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Wanapat M, Dagaew G, Sommai S, Matra M, Suriyapha C, Prachumchai R, Muslykhah U, Phupaboon S. The application of omics technologies for understanding tropical plants-based bioactive compounds in ruminants: a review. J Anim Sci Biotechnol 2024; 15:58. [PMID: 38689368 PMCID: PMC11062008 DOI: 10.1186/s40104-024-01017-4] [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: 11/11/2023] [Accepted: 02/29/2024] [Indexed: 05/02/2024] Open
Abstract
Finding out how diet impacts health and metabolism while concentrating on the functional qualities and bioactive components of food is the crucial scientific objective of nutritional research. The complex relationship between metabolism and nutrition could be investigated with cutting-edge "omics" and bioinformatics techniques. This review paper provides an overview of the use of omics technologies in nutritional research, with a particular emphasis on the new applications of transcriptomics, proteomics, metabolomics, and genomes in functional and biological activity research on ruminant livestock and products in the tropical regions. A wealth of knowledge has been uncovered regarding the regulation and use of numerous physiological and pathological processes by gene, mRNA, protein, and metabolite expressions under various physiological situations and guidelines. In particular, the components of meat and milk were assessed using omics research utilizing the various methods of transcriptomics, proteomics, metabolomics, and genomes. The goal of this review is to use omics technologies-which have been steadily gaining popularity as technological tools-to develop new nutritional, genetic, and leadership strategies to improve animal products and their quality control. We also present an overview of the new applications of omics technologies in cattle production and employ nutriomics and foodomics technologies to investigate the microbes in the rumen ecology. Thus, the application of state-of-the-art omics technology may aid in our understanding of how species and/or breeds adapt, and the sustainability of tropical animal production, in the long run, is becoming increasingly important as a means of mitigating the consequences of climate change.
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Affiliation(s)
- Metha Wanapat
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Gamonmas Dagaew
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Sukruthai Sommai
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Maharach Matra
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Chaichana Suriyapha
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Rittikeard Prachumchai
- Department of Animal Science, Faculty of Agricultural Technology, University of Technology Thanyaburi, Rajamangala Pathum Thani, 12130, Thailand
| | - Uswatun Muslykhah
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Srisan Phupaboon
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand.
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Liu T, Bu Z, Xiang K, Jia Y, Du S. Effects of non-pelleted or pelleted low-native grass and pelleted high-native grass diets on meat quality by regulating the rumen microbiota in lambs. Microbiol Spectr 2024; 12:e0375823. [PMID: 38363135 PMCID: PMC10986533 DOI: 10.1128/spectrum.03758-23] [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: 10/23/2023] [Accepted: 01/30/2024] [Indexed: 02/17/2024] Open
Abstract
Diet modulates the rumen microbiota, which in turn can impact the animal performance. The rumen microbiota is increasingly recognized for its crucial role in regulating the growth and meat quality of the host. Nevertheless, the mechanism by which the rumen microbiome influences the fatty acid and amino acid profiles of lambs in the grass feeding system remains unclear. This study aimed to evaluate the effects of different native grass-based diets on animal performance, meat quality, fatty acid compositions, amino acid profiles, and rumen microbiota of lamb. Seventy-two Ujumqin lambs were randomly assigned into three treatments according to the initial body weight (27.39 ± 0.51 kg) and age (6 months ± 6 days). The lambs received three diets: (i) non-pelleted native grass hay with 40% concentrate diet; the native grass and concentrate were fed individually; (ii) pelleted native grass hay with 40% concentrate diet (PHLC); (iii) pelleted native grass hay with 60% concentrate diet (PHHC). The results showed that among the three groups, the PHHC and PHLC diets had markedly (P < 0.05) higher average daily gain and pH45 min, respectively. All amino acid levels were significantly (P < 0.05) decreased in the PHHC diet than in the PHLC diet. The principal coordinate analysis of the ruminal microbiota indicated the markedly distinct separation (P = 0.001) among the three groups. In addition, the correlation analysis showed that the Rikenellaceae_RC9_gut_group, Prevotellaceae_UCG-003, Succinivibrio, and Succiniclasticum were significantly (P < 0.05) associated with most of the fatty acid and amino acid profiles. The correlation analysis of the association of microbiome with the meat quality provides us with a comprehensive understanding of the composition and function of the rumen microbial community, and these findings will contribute to the direction of future research in lamb. IMPORTANCE Diet modulates the gut microbiome, which in turn impact the meat quality, yet few studies investigate the correlation between the rumen microbiome and the fatty acid profile of meat. Here, the current study develops an experiment to investigate the correlation of the rumen microbiome and fatty acid profile of meat: rumen microbiome responses to feed type and meat quality. The results indicated a unique microbiota in the rumen of lamb in response to diets and meat quality. Associations between utilization and production were widely identified among the affected microbiome and meat quality, and these findings will contribute to the direction of future research in lamb.
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Affiliation(s)
- Tingyu Liu
- College of Agriculture, Inner Mongolia University of Nationalities, Tongliao, China
| | - Zhenkun Bu
- Guangdong Laboratory of Lingnan Modern Agriculture, Agriculture Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agriculture Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Kaifeng Xiang
- Forest and Grassland Protection and Development Center, Chifeng, China
| | - Yushan Jia
- Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization, Ministry of Agriculture, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Shuai Du
- Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization, Ministry of Agriculture, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
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Davoudkhani M, Rubino F, Creevey CJ, Ahvenjärvi S, Bayat AR, Tapio I, Belanche A, Muñoz-Tamayo R. Integrating microbial abundance time series with fermentation dynamics of the rumen microbiome via mathematical modelling. PLoS One 2024; 19:e0298930. [PMID: 38507436 PMCID: PMC10954177 DOI: 10.1371/journal.pone.0298930] [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: 10/06/2023] [Accepted: 02/02/2024] [Indexed: 03/22/2024] Open
Abstract
The rumen represents a dynamic microbial ecosystem where fermentation metabolites and microbial concentrations change over time in response to dietary changes. The integration of microbial genomic knowledge and dynamic modelling can enhance our system-level understanding of rumen ecosystem's function. However, such an integration between dynamic models and rumen microbiota data is lacking. The objective of this work was to integrate rumen microbiota time series determined by 16S rRNA gene amplicon sequencing into a dynamic modelling framework to link microbial data to the dynamics of the volatile fatty acids (VFA) production during fermentation. For that, we used the theory of state observers to develop a model that estimates the dynamics of VFA from the data of microbial functional proxies associated with the specific production of each VFA. We determined the microbial proxies using CowPi to infer the functional potential of the rumen microbiota and extrapolate their functional modules from KEGG (Kyoto Encyclopedia of Genes and Genomes). The approach was challenged using data from an in vitro RUSITEC experiment and from an in vivo experiment with four cows. The model performance was evaluated by the coefficient of variation of the root mean square error (CRMSE). For the in vitro case study, the mean CVRMSE were 9.8% for acetate, 14% for butyrate and 14.5% for propionate. For the in vivo case study, the mean CVRMSE were 16.4% for acetate, 15.8% for butyrate and 19.8% for propionate. The mean CVRMSE for the VFA molar fractions were 3.1% for acetate, 3.8% for butyrate and 8.9% for propionate. Ours results show the promising application of state observers integrated with microbiota time series data for predicting rumen microbial metabolism.
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Affiliation(s)
- Mohsen Davoudkhani
- INRAE, AgroParisTech, UMR Modélisation Systémique Appliquée aux Ruminants, Université Paris-Saclay, Palaiseau, France
| | - Francesco Rubino
- Institute of Global Food Security, School of Biological Sciences, Queen’s University Belfast, Northern Ireland, United Kingdom
| | - Christopher J. Creevey
- Institute of Global Food Security, School of Biological Sciences, Queen’s University Belfast, Northern Ireland, United Kingdom
| | - Seppo Ahvenjärvi
- Animal Nutrition, Production Systems, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Ali R. Bayat
- Animal Nutrition, Production Systems, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Ilma Tapio
- Genomics and Breeding, Production Systems, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Alejandro Belanche
- Departamento de Producción Animal y Ciencia de los Alimentos, Universidad de Zaragoza, Zaragoza, Spain
| | - Rafael Muñoz-Tamayo
- INRAE, AgroParisTech, UMR Modélisation Systémique Appliquée aux Ruminants, Université Paris-Saclay, Palaiseau, France
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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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Wu Y, Jiao C, Diao Q, Tu Y. Effect of Dietary and Age Changes on Ruminal Microbial Diversity in Holstein Calves. Microorganisms 2023; 12:12. [PMID: 38276181 PMCID: PMC10818949 DOI: 10.3390/microorganisms12010012] [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: 11/02/2023] [Revised: 12/01/2023] [Accepted: 12/03/2023] [Indexed: 01/27/2024] Open
Abstract
Ruminal microorganisms play a crucial role in the energy supply of ruminants and animal performance. We analyzed the variations in rumen bacteria and fungi at 45 d, 75 d, and 105 d by using 16SrRNA and ITS sequencing data and investigated their correlation with rumen fermentation. According to the results, rumen microflora tended to gradually mature with age, and bacterial and fungal establishment gradually stabilized. Upon comparing the three periods, the concentration of propionic acid increased significantly (p < 0.05) after weaning, and weaning accompanied by a transition in diet remarkably decreased (p < 0.05) rumen diversity in the short term and induced a corresponding change in the rumen microbiota composition. Bacteroidota, Actinobacteriota, and Firmicutes were the core bacterial phyla for all age periods. Ruminococcus, NK4A214_group, Sharpea, Rikenellaceae_RC9_gut_group, and norank_f__Butyricicoccaceae were the markedly abundant bacterial genera in pre-weaning. After weaning, the relative abundance of Erysipelotrichaceae_ UCG-002, Eubacterium_ruminantium_group, and Solobacterium significantly increased (p < 0.05). The relative abundance of Acetitomaculum increased with age with the greatest abundance noted at 105 d (37%). The dominant fungal phyla were Ascomycota and Basidiomycota, and Aspergillus and Xeromyces were the most abundant fungal genera after weaning. Trichomonascus, Phialosimplex, and Talaromyces were enriched at 105 d. However, the low abundance of Neocallimastigomycota was not detected throughout the study, which is worthy of further investigation. In addition, correlations were observed between age-related abundances of specific genera and microbiota functions and rumen fermentation-related parameters. This study revealed that rumen microbiota and rumen fermentation capacity are correlated, which contributed to a better understanding of the effects of age and diet on rumen microbiology and fermentation in calves.
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Affiliation(s)
| | | | | | - Yan Tu
- Key Laboratory for Dairy Cow Nutrition, Institute of Feed Research of Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (C.J.); (Q.D.)
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6
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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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7
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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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Chen M, Xie W, Zhou S, Ma N, Wang Y, Huang J, Shen X, Chang G. A high-concentrate diet induces colonic inflammation and barrier damage in Hu sheep. J Dairy Sci 2023; 106:9644-9662. [PMID: 37641289 DOI: 10.3168/jds.2023-23359] [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: 02/08/2023] [Accepted: 05/15/2023] [Indexed: 08/31/2023]
Abstract
Long-term feeding of a high-concentrate diet can induce subacute ruminal acidosis (SARA) in ruminants, which further leads to systemic inflammatory response. However, few studies have examined the effects of feeding a high-concentrate diet on the hindgut of ruminants. The purpose of this study was to investigate the effects of a high-concentrate diet on the composition of gut microbiota in colonic contents, inflammatory response, and barrier damage in the colon tissue of ruminants. A total of 12 healthy multiparous lactating Hu sheep were randomly allotted into the following 2 groups: a high-concentrate (HC) group (concentrate:forage = 7:3) and a low-concentrate (LC) group (concentrate:forage = 3:7). All sheep were fitted with ruminal fistulas. The formal feeding experiment lasted for 8 wk. After the feeding experiment, rumen fluid, portal vein blood, hepatic vein blood, colonic contents, and colon tissue samples were collected. The results showed that feeding the HC diet induced SARA in Hu sheep and significantly reduced pH in the colonic contents. The abundances of Firmicutes, Verrucomicrobiota, and Actinobacteriota decreased significantly, whereas those of Bacteroidota, Spirochaetota, and Fibrobacterota significantly increased in colonic contents. At the genus level, the relative abundances of 29 genera were significantly altered depending on the different type of diets. Analysis of the 10 bacterial genera with high relative abundance revealed that feeding the HC diet significantly reduced the abundance of UCG-005, Christensenellaceae R-7 group, UCG-010-norank, Monoglobus, [Eubacterium] coprostanoligenes group_norank, and Alistipes, whereas the abundances of Rikenellaceae RC9 gut group, Treponema, Bacteroides, and Prevotella increased. Compared with the LC group, feeding the HC diet significantly increased the concentration of LPS in rumen fluid, portal vein blood, hepatic vein blood, and colonic contents, and significantly upregulated the mRNA expression levels of proinflammatory cytokines in colon tissue, including TNF-α, IL-1β, IL-6, and IL-8, indicating the occurrence of inflammatory response in the colon tissue. In addition, the structure of colonic epithelial cells was loose, the intercellular space became larger, epithelial cells were exfoliated, and the mRNA and protein abundances of ZO-1, occludin, claudin-1, claudin-3, and claudin-4 were significantly decreased in the HC group, which was consistent with the results of immunohistochemistry. Furthermore, feeding the HC diet increased the ratios of DNA methylation and chromatin compaction in the promoter regions of occludin and claudin-1, which in turn inhibited their transcriptional expression. Therefore, the present study demonstrated that feeding an HC diet induced SARA in Hu sheep, altered the composition and structure of the microbial community in the colonic contents, induced an inflammatory response, and disrupted the intestinal mucosal barrier in the colonic tissue.
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Affiliation(s)
- Mengru Chen
- Ministry of Education Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, P. R. China 210095
| | - Wan Xie
- Ministry of Education Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, P. R. China 210095
| | - Shendong Zhou
- Ministry of Education Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, P. R. China 210095
| | - Nana Ma
- Ministry of Education Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, P. R. China 210095
| | - Yan Wang
- Ministry of Education Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, P. R. China 210095
| | - Jie Huang
- Huzhou Research Institute of Hu Sheep, Huzhou Academy of Agricultural Science, Huzhou, Zhejiang, P. R. China 313099
| | - Xiangzhen Shen
- Ministry of Education Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, P. R. China 210095
| | - Guangjun Chang
- Ministry of Education Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, P. R. China 210095.
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9
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Low KE, Tingley JP, Klassen L, King ML, Xing X, Watt C, Hoover SER, Gorzelak M, Abbott DW. Carbohydrate flow through agricultural ecosystems: Implications for synthesis and microbial conversion of carbohydrates. Biotechnol Adv 2023; 69:108245. [PMID: 37652144 DOI: 10.1016/j.biotechadv.2023.108245] [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: 08/04/2022] [Revised: 08/10/2023] [Accepted: 08/25/2023] [Indexed: 09/02/2023]
Abstract
Carbohydrates are chemically and structurally diverse biomolecules, serving numerous and varied roles in agricultural ecosystems. Crops and horticulture products are inherent sources of carbohydrates that are consumed by humans and non-human animals alike; however carbohydrates are also present in other agricultural materials, such as soil and compost, human and animal tissues, milk and dairy products, and honey. The biosynthesis, modification, and flow of carbohydrates within and between agricultural ecosystems is intimately related with microbial communities that colonize and thrive within these environments. Recent advances in -omics techniques have ushered in a new era for microbial ecology by illuminating the functional potential for carbohydrate metabolism encoded within microbial genomes, while agricultural glycomics is providing fresh perspective on carbohydrate-microbe interactions and how they influence the flow of functionalized carbon. Indeed, carbohydrates and carbohydrate-active enzymes are interventions with unrealized potential for improving carbon sequestration, soil fertility and stability, developing alternatives to antimicrobials, and circular production systems. In this manner, glycomics represents a new frontier for carbohydrate-based biotechnological solutions for agricultural systems facing escalating challenges, such as the changing climate.
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Affiliation(s)
- Kristin E Low
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Jeffrey P Tingley
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Leeann Klassen
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Marissa L King
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Xiaohui Xing
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Caitlin Watt
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Shelley E R Hoover
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Monika Gorzelak
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - D Wade Abbott
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada.
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10
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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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11
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Bleke CA, Gese EM, Roberts SB, Villalba JJ. Seasonal shifts in pronghorn antelope (Antilocapra americana) diets under a new lens: Examining diet composition using a molecular technique. PLoS One 2023; 18:e0292725. [PMID: 37819912 PMCID: PMC10566741 DOI: 10.1371/journal.pone.0292725] [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: 11/08/2022] [Accepted: 09/27/2023] [Indexed: 10/13/2023] Open
Abstract
Foraging is one of the most fundamental activities contributing to the maximization of an animal's fitness, and thus herbivores must optimize their diet selection and intake to meet their nutrient demands for survival, growth, and reproduction. Using plant DNA barcoding, we determined diet composition of five subpopulations of adult female pronghorn antelope (Antilocapra americana) grazing rangelands in southern and southeastern Idaho, USA. Fecal samples were collected for two years (2018-2019), and across metabolically-important adult female life history stages (late gestation, early lactation, breeding season). Plant DNA barcoding yielded 137 detected species within pronghorn diets across subpopulations and sampling periods with forbs being the most abundant. Pronghorn dietary functional group composition ranged from 52.2-60.3% from forbs followed by shrubs (22.6-28.2%), graminoids (8.7-15.7%), and legumes (5.5-9.6%). Dietary protein intake was also highest from forbs and ranged from 32.4-62.4% followed by graminoids (1.2-43.1%), shrubs (18.7-21.3%), and legumes (2.6-7.4%). We found significant intra- and interannual differences in the mean number of genera-based plant detections in pronghorn diets. Dietary protein intake of cultivated legumes (e.g., alfalfa [Medicago sativa] and sainfoin [Onobrychis viciifolia]) was lower than expected, ranging from <1.0-30.8%, suggesting that even within an agricultural-dominated landscape, factors other than plant nutritional composition contributed to pronghorn diets. Although the plant DNA barcoding technique exhibits limitations, it demonstrated potential for elucidating pronghorn dietary species richness, particularly for plants consumed in small proportions, as well as for observing temporal fluctuations in functional group composition and dietary protein intake explained through the interplay between environmental factors, plant chemical composition, and the animals' physiological needs.
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Affiliation(s)
- Cole A. Bleke
- Department of Wildland Resources, Utah State University, Logan, Utah, United States of America
| | - Eric M. Gese
- U.S. Department of Agriculture, Wildlife Services, National Wildlife Research Center, Utah Field Station, Logan, Utah, United States of America
| | - Shane B. Roberts
- Idaho Department of Fish and Game, Boise, Idaho, United States of America
| | - Juan J. Villalba
- Department of Wildland Resources, Utah State University, Logan, Utah, United States of America
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12
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Fonseca PAS, Lam S, Chen Y, Waters SM, Guan LL, Cánovas A. Multi-breed host rumen epithelium transcriptome and microbiome associations and their relationship with beef cattle feed efficiency. Sci Rep 2023; 13:16209. [PMID: 37758745 PMCID: PMC10533831 DOI: 10.1038/s41598-023-43097-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 09/19/2023] [Indexed: 09/29/2023] Open
Abstract
Understanding host-microbial interactions in the rumen and its influence on desirable production traits may lead to potential microbiota manipulation or genetic selection for improved cattle feed efficiency. This study investigated the host transcriptome and its correlation with the rumen archaea and bacteria differential abundance of two pure beef cattle breeds (Angus and Charolais) and one composite beef hybrid (Kinsella) divergent for residual feed intake (RFI; low-RFI vs. high-RFI). Using RNA-Sequencing of rumen tissue and 16S rRNA gene amplicon sequencing, differentially expressed genes (FDR ≤ 0.05, |log2(Fold-change) >|2) and differentially abundant (p-value < 0.05) archaea and bacteria amplicon sequence variants (ASV) were determined. Significant correlations between gene expression and ASVs (p-value < 0.05) were determine using Spearman correlation. Interesting associations with muscle contraction and the modulation of the immune system were observed for the genes correlated with bacterial ASVs. Potential functional candidate genes for feed efficiency status were identified for Angus (CCL17, CCR3, and CXCL10), Charolais (KCNK9, GGT1 and IL6), and Kinsella breed (ESR2). The results obtained here provide more insights regarding the applicability of target host and rumen microbial traits for the selection and breeding of more feed efficient beef cattle.
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Grants
- Beef Farmers of Ontario, Genome Canada and the Sustainable Beef and Forage Science Cluster funded by the Canadian Beef Cattle Check-Off, Beef Cattle Research Council (BCRC), Alberta Beef Producers, Alberta Cattle Feeders’ Association, Beef Farmers of Ontario, La Fédération des Productuers de bovins du Québec, and Agriculture and Agri-Food Canada’s Canadian Agricultural Partnership
- Ontario Ministry of Agriculture, Food, and Rural Affairs (OMAFRA), Ontario Ministry of Research and Innovation, and the Ontario Agri-Food Innovation Alliance
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Affiliation(s)
- P A S Fonseca
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - S Lam
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Y Chen
- Livestock Gentec, Department of Agriculture, Food & Nutritional Science, University of Alberta, Edmonton, AB, T6H 2P5, Canada
| | - S M Waters
- Teagasc, Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Grange, Dunsany, C15 PW93, Co. Meath, Ireland
| | - L L Guan
- Livestock Gentec, Department of Agriculture, Food & Nutritional Science, University of Alberta, Edmonton, AB, T6H 2P5, Canada
| | - A Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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13
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Vasco-Correa J, Zuleta-Correa A, Gómez-León J, Pérez-Taborda JA. Advances in microbial pretreatment for biorefining of perennial grasses. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12639-5. [PMID: 37410135 DOI: 10.1007/s00253-023-12639-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/09/2023] [Accepted: 06/15/2023] [Indexed: 07/07/2023]
Abstract
Perennial grasses are potentially abundant sources of biomass for biorefineries, which can produce high yields with low input requirements, and many added environmental benefits. However, perennial grasses are highly recalcitrant to biodegradation and may require pretreatment before undergoing many biorefining pathways. Microbial pretreatment uses the ability of microorganisms or their enzymes to deconstruct plant biomass and enhance its biodegradability. This process can enhance the enzymatic digestibility of perennial grasses, enabling saccharification with cellulolytic enzymes to produce fermentable sugars and derived fermentation products. Similarly, microbial pretreatment can increase the methanation rate when the grasses are used to produce biogas through anaerobic digestion. Microorganisms can also increase the digestibility of the grasses to improve their quality as animal feed, enhance the properties of grass pellets, and improve biomass thermochemical conversion. Metabolites produced by fungi or bacteria during microbial pretreatment, such as ligninolytic and cellulolytic enzymes, can be further recovered as added-value products. Additionally, the action of the microorganisms can release chemicals with commercialization potential, such as hydroxycinnamic acids and oligosaccharides, from the grasses. This review explores the recent advances and remaining challenges in using microbial pretreatment for perennial grasses with the goal of obtaining added-value products through biorefining. It emphasizes recent trends in microbial pretreatment such as the use of microorganisms as part of microbial consortia or in unsterilized systems, the use and development of microorganisms and consortia capable of performing more than one biorefining step, and the use of cell-free systems based on microbial enzymes. KEY POINTS: • Microorganisms or enzymes can reduce the recalcitrance of grasses for biorefining • Microbial pretreatment effectiveness depends on the grass-microbe interaction • Microbial pretreatment can generate value added co-products to enhance feasibility.
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Affiliation(s)
- Juliana Vasco-Correa
- Department of Agricultural and Biological Engineering, Penn State University, University Park, PA, USA.
- Sociedad Colombiana de Ingeniería Física (SCIF), Pereira, Risaralda, Colombia.
| | - Ana Zuleta-Correa
- Marine Bioprospecting Line-BIM, Marine and Coastal Research Institute "José Benito Vives de Andréis" (INVEMAR), Santa Marta D.T.C.H, Magdalena, Colombia
| | - Javier Gómez-León
- Marine Bioprospecting Line-BIM, Marine and Coastal Research Institute "José Benito Vives de Andréis" (INVEMAR), Santa Marta D.T.C.H, Magdalena, Colombia
| | - Jaime Andrés Pérez-Taborda
- Sociedad Colombiana de Ingeniería Física (SCIF), Pereira, Risaralda, Colombia
- Grupo de Nanoestructuras y Física Aplicada (NANOUPAR), Universidad Nacional de Colombia Sede De La Paz, La Paz, Cesar, Colombia
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14
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Xiong Y, Wang X, Li X, Guo L, Yang F, Ni K. Exploring the rumen microbiota of Hu lambs in response to diet with paper mulberry. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12614-0. [PMID: 37306709 DOI: 10.1007/s00253-023-12614-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/26/2023] [Accepted: 05/31/2023] [Indexed: 06/13/2023]
Abstract
Paper mulberry (Broussonetia papyrifera), as a new woody forage with high-protein characteristic, is being widely used in ruminant feeding. However, little is known about the comprehensive microbiota picture of whole ruminal niches (liquid, solid, and epithelium) under paper mulberry diet. To gain a better understanding of feeding paper mulberry on the rumen microbiota, the effects of fresh paper mulberry, paper mulberry silage, or a conventional high-protein alfalfa silage on rumen fermentation products and microbiota in rumen niches of Hu lambs were studied. Forty-five Hu lambs were randomly divided into 3 treatments with 15 replicates in each treatment. No significant difference was observed among treatments in the average daily gain (ADG). The fresh paper mulberry treatment had lower (P < 0.05) pH and higher (P < 0.05) total volatile fatty acids (TVFA) compared with silage treatments, but the fermentation parameters did not show significant differences between paper mulberry silage and alfalfa silage treatments. The Shannon index did not show a significant difference (P < 0.05) among treatments except between fresh paper mulberry and alfalfa silage treatment in rumen epithelial niches. Butyrivibrio and Treponema were the predominant genera in the rumen epithelial fraction, while Prevotella and Rikenellaceae_RC9 dominated in both rumen liquid and solid fractions. These results indicated the paper mulberry supplement did not have distinct impact on the microbial diversity and growth performance compared with alfalfa silage, especially for paper mulberry silage, which might help us develop an alternative animal feeding strategy of replacing alfalfa with paper mulberry. KEY POINTS: • Feeding paper mulberry silage did not show significant impact on the growth performance compared with alfalfa silage treatment. • Feeding fresh paper mulberry reduced rumen pH value and increased total volatile fatty acid. • The microbial diversity did not show significant difference among treatments.
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Affiliation(s)
- Yi Xiong
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xin Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xiaomei Li
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Linna Guo
- College of Biological Engineering, Henan University of Technology, Zhengzhou, 450001, China
| | - Fuyu Yang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China.
- College of Animal Science, Guizhou University, Guiyang, 550525, China.
| | - Kuikui Ni
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China.
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15
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Guo Y, Liu M, Liu X, Zheng M, Xu X, Liu X, Gong J, Liu H, Liu J. Metagenomic and Untargeted Metabolomic Analysis of the Effect of Sporisorium reilianum Polysaccharide on Improving Obesity. Foods 2023; 12:foods12081578. [PMID: 37107373 PMCID: PMC10137368 DOI: 10.3390/foods12081578] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/01/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Gut microbiota plays an important role in the pathophysiology of obesity. Fungal polysaccharide can improve obesity, but the potential mechanism needs further study. This experiment studied the potential mechanism of polysaccharides from Sporisorium reilianum (SRP) to improve obesity in male Sprague Dawley (SD) rats fed with a high-fat diet (HFD) using metagenomics and untargeted metabolomics. After 8 weeks of SRP (100, 200, and 400 mg/kg/day) intervention, we analyzed the related index of obesity, gut microbiota, and untargeted metabolomics of rats. The obesity and serum lipid levels of rats treated with SRP were reduced, and lipid accumulation in the liver and adipocyte hypertrophy was improved, especially in rats treated with a high dose of SRP. SRP improved the composition and function of gut microbiota in rats fed with a high-fat diet, and decreased the ratio of Firmicutes to Bacteroides at the phylum level. At the genus level, the abundance of Lactobacillus increased and that of Bacteroides decreased. At the species level, the abundance of Lactobacillus crispatus, Lactobacillus helveticus, and Lactobacillus acidophilus increased, while the abundance of Lactobacillus reuteri and Staphylococcus xylosus decreased. The function of gut microbiota mainly regulated lipid metabolism and amino acid metabolism. The untargeted metabolomics indicated that 36 metabolites were related to the anti-obesity effect of SRP. Furthermore, linoleic acid metabolism, phenylalanine, tyrosine, and tryptophan biosynthesis, and the phenylalanine metabolism pathway played a role in improving obesity in those treated with SRP. The study results suggest that SRP significantly alleviated obesity via gut-microbiota-related metabolic pathways, and SRP could be used for the prevention and treatment of obesity.
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Affiliation(s)
- Yunlong Guo
- National Engineering Research Center for Wheat and Corn Deep Processing, College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China
| | - Meihong Liu
- National Engineering Research Center for Wheat and Corn Deep Processing, College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China
| | - Xin Liu
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun 130117, China
| | - Mingzhu Zheng
- National Engineering Research Center for Wheat and Corn Deep Processing, College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China
| | - Xiuying Xu
- National Engineering Research Center for Wheat and Corn Deep Processing, College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China
| | - Xiaokang Liu
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun 130117, China
| | - Jiyu Gong
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun 130117, China
| | - Huimin Liu
- National Engineering Research Center for Wheat and Corn Deep Processing, College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China
| | - Jingsheng Liu
- National Engineering Research Center for Wheat and Corn Deep Processing, College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China
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16
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Cui X, Wang Z, Fan Q, Chang S, Yan T, Hou F. Ligularia virgaurea improved nutrient digestion, ruminal fermentation, and bacterial composition in Tibetan sheep grazing on the Qinghai–Tibetan Plateau in winter. Anim Feed Sci Technol 2023. [DOI: 10.1016/j.anifeedsci.2023.115628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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17
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Andrighetto I, Serva L, Fossaluzza D, Marchesini G. Herd Level Yield Gap Analysis in a Local Scale Dairy Farming System: A Practical Approach to Discriminate between Nutritional and Other Constraining Factors. Animals (Basel) 2023; 13:ani13030523. [PMID: 36766412 PMCID: PMC9913683 DOI: 10.3390/ani13030523] [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: 12/21/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
This study performed a yield gap analysis to help farmers understand whether their constraints were mainly due to nutritional factors or management and health issues. Twenty-nine farms were periodically evaluated. Milk yield (MY), dry matter intake (DMI), total mixed ration (TMR) composition and homogeneity index (HI), TMR digestibility, income over feed cost (IOFC), and MY summer-winter ratio (SWR) were collected. Farms were divided and compared according to the average annual MY: Low (L), Medium (M) and High (H), characterised by <31.1, 31.1-36.7 and >36.7 kg/head/day. An ANOVA mixed model and a stepwise regression to assess the relationship between nutritional variables and MY were run. H farms showed higher IOFC (p < 0.001), DMI (p = 0.006), DDM (p < 0.001), digestible crude protein (DCP, p = 0.019), HI (p = 0.09), SWR (p = 0.041) and lower HI coefficient of variation (p = 0.04). The conversion of DDM into milk was higher in H and M farms. Stepwise regression for MY selected DDM and CP (R2 = 0.716, p < 0.05). M farms were mainly constrained by nutritional factors, whereas L farms were also affected by other factors such as those related to management and health.
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18
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Osorio-Doblado AM, Feldmann KP, Lourenco JM, Stewart RL, Smith WB, Tedeschi LO, Fluharty FL, Callaway TR. Forages and pastures symposium: forage biodegradation: advances in ruminal microbial ecology. J Anim Sci 2023; 101:skad178. [PMID: 37257501 PMCID: PMC10313095 DOI: 10.1093/jas/skad178] [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: 02/22/2023] [Accepted: 05/26/2023] [Indexed: 06/02/2023] Open
Abstract
The rumen microbial ecosystem provides ruminants a selective advantage, the ability to utilize forages, allowing them to flourish worldwide in various environments. For many years, our understanding of the ruminal microbial ecosystem was limited to understanding the microbes (usually only laboratory-amenable bacteria) grown in pure culture, meaning that much of our understanding of ruminal function remained a "black box." However, the ruminal degradation of plant cell walls is performed by a consortium of bacteria, archaea, protozoa, and fungi that produces a wide variety of carbohydrate-active enzymes (CAZymes) that are responsible for the catabolism of cellulose, hemicellulose, and pectin. The past 15 years have seen the development and implementation of numerous next-generation sequencing (NGS) approaches (e.g., pyrosequencing, Illumina, and shotgun sequencing), which have contributed significantly to a greater level of insight regarding the microbial ecology of ruminants fed a variety of forages. There has also been an increase in the utilization of liquid chromatography and mass spectrometry that revolutionized transcriptomic approaches, and further improvements in the measurement of fermentation intermediates and end products have advanced with metabolomics. These advanced NGS techniques along with other analytic approaches, such as metaproteomics, have been utilized to elucidate the specific role of microbial CAZymes in forage degradation. Other methods have provided new insights into dynamic changes in the ruminal microbial population fed different diets and how these changes impact the assortment of products presented to the host animal. As more omics-based data has accumulated on forage-fed ruminants, the sequence of events that occur during fiber colonization by the microbial consortium has become more apparent, with fungal populations and fibrolytic bacterial populations working in conjunction, as well as expanding understanding of the individual microbial contributions to degradation of plant cell walls and polysaccharide components. In the future, the ability to predict microbial population and enzymatic activity and end products will be able to support the development of dynamic predictive models of rumen forage degradation and fermentation. Consequently, it is imperative to understand the rumen's microbial population better to improve fiber degradation in ruminants and, thus, stimulate more sustainable production systems.
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Affiliation(s)
- A M Osorio-Doblado
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - K P Feldmann
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - J M Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - R L Stewart
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - W B Smith
- Department Animal Science, Auburn University, Auburn, AL, USA
| | - L O Tedeschi
- Department of Animal Science, Texas A&M University, College Station, TX, USA
| | - F L Fluharty
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - T R Callaway
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
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19
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Miller GA, Auffret MD, Roehe R, Nisbet H, Martínez-Álvaro M. Different microbial genera drive methane emissions in beef cattle fed with two extreme diets. Front Microbiol 2023; 14:1102400. [PMID: 37125186 PMCID: PMC10133469 DOI: 10.3389/fmicb.2023.1102400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/29/2023] [Indexed: 05/02/2023] Open
Abstract
The ratio of forage to concentrate in cattle feeding has a major influence on the composition of the microbiota in the rumen and on the mass of methane produced. Using methane measurements and microbiota data from 26 cattle we aimed to investigate the relationships between microbial relative abundances and methane emissions, and identify potential biomarkers, in animals fed two extreme diets - a poor quality fresh cut grass diet (GRASS) or a high concentrate total mixed ration (TMR). Direct comparisons of the effects of such extreme diets on the composition of rumen microbiota have rarely been studied. Data were analyzed considering their multivariate and compositional nature. Diet had a relevant effect on methane yield of +10.6 g of methane/kg of dry matter intake for GRASS with respect to TMR, and on the centered log-ratio transformed abundance of 22 microbial genera. When predicting methane yield based on the abundance of 28 and 25 selected microbial genera in GRASS and TMR, respectively, we achieved cross-validation prediction accuracies of 66.5 ± 9% and 85 ± 8%. Only the abundance of Fibrobacter had a consistent negative association with methane yield in both diets, whereas most microbial genera were associated with methane yield in only one of the two diets. This study highlights the stark contrast in the microbiota controlling methane yield between animals fed a high concentrate diet, such as that found on intensive finishing units, and a low-quality grass forage that is often found in extensive grazing systems. This contrast must be taken into consideration when developing strategies to reduce methane emissions by manipulation of the rumen microbial composition.
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Affiliation(s)
- Gemma A. Miller
- Scotland’s Rural College (SRUC), Edinburgh, United Kingdom
- Gemma A. Miller,
| | | | - Rainer Roehe
- Scotland’s Rural College (SRUC), Edinburgh, United Kingdom
| | - Holly Nisbet
- Scotland’s Rural College (SRUC), Edinburgh, United Kingdom
| | - Marina Martínez-Álvaro
- Institute for Animal Science and Technology, Universitat Politècnica de València, Valencia, Spain
- *Correspondence: Marina Martínez-Álvaro,
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20
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Takizawa S, Shinkai T, Saito K, Fukumoto N, Arai Y, Hirai T, Maruyama M, Takeda M. Effect of rumen microbiota transfaunation on the growth, rumen fermentation, and microbial community of early separated Japanese Black cattle. Anim Sci J 2023; 94:e13876. [PMID: 37818871 DOI: 10.1111/asj.13876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/20/2023] [Accepted: 09/07/2023] [Indexed: 10/13/2023]
Abstract
This study aimed to investigate the effect of rumen microbiota transfaunation on the growth, rumen fermentation, and the microbial community of Japanese Black cattle that were separated early from their dams. Here, 24 calves were separated from their dams immediately after calving, 12 of which were transfaunated via inoculation with rumen fluid from adult cattle at the age of 2 months while the remaining 12 were kept unfaunated (not-inoculated). Feed efficiency monitoring was performed during 7-10 months of age. Body weight and feed intake were not significantly different between the transfaunated and unfaunated cattle. Transfaunation increased the relative levels of acetate and butyrate but decreased those of propionate, which increased the non-glucogenic/glucogenic short-chain fatty acid ratio. Microbial 16S, 18S, and ITS ribosomal RNA gene amplicon analysis showed that rumen microbial diversity and composition differed between transfaunated and unfaunated cattle; transfaunation increased the abundance of acetate- and butyrate-producing bacteria, and decreased the abundance of bacterial genera associated with propionate production. Transfaunation also increased the abundance of Methanomassiliicoccaceae_group10 (1.94% vs. 0.05%) and Neocallimastix (27.1% vs. 6.8%) but decreased that of Methanomicrobium (<0.01% vs. 0.06%). Our findings indicate that rumen microbiota transfaunation shifts rumen fermentation toward acetate and butyrate production through a change in the rumen microbial composition in Japanese Black cattle.
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Affiliation(s)
- Shuhei Takizawa
- National Agriculture and Food Research Organization, Institute of Livestock and Grassland Science, Tsukuba, Japan
| | - Takumi Shinkai
- National Agriculture and Food Research Organization, Institute of Livestock and Grassland Science, Tsukuba, Japan
| | - Kunihiko Saito
- National Livestock Breeding Center Tokachi Station, Otofuke, Japan
| | - Natsuko Fukumoto
- National Livestock Breeding Center Tokachi Station, Otofuke, Japan
| | - Yukari Arai
- National Livestock Breeding Center Tokachi Station, Otofuke, Japan
- Ministry of Agriculture, Forestry and Fisheries, Tokyo, Japan
| | - Tomokazu Hirai
- National Livestock Breeding Center Tokachi Station, Otofuke, Japan
| | | | - Masayuki Takeda
- National Livestock Breeding Center Tokachi Station, Otofuke, Japan
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21
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Effects of Dietary Capsaicin and Yucca schidigera Extracts as Feed Additives on Rumen Fermentation and Microflora of Beef Cattle Fed with a Moderate-Energy Diet. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation9010030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Capsaicin (CAP) and Yucca schidigera extract (YSE) are two types of plant extracts that can change rumen fermentation. This study was conducted to investigate whether supplementation of beef cattle diets with CAP and YSE for 90 days would affect rumen fermentation and microflora. Forty-five healthy Angus steers (initial body weight = 510.54 ± 41.27 kg) were divided into three groups: control (CON), CAP, and YSE. Ammonia nitrogen (NH3-N) and total volatile fatty acid (TVFA) concentrations were significantly higher in the YSE group than in the CON group and significantly lower in the CAP group than in the CON group. At the phylum level, YSE increased the relative abundances of Bacteroidota and Patescibacteria and reduced that of Bacillota. At the genus level, CAP and YSE both increased the relative abundances of genera subordinate to Bacteroidota and decreased the relative abundances of genera subordinate to Bacillota. Our study shows that YSE and CAP have different effects on rumen fermentation and microflora after long-term supplementation.
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22
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Eto M, Yahara T, Kuroiwa A, Shioya K, Flores GE, Hamamura N. Dynamics of rumen microbiome in sika deer (Cervus nippon yakushimae) from unique subtropical ecosystem in Yakushima Island, Japan. Sci Rep 2022; 12:21623. [PMID: 36517661 PMCID: PMC9751099 DOI: 10.1038/s41598-022-26050-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 12/08/2022] [Indexed: 12/15/2022] Open
Abstract
Yaku sika deer (Cervus nippon yakushimae) are endemic to Yakushima Island, whose landscape covered with primary evergreen forest is recognized as a World Heritage Site. In this study, the rumen bacterial microbiota (RBM) of wild Yaku sika was characterized using high throughput sequencing of bacterial 16S rRNA genes combined with targeted cultivation and functional analyses. Comparative analyses of RBM datasets from other ruminant animals revealed distinct community structure among domesticated and wild ruminants. Wild Yaku sika RBM exhibited higher species richness than other sika deer (i.e. wild Ezo sika and domesticated sika deer), likely reflecting their dietary variations associated with unique ecosystem in the island. The Yaku sika RBM of high deer population density samples exhibited higher diversity and contained higher proportion of Firmicutes than those of lower density samples. Moreover, the highest abundance of tannase gene were observed in individuals from the highest population density area, consistent with the previous observation that Yaku sika in the high density areas expanded their feed to include tannin-rich unpalatable plants. This study indicated that RBM of unique wild Yaku sika contribute to the flexibility of dietary shift and thus maintaining nutritional status of Yaku sika under high density conditions.
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Affiliation(s)
- Misaki Eto
- grid.177174.30000 0001 2242 4849Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Fukuoka, 819-0395 Japan
| | - Tetsukazu Yahara
- grid.177174.30000 0001 2242 4849Department of Biology, Faculty of Science, Kyushu University, 744 Motooka, Fukuoka, 819-0395 Japan
| | - Arika Kuroiwa
- grid.177174.30000 0001 2242 4849Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Fukuoka, 819-0395 Japan
| | - Katsunori Shioya
- Kyushu Natural Environmental Research Co. Ltd, 1159-5 Haramizu Kikuyoumachi, Kikuchi-Gun, Kumamoto, 869-1102 Japan
| | - Gilberto E. Flores
- grid.253563.40000 0001 0657 9381Department of Biology, California State University, Northridge, 18111 Nordhoff Street, Northridge, CA 91330 USA
| | - Natsuko Hamamura
- grid.177174.30000 0001 2242 4849Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Fukuoka, 819-0395 Japan ,grid.177174.30000 0001 2242 4849Department of Biology, Faculty of Science, Kyushu University, 744 Motooka, Fukuoka, 819-0395 Japan
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23
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Koester LR, Hayman K, Anderson CJ, Tibbs-Cortes BW, Daniels KM, Seggerman FM, Gorden PJ, Lyte M, Schmitz-Esser S. Influence of a sodium-saccharin sweetener on the rumen content and rumen epithelium microbiota in dairy cattle during heat stress. J Anim Sci 2022; 101:6894547. [PMID: 36511453 PMCID: PMC9838801 DOI: 10.1093/jas/skac403] [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: 09/28/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022] Open
Abstract
The effect of a saccharin-based artificial sweetener was tested on animal performance measures and on the microbial communities associated with the rumen content and with the rumen epithelium during heat stress. Ten cannulated Holstein-Friesian milking dairy cattle were supplemented with 2 g of saccharin-based sweetener per day, top-dressed into individual feeders for a 7-day adaptation period followed by a 14-day heat stress period. A control group of ten additional cows subjected to the same environmental conditions but not supplemented with sweetener were included for comparison. 16S rRNA gene amplicon sequencing was performed on rumen content and rumen epithelium samples from all animals, and comparisons of rumen content microbiota and rumen epithelial microbiota were made between supplemented and control populations. Supplementation of the saccharin-based sweetener did not affect the rumen content microbiota, but differences in the rumen epithelial microbiota beta-diversity (PERMANOVA, P = 0.003, R2 = 0.12) and alpha-diversity (Chao species richness, P = 0.06 and Shannon diversity, P = 0.034) were detected between the supplemented and control experimental groups. Despite the changes detected in the microbial community, animal performance metrics including feed intake, milk yield, and short-chain fatty acid (acetic, propionic, and butyric acid) concentrations were not different between experimental groups. Thus, under the conditions applied, supplementation with a saccharin-based sweetener does not appear to affect animal performance under heat stress. Additionally, we detected differences in the rumen epithelial microbiota due to heat stress when comparing initial, prestressed microbial communities to the communities after heat stress. Importantly, the changes occurring in the rumen epithelial microbiota may have implications on barrier integrity, oxygen scavenging, and urease activity. This research adds insight into the impact of saccharin-based sweeteners on the rumen microbiota and the responsivity of the rumen epithelial microbiota to different stimuli, providing novel hypotheses for future research.
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Affiliation(s)
- Lucas R Koester
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA,Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA 50011, USA
| | - Kris Hayman
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA 50011, USA
| | - Chiron J Anderson
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA 50011, USA,Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Bienvenido W Tibbs-Cortes
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA 50011, USA,Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Karrie M Daniels
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA
| | - Faith M Seggerman
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA 50011, USA,Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Patrick J Gorden
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA 50011, USA
| | - Mark Lyte
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA
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24
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Mahayri TM, Fliegerová KO, Mattiello S, Celozzi S, Mrázek J, Mekadim C, Sechovcová H, Kvasnová S, Atallah E, Moniello G. Host Species Affects Bacterial Evenness, but Not Diversity: Comparison of Fecal Bacteria of Cows and Goats Offered the Same Diet. Animals (Basel) 2022; 12:ani12162011. [PMID: 36009603 PMCID: PMC9404439 DOI: 10.3390/ani12162011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/29/2022] [Accepted: 08/05/2022] [Indexed: 12/19/2022] Open
Abstract
Simple Summary Comparison of bacterial diversity and composition of feces from cows and goats offered the same pasture-based diet revealed that the animal species had no effect on bacterial species richness and diversity, but significantly affected species evenness. Both diet and host species influence the gut microbiome. Abstract The aim of this study was to compare the diversity and composition of fecal bacteria in goats and cows offered the same diet and to evaluate the influence of animal species on the gut microbiome. A total of 17 female goats (Blond Adamellan) and 16 female cows (Brown Swiss) kept on an organic farm were fed pasture and hay. Bacterial structure in feces was examined by high-throughput sequencing using the V4–V5 region of the 16S rRNA gene. The Alpha diversity measurements of the bacterial community showed no statistical differences in species richness and diversity between the two groups of ruminants. However, the Pielou evenness index revealed a significant difference and showed higher species evenness in cows compared to goats. Beta diversity measurements showed statistical dissimilarities and significant clustering of bacterial composition between goats and cows. Firmicutes were the dominant phylum in both goats and cows, followed by Bacteroidetes, Proteobacteria, and Spirochaetes. Linear discriminant analysis with effect size (LEfSe) showed a total of 36 significantly different taxa between goats and cows. Notably, the relative abundance of Ruminococcaceae UCG-005, Christensenellaceae R-7 group, Ruminococcaceae UCG-010, Ruminococcaceae UCG-009, Ruminococcaceae UCG-013, Ruminococcaceae UCG-014, Ruminococcus 1, Ruminococcaceae UCG-002, Lachnospiraceae NK4A136 group, Treponema 2, Lachnospiraceae AC2044 group, and Bacillus was higher in goats compared to cows. In contrast, the relative abundance of Turicibacter, Solibacillus, Alloprevotella, Prevotellaceae UCG-001, Negativibacillus, Lachnospiraceae UCG-006, and Eubacterium hallii group was higher in cows compared with goats. Our results suggest that diet shapes the bacterial community in feces, but the host species has a significant impact on community structure, as reflected primarily in the relative abundance of certain taxa.
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Affiliation(s)
- Tiziana Maria Mahayri
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, Czech Academy of Science, 14220 Prague, Czech Republic
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Kateřina Olša Fliegerová
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, Czech Academy of Science, 14220 Prague, Czech Republic
- Correspondence: ; Tel.: +420-267-090-504
| | - Silvana Mattiello
- Department of Agricultural and Environmental Sciences—Production, Landscape, Agroenergy, University of Milan, 20133 Milan, Italy
| | - Stefania Celozzi
- Department of Agricultural and Environmental Sciences—Production, Landscape, Agroenergy, University of Milan, 20133 Milan, Italy
| | - Jakub Mrázek
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, Czech Academy of Science, 14220 Prague, Czech Republic
| | - Chahrazed Mekadim
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, Czech Academy of Science, 14220 Prague, Czech Republic
| | - Hana Sechovcová
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, Czech Academy of Science, 14220 Prague, Czech Republic
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences in Prague, 16500 Prague, Czech Republic
| | - Simona Kvasnová
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, Czech Academy of Science, 14220 Prague, Czech Republic
| | - Elie Atallah
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Giuseppe Moniello
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
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25
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Ault-Seay TB, Brandt KJ, Henniger MT, Payton RR, Mathew DJ, Moorey SE, Schrick FN, Pohler KG, Smith TPL, Rhinehart JD, Schneider LG, McLean KJ, Myer PR. Bacterial Communities of the Uterus and Rumen During Heifer Development With Protein Supplementation. FRONTIERS IN ANIMAL SCIENCE 2022. [DOI: 10.3389/fanim.2022.903909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Bacterial communities play major roles in rumen and uterine function toward optimal animal performance and may be affected by changes occurring during heifer development such as nutritional supplementation for optimal growth and the attainment of puberty. The effect of different levels of protein supplementation on ruminal and uterine bacterial communities following weaning was examined through first breeding of heifers. Angus heifers (n = 39) were blocked by initial body weight (BW) and randomly assigned to one of three 163-day (d) crude protein (CP) supplementation diets including control (10% CP, n = 14), 20% CP (n = 11), or 40% CP (n = 14) treatment groups. Growth and development were monitored by body weight, with blood progesterone concentration determined every 14 d to determine pubertal status. Uterine flush and rumen fluid were collected on d 56, 112, and 163 relative to the start of supplementation. Bacterial DNA was extracted from fluid samples, the V1–V3 hypervariable region of the 16S rRNA gene was amplified, and amplicons were sequenced then processed in R 4.1. Statistical analyses were performed in SAS 9.4 with a GLIMMIX procedure utilizing fixed effects of protein, month, pubertal status, and interactions, with random effects including BW, interaction of BW and protein, and heifer within the interaction, and repeated measures of day. In the uterus, pubertal status and day of supplementation affected the observed amplicon sequence variants (ASVs) and led to clustering of samples in a principal coordinate analysis (PCoA; P < 0.05), but no effect of protein supplementation was observed. Ruminal samples clustered in PCoA (P = 0.001), and observed ASVs were impacted over time (P < 0.0001), but no effect of protein supplementation was detected. In contrast, protein supplementation, pubertal status, and day of supplementation affected the abundance of multiple phyla and genera in the uterus and rumen (P < 0.05). Temporal and pubertal status effects on the heifer’s uterine bacterial communities potentially indicate a maturing uterine microbiome. Protein supplementation did not impact microbial diversity measures but did affect the abundance of individual bacterial phyla and genera that may provide future opportunities to manipulate bacterial community composition and maximize productivity.
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26
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Savin KW, Moate PJ, Williams SRO, Bath C, Hemsworth J, Wang J, Ram D, Zawadzki J, Rochfort S, Cocks BG. Dietary wheat and reduced methane yield are linked to rumen microbiome changes in dairy cows. PLoS One 2022; 17:e0268157. [PMID: 35587477 PMCID: PMC9119556 DOI: 10.1371/journal.pone.0268157] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 04/24/2022] [Indexed: 12/13/2022] Open
Abstract
Fermentation of pasture grasses and grains in the rumen of dairy cows and other ruminants produces methane as a by-product, wasting energy and contributing to the atmospheric load of greenhouse gasses. Many feeding trials in farmed ruminants have tested the impact of dietary components on feed efficiency, productivity and methane yield (MeY). Such diets remodel the rumen microbiome, altering bacterial, archaeal, fungal and protozoan populations, with an altered fermentation outcome. In dairy cows, some dietary grains can reduce enteric methane production. This is especially true of wheat, in comparison to corn or barley. Using a feeding trial of cows fed rolled wheat, corn or barley grain, in combination with hay and canola, we identified wheat-associated changes in the ruminal microbiome. Ruminal methane production, pH and VFA concentration data together with 16S rRNA gene amplicon sequences were used to compare ruminal bacterial and archaeal populations across diets. Differential abundance analysis of clustered sequences (OTU) identified members of the bacterial families Lachnospiraceae, Acidaminococcaceae, Eubacteriaceae, Prevotellaceae, Selenomonadaceae, Anaerovoracaceae and Fibrobacteraceae having a strong preference for growth in wheat-fed cows. Within the methanogenic archaea, (at >99% 16S rRNA sequence identity) the growth of Methanobrevibacter millerae was favoured by the non-wheat diets, while Methanobrevibacter olleyae was unaffected. From the wheat-preferring bacteria, correlation analysis found OTU strongly linked to reduced MeY, reduced pH and raised propionic acid levels. OTU from the genera Shuttleworthia and Prevotella_7 and especially Selenomonadaceae had high anti-methane correlations. An OTU likely representing (100% sequence identity) the fumarate-reducing, hydrogen-utilising, rumen bacterium Mitsuokella jalaludinii, had an especially high negative correlation coefficient (-0.83) versus MeY and moderate correlation (-0.6) with rumen pH, strongly suggesting much of the MeY suppression is due to reduced hydrogen availablity. Other OTU, representing as yet unknown species from the Selenomonadaceae family and the genera Prevotella_7, Fibrobacter and Syntrophococcus also had high to moderate negative MeY correlations, but low correlation with pH. These latter likely represent bacterial species able to reduce MeY without causing greater ruminal acidity, making them excellent candidates, provided they can be isolated, for development as anti-methane probiotics.
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Affiliation(s)
- Keith W. Savin
- AgriBio Centre, Agriculture Victoria Research, Bundoora, Victoria, Australia
- * E-mail: ,
| | - Peter J. Moate
- Agriculture Victoria Research, Ellinbank, Victoria, Australia
| | | | - Carolyn Bath
- AgriBio Centre, Agriculture Victoria Research, Bundoora, Victoria, Australia
| | - Joanne Hemsworth
- AgriBio Centre, Agriculture Victoria Research, Bundoora, Victoria, Australia
| | - Jianghui Wang
- AgriBio Centre, Agriculture Victoria Research, Bundoora, Victoria, Australia
| | - Doris Ram
- AgriBio Centre, Agriculture Victoria Research, Bundoora, Victoria, Australia
| | - Jody Zawadzki
- AgriBio Centre, Agriculture Victoria Research, Bundoora, Victoria, Australia
| | - Simone Rochfort
- AgriBio Centre, Agriculture Victoria Research, Bundoora, Victoria, Australia
| | - Benjamin G. Cocks
- AgriBio Centre, Agriculture Victoria Research, Bundoora, Victoria, Australia
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27
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Dowd B, McDonnell D, Tuohy MG. Current Progress in Optimising Sustainable Energy Recovery From Cattle Paunch Contents, a Slaughterhouse Waste Product. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.722424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Paunch contents are the recalcitrant, lignocellulose-rich, partially-digested feed present in the rumen of ruminant animals. Cattle forage in Europe is primarily from perennial and Italian ryegrasses and/or white clover, so paunch contents from forage-fed cattle in Europe is enriched in these feedstuffs. Globally, due to its underutilisation, the potential energy in cattle paunch contents annually represents an energy loss of 23,216,548,750–27,804,250,000 Megajoules (MJ) and financial loss of up to ~€800,000,000. Therefore, this review aims to describe progress made to-date in optimising sustainable energy recovery from paunch contents. Furthermore, analyses to determine the economic feasibility/potential of recovering sustainable energy from paunch contents was carried out. The primary method used to recover sustainable energy from paunch contents to-date has involved biomethane production through anaerobic digestion (AD). The major bottleneck in its utilisation through AD is its recalcitrance, resulting in build-up of fibrous material. Pre-treatments partially degrade the lignocellulose in lignocellulose-rich wastes, reducing their recalcitrance. Enzyme systems could be inexpensive and more environmentally compatible than conventional solvent pre-treatments. A potential source of enzyme systems is the rumen microbiome, whose efficiency in lignocellulose degradation is attracting significant research interest. Therefore, the application of rumen fluid (liquid derived from dewatering of paunch contents) to improve biomethane production from AD of lignocellulosic wastes is included in this review. Analysis of a study where rumen fluid was used to pre-treat paper sludge from a paper mill prior to AD for biomethane production suggested economic feasibility for CHP combustion, with potential savings of ~€11,000 annually. Meta-genomic studies of bacterial/archaeal populations have been carried out to understand their ruminal functions. However, despite their importance in degrading lignocellulose in nature, rumen fungi remain comparatively under-investigated. Further investigation of rumen microbes, their cultivation and their enzyme systems, and the role of rumen fluid in degrading lignocellulosic wastes, could provide efficient pre-treatments and co-digestion strategies to maximise biomethane yield from a range of lignocellulosic wastes. This review describes current progress in optimising sustainable energy recovery from paunch contents, and the potential of rumen fluid as a pre-treatment and co-substrate to recover sustainable energy from lignocellulosic wastes using AD.
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28
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Bhujbal SK, Ghosh P, Vijay VK, Rathour R, Kumar M, Singh L, Kapley A. Biotechnological potential of rumen microbiota for sustainable bioconversion of lignocellulosic waste to biofuels and value-added products. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 814:152773. [PMID: 34979222 DOI: 10.1016/j.scitotenv.2021.152773] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/05/2021] [Accepted: 12/25/2021] [Indexed: 06/14/2023]
Abstract
Lignocellulosic biomass is an abundant resource with untapped potential for biofuel, enzymes, and chemical production. Its complex recalcitrant structure obstructs its bioconversion into biofuels and other value-added products. For improving its bioconversion efficiency, it is important to deconstruct its complex structure. In natural systems like rumen, diverse microbial communities carry out hydrolysis, acidogenesis, acetogenesis, and methanogenesis of lignocellulosic biomass through physical penetration, synergistic and enzymatic actions enhancing lignocellulose degradation activity. This review article aims to discuss comprehensively the rumen microbial ecosystem, their interactions, enzyme production, and applications for efficient bioconversion of lignocellulosic waste to biofuels. Furthermore, meta 'omics' approaches to elucidate the structure and functions of rumen microorganisms, fermentation mechanisms, microbe-microbe interactions, and host-microbe interactions have been discussed thoroughly. Additionally, feed additives' role in improving ruminal fermentation efficiency and reducing environmental nitrogen losses has been discussed. Finally, the current status of rumen microbiota applications and future perspectives for the development of rumen mimic bioreactors for efficient bioconversion of lignocellulosic wastes to biofuels and chemicals have been highlighted.
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Affiliation(s)
- Sachin Krushna Bhujbal
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Pooja Ghosh
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi 110016, India.
| | - Virendra Kumar Vijay
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Rashmi Rathour
- CSIR-National Environmental and Engineering Research Institute (CSIR-NEERI), Nagpur 440020, India
| | - Manish Kumar
- CSIR-National Environmental and Engineering Research Institute (CSIR-NEERI), Nagpur 440020, India
| | - Lal Singh
- CSIR-National Environmental and Engineering Research Institute (CSIR-NEERI), Nagpur 440020, India
| | - Atya Kapley
- CSIR-National Environmental and Engineering Research Institute (CSIR-NEERI), Nagpur 440020, India
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29
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Zhu Y, Bu D, Ma L. Integration of Multiplied Omics, a Step Forward in Systematic Dairy Research. Metabolites 2022; 12:metabo12030225. [PMID: 35323668 PMCID: PMC8955540 DOI: 10.3390/metabo12030225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 02/07/2023] Open
Abstract
Due to their unique multi-gastric digestion system highly adapted for rumination, dairy livestock has complicated physiology different from monogastric animals. However, the microbiome-based mechanism of the digestion system is congenial for biology approaches. Different omics and their integration have been widely applied in the dairy sciences since the previous decade for investigating their physiology, pathology, and the development of feed and management protocols. The rumen microbiome can digest dietary components into utilizable sugars, proteins, and volatile fatty acids, contributing to the energy intake and feed efficiency of dairy animals, which has become one target of the basis for omics applications in dairy science. Rumen, liver, and mammary gland are also frequently targeted in omics because of their crucial impact on dairy animals’ energy metabolism, production performance, and health status. The application of omics has made outstanding contributions to a more profound understanding of the physiology, etiology, and optimizing the management strategy of dairy animals, while the multi-omics method could draw information of different levels and organs together, providing an unprecedented broad scope on traits of dairy animals. This article reviewed recent omics and multi-omics researches on physiology, feeding, and pathology on dairy animals and also performed the potential of multi-omics on systematic dairy research.
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Affiliation(s)
- Yingkun Zhu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
- School of Agriculture & Food Science, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - Dengpan Bu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
- Joint Laboratory on Integrated Crop-Tree-Livestock Systems of the Chinese Academy of Agricultural Sciences (CAAS), Ethiopian Institute of Agricultural Research (EIAR), and World Agroforestry Center (ICRAF), Beijing 100193, China
- Correspondence: (D.B.); (L.M.)
| | - Lu Ma
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
- Correspondence: (D.B.); (L.M.)
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30
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Chen S, Holyoak M, Liu H, Bao H, Ma Y, Dou H, Jiang G. Effects of spatially heterogeneous warming on gut microbiota, nutrition and gene flow of a heat-sensitive ungulate population. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150537. [PMID: 34844317 DOI: 10.1016/j.scitotenv.2021.150537] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 09/19/2021] [Accepted: 09/19/2021] [Indexed: 06/13/2023]
Abstract
Effects of climate warming on trophic cascades are increasingly reported for large herbivores occupying northern latitudes. During the last 40 years, moose (Alces alces) in northeast China have lost nearly half of their historical distribution through their habitat shifting northwards. There are many possible causes of bottom-up and top-down effects of temperature and for moose in northeast China they are poorly understood. Of particular relevance are the effects of extrinsic environmental factors on gene flow, nutritional adaptions, and gut microbiota that occur as moose populations retreat northwards. We combined molecular biology, nutritional ecology and metagenomics to gain deeper mechanistic insights into the effects of temperature on moose populations. In this study, we revealed that the direction and intensity of gene flow is consistent with global warming driving retreats of moose populations. We interpret this as evidence for the northward movement of moose populations, with cooler northern populations receiving more immigrants and warmer southern populations supplying emigrants. Comparison across latitudes showed that warmer late spring temperatures were associated with plant community composition and facilitated related changes in moose protein and carbohydrate intake through altering forage availability, forage quality and diet composition. Furthermore, these nutrient shifts were accompanied by changes in gut microbial composition and functional pathways related to nutrient metabolism. This study provided insights into mechanisms driving effects of spatial heterogeneous warming on genetic, nutritional and physiological adaptions related to key demographic rates and patterns of survival of heat-sensitive ungulates along a latitude gradient. Understanding such changes helps to identify key habitat areas and plant species to ensure accurate assessment of population status and targeted management of moose populations.
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Affiliation(s)
- Shiyu Chen
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Marcel Holyoak
- Department of Environmental Science and Policy, University of California, Davis, CA 95616, USA
| | - Hui Liu
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; College of Forestry, Hainan University, Haikou 570228, China
| | - Heng Bao
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Yingjie Ma
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1-5 Beichenxi Road, Chaoyang, Beijing 100101, China
| | - Hongliang Dou
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China
| | - Guangshun Jiang
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China.
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31
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Gresner N, Rodehutscord M, Südekum KH. Amino acid pattern of rumen microorganisms in cattle fed mixed diets-An update. J Anim Physiol Anim Nutr (Berl) 2021; 106:752-771. [PMID: 34964170 DOI: 10.1111/jpn.13676] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 10/16/2021] [Accepted: 12/14/2021] [Indexed: 11/30/2022]
Abstract
Rumen microorganisms turn small N-containing compounds into amino acids (AA) and contribute considerably to the supply of AA absorbed from the small intestine. Previous studies summarized the literature on microbial AA patterns, most recently in 2017 (Sok et al. Journal of Dairy Science, 100, 5241-5249). The present study intended to identify the microbial AA pattern typical when feeding Central European diets and a maximum proportion of concentrate (PCO; dry matter (DM) basis) of 0.60. Data sets were created from the literature for liquid (LAB)- and particle (PAB)-associated bacteria, total bacteria and protozoa, including 16, 9, 27 and 8 studies and 36, 21, 60 and 18 diets respectively. Because the only differences detected between LAB and PAB were slightly higher Phe and lower Thr percentages in PAB (p < 0.05), results for bacteria were pooled. A further data set evaluated AA-N (AAN) as a proportion of total N in microbial fractions and a final data set estimated protozoal contributions to total microbial N (TMN) flow to the duodenum, which were used to calculate weighted TMN AA patterns. Protozoa showed higher Lys, Asp, Glu, Ile and Phe and lower Ala, Arg, Gly, Met, Ser, Thr and Val proportions than bacteria (p < 0.05). The AAN percentage of total N in bacteria and protozoa showed large, unexplained variations, averaging 79.0% and 70.6% (p > 0.05) respectively. Estimation of protozoal contribution to TMN resulted in a cattle-specific mixed model including PCO and DM intake (DMI) per unit of metabolic body size (kg0.75 ) as fixed effects (RMSE = 3.77). With moderate PCO and DMI between 80 and 180 g/kg0.75 , which corresponds to a DMI of approximately 10 to 25 kg in a cow with 650 kg body weight, protozoal contribution ranged between 9% and 26% of TMN. Within this range, the estimated protozoal contribution to TMN resulted in minor effects on the total microbial AA pattern.
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Affiliation(s)
- Nina Gresner
- Institute of Animal Science, University of Bonn, Bonn, Germany
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Effects of Selenium Supplementation on Rumen Microbiota, Rumen Fermentation, and Apparent Nutrient Digestibility of Ruminant Animals: A Review. FERMENTATION-BASEL 2021. [DOI: 10.3390/fermentation8010004] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Enzymes excreted by rumen microbiome facilitate the conversion of ingested plant materials into major nutrients (e.g., volatile fatty acids (VFA) and microbial proteins) required for animal growth. Diet, animal age, and health affect the structure of the rumen microbial community. Pathogenic organisms in the rumen negatively affect fermentation processes in favor of energy loss and animal deprivation of nutrients in ingested feed. Drawing from the ban on antibiotic use during the last decade, the livestock industry has been focused on increasing rumen microbial nutrient supply to ruminants through the use of natural supplements that are capable of promoting the activity of beneficial rumen microflora. Selenium (Se) is a trace mineral commonly used as a supplement to regulate animal metabolism. However, a clear understanding of its effects on rumen microbial composition and rumen fermentation is not available. This review summarized the available literature for the effects of Se on specific rumen microorganisms along with consequences for rumen fermentation and digestibility. Some positive effects on total VFA, the molar proportion of propionate, acetate to propionate ratio, ruminal NH3-N, pH, enzymatic activity, ruminal microbiome composition, and digestibility were recorded. Because Se nanoparticles (SeNPs) were more effective than other forms of Se, more studies are needed to compare the effectiveness of synthetic SeNPs and lactic acid bacteria enriched with sodium selenite as a biological source of SeNPs and probiotics. Future studies also need to evaluate the effect of dietary Se on methane emissions.
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Cristobal-Carballo O, McCoard SA, Cookson AL, Laven RA, Ganesh S, Lewis SJ, Muetzel S. Effect of Divergent Feeding Regimes During Early Life on the Rumen Microbiota in Calves. Front Microbiol 2021; 12:711040. [PMID: 34745024 PMCID: PMC8565576 DOI: 10.3389/fmicb.2021.711040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 08/31/2021] [Indexed: 12/16/2022] Open
Abstract
The objective of this study was to determine whether divergent feeding regimes during the first 41 weeks of the life of a calf are associated with long-term changes in the rumen microbiota and the associated fermentation end-products. Twenty-four calves (9 ± 5 days of age) were arranged in a 2 × 2 factorial design with two divergent treatments across three dietary phases. In phase 1 (P01), calves were offered a low-milk volume/concentrate starter diet with early weaning (CO) or high-milk volume/pasture diet and late weaning (FO). In phase 2 (P02), calves from both groups were randomly allocated to either high-quality (HQ) or low-quality (LQ) pasture grazing groups. In phase 3 (P03), calves were randomly allocated to one of two grazing groups and offered the same pasture-only diet. During each dietary phase, methane (CH4) and hydrogen (H2) emissions and dry matter intake (DMI) were measured in respiration chambers, and rumen samples for the evaluation of microbiota and short-chain fatty acid (SCFA) characterizations were collected. In P01, CO calves had a higher solid feed intake but a lower CH4 yield (yCH4) and acetate:propionate ratio (A:P) compared with FO calves. The ruminal bacterial community had lower proportions of cellulolytic bacteria in CO than FO calves. The archaeal community was dominated by Methanobrevibacter boviskoreani in CO calves and by Mbb. gottschalkii in FO calves. These differences, however, did not persist into P02. Calves offered HQ pastures had greater DMI and lower A:P ratio than calves offered LQ pastures, but yCH4 was similar between groups. The cellulolytic bacteria had lower proportions in HQ than LQ calves. In all groups, the archaeal community was dominated by Mbb. gottschalkii. No treatment interactions were observed in P02. In P03, all calves had similar DMI, CH4 and H2 emissions, SCFA proportions, and microbial compositions, and no interactions with previous treatments were observed. These results indicate that the rumen microbiota and associated fermentation end-products are driven by the diet consumed at the time of sampling and that previous dietary interventions do not lead to a detectable long-term microbial imprint or changes in rumen function.
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Affiliation(s)
- Omar Cristobal-Carballo
- Ruminant Nutrition and Physiology Team, AgResearch Grasslands, Palmerston North, New Zealand.,School of Veterinary Medicine, Massey University, Palmerston North, New Zealand
| | - Sue A McCoard
- Ruminant Nutrition and Physiology Team, AgResearch Grasslands, Palmerston North, New Zealand
| | - Adrian L Cookson
- Food System Integrity Team, AgResearch Grasslands, Palmerston North, New Zealand.,School of Veterinary Medicine, Massey University, Palmerston North, New Zealand
| | - Richard A Laven
- School of Veterinary Medicine, Massey University, Palmerston North, New Zealand
| | - Siva Ganesh
- Biostatistics Team, AgResearch Grasslands, Palmerston North, New Zealand
| | - Sarah J Lewis
- Ruminant Nutrition and Physiology Team, AgResearch Grasslands, Palmerston North, New Zealand
| | - Stefan Muetzel
- Ruminant Nutrition and Physiology Team, AgResearch Grasslands, Palmerston North, New Zealand
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Li Y, Zang Y, Zhao X, Liu L, Qiu Q, Ouyang K, Qu M. Dietary Supplementation With Creatine Pyruvate Alters Rumen Microbiota Protein Function in Heat-Stressed Beef Cattle. Front Microbiol 2021; 12:715088. [PMID: 34512594 PMCID: PMC8431830 DOI: 10.3389/fmicb.2021.715088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
Creatine pyruvate (CrPyr) is a new multifunctional nutrient that can provide both pyruvate and creatine. It has been shown to relieve the heat stress of beef cattle by improving antioxidant activity and rumen microbial protein synthesis, but the mechanism of CrPyr influencing rumen fermentation remains unclear. This study aimed to combine 16S rDNA sequencing and metaproteomics technologies to investigate the microbial composition and function in rumen fluid samples taken from heat-stressed beef cattle treated with or without 60 g/day CrPyr. 16S rDNA sequencing revealed that there were no significant differences in the α-diversity indices between the two groups. By analyzing the level profiles of 700 distinct proteins, we found that the CrPyr administration increased the expression of enzymes involved in specific metabolic pathways including (i) fatty acid β-oxidation; (ii) interconversion from pyruvate to phosphoenolpyruvate, oxaloacetate, acetyl-CoA, and malate; (iii) glycolysis/gluconeogenesis and citrate cycle metabolism; and (iv) biosynthesis of amino acids. These results indicated that the increased generation of adenosine triphosphate during fatty acid β-oxidation or citrate cycle and the up-regulation synthesis of microbial protein in rumen of beef cattle treated with CrPyr may help decrease oxidative stress, regulate energy metabolism, and further improve the rumen fermentation characteristic under heat stress.
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Affiliation(s)
- Yanjiao Li
- Jiangxi Province Key Laboratory of Animal Nutrition/Animal Nutrition and Feed Safety Innovation Team, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yitian Zang
- Jiangxi Province Key Laboratory of Animal Nutrition/Animal Nutrition and Feed Safety Innovation Team, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Xianghui Zhao
- Jiangxi Province Key Laboratory of Animal Nutrition/Animal Nutrition and Feed Safety Innovation Team, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Lin Liu
- Jiangxi Province Key Laboratory of Animal Nutrition/Animal Nutrition and Feed Safety Innovation Team, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Qinghua Qiu
- Jiangxi Province Key Laboratory of Animal Nutrition/Animal Nutrition and Feed Safety Innovation Team, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Kehui Ouyang
- Jiangxi Province Key Laboratory of Animal Nutrition/Animal Nutrition and Feed Safety Innovation Team, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Mingren Qu
- Jiangxi Province Key Laboratory of Animal Nutrition/Animal Nutrition and Feed Safety Innovation Team, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
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Effects of Age, Diet CP, NDF, EE, and Starch on the Rumen Bacteria Community and Function in Dairy Cattle. Microorganisms 2021; 9:microorganisms9081788. [PMID: 34442867 PMCID: PMC8400643 DOI: 10.3390/microorganisms9081788] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/09/2021] [Accepted: 08/17/2021] [Indexed: 01/22/2023] Open
Abstract
To understand the effects of diet and age on the rumen bacterial community and function, forty-eight dairy cattle at 1.5 (M1.5), 6 (M6), 9 (M9), 18 (M18), 23 (M23), and 27 (M27) months old were selected. Rumen fermentation profile, enzyme activity, and bacteria community in rumen fluid were measured. The acetate to propionate ratio (A/P) at M9, M18, and M23 was higher than other ages, and M6 was the lowest (p < 0.05). The total volatile fatty acid (TVFA) at M23 and M27 was higher than at other ages (p < 0.05). The urease at M18 was lower than at M1.5, M6, and M9, and the xylanase at M18 was higher than at M1.5, M23, and M27 (p < 0.05). Thirty-three bacteria were identified as biomarkers of the different groups based on the linear discriminant analysis (LDA) when the LDA score >4. The variation partitioning approach analysis showed that the age and diet had a 7.98 and 32.49% contribution to the rumen bacteria community variation, respectively. The richness of Succinivibrionaceae_UCG-002 and Fibrobacter were positive correlated with age (r > 0.60, p < 0.01) and positively correlated with TVFA and acetate (r > 0.50, p < 0.01). The Lachnospiraceae_AC2044_group, Pseudobutyrivibrio, and Saccharofermentans has a positive correlation (r > 0.80, p < 0.05) with diet fiber and a negative correlation (r < −0.80, p < 0.05) with diet protein and starch, which were also positively correlated with the acetate and A/P (r > 0.50, p < 0.01). The genera of Lachnospiraceae_AC2044_group, Pseudobutyrivibrio, and Saccharofermentans could be worked as the target bacteria to modulate the rumen fermentation by diet; meanwhile, the high age correlated bacteria such as Succinivibrionaceae_UCG-002 and Fibrobacter also should be considered when shaping the rumen function.
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36
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Rumen Bacterial Community of Grazing Lactating Yaks ( Poephagus grunniens) Supplemented with Concentrate Feed and/or Rumen-Protected Lysine and Methionine. Animals (Basel) 2021; 11:ani11082425. [PMID: 34438881 PMCID: PMC8388701 DOI: 10.3390/ani11082425] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/12/2021] [Accepted: 08/12/2021] [Indexed: 12/17/2022] Open
Abstract
Simple Summary Ruminal microorganisms, especially bacteria, play a vital role in utilizing fibrous material in ruminants. The yak is a bovid on the Qinghai-Tibet Plateau that traditionally only grazes natural pasture all year. During lactation, energy intake of yaks is often well below requirements, and yaks lose body weight. Today, to mitigate body weight losses during lactation, suckling yaks are often offered supplementary feed. This study examined the effect of dietary supplements on rumen bacteria in lactating yak. The yaks were offered supplementary concentrate feed (C), rumen-protected Lys and Met (RPA), or both (RPA+C). The ratio of the relative abundance of Firmicutes to Bacteroidetes in RPA+C was greater than in the RPA group, while there was no difference between C and RPA+C. The intakes of supplements resulted in a number of alterations in the abundances of bacteria at the genus level. When supplemented with C, yaks increased the concentration of ruminal total volatile fatty acids (VFAs), acetate, and butyrate. These results demonstrate that supplementary feed: (1) alters the composition of rumen microbiota and VFAs of lactating yaks; and (2) can be used to manipulate the composition of rumen microbiota. Abstract Traditionally, yaks graze only natural pasture all year round without supplements. Forage intake of lactating yaks is below energy and protein requirements, even in the summer, and suckling yaks lose a substantial amount of significant body weight. Today, to mitigate the loss in body weight, supplementary feed is being offered to lactating yaks. However, the effects of supplementary feed on ruminal bacterial communities in lactating yaks is unknown. In the current study, we examined the effect of supplementary feed on ruminal microbiota, using 16S rRNA sequencing, and on volatile fatty acids (VFAs). Twenty-four lactating yaks of similar body weight (218 ± 19.5 kg) and grazing natural pasture were divided randomly into four groups and received different supplements: (1) rumen-protected amino acids (RPA); (2) concentrate feed (C); (3) RPA plus C (RPA+C); and (4) no supplements (control-CON). The concentrations of total VFAs, acetate, and butyrate were greater (p < 0.05) when supplemented with concentrate feed (C and RPA+C) than without concentrate feed (CON and RPA). Bacteroidetes (B) and Firmicutes (F) were the dominant ruminal bacterial phyla in all groups. The ratio of relative abundance of F:B in RPA+C was greater than in the RPA group, while there was no difference between CON and RPC (interaction, p = 0.026). At the genus level, the relative abundances of Absconditabacteriales_SR1, Bacteroidales-RF16-group, Bacteroidales_BS11_gut_group, Prevotellaceae, and Rikenellaceae_RC9_gut_group were lesser (p < 0.05) with supplementary concentrate feed (C and RPA+C) than without concentrate feed (CON and RPA), whereas Butyrivibrio_2 and Pseudobutyrivibrio were greater (p < 0.05) with supplementary rumen-protected amino acids (RPA and RPA+C) than without rumen-protected amino acids (CON and C). These results demonstrate that supplementary feed: (1) alters the composition of rumen microbiota and concentrations of ruminal VFAs in lactating yaks; and (2) can be used to manipulate the composition of rumen microbiota.
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Roman-Garcia Y, Mitchell KE, Denton BL, Lee C, Socha MT, Wenner BA, Firkins JL. Conditions stimulating neutral detergent fiber degradation by dosing branched-chain volatile fatty acids. II: Relation with solid passage rate and pH on neutral detergent fiber degradation and microbial function in continuous culture. J Dairy Sci 2021; 104:9853-9867. [PMID: 34147227 DOI: 10.3168/jds.2021-20335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/02/2021] [Indexed: 11/19/2022]
Abstract
To support improving genetic potential for increased milk production, intake of digestible carbohydrate must also increase to provide digestible energy and microbial protein synthesis. We hypothesized that the provision of exogenous branched-chain volatile fatty acids (BCVFA) would improve both neutral detergent fiber (NDF) degradability and efficiency of microbial protein synthesis. However, BCVFA should be more beneficial with increasing efficiency of bacterial protein synthesis associated with increasing passage rate (kp). We also hypothesized that decreasing pH would increase the need for isobutyrate over 2-methylbutyrate. To study these effects independent from other sources of variation in vivo, we evaluated continuous cultures without (control) versus with BCVFA (0 vs. 2 mmol/d each of isobutyrate, isovalerate, and 2-methylbutyrate), low versus high kp of the particulate phase (2.5 vs. 5.0%/h), and high versus low pH (ranging from 6.3 to 6.8 diurnally vs. 5.7 to 6.2) in a 2 × 2 × 2 factorial arrangement of treatments. Diets were 50% forage pellets and 50% grain pellets administered twice daily. Without an interaction, NDF degradability tended to increase from 29.7 to 35.0% for main effects of control compared with BCVFA treatments. Provision of BCVFA increased methanogenesis, presumably resulting from improved NDF degradability. Decreasing pH decreased methane production. Total volatile fatty acid (VFA) and acetate production were decreased with increasing kp, even though true organic matter degradability and bacterial nitrogen flow were not affected by treatments. Decreasing pH decreased acetate but increased propionate and valerate production, probably resulting from a shift in bacterial taxa and associated VFA stoichiometry. Decreasing pH decreased isobutyrate and isovalerate production while increasing 2-methylbutyrate production on a net basis (subtracting doses). Supplementing BCVFA improved NDF degradability in continuous cultures administered moderate (15.4%) crude protein diets (excluding urea in buffer) without major interactions with culture pH and kp.
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Affiliation(s)
- Y Roman-Garcia
- Department of Animal Sciences, The Ohio State University, Columbus 43210
| | - K E Mitchell
- Department of Animal Sciences, The Ohio State University, Columbus 43210
| | - B L Denton
- Department of Animal Sciences, The Ohio State University, Columbus 43210
| | - C Lee
- Ohio Agricultural Research and Development Center, Wooster 44691
| | - M T Socha
- Zinpro Corporation, Eden Prairie, MN 55344
| | - B A Wenner
- Department of Animal Sciences, The Ohio State University, Columbus 43210
| | - J L Firkins
- Department of Animal Sciences, The Ohio State University, Columbus 43210.
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38
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Zhang K, Qian Q, Mao Y, Xu Y, Yang Y, Chen Y, Wang X. Characterization of growth phenotypes and gastrointestinal tract microbiota in sheep fed with caragana. J Appl Microbiol 2021; 131:2763-2779. [PMID: 33998744 DOI: 10.1111/jam.15138] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/22/2021] [Accepted: 05/10/2021] [Indexed: 01/15/2023]
Abstract
AIMS Using high-protein caragana as an unconventional feed supplement has promising application potential in livestock feeding programmes, and verifying its function is of great importance to guide efficient dietary management of livestock. METHODS AND RESULTS This study investigated the resulting changes in the growth, slaughter performance, serum physiological index, physical and chemical characteristics of meat, ruminal and intestine morphology and gastrointestinal tract microbiota in sheep fed with caragana (CAR), corn straw (COR) and alfalfa (ALF) diets. The CAR group showed an increased abundance of Christensenellaceae R-7 group, Marvinbryantia, Ruminococcaceae NK4A214, Lachnospiraceae UCG-002 and Desulfuromonas in the rumen compared with ALF, and CAR group mainly enhanced starch and sucrose metabolism, fructose and mannose metabolism, photosynthesis and d-alanine metabolism in the rumen compared with ALF. CONCLUSIONS CAR diet positively changed the fatty acid profile of longissimus dorsi muscle and significantly altered the composition and function of the microbiota in the rumen, ileum and cecum. SIGNIFICANCE AND IMPACT OF THE STUDY This study systematically demonstrated the feasibility of CAR as an alternative to ALF for animal fattening in a complete formula granulated feed and provided a fundamental basis for further research and development of CAR as an unconventional feed source for ruminants.
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Affiliation(s)
- K Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Q Qian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Y Mao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Y Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Y Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Y Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - X Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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Schmitz-Esser S. The Rumen Epithelial Microbiota: Possible Gatekeepers of the Rumen Epithelium and Its Potential Contributions to Epithelial Barrier Function and Animal Health and Performance. MEAT AND MUSCLE BIOLOGY 2021. [DOI: 10.22175/mmb.11672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Ruminants are characterized by their unique mode of digesting cellulose-rich plant material in their forestomach, the rumen, which is densely populated by diverse microorganisms that are crucial for the breakdown of plant material. Among ruminal microbial communities, the microorganisms in the rumen fluid or attached to feed particles have attracted considerable research interest. However, comparatively less is known about the microorganisms attached to the rumen epithelium. Generally, the tissue lining the gastrointestinal tract serves the dual role of absorbing nutrients while preventing the infiltration of unwanted compounds and molecules as well as microorganisms. The rumen epithelium fulfills critical physiological functions for the ruminant host in energy absorption, metabolism, and nutrient transport. Essential host metabolites, such as short-chain fatty acids, ammonia, urea, and minerals, are exchanged across the rumen wall, thereby exposing the rumen epithelial microbiota to these nutrients. The integrity of the gastrointestinal barrier is central to animal health and productivity. The integrity of the rumen epithelium can be compromised by high ruminal microbial fermentation activity resulting in decreased rumen pH or by stress conditions such as heat stress or feed restriction. It is important to keep in mind that feeding strategies in cattle have changed over the last decades in favor of energy- and nutrient-rich concentrates instead of fiber-rich forages. These dietary shifts support high milk yields and growth rates but raised concerns regarding a possibly compromised rumen function. This paper will provide an overview of the composition of rumen epithelial microbial communities under physiological and disease conditions and will provide insights into the knowledge about the function and in situ activity of rumen epithelial microorganisms and their relevance for animal health and production. Given that an impaired intestinal barrier will negatively affect economically significant phenotypes, a better understanding of rumen wall microbiota is urgently needed.
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Hinsu AT, Tulsani NJ, Panchal KJ, Pandit RJ, Jyotsana B, Dafale NA, Patil NV, Purohit HJ, Joshi CG, Jakhesara SJ. Characterizing rumen microbiota and CAZyme profile of Indian dromedary camel (Camelus dromedarius) in response to different roughages. Sci Rep 2021; 11:9400. [PMID: 33931716 PMCID: PMC8087840 DOI: 10.1038/s41598-021-88943-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 04/12/2021] [Indexed: 02/07/2023] Open
Abstract
In dromedary camels, which are pseudo-ruminants, rumen or C1 section of stomach is the main compartment involved in fiber degradation, as in true ruminants. However, as camels are adapted to the harsh and scarce grazing conditions of desert, their ruminal microbiota makes an interesting target of study. The present study was undertaken to generate the rumen microbial profile of Indian camel using 16S rRNA amplicon and shotgun metagenomics. The camels were fed three diets differing in the source of roughage. The comparative metagenomic analysis revealed greater proportions of significant differences between two fractions of rumen content followed by diet associated differences. Significant differences were also observed in the rumen microbiota collected at different time-points of the feeding trial. However, fraction related differences were more highlighted as compared to diet dependent changes in microbial profile from shotgun metagenomics data. Further, 16 genera were identified as part of the core rumen microbiome of Indian camels. Moreover, glycoside hydrolases were observed to be the most abundant among all Carbohydrate-Active enzymes and were dominated by GH2, GH3, GH13 and GH43. In all, this study describes the camel rumen microbiota under different dietary conditions with focus on taxonomic, functional, and Carbohydrate-Active enzymes profiles.
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Affiliation(s)
- Ankit T Hinsu
- Department of Animal Biotechnology, College of Veterinary Science & A.H., Anand Agricultural University, Anand, 388001, India
| | - Nilam J Tulsani
- Department of Animal Biotechnology, College of Veterinary Science & A.H., Anand Agricultural University, Anand, 388001, India
| | - Ketankumar J Panchal
- Department of Animal Biotechnology, College of Veterinary Science & A.H., Anand Agricultural University, Anand, 388001, India
| | - Ramesh J Pandit
- Department of Animal Biotechnology, College of Veterinary Science & A.H., Anand Agricultural University, Anand, 388001, India
| | | | - Nishant A Dafale
- ICAR-Central Arid Zone Research Institute, Jodhpur, 342003, India
| | - Niteen V Patil
- ICAR-National Research Centre On Camel, Bikaner, 334001, India.,ICAR-Central Arid Zone Research Institute, Jodhpur, 342003, India
| | - Hemant J Purohit
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, 440020, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Science & A.H., Anand Agricultural University, Anand, 388001, India.,Gujarat Biotechnology Research Centre, Gandhinagar, 382010, India
| | - Subhash J Jakhesara
- Department of Animal Biotechnology, College of Veterinary Science & A.H., Anand Agricultural University, Anand, 388001, India.
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Roman-Garcia Y, Denton BL, Mitchell KE, Lee C, Socha MT, Firkins JL. Conditions stimulating neutral detergent fiber degradation by dosing branched-chain volatile fatty acids. I: Comparison with branched-chain amino acids and forage source in ruminal batch cultures. J Dairy Sci 2021; 104:6739-6755. [PMID: 33814156 DOI: 10.3168/jds.2020-20054] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/18/2021] [Indexed: 01/13/2023]
Abstract
Three experiments assessed branched-chain volatile fatty acid (BCVFA) stimulation of neutral detergent fiber (NDF) disappearance after 24 h of incubation in batch cultures derived from ruminal fluid inocula that were enriched with particulate-phase bacteria. In experiment 1, a control was compared with 3 treatments with isomolar doses of all 3 BCVFA (plus valerate), all 3 branched-chain AA (BCAA), or half of each BCVFA and BCAA mix with either alfalfa or grass hays (50%) and ground corn grain (50%). A portion of the BCAA and BCVFA doses were enriched with 13C, and valerate (also enriched with 13C) was added with BCVFA. Although BCAA yielded a similar production of BCVFA compared with dosing BCVFA, equimolar substitution of BCVFA for BCAA decreased the percentage of N in bacterial pellets when alfalfa hay was fed but increased N when grass hay was fed. Substituting BCVFA for BCAA increased total fatty acid (FA) concentration with alfalfa hay. Dosing of BCAA or BCVFA did not affect total branched-chain FA, iso-FA, or anteiso-FA percentages in bacterial total FA, whereas numerous individual FA isomers and their 13C enrichments were affected by these treatments. Increasing recovery of the 13C dose from respective labeled BCVFA primers indicated facilitated BCVFA uptake and incorporation into FA compared with BCAA, whereas increased recovery of 13C from labeled BCAA in the bacteria pellet but not in the FA fraction suggested direct assimilation into bacterial protein. The BCVFA and valerate were dosed in varying combinations that either summed to 4 mM (experiment 2) or had only 1 mM no matter what combination (experiment 3). In general, grass hay was more responsive to stimulation in NDF digestibility by BCVFA than was alfalfa hay, which was attributed to the higher degradable protein in the latter. The net production of the BCVFA (after subtracting dose) was affected by source and combination of BCVFA. Isovalerate dosing tended to increase its own net production; in contrast, isobutyrate seemed to be used more when it was added alone, but 2-methylbutyrate seemed to be preferred over isobutyrate when 2-methylbutyrate was added. Results supported potential interactions, including potential feedback in production from feed BCAA or increased concentration-dependent competition for dosed BCVFA into cellular products. Under our conditions, the BCVFA appear to be more readily available than BCAA, probably because of regulated BCAA transport and metabolism. Valerate consistently provided no benefit. Using nonparametric ranking, all 3 BCVFA or either isovalerate or isobutyrate (both yielding iso-FA) should be combined with 2-methylbutyrate (yielding anteiso-FA) as a potential opportunity to improve NDF digestibility when rumen-degraded BCAA are limited in diets to decrease environmental impact from N in waste.
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Affiliation(s)
- Y Roman-Garcia
- Cargill Animal Nutrition, Innovation Campus, Elk River, MN 55330
| | - B L Denton
- Department of Animal Sciences, The Ohio State University, Columbus 43210
| | - K E Mitchell
- Department of Animal Sciences, The Ohio State University, Columbus 43210
| | - C Lee
- Department of Animal Sciences, The Ohio State University, Columbus 43210; Department of Animal Sciences, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster 44691
| | - M T Socha
- Zinpro Corporation, Eden Prairie, MN 55344
| | - J L Firkins
- Department of Animal Sciences, The Ohio State University, Columbus 43210.
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Bailoni L, Carraro L, Cardin M, Cardazzo B. Active Rumen Bacterial and Protozoal Communities Revealed by RNA-Based Amplicon Sequencing on Dairy Cows Fed Different Diets at Three Physiological Stages. Microorganisms 2021; 9:754. [PMID: 33918504 PMCID: PMC8066057 DOI: 10.3390/microorganisms9040754] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/29/2021] [Accepted: 04/01/2021] [Indexed: 12/12/2022] Open
Abstract
Seven Italian Simmental cows were monitored during three different physiological stages, namely late lactation (LL), dry period (DP), and postpartum (PP), to evaluate modifications in their metabolically-active rumen bacterial and protozoal communities using the RNA-based amplicon sequencing method. The bacterial community was dominated by seven phyla: Proteobacteria, Bacteroidetes, Firmicutes, Spirochaetes, Fibrobacteres, Verrucomicrobia, and Tenericutes. The relative abundance of the phylum Proteobacteria decreased from 47.60 to 28.15% from LL to DP and then increased to 33.24% in PP. An opposite pattern in LL, DP, and PP stages was observed for phyla Verrucomicrobia (from 0.96 to 4.30 to 1.69%), Elusimicrobia (from 0.32 to 2.84 to 0.25%), and SR1 (from 0.50 to 2.08 to 0.79%). The relative abundance of families Succinivibrionaceae and Prevotellaceae decreased in the DP, while Ruminococcaceae increased. Bacterial genera Prevotella and Treponema were least abundant in the DP as compared to LL and PP, while Ruminobacter and Succinimonas were most abundant in the DP. The rumen eukaryotic community was dominated by protozoal phylum Ciliophora, which showed a significant decrease in relative abundance from 97.6 to 93.9 to 92.6 in LL, DP, and PP, respectively. In conclusion, the physiological stage-dependent dietary changes resulted in a clear shift in metabolically-active rumen microbial communities.
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Affiliation(s)
- Lucia Bailoni
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Viale dell’Universitá 16, 35020 Legnaro, PD, Italy; (L.C.); (M.C.); (B.C.)
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43
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Gharechahi J, Vahidi MF, Bahram M, Han JL, Ding XZ, Salekdeh GH. Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions to utilize high lignocellulosic forages in the cattle rumen. THE ISME JOURNAL 2021; 15:1108-1120. [PMID: 33262428 PMCID: PMC8114923 DOI: 10.1038/s41396-020-00837-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 11/03/2020] [Accepted: 11/11/2020] [Indexed: 02/08/2023]
Abstract
Rumen microbiota play a key role in the digestion and utilization of plant materials by the ruminant species, which have important implications for greenhouse gas emission. Yet, little is known about the key taxa and potential gene functions involved in the digestion process. Here, we performed a genome-centric analysis of rumen microbiota attached to six different lignocellulosic biomasses in rumen-fistulated cattle. Our metagenome sequencing provided novel genomic insights into functional potential of 523 uncultured bacteria and 15 mostly uncultured archaea in the rumen. The assembled genomes belonged mainly to Bacteroidota, Firmicutes, Verrucomicrobiota, and Fibrobacterota and were enriched for genes related to the degradation of lignocellulosic polymers and the fermentation of degraded products into short chain volatile fatty acids. We also found a shift from copiotrophic to oligotrophic taxa during the course of rumen fermentation, potentially important for the digestion of recalcitrant lignocellulosic substrates in the physiochemically complex and varying environment of the rumen. Differential colonization of forages (the incubated lignocellulosic materials) by rumen microbiota suggests that taxonomic and metabolic diversification is an evolutionary adaptation to diverse lignocellulosic substrates constituting a major component of the cattle's diet. Our data also provide novel insights into the key role of unique microbial diversity and associated gene functions in the degradation of recalcitrant lignocellulosic materials in the rumen.
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Affiliation(s)
- Javad Gharechahi
- grid.411521.20000 0000 9975 294XHuman Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Farhad Vahidi
- grid.473705.20000 0001 0681 7351Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran
| | - Mohammad Bahram
- grid.6341.00000 0000 8578 2742Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51 Uppsala, Sweden ,grid.10939.320000 0001 0943 7661Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, 51005 Tartu, Estonia
| | - Jian-Lin Han
- grid.419369.00000 0000 9378 4481Livestock Genetics Program, International Livestock Research Institute (ILRI), 00100 Nairobi, Kenya ,grid.410727.70000 0001 0526 1937CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), 100193 Beijing, China
| | - Xue-Zhi Ding
- grid.410727.70000 0001 0526 1937Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), 730050 Lanzhou, China
| | - Ghasem Hosseini Salekdeh
- grid.473705.20000 0001 0681 7351Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran ,grid.1004.50000 0001 2158 5405Department of Molecular Sciences, Macquarie University, North Ryde, NSW Australia
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The Effect of a High-Grain Diet on the Rumen Microbiome of Goats with a Special Focus on Anaerobic Fungi. Microorganisms 2021; 9:microorganisms9010157. [PMID: 33445538 PMCID: PMC7827659 DOI: 10.3390/microorganisms9010157] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/11/2021] [Accepted: 01/11/2021] [Indexed: 12/17/2022] Open
Abstract
This work investigated the changes of the rumen microbiome of goats switched from a forage to a concentrate diet with special attention to anaerobic fungi (AF). Female goats were fed an alfalfa hay (AH) diet (0% grain; n = 4) for 20 days and were then abruptly shifted to a high-grain (HG) diet (40% corn grain, 60% AH; n = 4) and treated for another 10 days. Rumen content samples were collected from the cannulated animals at the end of each diet period (day 20 and 30). The microbiome structure was studied using high-throughput sequencing for bacteria, archaea (16S rRNA gene) and fungi (ITS2), accompanied by qPCR for each group. To further elucidate unclassified AF, clone library analyses were performed on the ITS1 spacer region. Rumen pH was significantly lower in HG diet fed goats, but did not induce subacute ruminal acidosis. HG diet altered prokaryotic communities, with a significant increase of Bacteroidetes and a decrease of Firmicutes. On the genus level Prevotella 1 was significantly boosted. Methanobrevibacter and Methanosphaera were the most abundant archaea regardless of the diet and HG induced a significant augmentation of unclassified Thermoplasmatales. For anaerobic fungi, HG triggered a considerable rise in Feramyces observed with both ITS markers, while a decline of Tahromyces was detected by ITS2 and decrease of Joblinomyces by ITS1 only. The uncultured BlackRhino group revealed by ITS1 and further elucidated in one sample by LSU analysis, formed a considerable part of the AF community of goats fed both diets. Results strongly indicate that the rumen ecosystem still acts as a source for novel microorganisms and unexplored microbial interactions and that initial rumen microbiota of the host animal considerably influences the reaction pattern upon diet change.
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45
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Li C, Zhang Q, Wang G, Niu X, Wang W, Li F, Li F, Zhang Z. The functional development of the rumen is influenced by weaning and associated with ruminal microbiota in lambs. Anim Biotechnol 2020; 33:612-628. [PMID: 32876516 DOI: 10.1080/10495398.2020.1812618] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Rumen development is critical for the development of early lambs. This work aims to evaluate the effects of abrupt weaning at day 21 on rumen fermentation, histomorphological traits and the ruminal microbiota compared with continuous suckling. Twelve pairs of artificially reared full-sib neonatal male Hu lambs were allocated to two groups, one of which was weaned at day 21 (EW group) and the other which was not weaned (CON group). At day 26 and day 49, six lambs from each group were randomly selected and sacrificed to collect ruminal contents and rumen tissue samples. Results showed that weaning influenced the fermentation parameters in the rumen, and altered the microbial community composition on day 49 (p < 0.05). Several genera were associated with rumen fermentation parameters (p < 0.05). Volatile fatty acid (VFA) concentration is the key parameter impacting microbiota composition. Weaning influenced the expression of genes associated with VFA metabolism and regulation of cell proliferation (p < 0.05). In conclusion, weaning significantly influenced the morphological and functional development of the rumen, and bacterial community composition. The microbial community composition was strongly associated with rumen weight and fermentation profiles, but not with morphological development.
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Affiliation(s)
- Chong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.,The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Qian Zhang
- Institute of Grassland Research of CAAS, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Guoxiu Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaolin Niu
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Weimin Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Fei Li
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Fadi Li
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Zhaocai Zhang
- Gansu Runmu Bio-Engineering Co., LTD, Yongchang, China
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46
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Fan W, Saito S, Matsumura S. Expression of the Tas1r3 and Pept1 genes in the digestive tract of wagyu cattle. Transl Anim Sci 2020; 4:txaa019. [PMID: 32705019 PMCID: PMC7201161 DOI: 10.1093/tas/txaa019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 02/07/2020] [Indexed: 01/26/2023] Open
Abstract
Animals have precise recognition systems for amino acids and peptides that regulate their feeding behavior as well as metabolic responses. Because of their particular gastrointestinal structure, ruminants are expected to have unique mechanisms of amino acid regulation in the digestive tract. To better understand these mechanisms in the ruminant digestive tract, the expression of Tas1r3 and Pept1 was studied along the gastrointestinal tract of Japanese Black cattle through quantitative RT-PCR and immunohistochemistry. Tas1r3 mRNA was detected ubiquitously along the gastrointestinal tract, and the most predominant expression was observed in the reticulum. In addition, the presence of Tas1r3 receptor was confirmed in the rumen through immunohistochemistry. The expression level of Pept1 mRNA was higher in the forestomach (rumen, reticulum, and omasum) and small intestine (duodenum) than that in the tongue, and predominant expression was observed in the rumen. By contrast, a negligible amount of Pept1 mRNA was detected in the abomasum and large intestine. Further studies on the roles of Tas1r3 and Pept1 in the digestive tract, in particular, in the four components of the stomach, will help us to understand the mechanisms of amino acids regulation in ruminants and provide the basis for formulating cattle diets to improve the health and productivity of cattle.
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Affiliation(s)
- Weihong Fan
- Graduate School of Natural Science and Technology, Gifu University, Yanagido, Gifu, Japan
| | - Shoichiro Saito
- Faculty of Applied Biological Sciences, Gifu University, Yanagido, Gifu, Japan
| | - Shuichi Matsumura
- Faculty of Applied Biological Sciences, Gifu University, Yanagido, Gifu, Japan
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47
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Ribeiro DM, Salama AAK, Vitor ACM, Argüello A, Moncau CT, Santos EM, Caja G, de Oliveira JS, Balieiro JCC, Hernández-Castellano LE, Zachut M, Poleti MD, Castro N, Alves SP, Almeida AM. The application of omics in ruminant production: a review in the tropical and sub-tropical animal production context. J Proteomics 2020; 227:103905. [PMID: 32712373 DOI: 10.1016/j.jprot.2020.103905] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 06/25/2020] [Accepted: 07/16/2020] [Indexed: 02/08/2023]
Abstract
The demand for animal products (e.g. dairy and beef) in tropical regions is expected to increase in parallel with the public demand for sustainable practices, due to factors such as population growth and climate change. The necessity to increase animal production output must be achieved with better management and production technologies. For this to happen, novel research methodologies, animal selection and postgenomic tools play a pivotal role. Indeed, improving breeder selection programs, the quality of meat and dairy products as well as animal health will contribute to higher sustainability and productivity. This would surely benefit regions where resource quality and quantity are increasingly unstable, and research is still very incipient, which is the case of many regions in the tropics. The purpose of this review is to demonstrate how omics-based approaches play a major role in animal science, particularly concerning ruminant production systems and research associated to the tropics and developing countries. SIGNIFICANCE: Environmental conditions in the tropics make livestock production harder, compared to temperate regions. Due to global warming, the sustainability of livestock production will become increasingly problematic. The use of novel omics technologies could generate useful information to understand adaptation mechanisms of resilient breeds and/or species. The application of omics to tropical animal production is still residual in the currently available literature. With this review, we aim to summarize the most notable results in the field whilst encouraging further research to deal with the future challenges that animal production in the tropics will need to face.
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Affiliation(s)
- David M Ribeiro
- LEAF Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, University of Lisbon, Lisboa, Portugal
| | - Ahmed A K Salama
- Group of Research in Ruminants (G2R), Department of Animal and Food Science, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
| | - Ana C M Vitor
- CIISA - Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Av. da Universidade Técnica, Lisboa, Portugal
| | - Anastasio Argüello
- Animal Production and Biotechnology group, Institute of Animal Health and Food Safety, Universidad de Las Palmas de Gran Canaria, 35413 Arucas, Spain
| | - Cristina T Moncau
- FZEA - Faculty of Animal Science and Food Engineering, University of São Paulo, Avenida Duque de Caxias Norte - 225, 13635-900 Pirassununga, SP, Brazil
| | - Edson M Santos
- Departamento de Zootecnia, Centro de Ciências Agrárias, Universidade Federal da Paraíba, Areia, PB, Brazil
| | - Gerardo Caja
- Group of Research in Ruminants (G2R), Department of Animal and Food Science, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
| | - Juliana S de Oliveira
- Departamento de Zootecnia, Centro de Ciências Agrárias, Universidade Federal da Paraíba, Areia, PB, Brazil
| | - Júlio C C Balieiro
- FMVZ - School of Veterinary Medicine and Animal Science, University of São Paulo, Avenida Duque de Caxias Norte - 225, 13635-900 Pirassununga, SP, Brazil
| | | | - Maya Zachut
- Department of Ruminant Science, Institute of Animal Sciences Agricultural Research Organization/Volcani Center, Rishon Lezion 7505101, Israel
| | - Mirele D Poleti
- FZEA - Faculty of Animal Science and Food Engineering, University of São Paulo, Avenida Duque de Caxias Norte - 225, 13635-900 Pirassununga, SP, Brazil
| | - Noemi Castro
- Animal Production and Biotechnology group, Institute of Animal Health and Food Safety, Universidad de Las Palmas de Gran Canaria, 35413 Arucas, Spain
| | - Susana P Alves
- CIISA - Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Av. da Universidade Técnica, Lisboa, Portugal
| | - André M Almeida
- LEAF Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, University of Lisbon, Lisboa, Portugal.
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48
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Wang L, Zhang K, Zhang C, Feng Y, Zhang X, Wang X, Wu G. Dynamics and stabilization of the rumen microbiome in yearling Tibetan sheep. Sci Rep 2019; 9:19620. [PMID: 31873173 PMCID: PMC6927978 DOI: 10.1038/s41598-019-56206-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 11/26/2019] [Indexed: 01/03/2023] Open
Abstract
The productivity of ruminants depends largely on rumen microbiota. However, there are few studies on the age-related succession of rumen microbial communities in grazing lambs. Here, we conducted 16 s rRNA gene sequencing for bacterial identification on rumen fluid samples from 27 Tibetan lambs at nine developmental stages (days (D) 0, 2, 7, 14, 28, 42, 56, 70, and 360, n = 3). We observed that Bacteroidetes and Proteobacteria populations were significantly changed during the growing lambs’ first year of life. Bacteroidetes abundance increased from 18.9% on D0 to 53.9% on D360. On the other hand, Proteobacteria abundance decreased significantly from 40.8% on D0 to 5.9% on D360. Prevotella_1 established an absolute advantage in the rumen after 7 days of age. The co-occurrence network showed that the different microbial of the rumen presented a complex synergistic and cumbersome relationship. A phylogenetic tree was constructed, indicating that during the colonization process, may occur a phenomenon in which bacteria with close kinship are preferentially colonized. Overall, this study provides new insights into the colonization of bacterial communities in lambs that will benefit the development of management strategies to promote colonization of target communities to improve functional development.
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Affiliation(s)
- Lei Wang
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, 810016, China.,State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
| | - Ke Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Chenguang Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yuzhe Feng
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, 810016, China
| | - Xiaowei Zhang
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, 810016, China
| | - Xiaolong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Guofang Wu
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, 810016, China. .,State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China.
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