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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 E, Liu L, Zhang Z, Qu M, Xue F. An Automated Sprinkler Cooling System Effectively Alleviates Heat Stress in Dairy Cows. Animals (Basel) 2024; 14:2586. [PMID: 39272371 DOI: 10.3390/ani14172586] [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: 06/14/2024] [Revised: 08/10/2024] [Accepted: 08/20/2024] [Indexed: 09/15/2024] Open
Abstract
(1) Background: Heat stress detrimentally restricted economic growth in dairy production. In particular, the cooling mechanism of the spraying system effectively reduced both environmental and shell temperatures. This study was designed to investigate the underlying modulatory mechanism of an automatic cooling system in alleviating heat-stressed dairy cows. (2) Methods: A total of 1208 multiparous dairy cows was randomly allocated into six barns, three of which were equipped with automatic sprinklers (SPs), while the other three were considered the controls (CONs). Each barn was considered a replicate. (3) Results: Body temperatures and milk somatic cell counts significantly decreased, while DMI, milk yield, and milk fat content significantly increased under SP treatment. Rumen fermentability was enhanced, embodied by the increased levels of total VFA, acetate, propionate, and butyrate after SP treatment. The rumen microbiota results showed the relative abundances of fiber-degrading bacteria, including the Fibrobacters, Saccharofermentans, Lachnospira, Pseudobutyrivibrio, Selenomonas, and Succinivibrio, which significantly increased after receiving the SP treatment. (4) Conclusions: This study demonstrated that SP effectively alleviated heat stress and improved production performances and milk quality through modulating the rumen microbiota composition and fermentation function of dairy cows.
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Affiliation(s)
- En Liu
- Jiangxi Province Key Laboratory of Animal Nutrition, Engineering Research Center of Feed Development, Jiangxi Agricultural University, Nanchang 330029, China
| | - Liping Liu
- School of Food Engineering, Anhui College of Science and Technology, Chuzhou 233100, China
| | - Zhili Zhang
- Modern Farming (Wuhe) Co., Ltd., Bengbu 233311, China
| | - Mingren Qu
- Jiangxi Province Key Laboratory of Animal Nutrition, Engineering Research Center of Feed Development, Jiangxi Agricultural University, Nanchang 330029, China
| | - Fuguang Xue
- Jiangxi Province Key Laboratory of Animal Nutrition, Engineering Research Center of Feed Development, Jiangxi Agricultural University, Nanchang 330029, China
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Lima J, Martínez-Álvaro M, Mattock J, Auffret MD, Duthie CA, Cleveland MA, Dewhurst RJ, Watson M, Roehe R. Temporal stability of the rumen microbiome and its longitudinal associations with performance traits in beef cattle. Sci Rep 2024; 14:20772. [PMID: 39237607 PMCID: PMC11377694 DOI: 10.1038/s41598-024-70770-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 08/21/2024] [Indexed: 09/07/2024] Open
Abstract
The rumen microbiome is the focus of a growing body of research, mostly based on investigation of rumen fluid samples collected once from each animal. Exploring the temporal stability of rumen microbiome profiles is imperative, as it enables evaluating the reliability of findings obtained through single-timepoint sampling. We explored the temporal stability of rumen microbiomes considering taxonomic and functional aspects across the 7-month growing-finishing phase spanning 6 timepoints. We identified a temporally stable core microbiome, encompassing 515 microbial genera (e.g., Methanobacterium) and 417 microbial KEGG genes (e.g., K00856-adenosine kinase). The temporally stable core microbiome profiles collected from all timepoints were strongly associated with production traits with substantial economic and environmental impact (e.g., average daily gain, daily feed intake, and methane emissions); 515 microbial genera explained 45-83%, and 417 microbial genes explained 44-83% of their phenotypic variation. Microbiome profiles influenced by the bovine genome explained 54-87% of the genetic variation of bovine traits. Overall, our results provide evidence that the temporally stable core microbiome identified can accurately predict host performance traits at phenotypic and genetic level based on a single timepoint sample taken as early as 7 months prior to slaughter.
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Affiliation(s)
- Joana Lima
- Scotland's Rural College, Edinburgh, UK.
| | | | - Jennifer Mattock
- The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | | | | | | | | | - Mick Watson
- The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
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Anbazhagan AN, Ge Y, Priyamvada S, Kumar A, Jayawardena D, Palani ARV, Husain N, Kulkarni N, Kapoor S, Kaur P, Majumder A, Lin YD, Maletta L, Gill RK, Alrefai WA, Saksena S, Zadeh K, Hong S, Mohamadzadeh M, Dudeja PK. A Direct Link Implicating Loss of SLC26A6 to Gut Microbial Dysbiosis, Compromised Barrier Integrity, and Inflammation. Gastroenterology 2024; 167:704-717.e3. [PMID: 38735402 DOI: 10.1053/j.gastro.2024.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/27/2024] [Accepted: 05/02/2024] [Indexed: 05/14/2024]
Abstract
BACKGROUND & AIMS Putative anion transporter-1 (PAT1, SLC26A6) plays a key role in intestinal oxalate and bicarbonate secretion. PAT1 knockout (PKO) mice exhibit hyperoxaluria and nephrolithiasis. Notably, diseases such as inflammatory bowel disease are also associated with higher risk of hyperoxaluria and nephrolithiasis. However, the potential role of PAT1 deficiency in gut-barrier integrity and susceptibility to colitis is currently elusive. METHODS Age-matched PKO and wild-type littermates were administered 3.5% dextran sulfate sodium in drinking water for 6 days. Ileum and colon of control and treated mice were harvested. Messenger RNA and protein expression of tight junction proteins were determined by reverse transcription polymerase chain reaction and western blotting. Severity of inflammation was assessed by measuring diarrheal phenotype, cytokine expression, and hematoxylin and eosin staining. Gut microbiome and associated metabolome were analyzed by 16S ribosomal RNA sequencing and mass spectrometry, respectively. RESULTS PKO mice exhibited significantly higher loss of body weight, gut permeability, colonic inflammation, and diarrhea in response to dextran sulfate sodium treatment. In addition, PKO mice showed microbial dysbiosis and significantly reduced levels of butyrate and butyrate-producing microbes compared with controls. Co-housing wild-type and PKO mice for 4 weeks resulted in PKO-like signatures on the expression of tight junction proteins in the colons of wild-type mice. CONCLUSIONS Our data demonstrate that loss of PAT1 disrupts gut microbiome and related metabolites, decreases gut-barrier integrity, and increases host susceptibility to intestinal inflammation. These findings, thus, highlight a novel role of the oxalate transporter PAT1 in promoting gut-barrier integrity, and its deficiency appears to contribute to the pathogenesis of inflammatory bowel diseases.
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Affiliation(s)
- Arivarasu N Anbazhagan
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Yong Ge
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health, San Antonio, Texas
| | - Shubha Priyamvada
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Anoop Kumar
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois; Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois
| | - Dulari Jayawardena
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Arvind Raj Vishnu Palani
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Nazim Husain
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Neelkanth Kulkarni
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Shaunik Kapoor
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Prabhdeep Kaur
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Apurba Majumder
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Yang-Ding Lin
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health, San Antonio, Texas
| | - Leeany Maletta
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health, San Antonio, Texas
| | - Ravinder K Gill
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois; Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois
| | - Waddah A Alrefai
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois; Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois
| | - Seema Saksena
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois; Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois
| | - Kimia Zadeh
- Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois
| | - Sungmo Hong
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health, San Antonio, Texas
| | - Mansour Mohamadzadeh
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health, San Antonio, Texas; South Texas Veterans Health Care System, San Antonio, Texas
| | - Pradeep K Dudeja
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois; Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois.
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Luecke SM, Aryee G, Holman DB, Schmidt KN, King LE, Crouse MS, Ward AK, Dahlen CR, Caton JS, Amat S. Effects of dietary restriction and one-carbon metabolite supplementation during the first 63 days of gestation on the maternal gut, vaginal, and blood microbiota in cattle. Anim Microbiome 2024; 6:48. [PMID: 39210404 PMCID: PMC11360793 DOI: 10.1186/s42523-024-00335-2] [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: 12/20/2023] [Accepted: 08/19/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Maternal diet quality and quantity have significant impacts on both maternal and fetal health and development. The composition and function of the maternal gut microbiome is also significantly influenced by diet; however, little is known about the impact of gestational nutrient restriction on the bovine maternal microbiome during early gestation, which is a critical stage for maternal microbiome-mediated fetal programming to take place. The objective of the present study was to evaluate the impacts of diet restriction and one-carbon metabolite (OCM) supplementation during early gestation on maternal ruminal, vaginal, and blood microbiota in cattle. Thirty-three beef heifers (approx. 14 months old) were used in a 2 × 2 factorial experiment with main factors of target gain (control [CON]; targeted 0.45 kg/d gain vs restricted [RES]; targeted - 0.23 kg/d gain), and OCM supplementation (+ OCM vs - OCM; n = 8/treatment; except n = 9 for RES-OCM). Heifers were individually fed, starting treatment at breeding (d 0) and concluding at d 63 of gestation. Ruminal fluid and vaginal swabs were collected on d - 2, d 35, and d 63 (at necropsy) and whole blood was collected on d 63 (necropsy). Bacterial microbiota was assessed using 16S rRNA gene (V3-V4) sequencing. RESULTS Overall ruminal microbiota structure was affected by gain, OCM, time, and their interactions. The RES heifers had greater microbial richness (observed ASVs) but neither Shannon nor Inverse Simpson diversity was significantly influenced by gain or OCM supplementation; however, on d 63, 34 bacterial genera showed differential abundance in the ruminal fluid, with 25 genera enriched in RES heifers as compared to CON heifers. In addition, the overall interaction network structure of the ruminal microbiota changed due to diet restriction. The vaginal microbiota community structure was influenced by gain and time. Overall microbial richness and diversity of the vaginal microbiota steadily increased as pregnancy progressed. The vaginal ecological network structure was distinctive between RES and CON heifers with genera-genera interactions being intensified in RES heifers. A relatively diverse bacterial community was detected in blood samples, and the composition of the blood microbiota differed from that of ruminal and vaginal microbiota. CONCLUSION Restricted dietary intake during early gestation induced significant alterations in the ruminal microbiota which also extended to the vaginal microbiota. The composition of these two microbial communities was largely unaffected by OCM supplementation. Blood associated microbiota was largely distinctive from the ruminal and vaginal microbiota.
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Affiliation(s)
- Sarah M Luecke
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA
| | - Godson Aryee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA
| | - Devin B Holman
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Kaycie N Schmidt
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA
| | - Layla E King
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND, USA
| | - Matthew S Crouse
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Alison K Ward
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND, USA
| | - Carl R Dahlen
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND, USA
| | - Joel S Caton
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND, USA
| | - Samat Amat
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA.
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Wu X, Zhang G, Zhang W, Zhou J, Cong H, Yang G, Liu G. Rumen microbiota helps Tibetan sheep obtain energy more efficiently to survive in the extreme environment of the Qinghai-Tibet Plateau. Front Microbiol 2024; 15:1431063. [PMID: 39113833 PMCID: PMC11303141 DOI: 10.3389/fmicb.2024.1431063] [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: 05/11/2024] [Accepted: 07/10/2024] [Indexed: 08/10/2024] Open
Abstract
Introduction T-sheep and H-sheep exhibit different environmental adaptability and production performance. The rumen microbiome has co-evolved with hosts and plays a vital role in nutrient digestion and energy metabolism. In our previous study, we found that T-sheep have a higher efficiency in energy metabolism than H-sheep, but the rumen microbial community remains unclear. Methods In this study, we determined the rumen bacterial profile and rumen fermentation parameters to reveal the bacterial profiles and predictive functions among breeds and diets with four different energy levels, as well as the correlation between bacterial profiles and rumen fermentation characteristics. Results The results showed that the rumen total volatile fatty acids (VFAs), acetate, butyrate, total branched-chain VFAs, iso-butyrate, and iso-valerate were higher in T-sheep than H-sheep. The alpha diversity of ruminal bacteria is not affected by dietary energy, but it shows a distinction between the sheep breeds. Specifically, T-sheep rumen bacteria exhibit higher alpha diversity than H-sheep. The beta diversity of ruminal bacteria is not influenced by dietary energy or sheep breeds, indicating similar communities of ruminal bacteria between different diets and sheep breeds. The phyla of Bacteroidetes and Firmicutes predominate in the rumen, with a higher relative abundance of Firmicutes observed in T-sheep than H-sheep. The two most abundant genera in the rumen were Prevotella 1 and Rikenellaceae RC9 gut group. Prevotella 1 is the predominant bacterial genus in the rumen of H-sheep, while the Rikenellaceae RC9 gut group dominates in the rumen of T-sheep. Microbial co-occurrence network analysis reveals that variations in rumen fermentation characteristics result from differences in module abundance, with a higher abundance of VFA-producing modules observed in the rumen of T-sheep. Microbial function prediction analysis showed that dietary energy rarely alters the functional composition of rumen bacteria. However, there were differences in the functions of rumen bacteria between sheep breeds, with T-sheep showing a greater emphasis on energy metabolism-related functions, while H-sheep showed a greater emphasis on protein metabolism-related functions. Discussion These findings provide evidence of the special rumen microbial community that helps T-sheep efficiently obtain energy from low-protein and low-energy diets, enabling them to survive in the extreme environment of the Qinghai-Tibet Plateau.
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Affiliation(s)
- Xiukun Wu
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Gaosen Zhang
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Wei Zhang
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Jianwei Zhou
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Haitao Cong
- Shandong Huakun Rural Revitalization Institute Co., Ltd., Jinan, China
| | - Guo Yang
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Guangxiu Liu
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
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Wang Z, Chen P, Liang Y, Wang F, Zhang Y. Negative energy balance affects perinatal ewe performance, rumen morphology, rumen flora structure, and placental function. J Anim Physiol Anim Nutr (Berl) 2024. [PMID: 38958108 DOI: 10.1111/jpn.14009] [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: 04/14/2024] [Revised: 05/14/2024] [Accepted: 06/09/2024] [Indexed: 07/04/2024]
Abstract
This study investigated the effects of negative energy balance (NEB) on perinatal ewes, with a focus on changes in growth performance, serum biochemical parameters, rumen fermentation, ruminal bacteria composition, placental phenotype-related indicators, and expression levels of genes related to placental function. Twenty ewes at 130 days of gestation were randomly allocated to either the positive energy balance (PEB) or NEB groups. In the experiment, ewes in the PEB group were fed the same amount as their intake during the pre-feeding baseline period, while ewes in the NEB group were restricted to 70% of their individual baseline feed intake. The experiment was conducted until 42 days postpartum, and five double-lamb ewes per group were selected for slaughter. The results demonstrated that NEB led to a significant decrease in body weight, carcass weight, and the birth and weaning weights of lambs (P < 0.05). Additionally, NEB caused alterations in serum biochemical parameters, such as increased non-esterified fatty acids and β-hydroxybutyrate levels and decreased cholesterol and albumin levels (P < 0.05). Rumen fermentation and epithelial parameters were also affected, with a reduction in the concentrations of acetic acid, butyric acid, total acid and a decrease in the length of the rumen papilla (P < 0.05). Moreover, NEB induced changes in the structure and composition of ruminal bacteria, with significant differences in α-diversity indices and rumen microbial community composition (P < 0.05). Gene expression in rumen papilla and ewe placenta was also affected, impacting genes associated with glucose and amino acid transport, proliferation, apoptosis, and angiogenesis (P < 0.05). These findings screened the key microbiota in the rumen of ewes following NEB and highlighted the critical genes associated with rumen function. Furthermore, this study revealed the impact of NEB on placental function in ewes, providing a foundation for investigating how nutrition in ewes influences reproductive performance. This research demonstrates how nutrition regulates reproductive performance by considering the combined perspectives of rumen microbiota and placental function.
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Affiliation(s)
- Zhibo Wang
- Institute of Goats and Sheep Science, Nanjing Agricultural University, Nanjing, China
| | - Peiyong Chen
- Institute of Goats and Sheep Science, Nanjing Agricultural University, Nanjing, China
| | - Yaxu Liang
- Institute of Goats and Sheep Science, Nanjing Agricultural University, Nanjing, China
| | - Feng Wang
- Institute of Goats and Sheep Science, Nanjing Agricultural University, Nanjing, China
| | - Yanli Zhang
- Institute of Goats and Sheep Science, Nanjing Agricultural University, Nanjing, China
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Federiconi A, Ghiaccio F, Mammi L, Cavallini D, Visentin G, Formigoni A, Palmonari A. Changes on the rumen microbial community composition in dairy cows subjected to an acidogenic diet. J Dairy Sci 2024:S0022-0302(24)00846-4. [PMID: 38825118 DOI: 10.3168/jds.2023-24599] [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: 12/22/2023] [Accepted: 04/21/2024] [Indexed: 06/04/2024]
Abstract
In modern breeding systems, cows are subjected to many stress factors. Animals fed with a high-grain diet may have a decreased rumen pH, which would lead to subacute ruminal acidosis syndrome. The aim of this study was to investigate the evolution of microbial community composition in cows undergoing a dietary stress challenge. Twelve cows were subjected to a challenge period consisted in a rapid change of ration, from a normal (45.4:54.6 forage: concentrate) to a high-grain content diet (24.8:75.2 forage: concentrate) to induce sub-acute ruminal acidosis. Individual rumen fluid content samples were collected before (T0), and during the challenge (T3, T14, T28). DNA from rumen contents was extracted, purified, and sequenced to evaluate Bacterial populations and sequencing was performed on Illumina MiSeq. The effect of animal conditions on rumen microbial community was quantified through a linear mixed model. The acidogenic diet created 2 main clusters: ruminal hypomotility (RH) and milk fat depression (MFD). The microbial composition did not differ in T0 between the 2 groups, while during the challenge Ruminococcus spp., Treponema spp., Methanobrevibacter spp., and Methanosphaera spp. concentrations increased in RH cows; Succinivibrio spp. and Butyrivibrio spp. concentrations increased in MFD cows. Prevotella spp. and Ruminococcus spp., were negatively correlated, while Christenellaceae family were positively correlated with both Methanobrevibacter spp. and Methanosphaera spp. Moreover, the same diet affected differently cows' microbiota composition, underlying the impact of the host effect. Other studies are necessary to deepen the relationship between microbiota composition and host.
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Affiliation(s)
- A Federiconi
- DIMEVET, Dipartimento di Scienze Mediche Veterinarie, Università di Bologna, 40064 Ozzano dell'Emilia, Italy.
| | - F Ghiaccio
- DIMEVET, Dipartimento di Scienze Mediche Veterinarie, Università di Bologna, 40064 Ozzano dell'Emilia, Italy
| | - L Mammi
- DIMEVET, Dipartimento di Scienze Mediche Veterinarie, Università di Bologna, 40064 Ozzano dell'Emilia, Italy
| | - D Cavallini
- DIMEVET, Dipartimento di Scienze Mediche Veterinarie, Università di Bologna, 40064 Ozzano dell'Emilia, Italy
| | - G Visentin
- DIMEVET, Dipartimento di Scienze Mediche Veterinarie, Università di Bologna, 40064 Ozzano dell'Emilia, Italy
| | - A Formigoni
- DIMEVET, Dipartimento di Scienze Mediche Veterinarie, Università di Bologna, 40064 Ozzano dell'Emilia, Italy
| | - A Palmonari
- DIMEVET, Dipartimento di Scienze Mediche Veterinarie, Università di Bologna, 40064 Ozzano dell'Emilia, Italy
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9
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He S, Zhang R, Wang R, Wu D, Dai S, Wang Z, Chen T, Mao H, Li Q. Responses of nutrient utilization, rumen fermentation and microorganisms to different roughage of dairy buffaloes. BMC Microbiol 2024; 24:188. [PMID: 38811906 PMCID: PMC11134657 DOI: 10.1186/s12866-024-03342-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 05/17/2024] [Indexed: 05/31/2024] Open
Abstract
Dairy buffaloes are typically fed a high-forage, low-quality diet with high fiber. These conditions result in an inherent energy and protein inefficiency. In order to make full and rational use of feed resources and improve the production level and breeding efficiency of dairy buffaloes, the effects of various roughages on nutrient digestibility, ruminal fermentation parameters, and microorganisms in dairy buffaloes were studied in this experiment. Three ternary hybrid buffaloes, with an average body weight of 365 ± 22.1 kg, were selected and fitted with permanent rumen fistulas. They were fed six different diets, each consisting of 1 kg concentrate supplement and one of six types of roughage, including alfalfa hay (A diet), oat hay (O diet), whole corn silage (W diet), king grass (K diet), sugarcane shoot silage (S diet), and rice straw hay (R diet) according to an incomplete Latin square design of 3 × 6, respectively. The pre-feeding period of each period was 12 d. From day 13 to 15 was the official experimental period. During the prefeeding period, free feed intake for each roughage was determined, and during the experiment, the roughage was fed at 90% of the voluntary feed intake. Digestion and metabolism tests were carried out using the total manure collection method to determine the feed intake and fecal output of each buffalo, and to collect feed and fecal samples for chemical analysis. On day 15, rumen fluid samples were collected two hours after morning feeding to determine rumen fermentation parameters and bacterial 16 S rRNA high-throughput sequencing was performed. The results showed that DM and OM digestibility were greatest for the W diet and lowest for the S diet. The rumen pH of the O diet was significantly greater than that of the W diet. The concentration of rumen fluid NH3-N (mg/dL) increased with increased CP content. The concentration of total volatile fatty acids (mmol/L) in the rumen decreased with increased NDF content but increased with increased NFC content. The relative abundances of Bacteroidetes, Firmicutes, and Spirochaetes were 57.03-74.84%, 14.29-21.86%, and 0.44-1.43% in the different quality roughage groups. Bacteroidetes were mainly Prevotellaceae1 and Rikenellaceae RC_gut_group with relative abundances of 30.17-45.75% and 3.23-7.82%. The relative abundance of Patescibacteria and Spirochaetes decreased with increasing roughage quality. These results provide a theoretical and practical basis for evaluating the nutritional value of dairy buffalo feed, utilizing feed resources, matching rations, feeding scientifically, and protecting animal health.
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Affiliation(s)
- Shichun He
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Ruiyun Zhang
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Rongjiao Wang
- Institute of Animal and Veterinary Medicine, Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, 617000, China
| | - Dongwang Wu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Sifan Dai
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Zibei Wang
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Tao Chen
- Animal Husbandry station in Mangshi, Dehong Prefecture, Mangshi, Yunnan, 678400, China
| | - Huaming Mao
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Qing Li
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China.
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10
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Li D, Li Q, Ma X, Wang H, Wang C, Wang H, Liu Z, Li T, Ma Y. Prickly ash seeds can promote healthy production of sheep by regulating the rumen microbial community. Front Microbiol 2024; 15:1364517. [PMID: 38832114 PMCID: PMC11144891 DOI: 10.3389/fmicb.2024.1364517] [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: 01/02/2024] [Accepted: 05/06/2024] [Indexed: 06/05/2024] Open
Abstract
This study aimed to investigate the effect of prickly ash seeds (PAS) on the microbial community found in rumen microbes of Hu sheep by adding different percentages of prickly ash seeds and to carry out research on the relation between rumen flora and production performance. Twenty-seven male lambs of Hu sheep were classified into three groups based on the content of prickly ash seeds (PAS) fed for 90 days, i.e., 0%, 3%, and 6%. At the end of the feeding trial, rumen fluid samples were collected from six sheep in each group for 16S amplicon sequencing. The results showed that the addition of prickly ash seeds significantly increased both Chao1 and ACE indices (P < 0.05), and the differences between groups were greater than those within groups. The relative content of Bacteriodota decreased, and the relative content of Fusobacteriota, Proteobacteria, Acidobacteriota, and Euryarchaeota increased. The relative content of Papillibacter and Saccharofermentans was increased at the genus level, and the relative content of Bacteroides and Ruminococcus was decreased. The test group given 3% of prickly ash seeds was superior to the test group given 6% of prickly ash seeds. In addition, the addition of 3% of prickly ash seeds improved the metabolism or immunity of sheep. Fusobacteriota and Acidobacteriota were positively correlated with total weight, dressing percentage, and average daily gain (ADG) and negatively correlated with average daily feed intake (ADFI), feed-to-gain ratio (F/G), and lightness (L*). Methanobrevibacter and Saccharofermentans were positively correlated with ADG and negatively correlated with ADFI and L*. In conclusion, under the present experimental conditions, the addition of prickly ash seeds increased the abundance and diversity of rumen microorganisms in Hu sheep and changed the relative abundance of some genera. However, the addition of 6% prickly ash seeds may negatively affect the digestive and immune functions in sheep rumen.
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Affiliation(s)
- Dengpan Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
| | - Qiao Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
| | - Xueyi Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
| | - Huihui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
| | - Chunhui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
| | - Haoyu Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
| | - Zhanjing Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Tianzhu County Animal Disease Prevention and Control Center, Wuwei, China
| | - Taotao Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
| | - Youji Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, China
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11
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Ungerfeld EM, Pitta D. Review: Biological consequences of the inhibition of rumen methanogenesis. Animal 2024:101170. [PMID: 38772773 DOI: 10.1016/j.animal.2024.101170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 05/23/2024] Open
Abstract
Decreasing enteric CH4 emissions from ruminants is important for containing global warming to 1.5 °C and avoid the worst consequences of climate change. However, the objective of mitigating enteric CH4 emissions is difficult to reconcile with the forecasted increase in production of ruminant meat and milk, unless CH4 production per animal and per kilogram of animal product are decreased substantially. Chemical compound 3-nitrooxypropanol and bromoform-containing red algae Asparagopsis are currently the most potent inhibitors of rumen methanogenesis, but their average efficacy would have to be increased to mitigate enteric CH4 emissions to contain global warming to 1.5 °C, if the demand for ruminant products increases as predicted. We propose that it may be possible to enhance the efficacy of inhibitors of methanogenesis through understanding the mechanisms that cause variation in their efficacy across studies. We also propose that a more thorough understanding of the effects of inhibiting methanogenesis on rumen and postabsorptive metabolism may help improve feed efficiency and cost-effectiveness as co-benefits of the methanogenesis inhibition intervention. For enhancing efficacy, we examine herein how different inhibitors of methanogenesis affect the composition of the rumen microbial community and discuss some mechanisms that may explain dissimilar sensitivities among methanogens to different types of inhibitors. For improving feed efficiency and cost-effectiveness, we discuss the consequences of inhibiting methanogenesis on rumen fermentation, and how changes in rumen fermentation can in turn affect postabsorptive metabolism and animal performance. The objectives of this review are to identify knowledge gaps of the consequences of inhibiting methanogenesis on rumen microbiology and rumen and postabsorptive metabolism, propose research to address those knowledge gaps and discuss the implications that this research can have for the efficacy and adoption of inhibitors of methanogenesis. Depending on its outcomes, research on the microbiological, biochemical, and metabolic consequences of the inhibition of rumen methanogenesis could help the adoption of feed additives inhibitors of methanogenesis to mitigate enteric CH4 emissions from ruminants to ameliorate climate change.
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Affiliation(s)
- E M Ungerfeld
- Centro Regional de Investigación Carillanca, Instituto de Investigaciones Agropecuarias INIA, Camino Cajón a Vilcún km 10, 4880000 Vilcún, La Araucanía, Chile.
| | - D Pitta
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, New Bolton Center, 19348 Kenneth Square, PA, United States
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12
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Duniere L, Frayssinet B, Achard C, Chevaux E, Plateau J. Conditioner application improves bedding quality and bacterial composition with potential beneficial impacts for dairy cow's health. Microbiol Spectr 2024; 12:e0426323. [PMID: 38376365 PMCID: PMC10994720 DOI: 10.1128/spectrum.04263-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 01/29/2024] [Indexed: 02/21/2024] Open
Abstract
Recycled manure solids (RMS) is used as bedding material in cow housing but can be at risk for pathogens development. Cows spend several hours per day lying down, contributing to the transfer of potential mastitis pathogens from the bedding to the udder. The effect of a bacterial conditioner (Manure Pro, MP) application was studied on RMS-bedding and milk qualities and on animal health. MP product was applied on bedding once a week for 3 months. Bedding and teat skin samples were collected from Control and MP groups at D01, D51, and D90 and analyzed through 16S rRNA amplicon sequencing. MP application modified bacterial profiles and diversity. Control bedding was significantly associated with potential mastitis pathogens, while no taxa of potential health risk were significantly detected in MP beddings. Functional prediction identified enrichment of metabolic pathways of agronomic interest in MP beddings. Significant associations with potential mastitis pathogens were mainly observed in Control teat skin samples. Finally, significantly better hygiene and lower Somatic Cell Counts in milk were observed for cows from MP group, while no group impact was observed on milk quality and microbiota. No dissemination of MP strains was observed from bedding to teats or milk. IMPORTANCE The use of Manure Pro (MP) conditioner improved recycled manure solids-bedding quality and this higher sanitary condition had further impacts on dairy cows' health with less potential mastitis pathogens significantly associated with bedding and teat skin samples of animals from MP group. The animals also presented an improved inflammation status, while milk quality was not modified. The use of MP conditioner on bedding may be of interest in controlling the risk of mastitis onset for dairy cows and further associated costs.
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Affiliation(s)
| | | | | | - Eric Chevaux
- Lallemand SAS, 19 rue des Briquetiers, Blagnac, France
| | - Julia Plateau
- Lallemand SAS, 19 rue des Briquetiers, Blagnac, France
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13
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Chettri D, Verma AK. Statistical optimization of cellulase production from Bacillus sp. YE16 isolated from yak dung of the Sikkim Himalayas for its application in bioethanol production using pretreated sugarcane bagasse. Microbiol Res 2024; 281:127623. [PMID: 38301380 DOI: 10.1016/j.micres.2024.127623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 11/03/2023] [Accepted: 01/13/2024] [Indexed: 02/03/2024]
Abstract
Cellulolytic bacteria were isolated from yak dung samples collected from different habitats of Sikkim, India. Isolate YE16 from the Yumthang Valley sample showed highest enzyme activity of 7.68 U/mL and was identified as Bacillus sp., which has a sequence similarity of 96.15% with B. velezensis. One factor at a time (OFAT) analysis revealed that an acidic pH of 5 with 37 °C temperature was optimum for maximum enzyme production after 36 hrs of incubation (13.88 U/mL), which was further increased after statistical optimization (34.70 U/mL). Media optimization based on response surface methodology predicted that Carboxymethyl cellulose (CMC) and MgSO4 at concentrations of 30 g/L and 0.525 g/L, respectively, at pH 5.5 to show CMCase activity of 30.612 U/mL, which was consistent with the observed value of 30.25 U/mL and confirmed the model. The crude enzyme also efficiently hydrolyzed alkaline pretreated sugarcane bagasse, releasing 7.09 g/L of glucose equivalent with an ethanol production of 3.05 g.
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Affiliation(s)
- Dixita Chettri
- Department of Microbiology, Sikkim University, Gangtok 737102, Sikkim, India
| | - Anil Kumar Verma
- Department of Microbiology, Sikkim University, Gangtok 737102, Sikkim, India.
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14
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Jiang B, Qin C, Xu Y, Song X, Fu Y, Li R, Liu Q, Shi D. Multi-omics reveals the mechanism of rumen microbiome and its metabolome together with host metabolome participating in the regulation of milk production traits in dairy buffaloes. Front Microbiol 2024; 15:1301292. [PMID: 38525073 PMCID: PMC10959287 DOI: 10.3389/fmicb.2024.1301292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 02/14/2024] [Indexed: 03/26/2024] Open
Abstract
Recently, it has been discovered that certain dairy buffaloes can produce higher milk yield and milk fat yield under the same feeding management conditions, which is a potential new trait. It is unknown to what extent, the rumen microbiome and its metabolites, as well as the host metabolism, contribute to milk yield and milk fat yield. Therefore, we will analyze the rumen microbiome and host-level potential regulatory mechanisms on milk yield and milk fat yield through rumen metagenomics, rumen metabolomics, and serum metabolomics experiments. Microbial metagenomics analysis revealed a significantly higher abundance of several species in the rumen of high-yield dairy buffaloes, which mainly belonged to genera, such as Prevotella, Butyrivibrio, Barnesiella, Lachnospiraceae, Ruminococcus, and Bacteroides. These species contribute to the degradation of diets and improve functions related to fatty acid biosynthesis and lipid metabolism. Furthermore, the rumen of high-yield dairy buffaloes exhibited a lower abundance of methanogenic bacteria and functions, which may produce less methane. Rumen metabolome analysis showed that high-yield dairy buffaloes had significantly higher concentrations of metabolites, including lipids, carbohydrates, and organic acids, as well as volatile fatty acids (VFAs), such as acetic acid and butyric acid. Meanwhile, several Prevotella, Butyrivibrio, Barnesiella, and Bacteroides species were significantly positively correlated with these metabolites. Serum metabolome analysis showed that high-yield dairy buffaloes had significantly higher concentrations of metabolites, mainly lipids and organic acids. Meanwhile, several Prevotella, Bacteroides, Barnesiella, Ruminococcus, and Butyrivibrio species were significantly positively correlated with these metabolites. The combined analysis showed that several species were present, including Prevotella.sp.CAG1031, Prevotella.sp.HUN102, Prevotella.sp.KHD1, Prevotella.phocaeensis, Butyrivibrio.sp.AE3009, Barnesiella.sp.An22, Bacteroides.sp.CAG927, and Bacteroidales.bacterium.52-46, which may play a crucial role in rumen and host lipid metabolism, contributing to milk yield and milk fat yield. The "omics-explainability" analysis revealed that the rumen microbial composition, functions, metabolites, and serum metabolites contributed 34.04, 47.13, 39.09, and 50.14%, respectively, to milk yield and milk fat yield. These findings demonstrate how the rumen microbiota and host jointly affect milk production traits in dairy buffaloes. This information is essential for developing targeted feeding management strategies to improve the quality and yield of buffalo milk.
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Affiliation(s)
- Bingxing Jiang
- School of Animal Science and Technology, Guangxi University, Nanning, China
| | - Chaobin Qin
- School of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yixue Xu
- School of Animal Science and Technology, Guangxi University, Nanning, China
| | - Xinhui Song
- School of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yiheng Fu
- School of Animal Science and Technology, Guangxi University, Nanning, China
| | - Ruijia Li
- School of Animal Science and Technology, Guangxi University, Nanning, China
| | - Qingyou Liu
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Deshun Shi
- School of Animal Science and Technology, Guangxi University, Nanning, China
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15
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Yu S, Zhao Y, Li L, Zhao H, Liu M, Jiang L. Flavonoids from citrus peel display potential synergistic effects on inhibiting rumen methanogenesis and ammoniagenesis: a microbiome perspective. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:21208-21223. [PMID: 38383931 DOI: 10.1007/s11356-024-32509-5] [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: 10/27/2023] [Accepted: 02/13/2024] [Indexed: 02/23/2024]
Abstract
Flavonoids have been recognized as potential phytochemicals to reduce enteric methane (CH4) production and improve rumen nitrogen efficiency in ruminants. We evaluated whether naringin, hesperidin, their combination, or a mixed citrus flavonoid extract (CFE) as additives can inhibit methanogenesis and ammoniagenesis in dairy cows using an in vitro rumen batch refermentation system. The rumen inocula from dairy cows were incubated in batch cultures with five groups: no addition (CON), hesperidin (20 g/kg DM), naringin (20 g/kg DM), hesperidin + naringin (10 g/kg DM of hesperidin + 10 g/kg DM of naringin), and CFE (20 g/kg DM). The combination of naringin plus hesperidin and CFE achieved greater reductions in CH4 and ammonia production compared to either naringin or hesperidin alone. Microbiome analysis revealed that the decrease in CH4 emissions may have been caused by both the direct inhibitory impact of citrus flavonoids on Methanobrevibacter and a simultaneous decrease in protozoa Isotricha abundance. The relatively lower proportion of Entodinium in naringin plus hesperidin or CFE was responsible for the lower ammonia concentration. These results suggest that citrus flavonoids possess potential synergistic effects on mitigating ruminal CH4 emissions by cows and improving nitrogen utilization.
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Affiliation(s)
- Shiqiang Yu
- Beijing Key Laboratory of Dairy Cow Nutrition, Animal Science and Technology College, Beijing University of Agriculture, No.7 Beinong Road, Changping District, Beijing, 102206, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuchao Zhao
- Beijing Key Laboratory of Dairy Cow Nutrition, Animal Science and Technology College, Beijing University of Agriculture, No.7 Beinong Road, Changping District, Beijing, 102206, China
| | - Liuxue Li
- Beijing Key Laboratory of Dairy Cow Nutrition, Animal Science and Technology College, Beijing University of Agriculture, No.7 Beinong Road, Changping District, Beijing, 102206, China
| | - Huiying Zhao
- Beijing Key Laboratory of Dairy Cow Nutrition, Animal Science and Technology College, Beijing University of Agriculture, No.7 Beinong Road, Changping District, Beijing, 102206, China
| | - Ming Liu
- Beijing Key Laboratory of Dairy Cow Nutrition, Animal Science and Technology College, Beijing University of Agriculture, No.7 Beinong Road, Changping District, Beijing, 102206, China
| | - Linshu Jiang
- Beijing Key Laboratory of Dairy Cow Nutrition, Animal Science and Technology College, Beijing University of Agriculture, No.7 Beinong Road, Changping District, Beijing, 102206, China.
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16
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Keum GB, Pandey S, Kim ES, Doo H, Kwak J, Ryu S, Choi Y, Kang J, Kim S, Kim HB. Understanding the Diversity and Roles of the Ruminal Microbiome. J Microbiol 2024; 62:217-230. [PMID: 38662310 DOI: 10.1007/s12275-024-00121-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 04/26/2024]
Abstract
The importance of ruminal microbiota in ruminants is emphasized, not only as a special symbiotic relationship with ruminants but also as an interactive and dynamic ecosystem established by the metabolites of various rumen microorganisms. Rumen microbial community is essential for life maintenance and production as they help decompose and utilize fiber that is difficult to digest, supplying about 70% of the energy needed by the host and 60-85% of the amino acids that reach the small intestine. Bacteria are the most abundant in the rumen, but protozoa, which are relatively large, account for 40-50% of the total microorganisms. However, the composition of these ruminal microbiota is not conserved or constant throughout life and is greatly influenced by the host. It is known that the initial colonization of calves immediately after birth is mainly influenced by the mother, and later changes depending on various factors such as diet, age, gender and breed. The initial rumen microbial community contains aerobic and facultative anaerobic bacteria due to the presence of oxygen, but as age increases, a hypoxic environment is created inside the rumen, and anaerobic bacteria become dominant in the rumen microbial community. As calves grow, taxonomic diversity increases, especially as they begin to consume solid food. Understanding the factors affecting the rumen microbial community and their effects and changes can lead to the early development and stabilization of the microbial community through the control of rumen microorganisms, and is expected to ultimately help improve host productivity and efficiency.
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Affiliation(s)
- Gi Beom Keum
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Sriniwas Pandey
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Eun Sol Kim
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Hyunok Doo
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Jinok Kwak
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Sumin Ryu
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Yejin Choi
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Juyoun Kang
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Sheena Kim
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea.
| | - Hyeun Bum Kim
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea.
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17
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Dhakal R, Neves ALA, Sapkota R, Khanal P, Ellegaard-Jensen L, Winding A, Hansen HH. Temporal dynamics of volatile fatty acids profile, methane production, and prokaryotic community in an in vitro rumen fermentation system fed with maize silage. Front Microbiol 2024; 15:1271599. [PMID: 38444805 PMCID: PMC10912478 DOI: 10.3389/fmicb.2024.1271599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 02/01/2024] [Indexed: 03/07/2024] Open
Abstract
Anaerobic in vitro fermentation is widely used to simulate rumen kinetics and study the microbiome and metabolite profiling in a controlled lab environment. However, a better understanding of the interplay between the temporal dynamics of fermentation kinetics, metabolic profiles, and microbial composition in in vitro rumen fermentation batch systems is required. To fill that knowledge gap, we conducted three in vitro rumen fermentations with maize silage as the substrate, monitoring total gas production (TGP), dry matter degradability (dDM), and methane (CH4) concentration at 6, 12, 24, 36, and 48 h in each fermentation. At each time point, we collected rumen fluid samples for microbiome analysis and volatile fatty acid (VFA) analysis. Amplicon sequencing of 16S rRNA genes (V4 region) was used to profile the prokaryotic community structure in the rumen during the fermentation process. As the fermentation time increased, dDM, TGP, VFA concentrations, CH4 concentration, and yield (mL CH4 per g DM at standard temperature and pressure (STP)) significantly increased. For the dependent variables, CH4 concentration and yield, as well as the independent variables TGP and dDM, polynomial equations were fitted. These equations explained over 85% of the data variability (R2 > 0.85) and suggest that TGP and dDM can be used as predictors to estimate CH4 production in rumen fermentation systems. Microbiome analysis revealed a dominance of Bacteroidota, Cyanobacteria, Desulfobacterota, Euryarchaeota, Fibrobacterota, Firmicutes, Patescibacteria, Proteobacteria, Spirochaetota, and Verrucomicrobiota. Significant temporal variations in Bacteroidota, Campylobacterota, Firmicutes, Proteobacteria, and Spirochaetota were detected. Estimates of alpha diversity based on species richness and the Shannon index showed no variation between fermentation time points. This study demonstrated that the in vitro fermentation characteristics of a given feed type (e.g., maize silage) can be predicted from a few parameters (CH4 concentration and yield, tVFA, acetic acid, and propionic acid) without running the actual in vitro trial if the rumen fluid is collected from similar donor cows. Although the dynamics of the rumen prokaryotes changed remarkably over time and in accordance with the fermentation kinetics, more time points between 0 and 24 h are required to provide more details about the microbial temporal dynamics at the onset of the fermentation.
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Affiliation(s)
- Rajan Dhakal
- Department of Veterinary and Animal Sciences, Production, Nutrition and Health, University of Copenhagen, Frederiksberg, Denmark
| | - André Luis Alves Neves
- Department of Veterinary and Animal Sciences, Production, Nutrition and Health, University of Copenhagen, Frederiksberg, Denmark
| | - Rumakanta Sapkota
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Prabhat Khanal
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | | | - Anne Winding
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Hanne Helene Hansen
- Department of Veterinary and Animal Sciences, Production, Nutrition and Health, University of Copenhagen, Frederiksberg, Denmark
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Roques S, Martinez-Fernandez G, Ramayo-Caldas Y, Popova M, Denman S, Meale SJ, Morgavi DP. Recent Advances in Enteric Methane Mitigation and the Long Road to Sustainable Ruminant Production. Annu Rev Anim Biosci 2024; 12:321-343. [PMID: 38079599 DOI: 10.1146/annurev-animal-021022-024931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Mitigation of methane emission, a potent greenhouse gas, is a worldwide priority to limit global warming. A substantial part of anthropogenic methane is emitted by the livestock sector, as methane is a normal product of ruminant digestion. We present the latest developments and challenges ahead of the main efficient mitigation strategies of enteric methane production in ruminants. Numerous mitigation strategies have been developed in the last decades, from dietary manipulation and breeding to targeting of methanogens, the microbes that produce methane. The most recent advances focus on specific inhibition of key enzymes involved in methanogenesis. But these inhibitors, although efficient, are not affordable and not adapted to the extensive farming systems prevalent in low- and middle-income countries. Effective global mitigation of methane emissions from livestock should be based not only on scientific progress but also on the feasibility and accessibility of mitigation strategies.
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Affiliation(s)
- Simon Roques
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, Saint-Genes-Champanelle, France; , ,
| | | | - Yuliaxis Ramayo-Caldas
- Animal Breeding and Genetics Program, Institute of Agrifood Research and Technology (IRTA), Torre Marimon, Caldes de Montbui, Spain;
| | - Milka Popova
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, Saint-Genes-Champanelle, France; , ,
| | - Stuart Denman
- Agriculture and Food, CSIRO, St. Lucia, Queensland, Australia; ,
| | - Sarah J Meale
- School of Agriculture and Food Sustainability, Faculty of Science, University of Queensland, Gatton, Queensland, Australia;
| | - Diego P Morgavi
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, Saint-Genes-Champanelle, France; , ,
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19
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Alem WT. Effect of herbal extracts in animal nutrition as feed additives. Heliyon 2024; 10:e24973. [PMID: 38322944 PMCID: PMC10845724 DOI: 10.1016/j.heliyon.2024.e24973] [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: 12/29/2022] [Revised: 12/01/2023] [Accepted: 01/17/2024] [Indexed: 02/08/2024] Open
Abstract
This paper is reviewed with the objective to understand the effect of herbal extracts on animal performance as feed additives. The number of both external and internal factors which affects the production and productivity of animals obviously includes nutrition as a major factor. Feed additives are products used in animal nutrition to increase the quality of feed and animal-derived foods, as well as the performance and the health of animals. Plant extracts as feed additives are described as herbal-derived components added to ration to improve livestock performance and product quality. Many herbal extracts contain chemical components that have antioxidant, antimicrobial, anti-inflammatory, anticoccidial and anthelmintic properties to improve ruminal microbial activity, diet palatability and stimulate digestion. Bioactive chemicals found in nature, such as flavonoids and glucosinolates isoprene derivatives, are primarily responsible for the qualities of plant extracts. Plant extracts are commonly added to feed to increase palatability, productivity and to inhibit lipid oxidation. When added to meals, herbal extracts aid to decrease rancidity, delay the generation of hazardous oxidation products, and retain nutritional quality. It is concluded that; herbal extracts are important to improve growth performance and product quality.
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20
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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.
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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
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21
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van Gastelen S, Yáñez-Ruiz D, Khelil-Arfa H, Blanchard A, Bannink A. Effect of a blend of cinnamaldehyde, eugenol, and Capsicum oleoresin on methane emission and lactation performance of Holstein-Friesian dairy cows. J Dairy Sci 2024; 107:857-869. [PMID: 37709037 DOI: 10.3168/jds.2023-23406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 08/23/2023] [Indexed: 09/16/2023]
Abstract
This study aimed to investigate the effect of administering a standardized blend of cinnamaldehyde, eugenol, and Capsicum oleoresin (CEC) to lactating dairy cattle for 84 d (i.e., 12 wk) on enteric CH4 emission, feed intake, milk yield and composition, and body weight. The experiment involved 56 Holstein-Friesian dairy cows (145 ± 31.1 d in milk at the start of the trial; mean ± standard deviation) in a randomized complete block design. Cows were blocked in pairs according to parity, lactation stage, and current milk yield, and randomly allocated to 1 of the 2 dietary treatments: a diet including 54.5 mg of CEC/kg of DM or a control diet without CEC. Diets were provided as partial mixed rations in feed bins, which automatically recorded individual feed intake. Additional concentrate was fed in the GreenFeed system that was used to measure emissions of CO2, CH4, and H2. Feeding CEC decreased CH4 yield (g/kg DMI) by on average 3.4% over the complete 12-wk period and by on average 3.9% from 6 wk after the start of supplementation onward. Feeding CEC simultaneously increased feed intake and body weight, and tended to increase milk protein content, whereas no negative responses were observed. These results must be further investigated and confirmed in longer-term in vivo experiments.
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Affiliation(s)
- Sanne van Gastelen
- Wageningen Livestock Research, Wageningen University & Research, 6700 AH Wageningen, the Netherlands.
| | | | | | | | - André Bannink
- Wageningen Livestock Research, Wageningen University & Research, 6700 AH Wageningen, the Netherlands
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22
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Zhao Y, Yu S, Tan J, Wang Y, Li L, Zhao H, Liu M, Jiang L. Bioconversion of citrus waste by long-term DMSO-cryopreserved rumen fluid to volatile fatty acids and biogas is feasible: A microbiome perspective. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 351:119693. [PMID: 38042069 DOI: 10.1016/j.jenvman.2023.119693] [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: 07/09/2023] [Revised: 11/07/2023] [Accepted: 11/21/2023] [Indexed: 12/04/2023]
Abstract
Preserving rumen fluid as the inoculum for anaerobic digestion of food waste is necessary when access to animal donors or slaughterhouses is limited. This study aims to compare two preservation methods relative to fresh ruminal inoculum: (1) cryoprotected with 5% dimethyl sulfoxide (DMSO) and stored at -20 °C and (2) frozen at -20 °C, both for 6 months. The fermentation activity of different inoculum was evaluated by rumen-based in vitro anaerobic fermentation tests (volatile fatty acids, biomass digestibility, and gas production). Citrus pomace was used as the substrate during a 96-h fermentation. The maximum volatile fatty acids, methane production, and citrus pomace digestibility from fresh rumen fluid were not significantly different from rumen fluid preserved with DMSO. Metagenome analysis revealed a significant difference in the rumen microbial composition and functions between fresh rumen fluid and frozen inoculum without DMSO. Storage of rumen fluid using -20 °C with DMSO demonstrated the less difference compared with fresh rumen fluid in microbial alpha diversity and taxa composition. The hierarchical clustering tree of CAZymes showed that DMSO cryoprotected fluid was clustered much closer to the fresh rumen fluid, showing more similarity in CAZyme profiles than frozen rumen fluid. The abundance of functional genes associated with carbohydrate metabolism and methane metabolism did not differ between fresh rumen fluid and the DMSO-20 °C, whereas the abundance of key functional genes significantly decreased in frozen rumen fluid. These findings suggest that using rumen liquid preserved using DMSO at -20 °C for 180 days is a feasible alternative to fresh rumen fluid. This would reduce the need for laboratories to maintain animal donors and/or reduce the frequency of collecting rumen fluid from slaughterhouses.
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Affiliation(s)
- Yuchao Zhao
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Shiqiang Yu
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Jian Tan
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Ying Wang
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Liuxue Li
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Huiying Zhao
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Ming Liu
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Linshu Jiang
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing, 102206, China.
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23
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Qi W, Xue MY, Jia MH, Zhang S, Yan Q, Sun HZ. - Invited Review - Understanding the functionality of the rumen microbiota: searching for better opportunities for rumen microbial manipulation. Anim Biosci 2024; 37:370-384. [PMID: 38186256 PMCID: PMC10838668 DOI: 10.5713/ab.23.0308] [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: 08/17/2023] [Accepted: 11/03/2023] [Indexed: 01/09/2024] Open
Abstract
Rumen microbiota play a central role in the digestive process of ruminants. Their remarkable ability to break down complex plant fibers and proteins, converting them into essential organic compounds that provide animals with energy and nutrition. Research on rumen microbiota not only contributes to improving animal production performance and enhancing feed utilization efficiency but also holds the potential to reduce methane emissions and environmental impact. Nevertheless, studies on rumen microbiota face numerous challenges, including complexity, difficulties in cultivation, and obstacles in functional analysis. This review provides an overview of microbial species involved in the degradation of macromolecules, the fermentation processes, and methane production in the rumen, all based on cultivation methods. Additionally, the review introduces the applications, advantages, and limitations of emerging omics technologies such as metagenomics, metatranscriptomics, metaproteomics, and metabolomics, in investigating the functionality of rumen microbiota. Finally, the article offers a forward-looking perspective on the new horizons and technologies in the field of rumen microbiota functional research. These emerging technologies, with continuous refinement and mutual complementation, have deepened our understanding of rumen microbiota functionality, thereby enabling effective manipulation of the rumen microbial community.
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Affiliation(s)
- Wenlingli Qi
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ming-Yuan Xue
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ming-Hui Jia
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shuxian Zhang
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Qiongxian Yan
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Hui-Zeng Sun
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
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24
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Lawther K, Santos FG, Oyama LB, Huws SA. - Invited Review - Chemical signalling within the rumen microbiome. Anim Biosci 2024; 37:337-345. [PMID: 38186253 PMCID: PMC10838665 DOI: 10.5713/ab.23.0374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/24/2023] [Accepted: 12/12/2023] [Indexed: 01/09/2024] Open
Abstract
Ruminants possess a specialized four-compartment forestomach, consisting of the reticulum, rumen, omasum, and abomasum. The rumen, the primary fermentative chamber, harbours a dynamic ecosystem comprising bacteria, protozoa, fungi, archaea, and bacteriophages. These microorganisms engage in diverse ecological interactions within the rumen microbiome, primarily benefiting the host animal by deriving energy from plant material breakdown. These interactions encompass symbiosis, such as mutualism and commensalism, as well as parasitism, predation, and competition. These ecological interactions are dependent on many factors, including the production of diverse molecules, such as those involved in quorum sensing (QS). QS is a density-dependent signalling mechanism involving the release of autoinducer (AIs) compounds, when cell density increases AIs bind to receptors causing the altered expression of certain genes. These AIs are classified as mainly being N-acyl-homoserine lactones (AHL; commonly used by Gram-negative bacteria) or autoinducer-2 based systems (AI-2; used by Gram-positive and Gram-negative bacteria); although other less common AI systems exist. Most of our understanding of QS at a gene-level comes from pure culture in vitro studies using bacterial pathogens, with much being unknown on a commensal bacterial and ecosystem level, especially in the context of the rumen microbiome. A small number of studies have explored QS in the rumen using 'omic' technologies, revealing a prevalence of AI-2 QS systems among rumen bacteria. Nevertheless, the implications of these signalling systems on gene regulation, rumen ecology, and ruminant characteristics are largely uncharted territory. Metatranscriptome data tracking the colonization of perennial ryegrass by rumen microbes suggest that these chemicals may influence transitions in bacterial diversity during colonization. The likelihood of undiscovered chemicals within the rumen microbial arsenal is high, with the identified chemicals representing only the tip of the iceberg. A comprehensive grasp of rumen microbial chemical signalling is crucial for addressing the challenges of food security and climate targets.
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Affiliation(s)
- Katie Lawther
- School of Biological Sciences/Institute for Global Food Security, Queen’s University Belfast, Belfast, BT9 5DL,
UK
| | - Fernanda Godoy Santos
- School of Biological Sciences/Institute for Global Food Security, Queen’s University Belfast, Belfast, BT9 5DL,
UK
| | - Linda B Oyama
- School of Biological Sciences/Institute for Global Food Security, Queen’s University Belfast, Belfast, BT9 5DL,
UK
| | - Sharon A Huws
- School of Biological Sciences/Institute for Global Food Security, Queen’s University Belfast, Belfast, BT9 5DL,
UK
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25
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Ricci S, Pacífico C, Kreuzer-Redmer S, Castillo-Lopez E, Rivera-Chacon R, Sener-Aydemir A, Rossi G, Galosi L, Biagini L, Schwartz-Zimmermann HE, Berthiller F, Reisinger N, Petri RM, Zebeli Q. Integrated microbiota-host-metabolome approaches reveal adaptive ruminal changes to prolonged high-grain feeding and phytogenic supplementation in cattle. FEMS Microbiol Ecol 2024; 100:fiae006. [PMID: 38281064 PMCID: PMC10858391 DOI: 10.1093/femsec/fiae006] [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: 04/17/2023] [Revised: 11/30/2023] [Accepted: 01/25/2024] [Indexed: 01/29/2024] Open
Abstract
Diets rich in readily fermentable carbohydrates primarily impact microbial composition and activity, but can also impair the ruminal epithelium barrier function. By combining microbiota, metabolome, and gene expression analysis, we evaluated the impact of feeding a 65% concentrate diet for 4 weeks, with or without a phytogenic feed additive (PFA), on the rumen ecosystem of cattle. The breaking point for rumen health seemed to be the second week of high grain (HG) diet, with a dysbiosis characterized by reduced alpha diversity. While we did not find changes in histological evaluations, genes related with epithelial proliferation (IGF-1, IGF-1R, EGFR, and TBP) and ZO-1 were affected by the HG feeding. Integrative analyses allowed us to define the main drivers of difference for the rumen ecosystem in response to a HG diet, identified as ZO-1, MyD88, and genus Prevotella 1. PFA supplementation reduced the concentration of potentially harmful compounds in the rumen (e.g. dopamine and 5-aminovaleric acid) and increased the tolerance of the epithelium toward the microbiota by altering the expression of TLR-2, IL-6, and IL-10. The particle-associated rumen liquid microbiota showed a quicker adaptation potential to prolonged HG feeding compared to the other microenvironments investigated, especially by the end of the experiment.
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Affiliation(s)
- Sara Ricci
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Cátia Pacífico
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Susanne Kreuzer-Redmer
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Ezequias Castillo-Lopez
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Raul Rivera-Chacon
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Arife Sener-Aydemir
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Giacomo Rossi
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Circonvallazione, 93/95, 62024 Matelica, MC, Italy
| | - Livio Galosi
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Circonvallazione, 93/95, 62024 Matelica, MC, Italy
| | - Lucia Biagini
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Circonvallazione, 93/95, 62024 Matelica, MC, Italy
| | - Heidi E Schwartz-Zimmermann
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Konrad-Lorenz-Straße 20, 3430 Tulln an der Donau, Austria
| | - Franz Berthiller
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Konrad-Lorenz-Straße 20, 3430 Tulln an der Donau, Austria
| | - Nicole Reisinger
- dsm-firmenich,
Animal Health and Nutrition R&D Center, Technopark 1, 3430 Tulln an der Donau, Austria
| | - Renee M Petri
- Agriculture and Agri-Food Canada,
Sherbrooke Research and Development Centre, 2000 College Street, Sherbrooke, Quebec J1M 0C8, Canada
| | - Qendrim Zebeli
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
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26
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Cabral LDS, Weimer PJ. Megasphaera elsdenii: Its Role in Ruminant Nutrition and Its Potential Industrial Application for Organic Acid Biosynthesis. Microorganisms 2024; 12:219. [PMID: 38276203 PMCID: PMC10819428 DOI: 10.3390/microorganisms12010219] [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: 12/27/2023] [Revised: 01/15/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
The Gram-negative, strictly anaerobic bacterium Megasphaera elsdenii was first isolated from the rumen in 1953 and is common in the mammalian gastrointestinal tract. Its ability to use either lactate or glucose as its major energy sources for growth has been well documented, although it can also ferment amino acids into ammonia and branched-chain fatty acids, which are growth factors for other bacteria. The ruminal abundance of M. elsdenii usually increases in animals fed grain-based diets due to its ability to use lactate (the product of rapid ruminal sugar fermentation), especially at a low ruminal pH (<5.5). M. elsdenii has been proposed as a potential dietary probiotic to prevent ruminal acidosis in feedlot cattle and high-producing dairy cows. However, this bacterium has also been associated with milk fat depression (MFD) in dairy cows, although proving a causative role has remained elusive. This review summarizes the unique physiology of this intriguing bacterium and its functional role in the ruminal community as well as its role in the health and productivity of the host animal. In addition to its effects in the rumen, the ability of M. elsdenii to produce C2-C7 carboxylic acids-potential precursors for industrial fuel and chemical production-is examined.
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Affiliation(s)
- Luciano da Silva Cabral
- Department of Animal Science and Rural Extension, Agronomy and Animal Science School, Federal University of Mato Grosso, Cuiabá 780600-900, Mato Grosso, Brazil;
| | - Paul J. Weimer
- Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA
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27
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Fu L, Liu L, Zhang L, Hu Y, Zeng Y, Ran Q, Zhou Y, Zhou P, Chen J, Loor JJ, Wang G, Dong X. Inoculation of Newborn Lambs with Ruminal Solids Derived from Adult Goats Reprograms the Development of Gut Microbiota and Serum Metabolome and Favors Growth Performance. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:983-998. [PMID: 38189273 PMCID: PMC10797616 DOI: 10.1021/acs.jafc.3c04632] [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: 07/06/2023] [Revised: 12/05/2023] [Accepted: 12/22/2023] [Indexed: 01/09/2024]
Abstract
Microbial transplantation in early life was a strategy to optimize the health and performance of livestock animals. This study aimed to investigate the effect of active ruminal solids microorganism supplementation on newborn lamb gut microbiota and serum metabolism. Twenty-four Youzhou dark newborn lambs were randomly divided into three groups: (1) newborn lambs fed with sterilized goat milk inoculated with sterilized normal saline (CON), supernatant from ruminal solids (SRS), or autoclaved supernatant from ruminal solids (ASRS). Results showed that SRS increased gut bacterial richness and community, downregulating the Firmicutes/Bacteroidetes ratio, and increased the abundance of some probiotics (Bacteroidetes, Spirochaetota, and Fibrobacterota), while reducing the abundance of Fusobacteriota, compared to the CON group. SRS also improved the plasma metabolic function, such as arachidonic acid metabolism, primary bile acid biosynthesis, and tryptophan metabolism and then actively promoted the levels of ALP and HLD. Our study indicated that inoculation with active ruminal solids significantly affected the intestinal microbial communities and metabolic characteristics, and these changes can improve the growing health of the newborn lamb. These findings provided an experimental and theoretical basis for the application of ruminal solid-attached microorganisms in the nutritional management of lambs reared for human consumption.
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Affiliation(s)
- Lin Fu
- Chongqing Academy
of Animal Sciences, Chongqing 402460, China
| | - Li Liu
- Chongqing Chemical Industry Vocational College, Chongqing 401228, China
- Chongqing Industry Polytechnic College, Chongqing 401127, China
| | - Li Zhang
- Chongqing Academy
of Animal Sciences, Chongqing 402460, China
| | - Yonghui Hu
- Wushan Animal Husbandry
Technology Promotion Station, Chongqing 404700, China
| | - Yu Zeng
- Chongqing Academy
of Animal Sciences, Chongqing 402460, China
| | - Qifan Ran
- Chongqing Academy
of Animal Sciences, Chongqing 402460, China
| | - Yan Zhou
- Chongqing Academy
of Animal Sciences, Chongqing 402460, China
| | - Peng Zhou
- Chongqing Academy
of Animal Sciences, Chongqing 402460, China
| | - Juncai Chen
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Juan J. Loor
- Mammalian
NutriPhysioGenomics, Department of Animal Sciences and Division of
Nutritional Sciences, University of Illinois, Urbana, Illinois 61801, United States
| | - Gaofu Wang
- Chongqing Academy
of Animal Sciences, Chongqing 402460, China
| | - Xianwen Dong
- Chongqing Academy
of Animal Sciences, Chongqing 402460, China
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Qiu S, Li K, He X, Gu M, Jiang X, Lu J, Ma Z, Liang X, Gan Q. The Effects of Composite Alkali-Stored Spent Hypsizygus marmoreus Substrate on Carcass Quality, Rumen Fermentation, and Rumen Microbial Diversity in Goats. Animals (Basel) 2024; 14:166. [PMID: 38200897 PMCID: PMC10778354 DOI: 10.3390/ani14010166] [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: 11/26/2023] [Revised: 12/21/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
The objective of this study was to investigate the effects of composite alkali-stored spent Hypsizygus marmoreus substrate (SHMS) on carcass quality, rumen fermentation, and rumen microbial diversity in goats. Twenty-four 6-month-old Chuanzhong black goats with similar body weights (20 ± 5 kg) were selected and randomly divided into four groups (n = 6 per group) and received four treatments: 0% (control group, CG); 20% (low-addition group, LG); 30% (moderate-addition group, MG); and 40% (high-addition group, HG) of SHMS-replaced silage corn and oat hay. The experiment lasted for 74 days (including a 14 d adaptation period and a 60 d treatment period). The results of this study showed that MG and HG significantly improved the marble score of goat meat (p < 0.05). The flesh color score significantly increased in each group (p < 0.05). The fat color scores significantly increased in LG and MG (p < 0.05). There were no significant effects on the pH value or shear force of the longissimus dorsi in each group (p > 0.05). The cooking loss in MG was higher than that in CG (p < 0.05). The histidine and tyrosine contents in each group of muscles significantly increased (p < 0.05), with no significant effect on fatty acids (p > 0.05). The rumen pH of MG significantly decreased (p < 0.05), while the total volatile fatty acids (TVFAs) and ammoniacal nitrogen (NH3-N) increased by 44.63% and 54.50%, respectively. The addition of the SHMS altered both the alpha and beta diversities of the rumen microbiota and significant differences in the composition and structure of the four microbial communities. The dominant bacterial phylum in each group were Firmicutes and Bacteroidetes, with Prevotella 1 as the dominant bacterial genus. Correlation analysis revealed that rumen bacteria are closely related to the animal carcass quality and rumen fermentation. In the PICRUSt prediction, 21 significantly different pathways were found, and the correlation network showed a positive correlation between the Prevotella 1 and 7 metabolic pathways, while the C5-branched dibasic acid metabolism was positively correlated with nine bacteria. In summary, feeding goats with an SHMS diet can improve the carcass quality, promote rumen fermentation, and alter the microbial structure. The research results can provide a scientific reference for the utilization of SHMS as feed in the goat industry.
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Affiliation(s)
- Shuiling Qiu
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.Q.); (K.L.); (X.H.); (M.G.); (X.J.); (J.L.); (Z.M.)
| | - Keyao Li
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.Q.); (K.L.); (X.H.); (M.G.); (X.J.); (J.L.); (Z.M.)
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Xiangbo He
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.Q.); (K.L.); (X.H.); (M.G.); (X.J.); (J.L.); (Z.M.)
| | - Mingming Gu
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.Q.); (K.L.); (X.H.); (M.G.); (X.J.); (J.L.); (Z.M.)
| | - Xinghui Jiang
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.Q.); (K.L.); (X.H.); (M.G.); (X.J.); (J.L.); (Z.M.)
| | - Jianing Lu
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.Q.); (K.L.); (X.H.); (M.G.); (X.J.); (J.L.); (Z.M.)
| | - Zhiyi Ma
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.Q.); (K.L.); (X.H.); (M.G.); (X.J.); (J.L.); (Z.M.)
| | - Xuewu Liang
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.Q.); (K.L.); (X.H.); (M.G.); (X.J.); (J.L.); (Z.M.)
| | - Qianfu Gan
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.Q.); (K.L.); (X.H.); (M.G.); (X.J.); (J.L.); (Z.M.)
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Belanche A, Palma-Hidalgo JM, Jiménez E, Yáñez-Ruiz DR. Enhancing rumen microbial diversity and its impact on energy and protein metabolism in forage-fed goats. Front Vet Sci 2023; 10:1272835. [PMID: 38179333 PMCID: PMC10764530 DOI: 10.3389/fvets.2023.1272835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/05/2023] [Indexed: 01/06/2024] Open
Abstract
Introduction This study explores if promoting a complex rumen microbiota represents an advantage or a handicap in the current dairy production systems in which ruminants are artificially reared in absence of contact with adult animals and fed preserved monophyte forage. Methods In order to promote a different rumen microbial diversity, a total of 36 newborn goat kids were artificially reared, divided in 4 groups and daily inoculated during 10 weeks with autoclaved rumen fluid (AUT), fresh rumen fluid from adult goats adapted to forage (RFF) or concentrate (RFC) diets, or absence of inoculation (CTL). At 6 months of age all animals were shifted to an oats hay diet to determine their ability to digest a low quality forage. Results and discussion Early life inoculation with fresh rumen fluid promoted an increase in the rumen overall microbial diversity which was detected later in life. As a result, at 6 months of age RFF and RFC animals had higher bacterial (+50 OTUs) and methanogens diversity (+4 OTUs) and the presence of a complex rumen protozoal community (+32 OTUs), whereas CTL animals remained protozoa-free. This superior rumen diversity and presence of rumen protozoa had beneficial effects on the energy metabolism allowing a faster adaptation to the forage diet, a higher forage digestion (+21% NDF digestibility) and an energetically favourable shift of the rumen fermentation pattern from acetate to butyrate (+92%) and propionate (+19%) production. These effects were associated with the presence of certain rumen bacterial taxa and a diverse protozoal community. On the contrary, the presence of rumen protozoa (mostly Entodinium) had a negative impact on the N metabolism leading to a higher bacterial protein breakdown in the rumen and lower microbial protein flow to the host based on purine derivatives urinary excretion (-17% to -54%). The inoculation with autoclaved rumen fluid, as source of fermentation products but not viable microbes, had smaller effects than using fresh inoculum. These findings suggest that enhancing rumen microbial diversity represents a desirable attribute when ruminants are fed forages in which the N supply does not represent a limiting factor for the rumen microbiota.
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Affiliation(s)
- Alejandro Belanche
- Estación Experimental del Zaidín (CSIC), Granada, Spain
- Department of Animal Production and Food Sciences, University of Zaragoza, Zaragoza, Spain
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Dixit S, Kumar S, Sharma R, Banakar PS, Singh M, Keshri A, Tyagi AK. Rumen multi-omics addressing diet-host-microbiome interplay in farm animals: a review. Anim Biotechnol 2023; 34:3187-3205. [PMID: 35713100 DOI: 10.1080/10495398.2022.2078979] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Continuous improvement in the living standards of developing countries, calls for an urgent need of high quality meat and dairy products. The farm animals have a micro-ecosystem in gastro-intestinal tract, comprising of a wide variety of flora and fauna which converts roughages and agricultural byproducts as well as nutrient rich concentrate sources into the useful products such as volatile fatty acids and microbial crude proteins. The microbial diversity changes according to composition of the feed, host species/breed and host's individual genetic makeup. From culture methods to next-generation sequencing technologies, the knowledge has emerged a lot to know-how of microbial world viz. their identification, enzymatic activities and metabolites which are the keys of ruminant's successful existence. The structural composition of ruminal community revealed through metagenomics can be elaborated by metatranscriptomics and metabolomics through deciphering their functional role in metabolism and their responses to the external and internal stimuli. These highly sophisticated analytical tools have made possible to correlate the differences in the feed efficiency, nutrients utilization and methane emissions to their rumen microbiome. The comprehensively understood rumen microbiome will enhance the knowledge in the fields of animal nutrition, biotechnology and climatology through deciphering the significance of each and every domain of residing microbial entity. The present review undertakes the recent investigations regarding rumen multi-omics viz. taxonomic and functional potential of microbial populations, host-diet-microbiome interactions and correlation with metabolic dynamics.
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Affiliation(s)
- Sonam Dixit
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - Sachin Kumar
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - Ritu Sharma
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - P S Banakar
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - Manvendra Singh
- Krishi Vigyan Kendra, Banda University of Agriculture and Technology, Banda, India
| | - Anchal Keshri
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - A K Tyagi
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
- Animal Nutrition and Physiology, Indian Council of Agricultural Research, New Delhi, India
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Muñoz-Tamayo R, Davoudkhani M, Fakih I, Robles-Rodriguez CE, Rubino F, Creevey CJ, Forano E. Review: Towards the next-generation models of the rumen microbiome for enhancing predictive power and guiding sustainable production strategies. Animal 2023; 17 Suppl 5:100984. [PMID: 37821326 DOI: 10.1016/j.animal.2023.100984] [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: 11/25/2022] [Revised: 09/01/2023] [Accepted: 09/07/2023] [Indexed: 10/13/2023] Open
Abstract
The rumen ecosystem harbours a galaxy of microbes working in syntrophy to carry out a metabolic cascade of hydrolytic and fermentative reactions. This fermentation process allows ruminants to harvest nutrients from a wide range of feedstuff otherwise inaccessible to the host. The interconnection between the ruminant and its rumen microbiota shapes key animal phenotypes such as feed efficiency and methane emissions and suggests the potential of reducing methane emissions and enhancing feed conversion into animal products by manipulating the rumen microbiota. Whilst significant technological progress in omics techniques has increased our knowledge of the rumen microbiota and its genome (microbiome), translating omics knowledge into effective microbial manipulation strategies remains a great challenge. This challenge can be addressed by modelling approaches integrating causality principles and thus going beyond current correlation-based approaches applied to analyse rumen microbial genomic data. However, existing rumen models are not yet adapted to capitalise on microbial genomic information. This gap between the rumen microbiota available omics data and the way microbial metabolism is represented in the existing rumen models needs to be filled to enhance rumen understanding and produce better predictive models with capabilities for guiding nutritional strategies. To fill this gap, the integration of computational biology tools and mathematical modelling frameworks is needed to translate the information of the metabolic potential of the rumen microbes (inferred from their genomes) into a mathematical object. In this paper, we aim to discuss the potential use of two modelling approaches for the integration of microbial genomic information into dynamic models. The first modelling approach explores the theory of state observers to integrate microbial time series data into rumen fermentation models. The second approach is based on the genome-scale network reconstructions of rumen microbes. For a given microorganism, the network reconstruction produces a stoichiometry matrix of the metabolism. This matrix is the core of the so-called genome-scale metabolic models which can be exploited by a plethora of methods comprised within the constraint-based reconstruction and analysis approaches. We will discuss how these methods can be used to produce the next-generation models of the rumen microbiome.
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Affiliation(s)
- R Muñoz-Tamayo
- Université Paris-Saclay, INRAE, AgroParisTech, UMR Modélisation Systémique Appliquée aux Ruminants, 91120 Palaiseau, France.
| | - M Davoudkhani
- Université Paris-Saclay, INRAE, AgroParisTech, UMR Modélisation Systémique Appliquée aux Ruminants, 91120 Palaiseau, France
| | - I Fakih
- Université Paris-Saclay, INRAE, AgroParisTech, UMR Modélisation Systémique Appliquée aux Ruminants, 91120 Palaiseau, France; Université Clermont Auvergne, INRAE, UMR 454 MEDIS, Clermont-Ferrand, France
| | | | - F Rubino
- Institute of Global Food Security, School of Biological Sciences, Queen's University Belfast, BT9 5DL Northern Ireland, UK
| | - C J Creevey
- Institute of Global Food Security, School of Biological Sciences, Queen's University Belfast, BT9 5DL Northern Ireland, UK
| | - E Forano
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, Clermont-Ferrand, France
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32
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Golder HM, Denman SE, McSweeney C, Celi P, Lean IJ. Effects of feed additives on rumen function and bacterial and archaeal communities during a starch and fructose challenge. J Dairy Sci 2023; 106:8787-8808. [PMID: 37678787 DOI: 10.3168/jds.2023-23486] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/18/2023] [Indexed: 09/09/2023]
Abstract
The objective of this study was to improve understandings of the rumen microbial ecosystem during ruminal acidosis and responses to feed additives to improve prudent use strategies for ruminal acidosis control. Rumen bacterial and archaeal community composition (BCC) and its associations with rumen fermentation measures were examined in Holstein heifers fed feed additives and challenged with starch and fructose. Heifers (n = 40) were randomly allocated to 5 treatment groups: (1) control (no additives); (2) virginiamycin (VM; 200 mg/d); (3) monensin (MT; 200 mg/d) + tylosin (110 mg/d); (4) monensin (MLY; 220 mg/d) + live yeast (5.0 × 1012 cfu/d); (5) sodium bicarbonate (BUF; 200 g/d) + magnesium oxide (30 g/d). Heifers were fed twice daily a 62% forage:38% concentrate total mixed ration at 1.25% of body weight (BW) dry matter (DM)/d for a 20-d adaptation period with their additive(s). Fructose (0.1% of BW/d) was added to the ration for the last 10 d of adaptation. On d 21 heifers were challenged once with a ration consisting of 1.0% of BW DM wheat and 0.2% of BW fructose plus their additive(s). A rumen sample was collected from each heifer via stomach tube weekly (d 0, 7, 14) and 5 times over a 3.6 h period at 5, 65, 115, 165, and 215 min after consumption of the challenge ration (d 21) and analyzed for pH, and ammonia, d- and l-lactate, volatile fatty acids (VFA), and histamine concentrations and total bacteria and archaea. The 16S rRNA gene spanning the V4 region was PCR amplified and sequenced. Alpha and β diversity and associations of relative abundances of taxa with rumen fermentation measures were evaluated. Rumen BCC shifted among treatment groups in the adaptation period and across the challenge sampling period, indicating the feed additives had different modes of action. The monensin-containing treatment groups, MT and MLY often had similar relative abundances of rumen bacterial phyla and families. The MLY treatment group was characterized in the challenge period by increased relative abundances of the lactate utilizing genera Anaerovibrio and Megasphaera. The MLY treatment group also had increased diversity of ruminal bacteria which may provide resilience to changes in substrates. The control and BUF treatment groups were most similar in BCC. A redundancy analysis showed the MLY treatment group differed from all other treatment groups and concentrations of histamine and valerate in the rumen were associated with the most variation in the microbiota, 5.3% and 4.8%, respectively. It was evident from the taxa common to all treatment groups that cattle have a core microbiota. Functional redundancy of rumen bacteria which was reflected in the greater sensitivity for the rumen BCC than rumen fermentation measures likely provide resilience to changes in substrate. This functional redundancy of microbes in cattle suggests that there is no single optimal ruminal microbial population and no universally superior feed additive(s). In summary, differences in modes of action suggest the potential for more targeted and improved prudent use of feed additives with no single feed additive(s) providing an optimal BCC in all heifers.
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Affiliation(s)
- H M Golder
- Scibus, Camden, New South Wales, 2570, Australia; Dairy Science Group, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camden, New South Wales, Australia, 2567.
| | - S E Denman
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD 4067, Australia
| | - C McSweeney
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD 4067, Australia
| | - P Celi
- Melbourne School of Land and Environment, The University of Melbourne, Parkville, VIC 3052, Australia
| | - I J Lean
- Scibus, Camden, New South Wales, 2570, Australia; Dairy Science Group, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camden, New South Wales, Australia, 2567
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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.
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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
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Wang RJ, He SC, Huang D, Wu DW, He SY, Guo TQ, Chen CG, Mao HM. Effects of king grass and rice straw hay on apparent digestibility and ruminal microorganisms of buffalo. Anim Biotechnol 2023; 34:1514-1523. [PMID: 35167410 DOI: 10.1080/10495398.2022.2036748] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
The purpose of this study was to explore the effects of Rice straw and King grass on apparent digestibility, ruminal bacterial, and fungus composition in buffaloes. Three ruminal fistulated buffaloes were used in a 3 × 2 Latin square design. The dietary treatments were king grass and straw hay. Experimental animals were kept in individual pens and concentrate was offered at 1 kg/d while roughage was fed ad libitum. Each period lasted for 15d, with the first 12d for an adaptation period, followed by a 3-day formal trial period. King grass has higher digestibility of protein. Rice straw has higher digestibility to cellulose. The results showed that when buffaloes were fed king grass and straw, Bacteroidetes were dominant in the rumen normal flora, but firmicutes were not. In addition, the results of this experiment suggest that increasing protein content in diets may be beneficial to increase the relative abundance of Proteobacteria. Similarly, higher dietary fiber content may be beneficial for increasing relative abundance of Prevotella and Staphylococcus. The dominant fungi in ruminal fluid 2 h after ingestion were aerobic fungi. These aerobic fungi most likely entered the rumen with food. Whether and how long aerobic fungi can survive in the rumen needs more research.
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Affiliation(s)
- Rong-Jiao Wang
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, P.R. China
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, P.R. China
| | - Shi-Chun He
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, P.R. China
| | - Dan Huang
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, P.R. China
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, P.R. China
| | - Dong-Wang Wu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, P.R. China
| | - Shao-Ying He
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, P.R. China
| | - Tai-Qing Guo
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, P.R. China
| | - Chang-Guo Chen
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, P.R. China
| | - Hua-Ming Mao
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, P.R. China
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Yu J, Li C, Li X, Liu K, Liu Z, Ni W, Zhou P, Wang L, Hu S. Isolation and functional analysis of acid-producing bacteria from bovine rumen. PeerJ 2023; 11:e16294. [PMID: 37868061 PMCID: PMC10590097 DOI: 10.7717/peerj.16294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/22/2023] [Indexed: 10/24/2023] Open
Abstract
Ruminants such as cattle rely mainly on microbes in the rumen to digest cellulose and hemicellulose from forage, and the digestion products are mainly absorbed and utilized by the host in the form of short chain fatty acids (SCFAs). This study aimed to isolate acid-producing strains from the cattle rumen and investigate their functions. A total of 980 strains of acid-producing bacteria were isolated from cattle rumen contents using a medium supplemented with bromocresol green. Combined with the test of acid production ability and 16S rRNA amplicon sequencing technology, five strains were selected based on their ability to produce relatively high levels of acid, including Bacillus pumillus, Enterococcus hirae, Enterococcus faecium, and Bacillus subtilis. Sheep were treated by gavage with a mixed bacterial suspension. The results showed that mixed bacteria significantly increased the body weight gain and feed conversion rate of sheep. To investigate the function of acid-producing bacteria in sheep, we used 16S rDNA sequencing technology to analyze the rumen microbes of sheep. We found that mixed bacteria changed the composition and abundance of sheep rumen bacteria. Among them, the abundance of Bacteroidota, Actinobacteriota, Acidobacteriota, and Proteobacteria was significantly increased, and the abundance of Firmicutes was significantly decreased, indicating that the changes in gut microbiota changed the function of the sheep rumen. The acid-producing bacteria isolated in this study can effectively promote the growth of ruminants, such as cattle and sheep, and can be used as additives to improve breeding efficiency, which lays a foundation for subsequent research on probiotics.
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Affiliation(s)
- Jinming Yu
- College of Life Science, Shihezi University, Shihezi, Xinjiang, China
| | - Cunyuan Li
- College of Life Science, Shihezi University, Shihezi, Xinjiang, China
| | - Xiaoyue Li
- College of Life Science, Shihezi University, Shihezi, Xinjiang, China
| | - Kaiping Liu
- College of Life Science, Shihezi University, Shihezi, Xinjiang, China
| | - Zhuang Liu
- College of Life Science, Shihezi University, Shihezi, Xinjiang, China
| | - Wei Ni
- College of Life Science, Shihezi University, Shihezi, Xinjiang, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, Xinjiang, China
| | - Ping Zhou
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, Xinjiang, China
| | - Limin Wang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, Xinjiang, China
| | - Shengwei Hu
- College of Life Science, Shihezi University, Shihezi, Xinjiang, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, Xinjiang, China
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Pfau AP, Shepherd EA, Martin MG, Ascolese S, Mason KM, Egert-McLean AM, Voy BH, Myer PR. Beta-Adrenergic Agonists, Dietary Protein, and Rumen Bacterial Community Interactions in Beef Cattle: A Review. Vet Sci 2023; 10:579. [PMID: 37756100 PMCID: PMC10537598 DOI: 10.3390/vetsci10090579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/01/2023] [Accepted: 09/13/2023] [Indexed: 09/28/2023] Open
Abstract
Improving beef production efficiency, sustainability, and food security is crucial for meeting the growing global demand for beef while minimizing environmental impact, conserving resources, ensuring economic viability, and promoting animal welfare. Beta-adrenergic agonists and dietary protein have been critical factors in beef cattle production. Beta-agonists enhance growth, improve feed efficiency, and influence carcass composition, while dietary protein provides the necessary nutrients for muscle development and overall health. A balanced approach to their use and incorporation into cattle diets can lead to more efficient and sustainable beef production. However, microbiome technologies play an increasingly important role in beef cattle production, particularly by optimizing rumen fermentation, enhancing nutrient utilization, supporting gut health, and enhancing feed efficiency. Therefore, optimizing rumen fermentation, diet, and growth-promoting technologies has the potential to increase energy capture and improve performance. This review addresses the interactions among beta-adrenergic agonists, protein level and source, and the ruminal microbiome. By adopting innovative technologies, sustainable practices, and responsible management strategies, the beef industry can contribute to a more secure and sustainable food future. Continued research and development in this field can lead to innovative solutions that benefit both producers and the environment.
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Affiliation(s)
| | | | | | | | | | | | | | - Phillip R. Myer
- Department of Animal Science, University of Tennessee, Knoxville, TN 37996, USA
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Boggio GM, Christensen OF, Legarra A, Meynadier A, Marie-Etancelin C. Microbiability of milk composition and genetic control of microbiota effects in sheep. J Dairy Sci 2023; 106:6288-6298. [PMID: 37474364 DOI: 10.3168/jds.2022-22948] [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: 10/26/2022] [Accepted: 02/28/2023] [Indexed: 07/22/2023]
Abstract
Recently, high-dimensional omics data are becoming available in larger quantities, and models have been developed that integrate them with genomics to understand in finer detail the relationship between genotype and phenotype, and thus improve the performance of genetic evaluations. Our objectives are to quantify the effect of the inclusion of microbiome data in the genetic evaluation for dairy traits in sheep, through the estimation of the heritability, microbiability, and how the microbiome effect on dairy traits decomposes into genetic and nongenetic parts. In this study we analyzed milk and rumen samples of 795 Lacaune dairy ewes. We included, as phenotype, dairy traits and milk fatty acids and proteins composition; as omics measurements, 16S rRNA rumen bacterial abundances; and as genotyping, 54K SNP chip for all ewes. Two nested genomic models were used: a first model to predict the individual contributions of the genetic and microbial abundances to phenotypes, and a second model to predict the additive genetic effect of the microbial community. In addition, microbiome-wide association studies for all dairy traits were applied using the 2,059 rumen bacterial abundances, and the genetic correlations between microbiome principal components and dairy traits were estimated. Results showed that in general the inclusion of both genetic and microbiome effect did not improve the fit of the model compared with the model with the genetic effect only. In addition, for all dairy traits the total heritability was equal to the direct heritability after fitting microbiota effects, due to a microbiability being almost zero for most dairy traits and heritability of the microbial community was very close to zero. Microbiome-wide association studies did not show operational taxonomic units with major effect for any of the dairy traits evaluated, and the genetic correlations between the first 5 principal components and dairy traits were low to moderate. So far, we can conclude that, using a substantial data set of 795 Lacaune dairy ewes, rumen bacterial abundances do not provide improved genetic evaluation for dairy traits in sheep.
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Affiliation(s)
- G Martinez Boggio
- GenPhySE, Université de Toulouse, INRAE-ENVT, 31326, Castanet-Tolosan, France.
| | - O F Christensen
- Center for Quantitative Genetics and Genomics, Aarhus University, DK-8000 Aarhus C, Denmark
| | - A Legarra
- GenPhySE, Université de Toulouse, INRAE-ENVT, 31326, Castanet-Tolosan, France
| | - A Meynadier
- GenPhySE, Université de Toulouse, INRAE-ENVT, 31326, Castanet-Tolosan, France
| | - C Marie-Etancelin
- GenPhySE, Université de Toulouse, INRAE-ENVT, 31326, Castanet-Tolosan, France.
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Palma-Hidalgo JM, Belanche A, Jiménez E, Newbold CJ, Denman SE, Yáñez-Ruiz DR. Multi-omics in vitro study of the salivary modulation of the goat rumen microbiome. Animal 2023; 17:100895. [PMID: 37515965 DOI: 10.1016/j.animal.2023.100895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 06/17/2023] [Accepted: 06/19/2023] [Indexed: 07/31/2023] Open
Abstract
Ruminants are able to produce large quantities of saliva which enter into the rumen and salivary components exert different physiological functions. Although previous research has indicated that salivary immunoglobulins can partially modulate the rumen microbial activity, the role of the salivary components other than ions on the rumen microbial ecosystem has not been thoroughly investigated in ruminants. To investigate this modulatory activity, a total of 16 semi-continuous in vitro cultures with oats hay and concentrate were used to incubate rumen fluid from four donor goats with autoclaved saliva (AUT) as negative control, saliva from the same rumen fluid donor (OWN) as positive control, and either goat (GOAT) or sheep (SHEEP) saliva as experimental interventions. Fermentation was monitored throughout 7 days of incubation and the microbiome and metabolome were analysed at the end of this incubation by Next-Generation sequencing and liquid chromatography coupled with mass spectrometry, respectively. Characterisation of the proteome and metabolome of the different salivas used for the incubation showed a high inter-animal variability in terms of metabolites and proteins, including immunoglobulins. Incubation with AUT saliva promoted lower fermentative activity in terms of gas production (-9.4%) and highly divergent prokaryotic community in comparison with other treatments (OWN, GOAT and SHEEP) suggesting a modulatory effect derived from the presence of bioactive salivary components. Microbial alpha-diversity at amplicon sequence variant (ASV) level was unaffected by treatment. However, some differences were found in the microbial communities across treatments, which were mostly caused by a greater abundance of Proteobacteria and Rikenellacea in the AUT treatment and lower of Prevotellaceae. These bacteria, which are key in the rumen metabolism, had greater abundances in GOAT and SHEEP treatments. Incubation with GOAT saliva led to a lower protozoal concentration and propionate molar proportion indicating a capacity to modulate the rumen microbial ecosystem. The metabolomics analysis showed that the AUT samples were clustered apart from the rest indicating different metabolic pathways were promoted in this treatment. These results suggest that specific salivary components contribute to host-associated role in selecting the rumen commensal microbiota and its activity. These findings could open the possibility of developing new strategies to modulate the saliva composition as a way to manipulate the rumen function and activity.
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Affiliation(s)
- Juan Manuel Palma-Hidalgo
- Estación Experimental del Zaidín (CSIC), Profesor Albareda 1, 18008 Granada, Spain; Scotland's Rural College (SRUC), Peter Wilson Building King's Buildings, W Mains Rd, Edinburgh EH9 3JG, United Kingdom
| | - Alejandro Belanche
- Estación Experimental del Zaidín (CSIC), Profesor Albareda 1, 18008 Granada, Spain; Departamento de Producción Animal y Ciencia de los Alimentos, IA2, Universidad de Zaragoza, Miguel Servet 177, 50013 Zaragoza, Spain
| | - Elisabeth Jiménez
- Estación Experimental del Zaidín (CSIC), Profesor Albareda 1, 18008 Granada, Spain
| | - Charles J Newbold
- Scotland's Rural College (SRUC), Peter Wilson Building King's Buildings, W Mains Rd, Edinburgh EH9 3JG, United Kingdom
| | - Stuart E Denman
- CSIRO Livestock Industries, Queensland Bioscience Precinct, St Lucia, Qld, Australia
| | - David R Yáñez-Ruiz
- Estación Experimental del Zaidín (CSIC), Profesor Albareda 1, 18008 Granada, Spain.
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Floridia V, Giuffrè L, Giosa D, Arfuso F, Aragona F, Fazio F, Chen C, Song C, Romeo O, D'Alessandro E. Comparison of the Faecal Microbiota Composition Following a Dairy By-Product Supplemented Diet in Nero Siciliano and Large White × Landrace Pig Breeds. Animals (Basel) 2023; 13:2323. [PMID: 37508100 PMCID: PMC10376647 DOI: 10.3390/ani13142323] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/11/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
The current study compared the faecal microbiota composition of two pig breeds (autochthonous vs. commercial) to understand what happens after the integration of liquid whey in the diet and what the role of the host genetic is. The trial was conducted for 60 days, and the faecal microbiota composition was investigated at three time points, T0, T1 (after 30 days) and T2 (after 60 days) in 30 female pigs (20 commercial crossbred and 10 Nero Siciliano pigs). The animals were divided into four groups (two control and two treatment groups). Generally, in both breeds, Firmicutes (51%) and Bacteroidota (36%) were the most abundant phylum whereas Prevotella, Treponema and Lactobacillus were the most abundant genera. The two breeds have a different reaction to a liquid whey diet. In fact, as shown by PERMANOVA analysis, the liquid whey significantly (p < 0.001) affects the microbiota composition of crossbreeds while not having an effect on the microbiota of the Nero Siciliano. Despite this, in both breeds Bifidobacterium and Ruminococcus have been positively influenced by liquid whey and they promote intestinal health, improve immunity, increase performance, and feed efficiency. In conclusion, the integration of liquid whey had a different effect on the Nero Siciliano and crossbred pig breeds, emphasizing the importance of the host genetic profile in determining the faecal bacterial composition.
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Affiliation(s)
- Viviana Floridia
- Animal Production Unit, Department of Veterinary Sciences, University of Messina, Viale Palatucci 13, 98168 Messina, Italy
| | - Letterio Giuffrè
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D'Alcontres 31, 98166 Messina, Italy
| | - Domenico Giosa
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D'Alcontres 31, 98166 Messina, Italy
| | - Francesca Arfuso
- Animal Production Unit, Department of Veterinary Sciences, University of Messina, Viale Palatucci 13, 98168 Messina, Italy
| | - Francesca Aragona
- Animal Production Unit, Department of Veterinary Sciences, University of Messina, Viale Palatucci 13, 98168 Messina, Italy
| | - Francesco Fazio
- Animal Production Unit, Department of Veterinary Sciences, University of Messina, Viale Palatucci 13, 98168 Messina, Italy
| | - Cai Chen
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China
| | - Chengy Song
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China
| | - Orazio Romeo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D'Alcontres 31, 98166 Messina, Italy
| | - Enrico D'Alessandro
- Animal Production Unit, Department of Veterinary Sciences, University of Messina, Viale Palatucci 13, 98168 Messina, Italy
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St-Pierre B, Perez Palencia JY, Samuel RS. Impact of Early Weaning on Development of the Swine Gut Microbiome. Microorganisms 2023; 11:1753. [PMID: 37512925 PMCID: PMC10385335 DOI: 10.3390/microorganisms11071753] [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: 06/18/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023] Open
Abstract
Considering that pigs are naturally weaned between 12 and 18 weeks of age, the common practice in the modern swine industry of weaning as early as between two and four weeks of age increases challenges during this transition period. Indeed, young pigs with an immature gut are suddenly separated from the sow, switched from milk to a diet consisting of only solid ingredients, and subjected to a new social hierarchy from mixing multiple litters. From the perspective of host gut development, weaning under these conditions causes a regression in histological structure as well as in digestive and barrier functions. While the gut is the main center of immunity in mature animals, the underdeveloped gut of early weaned pigs has yet to contribute to this function until seven weeks of age. The gut microbiota or microbiome, an essential contributor to the health and nutrition of their animal host, undergoes dramatic alterations during this transition, and this descriptive review aims to present a microbial ecology-based perspective on these events. Indeed, as gut microbial communities are dependent on cross-feeding relationships, the change in substrate availability triggers a cascade of succession events until a stable composition is reached. During this process, the gut microbiota is unstable and prone to dysbiosis, which can devolve into a diseased state. One potential strategy to accelerate maturation of the gut microbiome would be to identify microbial species that are critical to mature swine gut microbiomes, and develop strategies to facilitate their establishment in early post-weaning microbial communities.
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Affiliation(s)
- Benoit St-Pierre
- Department of Animal Science, South Dakota State University, Animal Science Complex, Box 2170, Brookings, SD 57007, USA
| | - Jorge Yair Perez Palencia
- Department of Animal Science, South Dakota State University, Animal Science Complex, Box 2170, Brookings, SD 57007, USA
| | - Ryan S Samuel
- Department of Animal Science, South Dakota State University, Animal Science Complex, Box 2170, Brookings, SD 57007, USA
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41
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Li S, Liu Y, Zeng H, Wang C, Han Z. Dietary Palygorskite-Based Antibacterial Agent Supplementation as an Alternative to Antibiotics Improves Growth Performance, Blood Parameters, and Rumen Microbiota in Sheep. Antibiotics (Basel) 2023; 12:1144. [PMID: 37508240 PMCID: PMC10376601 DOI: 10.3390/antibiotics12071144] [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: 05/31/2023] [Revised: 06/29/2023] [Accepted: 07/01/2023] [Indexed: 07/30/2023] Open
Abstract
This research aimed to investigate the effects of a palygorskite-based antibacterial agent (PAA) as an alternative to antibiotics on growth performance, blood parameters, and rumen microbiota in sheep. A total of 120 sheep were randomly divided into five groups of six replicates with four sheep each. Sheep were fed a basal diet, an antibiotic diet supplemented with 500 g/t chlortetracycline (CTC), and a basal diet supplemented with 500, 1000, and 2000 g/t PAA for 80 d, respectively. Supplementation with 2000 g/t PAA and 500 g/t CTC increased the average daily gain (ADG) of sheep compared with the control group (p < 0.05). Diets supplemented with 2000 g/t PAA and 500 g/t CTC reduced (p < 0.05) the feed:gain ratio (F/G ratio) in the overall periods. Dietary supplementation with 1000 g/t PAA significantly increased albumin and total protein (p < 0.05). A significant positive correlation was found between growth hormone concentration and PAA supplementation (p < 0.05). In addition, compared to the control group, the CTC group had higher growth hormone concentration and lower lipopolysaccharide concentration (p < 0.05). No difference was observed between the five groups in terms of rumen fermentation characteristics (p > 0.05). At the phylum level, the relative abundance of Proteobacteria was lower in the PAA 2000 and CTC 500 groups than in the control and PAA 500 groups (p < 0.05). At the genus level, a significant decrease (p < 0.05) in the relative abundance of RuminococcaceaeUCG-010 was observed in the PAA 1000, PAA 2000, and CTC 500 groups compared with that in the control group. In addition, the relative abundance of Prevotella1 (p < 0.05) was higher in the PAA 2000 group than in the control group. These findings indicate that dietary supplementation with PAA has ameliorative effects on growth performance, blood parameters, and rumen microbiota, with an optimal dosage of 2000 g/t for sheep.
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Affiliation(s)
- Shujie Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yue Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Hanfang Zeng
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Chanjian Wang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhaoyu Han
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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Luecke SM, Holman DB, Schmidt KN, Gzyl KE, Hurlbert JL, Menezes ACB, Bochantin KA, Kirsch JD, Baumgaertner F, Sedivec KK, Swanson KC, Dahlen CR, Amat S. Whole-body microbiota of newborn calves and their response to prenatal vitamin and mineral supplementation. Front Microbiol 2023; 14:1207601. [PMID: 37434710 PMCID: PMC10331429 DOI: 10.3389/fmicb.2023.1207601] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/08/2023] [Indexed: 07/13/2023] Open
Abstract
Early life microbial colonization and factors affecting colonization patterns are gaining interest due to recent developments suggesting that early life microbiome may play a role in Developmental Origins of Health and Disease. In cattle, limited information exists on the early microbial colonization of anatomical sites involved in bovine health beyond the gastrointestinal tract. Here, we investigated 1) the initial microbial colonization of seven different anatomical locations in newborn calves and 2) whether these early life microbial communities and 3) serum cytokine profiles are influenced by prenatal vitamin and mineral (VTM) supplementation. Samples were collected from the hoof, liver, lung, nasal cavity, eye, rumen (tissue and fluid), and vagina of beef calves that were born from dams that either received or did not receive VTM supplementation throughout gestation (n = 7/group). Calves were separated from dams immediately after birth and fed commercial colostrum and milk replacer until euthanasia at 30 h post-initial colostrum feeding. The microbiota of all samples was assessed using 16S rRNA gene sequencing and qPCR. Calf serum was subjected to multiplex quantification of 15 bovine cytokines and chemokines. Our results indicated that the hoof, eye, liver, lung, nasal cavity, and vagina of newborn calves were colonized by site-specific microbiota, whose community structure differed from the ruminal-associated communities (0.64 ≥ R2 ≥ 0.12, p ≤ 0.003). The ruminal fluid microbial community was the only one that differed by treatment (p < 0.01). However, differences (p < 0.05) by treatment were detected in microbial richness (vagina); diversity (ruminal tissue, fluid, and eye); composition at the phylum and genus level (ruminal tissue, fluid, and vagina); and in total bacterial abundance (eye and vagina). From serum cytokines evaluated, concentration of chemokine IP-10 was greater (p = 0.02) in VTM calves compared to control calves. Overall, our results suggest that upon birth, the whole-body of newborn calves are colonized by relatively rich, diverse, and site-specific bacterial communities. Noticeable differences were observed in ruminal, vaginal, and ocular microbiota of newborn calves in response to prenatal VTM supplementation. These findings can derive future hypotheses regarding the initial microbial colonization of different body sites, and on maternal micronutrient consumption as a factor that may influence early life microbial colonization.
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Affiliation(s)
- Sarah M. Luecke
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, United States
| | - Devin B. Holman
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Kaycie N. Schmidt
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, United States
| | - Katherine E. Gzyl
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Jennifer L. Hurlbert
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND, United States
| | - Ana Clara B. Menezes
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND, United States
| | - Kerri A. Bochantin
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND, United States
| | - James D. Kirsch
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND, United States
| | - Friederike Baumgaertner
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND, United States
| | - Kevin K. Sedivec
- Central Grasslands Research Extension Center, North Dakota State University, Streeter, ND, United States
| | - Kendall C. Swanson
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND, United States
| | - Carl R. Dahlen
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND, United States
| | - Samat Amat
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, United States
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Belanche A, Arturo-Schaan M, Leboeuf L, Yáñez-Ruiz D, Martín-García I. Early life supplementation with a natural blend containing turmeric, thymol, and yeast cell wall components to optimize rumen anatomical and microbiological development and productivity in dairy goats. J Dairy Sci 2023:S0022-0302(23)00267-9. [PMID: 37225586 DOI: 10.3168/jds.2022-22621] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 01/20/2023] [Indexed: 05/26/2023]
Abstract
Ruminants are born with an anatomically, microbiologically, and metabolically immature rumen. Optimizing the rearing of young ruminants represent an important challenge in intensive dairy farms. Therefore, the objective of this study was to evaluate the effects of dietary supplementation of young ruminants with a plant extract blend containing turmeric, thymol, and yeast cell wall components such as mannan oligosaccharides and β-glucans. One hundred newborn female goat kids were randomly allocated to 2 experimental treatments, which were unsupplemented (CTL) or supplemented with the blend containing plant extracts and yeast cell wall components (PEY). All animas were fed with milk replacer, concentrate feed, and oat hay, and were weaned at 8 wk of age. Dietary treatments lasted from wk 1 to 22 and 10 animals from each treatment were randomly selected to monitor feed intake, digestibility, and health-related indicators. These latter animals were euthanized at wk 22 of age to study the rumen anatomical, papillary, and microbiological development, whereas the remaining animals were monitored for reproductive performance and milk yield during the first lactation. Results indicated that PEY supplementation did not lead to feed intake or health issues because PEY animals tended to have a higher concentrate intake and lower diarrheal incidence than CTL animals. No differences between treatments were noted in terms of feed digestibility, rumen microbial protein synthesis, health-related metabolites, or blood cell counts. Supplementation with PEY promoted a higher rumen empty weight, and rumen relative proportion to the total digestive tract weight, than CTL animals. This was accompanied with a higher rumen papillary development in terms of papillae length and surface area in the cranial ventral and caudal ventral sacs, respectively. The PEY animals also had higher expression of the MCT1 gene, which is related to volatile fatty acid absorption by the rumen epithelium, than CTL animals. The antimicrobial effects of the turmeric and thymol could explain the decreased the rumen absolute abundance of protozoa and anaerobic fungi. This antimicrobial modulation led to a change in the bacterial community structure, a decrease in the bacteria richness, and to the disappearance (i.e., Prevotellaceae_UCG-004, Bacteroidetes_BD2-2, Papillibacter, Schwartzia, and Absconditabacteriales_SR1) or decline of certain bacterial taxa (i.e., Prevotellaceae_NK3B31_group, and Clostridia_UCG-014). Supplementation with PEY also decreased the relative abundance of fibrolytic (i.e., Fibrobacter succinogenes and Eubacterium ruminantium) and increased amylolytic bacteria (Selenomonas ruminantium). Although these microbial changes were not accompanied with significant differences in the rumen fermentation, this supplementation led to increased body weight gain during the preweaning period, higher body weight during the postweaning period, and higher fertility rate during the first gestation. On the contrary, no residual effects of this nutritional intervention were noted on the milk yield and milk components during the first lactation. In conclusion, supplementation with this blend of plant extracts and yeast cell wall component in early life could be considered as a sustainable nutritional strategy to increase body weight gain and optimize the rumen anatomical and microbiological development in young ruminants, despite having minor productive implications later in life.
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Affiliation(s)
- Alejandro Belanche
- Estación Experimental del Zaidín (CSIC), Prof. Albareda 1, 18008, Granada, Spain; Department of Animal Production and Food Sciences, University of Zaragoza, Miguel Servet 177, 50013, Zaragoza, Spain.
| | | | - Lara Leboeuf
- CCPA group, ZA Bois de Teillay, 35150, Janzé, France
| | - David Yáñez-Ruiz
- Estación Experimental del Zaidín (CSIC), Prof. Albareda 1, 18008, Granada, Spain
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Winders TM, Holman DB, Schmidt KN, Luecke SM, Smith DJ, Neville BW, Dahlen CR, Swanson KC, Amat S. Feeding hempseed cake alters the bovine gut, respiratory and reproductive microbiota. Sci Rep 2023; 13:8121. [PMID: 37208436 DOI: 10.1038/s41598-023-35241-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 05/15/2023] [Indexed: 05/21/2023] Open
Abstract
A growing number of studies have investigated the feasibility of utilizing hemp by-products as livestock feedstuffs; however, their impact on livestock microbiomes remains unexplored. Here, we evaluated the effects of feeding hempseed cake on the gastrointestinal, respiratory, and reproductive microbiota in beef heifers. Angus-crossbred heifers (19-months old, initial body weight = 494 ± 10 kg [SE]) were fed a corn-based finishing diet containing 20% hempseed cake as a substitute for 20% corn dried distillers' grains with solubles (DM basis; Control; n = 16/group) for 111 days until slaughter. Ruminal fluid and deep nasopharyngeal swabs (days 0, 7, 42, 70 and 98), and vaginal and uterine swabs (at slaughter) were collected, and the microbiota assessed using 16S rRNA gene sequencing. Diet affected the community structure of the ruminal (d 7-98; 0.06 ≤ R2 ≤ 0.12; P < 0.05), nasopharyngeal (d 98; R2 = 0.18; P < 0.001), and vaginal (R2 = 0.06; P < 0.01) microbiota. Heifers fed hempseed cake had increased microbial diversity in the rumen, reduced microbial richness in the vagina, and greater microbial diversity and richness in the uterus. In addition to the distinct microbial communities in the rumen, nasopharynx, vagina and uterus, we identified 28 core taxa that were shared (≥ 60% of all samples) across these sampling locations. Feeding hempseed cake appeared to alter the bovine gut, respiratory and reproductive microbiota. Our results suggest that future research aiming to evaluate the use of hemp by-products in livestock diet should consider their impact on animal microbiome and microbiome mediated animal health and reproductive efficiency. Our findings also highlight the need for research evaluating the impact of hemp-associated food and personal care products on the human microbiome.
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Affiliation(s)
- Thomas M Winders
- Department of Animal Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Devin B Holman
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, 6000 C & E Trail, Lacombe, AB, T4L 1W1, Canada
| | - Kaycie N Schmidt
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Sarah M Luecke
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - David J Smith
- USDA ARS, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA
| | - Bryan W Neville
- USDA-ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Carl R Dahlen
- Department of Animal Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA
- Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Kendall C Swanson
- Department of Animal Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Samat Amat
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA.
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Gharechahi J, Vahidi MF, Sharifi G, Ariaeenejad S, Ding XZ, Han JL, Salekdeh GH. Lignocellulose degradation by rumen bacterial communities: New insights from metagenome analyses. ENVIRONMENTAL RESEARCH 2023; 229:115925. [PMID: 37086884 DOI: 10.1016/j.envres.2023.115925] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/26/2023] [Accepted: 04/15/2023] [Indexed: 05/03/2023]
Abstract
Ruminant animals house a dense and diverse community of microorganisms in their rumen, an enlarged compartment in their stomach, which provides a supportive environment for the storage and microbial fermentation of ingested feeds dominated by plant materials. The rumen microbiota has acquired diverse and functionally overlapped enzymes for the degradation of plant cell wall polysaccharides. In rumen Bacteroidetes, enzymes involved in degradation are clustered into polysaccharide utilization loci to facilitate coordinated expression when target polysaccharides are available. Firmicutes use free enzymes and cellulosomes to degrade the polysaccharides. Fibrobacters either aggregate lignocellulose-degrading enzymes on their cell surface or release them into the extracellular medium in membrane vesicles, a mechanism that has proven extremely effective in the breakdown of recalcitrant cellulose. Based on current metagenomic analyses, rumen Bacteroidetes and Firmicutes are categorized as generalist microbes that can degrade a wide range of polysaccharides, while other members adapted toward specific polysaccharides. Particularly, there is ample evidence that Verrucomicrobia and Spirochaetes have evolved enzyme systems for the breakdown of complex polysaccharides such as xyloglucans, peptidoglycans, and pectin. It is concluded that diversity in degradation mechanisms is required to ensure that every component in feeds is efficiently degraded, which is key to harvesting maximum energy by host animals.
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Affiliation(s)
- Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Farhad Vahidi
- Animal Science Research Department, Qom Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Qom, Iran
| | - Golandam Sharifi
- Department of Basic Sciences, Encyclopedia Research Center, Institute for Humanities and Cultural Studies, Tehran, Iran
| | - Shohreh Ariaeenejad
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, And Extension Organization, Karaj, Iran
| | - Xue-Zhi Ding
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, 730050, China
| | - Jian-Lin Han
- Livestock Genetics Program, International Livestock Research, Institute (ILRI), 00100, Nairobi, Kenya; CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, And Extension Organization, Karaj, Iran; School of Natural Sciences, Macquarie University, North Ryde, NSW, Australia.
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Li Q, Fei HL, Luo ZH, Gao SM, Wang PD, Lan LY, Zhao XF, Huang LN, Fan PF. Gut microbiome responds compositionally and functionally to the seasonal diet variations in wild gibbons. NPJ Biofilms Microbiomes 2023; 9:21. [PMID: 37085482 PMCID: PMC10121652 DOI: 10.1038/s41522-023-00388-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 04/11/2023] [Indexed: 04/23/2023] Open
Abstract
Wild animals may encounter multiple challenges especially food shortage and altered diet composition in their suboptimal ranges. Yet, how the gut microbiome responds to dietary changes remains poorly understood. Prior studies on wild animal microbiomes have typically leaned upon relatively coarse dietary records and individually unresolved fecal samples. Here, we conducted a longitudinal study integrating 514 time-series individually recognized fecal samples with parallel fine-grained dietary data from two Skywalker hoolock gibbon (Hoolock tianxing) groups populating high-altitude mountainous forests in western Yunnan Province, China. 16S rRNA gene amplicon sequencing showed a remarkable seasonal fluctuation in the gibbons' gut microbial community structure both across individuals and between the social groups, especially driven by the relative abundances of Lanchnospiraceae and Oscillospiraceae associated with fluctuating consumption of leaf. Metagenomic functional profiling revealed that diverse metabolisms associated with cellulose degradation and short-chain fatty acids (SCFAs) production were enriched in the high-leaf periods possibly to compensate for energy intake. Genome-resolved metagenomics further enabled the resolving metabolic capacities associated with carbohydrate breakdown among community members which exhibited a high degree of functional redundancy. Our results highlight a taxonomically and functionally sensitive gut microbiome actively responding to the seasonally shifting diet, facilitating the survival and reproduction of the endangered gibbon species in their suboptimal habitats.
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Affiliation(s)
- Qi Li
- School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, P.R. China
| | - Han-Lan Fei
- School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, P.R. China
- College of Life Science, China West Normal University, 637002, Nanchong, P.R. China
| | - Zhen-Hao Luo
- School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, P.R. China
| | - Shao-Ming Gao
- School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, P.R. China
| | - Pan-Deng Wang
- School of Ecology, Shenzhen Campus of Sun Yat-sen University, 518107, Shenzhen, P.R. China
| | - Li-Ying Lan
- School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, P.R. China
| | - Xin-Feng Zhao
- School of Life Sciences, South China Normal University, 510631, Guangzhou, P.R. China
| | - Li-Nan Huang
- School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, P.R. China.
| | - Peng-Fei Fan
- School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, P.R. China.
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Shen J, Zheng W, Xu Y, Yu Z. The inhibition of high ammonia to in vitro rumen fermentation is pH dependent. Front Vet Sci 2023; 10:1163021. [PMID: 37065225 PMCID: PMC10097989 DOI: 10.3389/fvets.2023.1163021] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 03/14/2023] [Indexed: 04/03/2023] Open
Abstract
Ammonia is an important rumen internal environment indicator. In livestock production, feeding a large amount of non-protein nitrogen to ruminants will create high ammonia stress to the animals, which increases the risk of ammonia toxicity. However, the effects of ammonia toxicity on rumen microbiota and fermentation are still unknown. In this study, an in vitro rumen fermentation technique was used to investigate the effects of different concentrations of ammonia on rumen microbiota and fermentation. To achieve the four final total ammonia nitrogen (TAN) concentrations of 0, 8, 32, and 128 mmol/L, ammonium chloride (NH4Cl) was added at 0, 42.8, 171.2, and 686.8 mg/100 mL, and urea was added at 0, 24, 96, and 384 mg/100 mL. Urea hydrolysis increased, while NH4Cl dissociation slightly reduced the pH. At similar concentrations of TAN, the increased pH of the rumen culture by urea addition resulted in a much higher free ammonia nitrogen (FAN) concentration compared to NH4Cl addition. Pearson correlation analysis revealed a strong negative correlation between FAN and microbial populations (total bacteria, protozoa, fungi, and methanogens) and in vitro rumen fermentation profiles (gas production, dry matter digestibility, total volatile fatty acid, acetate, propionate, etc.), and a much weaker correlation between TAN and the above indicators. Additionally, bacterial community structure changed differently in response to TAN concentrations. High TAN increased Gram-positive Firmicutes and Actinobacteria but reduced Gram-negative Fibrobacteres and Spirochaetes. The current study demonstrated that the inhibition of in vitro rumen fermentation by high ammonia was pH-dependent and was associated with variations of rumen microbial populations and communities.
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Affiliation(s)
- Junshi Shen
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Junshi Shen
| | - Wenjin Zheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yixuan Xu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State University, Columbus, OH, United States
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Lee MD, Pedroso AA, Lumpkins B, Cho Y, Maurer JJ. Pioneer colonizers: Bacteria that alter the chicken intestinal morphology and development of the microbiota. Front Physiol 2023; 14:1139321. [PMID: 37064908 PMCID: PMC10090334 DOI: 10.3389/fphys.2023.1139321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/14/2023] [Indexed: 03/31/2023] Open
Abstract
Microbes commonly administered to chickens facilitate development of a beneficial microbiome that improves gut function, feed conversion and reduces pathogen colonization. Competitive exclusion products, derived from the cecal contents of hens and shown to reduce Salmonella colonization in chicks, possess important pioneer-colonizing bacteria needed for proper intestinal development and animal growth. We hypothesized that inoculation of these pioneer-colonizing bacteria to day of hatch chicks would enhance the development of their intestinal anatomy and microbiome. A competitive exclusion product was administered to broiler chickens, in their drinking water, at day of hatch, and its impact on intestinal morphometrics, intestinal microbiome, and production parameters, was assessed relative to a control, no treatment group. 16S rRNA gene, terminal restriction fragment length polymorphism (T-RFLP) was used to assess ileal community composition. The competitive exclusion product, administered on day of hatch, increased villus height, villus height/width ratio and goblet cell production ∼1.25-fold and expression of enterocyte sugar transporters 1.25 to 1.5-fold in chickens at 3 days of age, compared to the control group. As a next step, chicks were inoculated with a defined formulation, containing Bacteroidia and Clostridia representing pioneer-colonizing bacteria of the two major bacterial phyla present in the competitive exclusion product. The defined formulation, containing both groups of bacteria, were shown, dependent on age, to improve villus height (jejunum: 1.14 to 1.46-fold; ileum: 1.17-fold), goblet cell numbers (ileum 1.32 to 2.51-fold), and feed efficiency (1.18-fold, day 1) while decreasing Lactobacillus ileal abundance by one-third to half in birds at 16 and 42 days of age, respectively; compared to the phosphate buffered saline treatment group. Therefore, specific probiotic formulations containing pioneer colonizing species can provide benefits in intestinal development, feed efficiency and body weight gain.
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Affiliation(s)
- Margie D. Lee
- Virginia Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States
- Poultry Diagnostic and Research Center, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
- *Correspondence: Margie D. Lee,
| | - Adriana A. Pedroso
- Poultry Diagnostic and Research Center, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Brett Lumpkins
- Department of Poultry Science, College of Agricultural and Environmental Sciences, University of Georgia, Athens, GA, United States
| | - Youngjae Cho
- Poultry Diagnostic and Research Center, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - John J. Maurer
- Poultry Diagnostic and Research Center, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
- Department of Animal and Poultry Sciences, College of Agriculture and Life Sciences, Virginia Tech, Blacksburg, VA, United States
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Li Y, Gao J, Xue Y, Sun R, Sun X, Sun Z, Liu S, Tan Z, Zhu W, Cheng Y. Nutrient availability of roughages in isocaloric and isonitrogenous diets alters the bacterial networks in the whole gastrointestinal tract of Hu sheep. BMC Microbiol 2023; 23:70. [PMID: 36922757 PMCID: PMC10015938 DOI: 10.1186/s12866-023-02814-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/06/2023] [Indexed: 03/17/2023] Open
Abstract
BACKGROUND The nutrient availability of roughages could affect the dietary utilization efficiency of ruminants even in isocaloric and isonitrogenous diets. Here, we analyzed the bacterial composition and their metabolic pathways in the gastrointestinal tracts (GITs) of Hu sheep fed with wheat straw (WS) instead of alfalfa (AL) in isocaloric and isonitrogenous diets, trying to explore the reasons from the perspective of GITs bacterial network structure changes. RESULTS We employed 16S rRNA gene sequencing in combination with the Kruskal-Wallis test, Spearman correlation analysis, and other statistical methods to describe the microbiota composition in the GITs of Hu sheep. The results showed after the roughage was replaced from AL to WS, the most positive response occurred in the rumen microbiota, resulting in a more obvious microbiological and functional redundancy phenomenon. Whereas extended biogeographic studies of the GITs bacterial community found opposite results for the hindgut microbiota and metabolism networks compared to the forestomach. The abundance of fiber-degrading bacteria such as Prevotella, Oscillospiraceae NK4A214 group, and Treponema was significantly increased in GITs, but low-efficiency crude fiber degradation inhibited energy use efficiency, the pentose phosphate pathway, gluconeogenesis, and volatile acid synthesis. In addition, dietary shifting from AL to WS decreased the abundance of beneficial bacteria such as the Lachnospiraceae NK3A20 group and Alistipes, thereby enhancing the underlying inflammatory response. CONCLUSIONS These findings suggest that feeding untreated WS affected the structure and function of the bacterial network in the GITs due to limited total digestible nutrients, and in particular increases the complexity of the rumen bacterial network, and limit the abundance of bacteria involved in the crude fiber degradation in the hindgut.
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Affiliation(s)
- Yuqi Li
- 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
| | - Yihan Xue
- Laboratory of Gastrointestinal Microbiology, National Center for International Research On Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruolin Sun
- Laboratory of Gastrointestinal Microbiology, National Center for International Research On Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoni Sun
- Laboratory of Gastrointestinal Microbiology, National Center for International Research On Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhanying Sun
- 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, Nyingchi, 860000, China
| | - Zhankun Tan
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Nyingchi, 860000, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research On Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research On Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China.
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50
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Soltis MP, Moorey SE, Egert-McLean AM, Voy BH, Shepherd EA, Myer PR. Rumen Biogeographical Regions and Microbiome Variation. Microorganisms 2023; 11:microorganisms11030747. [PMID: 36985320 PMCID: PMC10057925 DOI: 10.3390/microorganisms11030747] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/01/2023] [Accepted: 03/11/2023] [Indexed: 03/15/2023] Open
Abstract
The rumen is a complex organ that is critical for its host to convert low-quality feedstuffs into energy. The conversion of lignocellulosic biomass to volatile fatty acids and other end products is primarily driven by the rumen microbiome and its interaction with the host. Importantly, the rumen is demarcated into five distinct rumen sacs as a result of anatomical structure, resulting in variable physiology among the sacs. However, rumen nutritional and microbiome studies have historically focused on the bulk content or fluids sampled from single regions within the rumen. Examining the rumen microbiome from only one or two biogeographical regions is likely not sufficient to provide a comprehensive analysis of the rumen microbiome and its fermentative capacity. Rumen biogeography, digesta fraction, and microbial rumen–tissue association all impact the diversity and function of the entirety of the rumen microbiome. Therefore, this review discusses the importance of the rumen biographical regions and their contribution to microbiome variation.
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