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Fregulia P, Campos MM, Dhakal R, Dias RJP, Neves ALA. Feed efficiency and enteric methane emissions indices are inconsistent with the outcomes of the rumen microbiome composition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:175263. [PMID: 39102957 DOI: 10.1016/j.scitotenv.2024.175263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/23/2024] [Accepted: 08/01/2024] [Indexed: 08/07/2024]
Abstract
The correlation between enteric methane emissions (eME) and feed efficiency (FE) in cattle is linked to the anaerobic fermentation of feedstuffs that occurs in the rumen. Several mathematical indices have been developed to predict feed efficiency and identify low methane emitters in herds. To investigate this, the current study aimed to evaluate the rumen microbial composition in the same group of animals ranked according to six different indices (three indices for FE and three for eME). Thirty-three heifers were ranked into three groups, each consisting of 11 animals, based on FE (feed conversion efficiency - FCE, residual weight gain - RG, and residual feed intake - RFI) and eME indices (production, yield, and intensity). Rumen fluids were collected using a stomach tube and analyzed using 16S rRNA and 18S rRNA, targeting rumen bacteria, archaea, and protozoa. The sequencing analysis revealed that the presence of unique microbial species in the rumen varies across animals ranked by the FE and eME indices. The High RG group harbored 17 unique prokaryotic taxa, while the High FCE group contained only seven. Significant differences existed in the microbial profiles of the animals based on the FE and eME indices. For instance, Raoultibacter was more abundant in the Intermediate RFI group but less so in the Intermediate RG and Intermediate FCE groups. The abundance of Entodinium was higher while Diplodinium was lower in the High FCE group, in contrast to the High RG and High RFI groups. Methanobrevibacter exhibited similar abundances across eME indices. However, the heifers did not demonstrate the same production, yield, and intensity of eME. The present findings underscore the importance of standardizing the FE and eME indices. This standardization is crucial for ensuring consistent and reliable assessments of the composition and function of the rumen microbiome across different herds.
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Affiliation(s)
- Priscila Fregulia
- Laboratório de Protozoologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, 36036-900 Juiz de Fora, Minas Gerais, Brazil; Programa de Pós-graduação em Biodiversidade e Conservação da Natureza, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - Mariana Magalhães Campos
- Brazilian Agricultural Research Corporation (Empresa Brasileira de Pesquisa Agropecuária, EMBRAPA), National Center for Research on Dairy Cattle, Juiz de Fora, Brazil
| | - Rajan Dhakal
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark
| | - Roberto Júnio Pedroso Dias
- Laboratório de Protozoologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, 36036-900 Juiz de Fora, Minas Gerais, Brazil; Programa de Pós-graduação em Biodiversidade e Conservação da Natureza, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - André Luis Alves Neves
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark.
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Liu Q, Zhang Y, Zhang J, Du Z, He B, Qin J, Zhang L, Zhang J. Organic Iodine Improves the Growth Performance and Gut Health of Fujian Yellow Rabbits. Animals (Basel) 2024; 14:1935. [PMID: 38998047 PMCID: PMC11240724 DOI: 10.3390/ani14131935] [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: 04/09/2024] [Revised: 06/05/2024] [Accepted: 06/25/2024] [Indexed: 07/14/2024] Open
Abstract
Organic iodine is a new trace element additive that is highly efficient in regulating cell growth, function, and metabolism. This study demonstrated that organic iodine improves the growth performance and gut health of Fujian yellow rabbits. A total of 160 healthy rabbits of similar weight were randomly divided into four groups, which were treated with organic iodine (0, 0.5, 1.0, and 1.5 mg/kg) for 60 days. Our results indicated that organic iodine improved the growth performance, including significantly increased BW, ADG, and ADFI, and decreased F/G notably. Organic iodine improved the content of T3, T4, IgM, IgA, and IgM in serum, and intestinal mucosal immunity (IL-1α, IL-2, and sIgA). Organic iodine supplementation ameliorated gut morphometry and morphology, such as higher villus height and lower crypt depth. Organic iodine increased the amount of goblet cells significantly. The 0.5 mg/kg organic iodine most increased the activities of amylase, cellulase, and trypsin in caecum. Organic iodine induced more active caecum fermentation, higher NH3-N, acetic acid, propionic acid, and butyric acid, while lowering PH. In conclusion, organic iodine improved the growth performance and gut morphometry and morphology, and increased caecum enzyme activities, active caecum fermentation, and intestinal immunity of Fujian yellow rabbits.
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Affiliation(s)
- Qinghua Liu
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yeqiu Zhang
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jie Zhang
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhijian Du
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Bixian He
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Juanqing Qin
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liping Zhang
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jing Zhang
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Park T. - Invited Review - Ruminal ciliates as modulators of the rumen microbiome. Anim Biosci 2024; 37:385-395. [PMID: 38186255 PMCID: PMC10838670 DOI: 10.5713/ab.23.0309] [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: 08/18/2023] [Accepted: 11/22/2023] [Indexed: 01/09/2024] Open
Abstract
Ruminal ciliates are a fundamental constituent within the rumen microbiome of ruminant animals. The complex interactions between ruminal ciliates and other microbial guilds within the rumen ecosystems are of paramount importance for facilitating the digestion and fermentation processes of ingested feed components. This review underscores the significance of ruminal ciliates by exploring their impact on key factors, such as methane production, nitrogen utilization efficiency, feed efficiency, and other animal performance measurements. Various methods are employed in the study of ruminal ciliates including culture techniques and molecular approaches. This review highlights the pressing need for further investigations to discern the distinct roles of various ciliate species, particularly relating to methane mitigation and the enhancement of nitrogen utilization efficiency. The promotion of establishing robust reference databases tailored specifically to ruminal ciliates is encouraged, alongside the utilization of genomics and transcriptomics that can highlight their functional contributions to the rumen microbiome. Collectively, the progressive advancement in knowledge concerning ruminal ciliates and their inherent biological significance will be helpful in the pursuit of optimizing rumen functionality and refining animal production outcomes.
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Affiliation(s)
- Tansol Park
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Korea
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Le Graverand Q, Marie-Etancelin C, Meynadier A, Weisbecker JL, Marcon D, Tortereau F. Predicting feed efficiency traits in growing lambs from their ruminal microbiota. Animal 2023; 17:100824. [PMID: 37224614 DOI: 10.1016/j.animal.2023.100824] [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: 12/13/2022] [Revised: 04/07/2023] [Accepted: 04/14/2023] [Indexed: 05/26/2023] Open
Abstract
Selecting feed-efficient sheep could improve the sustainability of this livestock production. However, most sheep breeding companies cannot afford to record feed intake to select feed-efficient animals. Past studies underlined the potential of omics data, including microbiota metabarcoding data, as proxies for feed efficiency. The study involved 277 Romane lambs from two lines divergently selected for residual feed intake (RFI). There were two objectives: check the consequences of selecting for feed efficiency over the rumen microbiota, and assess the predictive ability of the rumen microbiota for host traits. The study assessed two contrasting diets (concentrate diet and mixed diet) and two microbial groups (prokaryotes and eukaryotes). Discriminant analyses did not highlight any significant effect of sheep selection for residual feed intake on the rumen microbiota composition. Indeed, prokaryotic and eukaryotic microbiota compositions poorly discriminated the RFI lines, with averaged balanced error rates ranging from 45% to 55%. Correlations between host traits (feed efficiency and production traits) and their predictions from microbiota data varied between -0.07 and 0.56, depending on the trait, diet and sequencing. Feed intake was the most accurately predicted trait. However, predictions from fixed effects and BW were more accurate than or as accurate as predictions from the microbiota. Environmental effects can greatly affect the variability of microbiota compositions. Considering batch and environmental effects should be paramount when the predictive ability of the microbiota is assessed. This study argues why metabarcoding the rumen microbiota is not the best way to predict meat sheep production traits: fixed effects and BW were more cost-effective proxies and they led to similar or better predictive accuracies than microbiota metabarcoding (16S and 18S sequencing).
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Affiliation(s)
- Q Le Graverand
- GenPhySE, Université de Toulouse, INRAE, ENVT, 24 Chemin de Borde-Rouge-Auzeville CS 52627, F-31326 Castanet-Tolosan, France.
| | - C Marie-Etancelin
- GenPhySE, Université de Toulouse, INRAE, ENVT, 24 Chemin de Borde-Rouge-Auzeville CS 52627, F-31326 Castanet-Tolosan, France
| | - A Meynadier
- GenPhySE, Université de Toulouse, INRAE, ENVT, 24 Chemin de Borde-Rouge-Auzeville CS 52627, F-31326 Castanet-Tolosan, France
| | - J-L Weisbecker
- GenPhySE, Université de Toulouse, INRAE, ENVT, 24 Chemin de Borde-Rouge-Auzeville CS 52627, F-31326 Castanet-Tolosan, France
| | - D Marcon
- INRAE, Unité Expérimentale P3R, Domaine de la Sapinière, F-18390 Osmoy, France
| | - F Tortereau
- GenPhySE, Université de Toulouse, INRAE, ENVT, 24 Chemin de Borde-Rouge-Auzeville CS 52627, F-31326 Castanet-Tolosan, France
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Fregulia P, Campos MM, Dias RJP, Liu J, Guo W, Pereira LGR, Machado MA, Faza DRDLR, Guan LL, Garnsworthy PC, Neves ALA. Taxonomic and predicted functional signatures reveal linkages between the rumen microbiota and feed efficiency in dairy cattle raised in tropical areas. Front Microbiol 2022; 13:1025173. [PMID: 36523842 PMCID: PMC9745175 DOI: 10.3389/fmicb.2022.1025173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 11/07/2022] [Indexed: 08/27/2023] Open
Abstract
Ruminants digest plant biomass more efficiently than monogastric animals due to their symbiotic relationship with a complex microbiota residing in the rumen environment. What remains unclear is the relationship between the rumen microbial taxonomic and functional composition and feed efficiency (FE), especially in crossbred dairy cattle (Holstein x Gyr) raised under tropical conditions. In this study, we selected twenty-two F1 Holstein x Gyr heifers and grouped them according to their residual feed intake (RFI) ranking, high efficiency (HE) (n = 11) and low efficiency (LE) (n = 11), to investigate the effect of FE on the rumen microbial taxa and their functions. Rumen fluids were collected using a stomach tube apparatus and analyzed using amplicon sequencing targeting the 16S (bacteria and archaea) and 18S (protozoa) rRNA genes. Alpha-diversity and beta-diversity analysis revealed no significant difference in the rumen microbiota between the HE and LE animals. Multivariate analysis (sPLS-DA) showed a clear separation of two clusters in bacterial taxonomic profiles related to each FE group, but in archaeal and protozoal profiles, the clusters overlapped. The sPLS-DA also revealed a clear separation in functional profiles for bacteria, archaea, and protozoa between the HE and LE animals. Microbial taxa were differently related to HE (e.g., Howardella and Shuttleworthia) and LE animals (e.g., Eremoplastron and Methanobrevibacter), and predicted functions were significatively different for each FE group (e.g., K03395-signaling and cellular process was strongly related to HE animals, and K13643-genetic information processing was related to LE animals). This study demonstrates that differences in the rumen microbiome relative to FE ranking are not directly observed from diversity indices (Faith's Phylogenetic Diversity, Pielou's Evenness, Shannon's diversity, weighted UniFrac distance, Jaccard index, and Bray-Curtis dissimilarity), but from targeted identification of specific taxa and microbial functions characterizing each FE group. These results shed light on the role of rumen microbial taxonomic and functional profiles in crossbred Holstein × Gyr dairy cattle raised in tropical conditions, creating the possibility of using the microbial signature of the HE group as a biological tool for the development of biomarkers that improve FE in ruminants.
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Affiliation(s)
- Priscila Fregulia
- Laboratório de Protozoologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
- Programa de Pós-Graduação em Biodiversidade e Conservação da Natureza, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Mariana Magalhães Campos
- Brazilian Agricultural Research Corporation (Empresa Brasileira de Pesquisa Agropecuária, EMBRAPA), National Center for Research on Dairy Cattle, Juiz de Fora, Minas Gerais, Brazil
| | - Roberto Júnio Pedroso Dias
- Laboratório de Protozoologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
- Programa de Pós-Graduação em Biodiversidade e Conservação da Natureza, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Junhong Liu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Wei Guo
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
| | - Luiz Gustavo Ribeiro Pereira
- Brazilian Agricultural Research Corporation (Empresa Brasileira de Pesquisa Agropecuária, EMBRAPA), National Center for Research on Dairy Cattle, Juiz de Fora, Minas Gerais, Brazil
| | - Marco Antônio Machado
- Brazilian Agricultural Research Corporation (Empresa Brasileira de Pesquisa Agropecuária, EMBRAPA), National Center for Research on Dairy Cattle, Juiz de Fora, Minas Gerais, Brazil
| | - Daniele Ribeiro de Lima Reis Faza
- Brazilian Agricultural Research Corporation (Empresa Brasileira de Pesquisa Agropecuária, EMBRAPA), National Center for Research on Dairy Cattle, Juiz de Fora, Minas Gerais, Brazil
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Phil C. Garnsworthy
- School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - André Luis Alves Neves
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
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