked. This study investigated the effect of 6-MBOA on the cecal microbiota of adult male Brandt’s voles (Lasiopodomys brandtii), to evaluate its effect on the physiology of mammalian herbivores. The growth of voles was inhibited by 6-MBOA. A low dose of 6-MBOA enhanced the observed species, as well as the Chao1 and abundance-based coverage estimator (ACE) indices and introduced changes in the structure of cecal microbiota. The abundance of the phylum Tenericutes, classes Mollicutes and Negativicutes, order Selenomonadales, families Ruminococcaceae and Veillonellaceae, genera Quinella, Caproiciproducens, Anaerofilum, Harryflintia, and unidentified Spirochaetaceae in the cecal microbiota was enhanced upon administration of a low dose of 6-MBOA, which also inhibited glucose metabolism and protein digestion and absorption in the cecal microbiota. 6-MBOA treatment also stimulated butyrate production and dose-dependently enhanced the metabolism of xenobiotics in the cecal microbiome. Our findings indicate that 6-MBOA can affect Brandt’s voles by inducing changes in the abundance of cecal bacteria, thereby, altering the contents of short-chain fatty acids (SCFAs) and pathway intermediates, ultimately inhibiting the growth of voles. Our research suggests that 6-MBOA could potentially act as a digestion-inhibiting PSM in the interaction between mammalian herbivores and plants.
Collapse
Affiliation(s)
- Xin Dai
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Lin Chen
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Mengyue Liu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Ying Liu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Siqi Jiang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Tingting Xu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Aiqin Wang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Shengmei Yang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Wanhong Wei
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| |
Collapse
|
44
|
Hummel GL, Austin K, Cunningham-Hollinger HC. Comparing the maternal-fetal microbiome of humans and cattle: a translational assessment of the reproductive, placental, and fetal gut microbiomes. Biol Reprod 2022; 107:371-381. [PMID: 35412586 DOI: 10.1093/biolre/ioac067] [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: 11/12/2021] [Revised: 03/23/2022] [Accepted: 04/28/2022] [Indexed: 11/13/2022] Open
Abstract
An analysis of sites within the maternal reproductive microbiome that potentially contribute to fetal gut microbial colonization, with a special focus on the comparison between humans and cattle.
Collapse
Affiliation(s)
- Gwendolynn L Hummel
- Department of Animal and Veterinary Science, University of Wyoming, Laramie, WY, 82071
| | - Kathleen Austin
- Department of Animal and Veterinary Science, University of Wyoming, Laramie, WY, 82071
| | | |
Collapse
|
45
|
Martínez-Álvaro M, Auffret MD, Duthie CA, Dewhurst RJ, Cleveland MA, Watson M, Roehe R. Bovine host genome acts on rumen microbiome function linked to methane emissions. Commun Biol 2022; 5:350. [PMID: 35414107 PMCID: PMC9005536 DOI: 10.1038/s42003-022-03293-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 03/17/2022] [Indexed: 12/28/2022] Open
Abstract
Our study provides substantial evidence that the host genome affects the comprehensive function of the microbiome in the rumen of bovines. Of 1,107/225/1,141 rumen microbial genera/metagenome assembled uncultured genomes (RUGs)/genes identified from whole metagenomics sequencing, 194/14/337 had significant host genomic effects (heritabilities ranging from 0.13 to 0.61), revealing that substantial variation of the microbiome is under host genomic control. We found 29/22/115 microbial genera/RUGs/genes host-genomically correlated (|0.59| to |0.93|) with emissions of the potent greenhouse gas methane (CH4), highlighting the strength of a common host genomic control of specific microbial processes and CH4. Only one of these microbial genes was directly involved in methanogenesis (cofG), whereas others were involved in providing substrates for archaea (e.g. bcd and pccB), important microbial interspecies communication mechanisms (ABC.PE.P), host-microbiome interaction (TSTA3) and genetic information processes (RP-L35). In our population, selection based on abundances of the 30 most informative microbial genes provided a mitigation potential of 17% of mean CH4 emissions per generation, which is higher than for selection based on measured CH4 using respiration chambers (13%), indicating the high potential of microbiome-driven breeding to cumulatively reduce CH4 emissions and mitigate climate change.
Collapse
Affiliation(s)
| | | | | | | | | | - Mick Watson
- The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | | |
Collapse
|
46
|
Min BR, Lee S, Jung H, Miller DN, Chen R. Enteric Methane Emissions and Animal Performance in Dairy and Beef Cattle Production: Strategies, Opportunities, and Impact of Reducing Emissions. Animals (Basel) 2022; 12:948. [PMID: 35454195 PMCID: PMC9030782 DOI: 10.3390/ani12080948] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/27/2022] [Accepted: 03/29/2022] [Indexed: 01/14/2023] Open
Abstract
Enteric methane (CH4) emissions produced by microbial fermentation in the rumen resulting in the emission of greenhouse gases (GHG) into the atmosphere. The GHG emissions reduction from the livestock industry can be attained by increasing production efficiency and improving feed efficiency, by lowering the emission intensity of production, or by combining the two. In this work, information was compiled from peer-reviewed studies to analyze CH4 emissions calculated per unit of milk production, energy-corrected milk (ECM), average daily gain (ADG), dry matter intake (DMI), and gross energy intake (GEI), and related emissions to rumen fermentation profiles (volatile fatty acids [VFA], hydrogen [H2]) and microflora activities in the rumen of beef and dairy cattle. For dairy cattle, there was a positive correlation (p < 0.001) between CH4 emissions and DMI (R2 = 0.44), milk production (R2 = 0.37; p < 0.001), ECM (R2 = 0.46), GEI (R2 = 0.50), and acetate/propionate (A/P) ratio (R2 = 0.45). For beef cattle, CH4 emissions were positively correlated (p < 0.05−0.001) with DMI (R2 = 0.37) and GEI (R2 = 0.74). Additionally, the ADG (R2 = 0.19; p < 0.01) and A/P ratio (R2 = 0.15; p < 0.05) were significantly associated with CH4 emission in beef steers. This information may lead to cost-effective methods to reduce enteric CH4 production from cattle. We conclude that enteric CH4 emissions per unit of ECM, GEI, and ADG, as well as rumen fermentation profiles, show great potential for estimating enteric CH4 emissions.
Collapse
Affiliation(s)
- Byeng-Ryel Min
- College of Agriculture, Environment and Nutrition Sciences, Tuskegee University, Tuskegee, AL 36088, USA;
| | - Seul Lee
- Animal Nutrition & Physiology Division, National Institute of Animal Science, Rural Development Administration, Wanju-gun 55365, Jeollabuk-do, Korea; (S.L.); (H.J.)
| | - Hyunjung Jung
- Animal Nutrition & Physiology Division, National Institute of Animal Science, Rural Development Administration, Wanju-gun 55365, Jeollabuk-do, Korea; (S.L.); (H.J.)
| | - Daniel N. Miller
- Agroecosystem Management Research Unit, USDA/ARS, 354 Filly Hall, Lincoln, NE 68583, USA;
| | - Rui Chen
- College of Agriculture, Environment and Nutrition Sciences, Tuskegee University, Tuskegee, AL 36088, USA;
| |
Collapse
|
47
|
Miura H, Takeda M, Yamaguchi M, Ohtani Y, Endo G, Masuda Y, Ito K, Nagura Y, Iwashita K, Mitani T, Suzuki Y, Kobayashi Y, Koike S. Application of MinION Amplicon Sequencing to Buccal Swab Samples for Improving Resolution and Throughput of Rumen Microbiota Analysis. Front Microbiol 2022; 13:783058. [PMID: 35401463 PMCID: PMC8989143 DOI: 10.3389/fmicb.2022.783058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 03/02/2022] [Indexed: 11/17/2022] Open
Abstract
The Illumina MiSeq platform has been widely used as a standard method for studying the rumen microbiota. However, the low resolution of taxonomic identification is the only disadvantage of MiSeq amplicon sequencing, as it targets a part of the 16S rRNA gene. In the present study, we performed three experiments to establish a high-resolution and high-throughput rumen microbial profiling approach using a combination of MinION platform and buccal swab sample, which is a proxy for rumen contents. In experiment 1, rumen contents and buccal swab samples were collected simultaneously from cannulated cattle (n = 6) and used for microbiota analysis using three different analytical workflows: amplicon sequencing of the V3–V4 region of the 16S rRNA gene using MiSeq and amplicon sequencing of near full-length 16S rRNA gene using MinION or PacBio Sequel II. All reads derived from the MinION and PacBio platforms were classified at the species-level. In experiment 2, rumen fluid samples were collected from beef cattle (n = 28) and used for 16S rRNA gene amplicon sequencing using the MinION platform to evaluate this sequencing platform for rumen microbiota analysis. We confirmed that the MinION platform allowed species-level taxa assignment for the predominant bacterial groups, which were previously identified at the family- and genus-level using the MiSeq platform. In experiment 3, buccal swab samples were collected from beef cattle (n = 30) and used for 16S rRNA gene amplicon sequencing using the MinION platform to validate the applicability of a combination of the MinION platform and buccal swab samples for rumen microbiota analysis. The distribution of predominant bacterial taxa in the buccal swab samples was similar to that in the rumen samples observed in experiment 2. Based on these results, we concluded that the combination of the MinION platform and buccal swab samples may be potentially applied for rumen microbial analysis in large-scale studies.
Collapse
Affiliation(s)
- Hiroto Miura
- Graduate School of Agriculture, Hokkaido University, Hokkaido, Japan
| | | | - Megumi Yamaguchi
- Graduate School of Agriculture, Hokkaido University, Hokkaido, Japan
| | | | - Go Endo
- Field Science Center for Northern Biosphere, Hokkaido University, Hokkaido, Japan
| | - Yasuhisa Masuda
- Field Science Center for Northern Biosphere, Hokkaido University, Hokkaido, Japan
| | - Kaede Ito
- Field Science Center for Northern Biosphere, Hokkaido University, Hokkaido, Japan
| | - Yoshio Nagura
- Field Science Center for Northern Biosphere, Hokkaido University, Hokkaido, Japan
| | | | - Tomohiro Mitani
- Field Science Center for Northern Biosphere, Hokkaido University, Hokkaido, Japan
| | - Yutaka Suzuki
- Graduate School of Agriculture, Hokkaido University, Hokkaido, Japan
| | - Yasuo Kobayashi
- Graduate School of Agriculture, Hokkaido University, Hokkaido, Japan
| | - Satoshi Koike
- Graduate School of Agriculture, Hokkaido University, Hokkaido, Japan
- *Correspondence: Satoshi Koike,
| |
Collapse
|
48
|
Cardinale S, Kadarmideen HN. Host Genome-Metagenome Analyses Using Combinatorial Network Methods Reveal Key Metagenomic and Host Genetic Features for Methane Emission and Feed Efficiency in Cattle. Front Genet 2022; 13:795717. [PMID: 35281842 PMCID: PMC8905538 DOI: 10.3389/fgene.2022.795717] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 01/10/2022] [Indexed: 12/22/2022] Open
Abstract
Cattle production is one of the key contributors to global warming due to methane emission, which is a by-product of converting feed stuff into milk and meat for human consumption. Rumen hosts numerous microbial communities that are involved in the digestive process, leading to notable amounts of methane emission. The key factors underlying differences in methane emission between individual animals are due to, among other factors, both specific enrichments of certain microbial communities and host genetic factors that influence the microbial abundances. The detection of such factors involves various biostatistical and bioinformatics methods. In this study, our main objective was to reanalyze a publicly available data set using our proprietary Synomics Insights platform that is based on novel combinatorial network and machine learning methods to detect key metagenomic and host genetic features for methane emission and residual feed intake (RFI) in dairy cattle. The other objective was to compare the results with publicly available standard tools, such as those found in the microbiome bioinformatics platform QIIME2 and classic GWAS analysis. The data set used was publicly available and comprised 1,016 dairy cows with 16S short read sequencing data from two dairy cow breeds: Holstein and Nordic Reds. Host genomic data consisted of both 50 k and 150 k SNP arrays. Although several traits were analyzed by the original authors, here, we considered only methane emission as key phenotype for associating microbial communities and host genetic factors. The Synomics Insights platform is based on combinatorial methods that can identify taxa that are differentially abundant between animals showing high or low methane emission or RFI. Focusing exclusively on enriched taxa, for methane emission, the study identified 26 order-level taxa that combinatorial networks reported as significantly enriched either in high or low emitters. Additionally, a Z-test on proportions found 21/26 (81%) of these taxa were differentially enriched between high and low emitters (p value <.05). In particular, the phylum of Proteobacteria and the order Desulfovibrionales were found enriched in high emitters while the order Veillonellales was found to be more abundant in low emitters as previously reported for cattle (Wallace et al., 2015). In comparison, using the publicly available tool ANCOM only the order Methanosarcinales could be identified as differentially abundant between the two groups. We also investigated a link between host genome and rumen microbiome by applying our Synomics Insights platform and comparing it with an industry standard GWAS method. This resulted in the identification of genetic determinants in cows that are associated with changes in heritable components of the rumen microbiome. Only four key SNPs were found by both our platform and GWAS, whereas the Synomics Insights platform identified 1,290 significant SNPs that were not found by GWAS. Gene Ontology (GO) analysis found transcription factor as the dominant biological function. We estimated heritability of a core 73 taxa from the original set of 150 core order-level taxonomies and showed that some species are medium to highly heritable (0.25–0.62), paving the way for selective breeding of animals with desirable core microbiome characteristics. We identified a set of 113 key SNPs associated with >90% of these core heritable taxonomies. Finally, we have characterized a small set (<10) of SNPs strongly associated with key heritable bacterial orders with known role in methanogenesis, such as Desulfobacterales and Methanobacteriales.
Collapse
Affiliation(s)
- Stefano Cardinale
- Synomics Ltd, Hanborough Business Park, Long Hanborough, United Kingdom
| | | |
Collapse
|
49
|
Kelly WJ, Mackie RI, Attwood GT, Janssen PH, McAllister TA, Leahy SC. Hydrogen and formate production and utilisation in the rumen and the human colon. Anim Microbiome 2022; 4:22. [PMID: 35287765 PMCID: PMC8919644 DOI: 10.1186/s42523-022-00174-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/02/2022] [Indexed: 12/31/2022] Open
Abstract
Molecular hydrogen (H2) and formate (HCOO−) are metabolic end products of many primary fermenters in the mammalian gut. Both play a vital role in fermentation where they are electron sinks for individual microbes in an anaerobic environment that lacks external electron acceptors. If H2 and/or formate accumulate within the gut ecosystem, the ability of primary fermenters to regenerate electron carriers may be inhibited and microbial metabolism and growth disrupted. Consequently, H2- and/or formate-consuming microbes such as methanogens and homoacetogens play a key role in maintaining the metabolic efficiency of primary fermenters. There is increasing interest in identifying approaches to manipulate mammalian gut environments for the benefit of the host and the environment. As H2 and formate are important mediators of interspecies interactions, an understanding of their production and utilisation could be a significant entry point for the development of successful interventions. Ruminant methane mitigation approaches are discussed as a model to help understand the fate of H2 and formate in gut systems.
Collapse
|
50
|
Arce-Recinos C, Ojeda-Robertos NF, Garcia-Herrera RA, Ramos-Juarez JA, Piñeiro-Vázquez ÁT, Canul-Solís JR, Castillo-Sanchez LE, Casanova-Lugo F, Vargas-Bello-Pérez E, Chay-Canul AJ. Residual Feed Intake and Rumen Metabolism in Growing Pelibuey Sheep. Animals (Basel) 2022; 12:ani12050572. [PMID: 35268141 PMCID: PMC8909271 DOI: 10.3390/ani12050572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/28/2022] [Accepted: 02/04/2022] [Indexed: 11/16/2022] Open
Abstract
This study was carried out to evaluate the residual feed intake (RFI), volatile fatty acid (VFA) production and enteric methane (CH4) from growing Pelibuey sheep. In this case, 12 non-castrated Pelibuey with an initial average live weight (LW) of 21.17 ± 3.87 kg and an age of 3 months, were housed in individual pens and fed a basal diet with 16% of crude protein and 11 MJ ME for 45 days. Dry matter intake (DMI) was measured and the daily weight gain (DWG) was calculated using a linear regression between the LW and experimental period. Mean metabolic live weight (LW0.75) was calculated. RFI was determined by linear regression with DWG and LW0.75 as independent variables. Lambs were classified as low, medium, and high RFI. Feed efficiency was determined as DWG/DMI. For determining rumen pH, ammonia nitrogen concentration NH3-N), and VFA, ruminal fluid was obtained using an esophageal probe on day 40. Feed intake of low RFI lambs was approximately 16% lower (p < 0.05) while growth rate was not significantly different. Their average energy loss, expressed as CH4 production per kilogram of metabolic weight, was 17% lower (p < 0.05).
Collapse
Affiliation(s)
- Carlos Arce-Recinos
- División Académica de Ciencias Agropecuarias, Universidad Juárez Autónoma de Tabasco, Carretera Villahermosa-Teapa, Km 25, R/A, La Huasteca 2ª Sección, Villahermosa 86280, Tabasco, Mexico; (C.A.-R.); (N.F.O.-R.); (R.A.G.-H.)
- Colegio de Postgraduados, Campus Tabasco, Periférico Carlos A. Molina, Km 3.5, Carretera Cárdenas-Huimanguillo, H. Cárdenas 86500, Tabasco, Mexico;
| | - Nadia Florencia Ojeda-Robertos
- División Académica de Ciencias Agropecuarias, Universidad Juárez Autónoma de Tabasco, Carretera Villahermosa-Teapa, Km 25, R/A, La Huasteca 2ª Sección, Villahermosa 86280, Tabasco, Mexico; (C.A.-R.); (N.F.O.-R.); (R.A.G.-H.)
| | - Ricardo Alfonso Garcia-Herrera
- División Académica de Ciencias Agropecuarias, Universidad Juárez Autónoma de Tabasco, Carretera Villahermosa-Teapa, Km 25, R/A, La Huasteca 2ª Sección, Villahermosa 86280, Tabasco, Mexico; (C.A.-R.); (N.F.O.-R.); (R.A.G.-H.)
| | - Jesús Alberto Ramos-Juarez
- Colegio de Postgraduados, Campus Tabasco, Periférico Carlos A. Molina, Km 3.5, Carretera Cárdenas-Huimanguillo, H. Cárdenas 86500, Tabasco, Mexico;
| | - Ángel Trinidad Piñeiro-Vázquez
- Tecnológico Nacional de México, Instituto Tecnológico de Conkal, Avenida Tecnológico s/n, Conkal 97345, Yucatán, Mexico;
| | - Jorge Rodolfo Canul-Solís
- Tecnológico Nacional de México, Instituto Tecnológico de Tizimín, Tizimín 97702, Yucatán, Mexico; (J.R.C.-S.); (L.E.C.-S.)
| | - Luis Enrique Castillo-Sanchez
- Tecnológico Nacional de México, Instituto Tecnológico de Tizimín, Tizimín 97702, Yucatán, Mexico; (J.R.C.-S.); (L.E.C.-S.)
| | - Fernando Casanova-Lugo
- Tecnológico Nacional de Mexico, Instituto Tecnológico de la Zona Maya, Othón P. Blanco 77965, Quintana Roo, Mexico;
| | - Einar Vargas-Bello-Pérez
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark
- Correspondence: (E.V.-B.-P.); (A.J.C.-C.); Tel.: +52-(993)-358-1585 or +52-(993)-142-9151 (A.J.C.-C.); Fax: +52-(993)-142-9150 (A.J.C.-C.)
| | - Alfonso Juventino Chay-Canul
- División Académica de Ciencias Agropecuarias, Universidad Juárez Autónoma de Tabasco, Carretera Villahermosa-Teapa, Km 25, R/A, La Huasteca 2ª Sección, Villahermosa 86280, Tabasco, Mexico; (C.A.-R.); (N.F.O.-R.); (R.A.G.-H.)
- Correspondence: (E.V.-B.-P.); (A.J.C.-C.); Tel.: +52-(993)-358-1585 or +52-(993)-142-9151 (A.J.C.-C.); Fax: +52-(993)-142-9150 (A.J.C.-C.)
| |
Collapse
|