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Kibegwa FM, Bett RC, Gachuiri CK, Machuka E, Stomeo F, Mujibi FD. Diversity and functional analysis of rumen and fecal microbial communities associated with dietary changes in crossbreed dairy cattle. PLoS One 2023; 18:e0274371. [PMID: 36638091 PMCID: PMC9838872 DOI: 10.1371/journal.pone.0274371] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 12/29/2022] [Indexed: 01/14/2023] Open
Abstract
The objective of this study was to investigate the effect of varying roughage and concentrate proportions, in diet of crossbreed dairy cattle, on the composition and associated functional genes of rumen and fecal microbiota. We also explored fecal samples as a proxy for rumen liquor samples. Six crossbred dairy cattle were reared on three diets with an increasing concentrate and reducing roughage amount in three consecutive 10-day periods. After each period, individual rumen liquor and fecal samples were collected and analyzed through shotgun metagenomic sequencing. Average relative abundance of identified Operational Taxonomic Units (OTU) and microbial functional roles from all animals were compared between diets and sample types (fecal and rumen liquor). Results indicated that dietary modifications significantly affected several rumen and fecal microbial OTUs. In the rumen, an increase in dietary concentrate resulted in an upsurge in the abundance of Proteobacteria, while reducing the proportions of Bacteroidetes and Firmicutes. Conversely, changes in microbial composition in fecal samples were not consistent with dietary modification patterns. Microbial functional pathway classification identified that carbohydrate metabolism and protein metabolism pathways dominated microbial roles. Assessment of dietary effects on the predicted functional roles of these microbiota revealed that a high amount of dietary concentrate resulted in an increase in central carbohydrate metabolism and a corresponding reduction in protein synthesis. Moreover, we identified several microbial stress-related responses linked to dietary changes. Bacteroides and Clostridium genera were the principal hosts of these microbial functions. Therefore, the roughage to concentrate proportion has more influence on the microbial composition and microbial functional genes in rumen samples than fecal samples. As such, we did not establish a significant relationship between the rumen and fecal metagenome profiles, and the rumen and fecal microbiota from one animal did not correlate more than those from different animals.
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Affiliation(s)
- Felix M. Kibegwa
- Department of Animal Production, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, Kenya
- * E-mail:
| | - Rawlynce C. Bett
- Department of Animal Production, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, Kenya
| | - Charles K. Gachuiri
- Department of Animal Production, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, Kenya
| | - Eunice Machuka
- Biosciences Eastern and Central Africa—International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Francesca Stomeo
- Biosciences Eastern and Central Africa—International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
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Liu J, Bai Y, Liu F, Kohn RA, Tadesse DA, Sarria S, Li RW, Song J. Rumen Microbial Predictors for Short-Chain Fatty Acid Levels and the Grass-Fed Regimen in Angus Cattle. Animals (Basel) 2022; 12:2995. [PMID: 36359118 PMCID: PMC9656057 DOI: 10.3390/ani12212995] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/13/2022] [Accepted: 10/20/2022] [Indexed: 10/12/2023] Open
Abstract
The health benefits of grass-fed beef are well documented. However, the rumen microbiome features in beef steers raised in a grass-fed regimen have yet to be identified. This study examined the rumen microbiome profile in the feeding regimes. Our findings show that the rumen microbiome of the grass-fed cattle demonstrated greater species diversity and harbored significantly higher microbial alpha diversity, including multiple species richness and evenness indices, than the grain-fed cattle. Global network analysis unveiled that grass-fed cattle's rumen microbial interaction networks had higher modularity, suggesting a more resilient and stable microbial community under this feeding regimen. Using the analysis of compositions of microbiomes with a bias correction (ANCOM-BC) algorithm, the abundance of multiple unclassified genera, such as those belonging to Planctomycetes, LD1-PB3, SR1, Lachnospira, and Sutterella, were significantly enriched in the rumen of grass-fed steers. Sutterella was also the critical genus able to distinguish the two feeding regimens by Random Forest. A rumen microbial predictor consisting of an unclassified genus in the candidate division SR1 (numerator) and an unclassified genus in the order Bacteroidales (denominator) accurately distinguished the two feeding schemes. Multiple microbial signatures or balances strongly correlated with various levels of SCFA in the rumen. For example, a balance represented by the log abundance ratio of Sutterella to Desulfovibrio was strongly associated with acetate-to-propionate proportions in the rumen (R2 = 0.87), which could be developed as a valuable biomarker for optimizing milk fat yield and cattle growth. Therefore, our findings provided novel insights into microbial interactions in the rumen under different feed schemes and their ecophysiological implications. These findings will help to develop rumen manipulation strategies to improve feed conversion ratios and average daily weight gains for grass- or pasture-fed cattle production.
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Affiliation(s)
- Jianan Liu
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Ying Bai
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan 056038, China
| | - Fang Liu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Richard A. Kohn
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Daniel A. Tadesse
- Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Laurel, MD 20708, USA
| | - Saul Sarria
- Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Laurel, MD 20708, USA
| | - Robert W. Li
- United States Department of Agriculture, Agriculture Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705, USA
| | - Jiuzhou Song
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742, USA
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Combination of Medium- and High-Pressure Liquid Chromatography for Isolation of L-tryptophan (Q-marker) from Medicago sativa Extract. SEPARATIONS 2022. [DOI: 10.3390/separations9090240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Medicago sativa (alfalfa) is a widely used animal feed. However, its quality has been difficult to control due to the lack of appropriate marker compounds. Therefore, it is very necessary to select an appropriate quality marker (Q-marker) to control its quality. In this study, medium-pressure liquid chromatography and high-pressure liquid chromatography were employed to effectively prepare the separation of the Q-marker (L-tryptophan) from Medicago sativa. Firstly, using MCI GEL® CHP20P as the stationary phase, 2.5 g of the target fraction Fr3 was enriched from crude Medicago sativa extract (2.9 kg) by medium-pressure liquid chromatography. Secondly, Sephadex LH-20 was used to further separate Fr3 fractions, and the Fr34 fraction (358.3 mg) was enriched after 14 repetitions. Lastly, using the ReproSil-Pur C18 AQ preparative column, 63.4 mg of L-tryptophan was obtained by high-pressure liquid chromatography, and the purity was above 95%. The results showed that medium-pressure liquid chromatography (MCI GEL® CHP20P and Sephadex LH-20) combined with high-pressure liquid chromatography (ReproSil-Pur C18 AQ) could be used to effectively prepare the Q-marker from natural products with satisfactory purity.
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Zhang R, Liu J, Jiang L, Wang X, Mao S. The Remodeling Effects of High-Concentrate Diets on Microbial Composition and Function in the Hindgut of Dairy Cows. Front Nutr 2022; 8:809406. [PMID: 35178417 PMCID: PMC8845480 DOI: 10.3389/fnut.2021.809406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/15/2021] [Indexed: 01/22/2023] Open
Abstract
At present, research on high-concentrate (HC) diets mostly focused on the rumen, and there is a paucity of information on the hindgut microbiota of dairy cows. In the present study, a 2 × 2 crossover design with four healthy Holstein cows was used, and the metagenomics approach was adopted to reveal the remodeling effects of HC diets on hindgut microbiota and their metabolic functions. Results showed that, compared with the low-concentrate (LC) diets, HC diets have markedly decreased (p < 0.05) the abundance of cellulolytic bacteria (such as Fibrobacter, Ruminococcus, and Ruminiclostridium) and methanogens (such as Methanobrevibacter, Methanosarcina, and Methanosphaera); and correspondingly, HC diets have significantly reduced (p < 0.05) the abundance of carbohydrate-active enzymes (CAZy) related to hemicellulases (GH10, GH11, and GH54) and cellulases (GH1, GH44, and GH45) and increased the abundance of one oligosaccharide-degrading enzyme (GH32). Furthermore, 62 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of hindgut microbiota were affected (p < 0.05) by different dietary treatments, and the major pathways altered by HC diets were “Methane metabolism” (enriched in the LC group), “Lipid metabolism” (enriched in the HC group), and several sub-pathways in “Amino acid metabolism” (such as Phenylalanine metabolism, and Phenylalanine, tyrosine, and tryptophan biosynthesis). Also, the microbial genes involved in the pathways “Methane metabolism” (except 1 gene), “Tryptophan metabolism”, and “Phenylalanine metabolism” were all decreased (p < 0.05) in the present study. These findings suggested that HC diets caused the remodeling of hindgut microbiota and its potential functions, and these results may benefit in gaining a deeper understanding of the impact of HC diets on the hindgut microbiota of dairy cows.
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Affiliation(s)
- Ruiyang Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Junhua Liu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Linshu Jiang
- Beijing University of Agriculture, Beijing, China
| | - Xinfeng Wang
- College of Animal Science and Technology, Shihezi University, Shihezi, China
- *Correspondence: Xinfeng Wang
| | - Shengyong Mao
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- College of Animal Science and Technology, Shihezi University, Shihezi, China
- Shengyong Mao
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Castillo C, Hernández J. Ruminal Fistulation and Cannulation: A Necessary Procedure for the Advancement of Biotechnological Research in Ruminants. Animals (Basel) 2021; 11:ani11071870. [PMID: 34201623 PMCID: PMC8300264 DOI: 10.3390/ani11071870] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/11/2021] [Accepted: 06/15/2021] [Indexed: 11/18/2022] Open
Abstract
Simple Summary This article addresses the role of ruminal fistulation and cannulation as an essential procedure in the advancement of research related to several items: fermentation in the ruminant forestomach, effects of new food sources, rumen diseases as well as the minimization of methane emissions, implicated in the so-called greenhouse gases. The aim is also to diminish the alarmist news promoted by animalist sectors, which accuse this technique of being an act of cruelty. This paper describes the importance of this procedure as a necessary in vivo tool for biotechnological research. In addition, we highlight the necessary management measures to ensure animal welfare. This review ends with a description of current in vitro methods as an alternative to in vivo studies, assessing their applicability as a complementary tool to the knowledge of rumen dynamics. Abstract Rumen content is a complex mixture of feed, water, fermentation products, and living organisms such as bacteria, fungi, and protozoa, which vary over time and with different feeds. As it is impossible to reproduce this complex system in the laboratory, surgical fistulation and cannulation of the rumen is a powerful tool for the study (in vivo and in situ) of the physiology and biochemistry of the ruminant digestive system. Rumen fistulation in cattle, sheep, and goats has been performed extensively to advance our understanding of digestive physiology and development, nutrient degradability, and rumen microbial populations. The literature reports several fistulation and cannulation procedures in ruminants, which is not the focus of this paper. However, this method questions the ethical principles that alter the opinions of certain animal groups or those opposed to animal experimentation. In this article, we analyze the objectives of fistulation and cannulation of ruminants and the care needed to ensure that the welfare of the animal is maintained at all times. Due to the ethical issues raised by this technique, several in vitro digestion methods for simulating ruminal fermentation have been developed. The most relevant ones are described in this article. Independently of the procedure, we want to point out that research carried out with animals is obliged by legislation to follow strict ethical protocols, following the well-being and health status of the animal at all times.
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Xing BS, Cao S, Han Y, Wang XC, Wen J, Zhang K. A comparative study of artificial cow and sheep rumen fermentation of corn straw and food waste: Batch and continuous operation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 745:140731. [PMID: 32717608 DOI: 10.1016/j.scitotenv.2020.140731] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 06/11/2023]
Abstract
To optimize the artificial rumen microorganism sources and develop a stable artificial rumen system, batch and continuous operation were investigated with corn straw and food waste as substrates. The batch trials evaluated the volatile fatty acid (VFA) yield, biogas production, and lignocellulose degradation efficiency. The continuous test evaluated the performance of the artificial cow and sheep rumen systems using a dynamic membrane bioreactor (DMBR) with a stepwise organic loading rate at mesophilic temperature. The anaerobic digestion (AD) of the lignocellulose biomass after rumen fermentation pretreatment and of the permeate from the artificial rumen system were also evaluated for CH4 production. The results indicated that the cow rumen microorganisms were more suitable than sheep rumen microorganisms for lignocellulosic biomass pretreatment and maximized the CH4 yield through the AD process without inhibition. After approximately four months of continuous operation, a stable and continuous artificial rumen system for lignocellulosic biomass degradation was achieved with cow rumen fluid as inoculum. Based on analysis of the core lignocellulose-degrading enzyme levels and gel filtration chromatography, the cow rumen microorganisms could secrete more extracellular multienzyme complexes to hydrolyze lignocellulosic biomass than the sheep rumen microorganisms in vitro. During the batch and continuous operations, a high diversity and similar richness of bacteria and fungi demonstrated that the cow rumen microorganisms can be used as a preferred inoculum for the artificial rumen system. The use of an artificial cow rumen system with a DMBR is a promising way to construct a stable and continuous artificial rumen system to biodegrade lignocellulosic biomass for biogas production.
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Affiliation(s)
- Bao-Shan Xing
- International Science and Technology Cooperation Center for Urban Alternative Water Resources Development, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Engineering Technology Research Center for Wastewater Treatment and Reuse, Shaanxi, Key Laboratory of Environmental Engineering, Shaanxi, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, China
| | - Sifan Cao
- International Science and Technology Cooperation Center for Urban Alternative Water Resources Development, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Engineering Technology Research Center for Wastewater Treatment and Reuse, Shaanxi, Key Laboratory of Environmental Engineering, Shaanxi, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, China
| | - Yule Han
- International Science and Technology Cooperation Center for Urban Alternative Water Resources Development, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Engineering Technology Research Center for Wastewater Treatment and Reuse, Shaanxi, Key Laboratory of Environmental Engineering, Shaanxi, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, China
| | - Xiaochang C Wang
- International Science and Technology Cooperation Center for Urban Alternative Water Resources Development, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Engineering Technology Research Center for Wastewater Treatment and Reuse, Shaanxi, Key Laboratory of Environmental Engineering, Shaanxi, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, China.
| | - Junwei Wen
- International Science and Technology Cooperation Center for Urban Alternative Water Resources Development, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Engineering Technology Research Center for Wastewater Treatment and Reuse, Shaanxi, Key Laboratory of Environmental Engineering, Shaanxi, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, China
| | - Kaidi Zhang
- International Science and Technology Cooperation Center for Urban Alternative Water Resources Development, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Engineering Technology Research Center for Wastewater Treatment and Reuse, Shaanxi, Key Laboratory of Environmental Engineering, Shaanxi, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, China
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Serra V, Gammuto L, Nitla V, Castelli M, Lanzoni O, Sassera D, Bandi C, Sandeep BV, Verni F, Modeo L, Petroni G. Morphology, ultrastructure, genomics, and phylogeny of Euplotes vanleeuwenhoeki sp. nov. and its ultra-reduced endosymbiont "Candidatus Pinguicoccus supinus" sp. nov. Sci Rep 2020; 10:20311. [PMID: 33219271 PMCID: PMC7679464 DOI: 10.1038/s41598-020-76348-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/30/2020] [Indexed: 01/30/2023] Open
Abstract
Taxonomy is the science of defining and naming groups of biological organisms based on shared characteristics and, more recently, on evolutionary relationships. With the birth of novel genomics/bioinformatics techniques and the increasing interest in microbiome studies, a further advance of taxonomic discipline appears not only possible but highly desirable. The present work proposes a new approach to modern taxonomy, consisting in the inclusion of novel descriptors in the organism characterization: (1) the presence of associated microorganisms (e.g.: symbionts, microbiome), (2) the mitochondrial genome of the host, (3) the symbiont genome. This approach aims to provide a deeper comprehension of the evolutionary/ecological dimensions of organisms since their very first description. Particularly interesting, are those complexes formed by the host plus associated microorganisms, that in the present study we refer to as "holobionts". We illustrate this approach through the description of the ciliate Euplotes vanleeuwenhoeki sp. nov. and its bacterial endosymbiont "Candidatus Pinguicoccus supinus" gen. nov., sp. nov. The endosymbiont possesses an extremely reduced genome (~ 163 kbp); intriguingly, this suggests a high integration between host and symbiont.
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Affiliation(s)
- Valentina Serra
- Department of Biology, University of Pisa, Via Volta 4/6, 56126, Pisa, Italy
| | - Leandro Gammuto
- Department of Biology, University of Pisa, Via Volta 4/6, 56126, Pisa, Italy
| | - Venkatamahesh Nitla
- Department of Biology, University of Pisa, Via Volta 4/6, 56126, Pisa, Italy
| | - Michele Castelli
- Department of Biosciences, Romeo and Enrica Invernizzi Pediatric Research Center, University of Milan, Milan, Italy
- Department of Biology and Biotechnology "Lazzaro Spallanzani", Pavia University, Pavia, Italy
| | - Olivia Lanzoni
- Department of Biology, University of Pisa, Via Volta 4/6, 56126, Pisa, Italy
| | - Davide Sassera
- Department of Biology and Biotechnology "Lazzaro Spallanzani", Pavia University, Pavia, Italy
| | - Claudio Bandi
- Department of Biosciences, Romeo and Enrica Invernizzi Pediatric Research Center, University of Milan, Milan, Italy
| | | | - Franco Verni
- Department of Biology, University of Pisa, Via Volta 4/6, 56126, Pisa, Italy
| | - Letizia Modeo
- Department of Biology, University of Pisa, Via Volta 4/6, 56126, Pisa, Italy.
- CIME, Centro Interdipartimentale di Microscopia Elettronica, Università di Pisa, Pisa, Italy.
- CISUP, Centro per l'Integrazione della Strumentazione dell'Università di Pisa, Pisa, India.
| | - Giulio Petroni
- Department of Biology, University of Pisa, Via Volta 4/6, 56126, Pisa, Italy.
- CIME, Centro Interdipartimentale di Microscopia Elettronica, Università di Pisa, Pisa, Italy.
- CISUP, Centro per l'Integrazione della Strumentazione dell'Università di Pisa, Pisa, India.
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Mahmood M, Petri RM, Gavrău A, Zebeli Q, Khiaosa‐ard R. Betaine addition as a potent ruminal fermentation modulator under hyperthermal and hyperosmotic conditions in vitro. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2020; 100:2261-2271. [PMID: 31917480 PMCID: PMC7078755 DOI: 10.1002/jsfa.10255] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 12/02/2019] [Accepted: 01/06/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Climatic and dietary shifts predispose ruminal microbes to hyperthermal and hyperosmotic stress, leading to poor fermentation and subsequently adverse effects on ruminant productivity. Betaine may function as substrate, osmolyte, antioxidant, and methyl donor for microbes. However, its effect depends on the extent of microbial catabolism. This study revealed the ruminal disappearance kinetics of betaine and its dose effect on ruminal fermentation during thermal and osmotic stress using a rumen simulation technique. RESULTS Three different betaine doses were used: 0, 50, and 286 mg L-1 ; each was assigned to two incubation temperatures (39.5 and 42 °C) and two osmotic conditions (295 and 420 mOsmol kg-1 ). Betaine disappeared rapidly within the first 6 h of incubation; however, the rate was lower during hyperosmotic stress (P < 0.05), the stress condition that also suppressed the overall fermentation and degradation of organic nutrients and decreased the bacterial diversity (P < 0.001). During hyperosmotic stress, betaine shifted the fermentation pathway to more propionate (P < 0.05). Betaine counteracted the negative effect of hyperthermal stress on total short-chain fatty acid concentration (P < 0.05) without affecting the composition. Both stress conditions shifted the bacterial composition, but the effect of betaine was minimal. CONCLUSION Despite its rapid ruminal disappearance, betaine modulated microbial fermentation in different ways depending on stress conditions, indicating the plasticity of the betaine effect in response to various kinds of physicochemical stress. Although betaine did not affect the abundance of ruminal microbiota, the enhanced fermentation suggests an improved microbial metabolic activity under stress conditions. © 2020 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Mubarik Mahmood
- Department for Farm Animals and Veterinary Public HealthInstitute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine ViennaViennaAustria
- Section of Animal Nutrition, Department of Animal SciencesUniversity of Veterinary and Animal Sciences, Lahore sub‐campus JhangJhangPakistan
| | - Renée Maxine Petri
- Department for Farm Animals and Veterinary Public HealthInstitute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine ViennaViennaAustria
| | - Ana Gavrău
- AGRANA Sales & Marketing GmbHViennaAustria
| | - Qendrim Zebeli
- Department for Farm Animals and Veterinary Public HealthInstitute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine ViennaViennaAustria
| | - Ratchaneewan Khiaosa‐ard
- Department for Farm Animals and Veterinary Public HealthInstitute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine ViennaViennaAustria
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9
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Lan W, Yang C. Ruminal methane production: Associated microorganisms and the potential of applying hydrogen-utilizing bacteria for mitigation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 654:1270-1283. [PMID: 30841400 DOI: 10.1016/j.scitotenv.2018.11.180] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/12/2018] [Accepted: 11/12/2018] [Indexed: 05/16/2023]
Abstract
Methane emission from ruminants not only causes serious environmental problems, but also represents a significant source of energy loss to animals. The increasing demand for sustainable animal production is driving researchers to explore proper strategies to mitigate ruminal methanogenesis. Since hydrogen is the primary substrate of ruminal methanogenesis, hydrogen metabolism and its associated microbiome in the rumen may closely relate to low- and high-methane phenotypes. Using candidate microbes that can compete with methanogens and redirect hydrogen away from methanogenesis as ruminal methane mitigants are promising avenues for methane mitigation, which can both prevent the adverse effects deriving from chemical additives such as toxicity and resistance, and increase the retention of feed energy. This review describes the ruminal microbial ecosystem and its association with methane production, as well as the effects of interspecies hydrogen transfer on methanogenesis. It provides a scientific perspective on using bacteria that are involved in hydrogen utilization as ruminal modifiers to decrease methanogenesis. This information will be helpful in better understanding the key role of ruminal microbiomes and their relationship with methane production and, therefore, will form the basis of valuable and eco-friendly methane mitigation methods while improving animal productivity.
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Affiliation(s)
- Wei Lan
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China; MoE Key Laboratory of Molecular Animal Nutrition, China
| | - Chunlei Yang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China; MoE Key Laboratory of Molecular Animal Nutrition, China.
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Mir RA, Kleinhenz MD, Coetzee JF, Allen HK, Kudva IT. Fecal microbiota changes associated with dehorning and castration stress primarily affects light-weight dairy calves. PLoS One 2019; 14:e0210203. [PMID: 30673718 PMCID: PMC6344101 DOI: 10.1371/journal.pone.0210203] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 12/18/2018] [Indexed: 12/31/2022] Open
Abstract
Gastrointestinal tract (GIT) microbiota and stress can impact animal health. Studies have shown that perturbations in the GIT microbiota can influence host health and productivity by affecting physiological homeostasis, metabolism, hematopoiesis and inflammation. The present study aimed to evaluate possible effects of dehorning and castration stress on the GIT microbiota of dairy calves. Dehorning and castration are routinely performed on over 90% of dairy farms, and analgesics like flunixin meglumine (FLU) are given at the time of these procedures to reduce pain. We analyzed fecal microbiota of 24 weaned male dairy calves at two different stages in their life (at 10 weeks for dehorning and 36 weeks age for castration) to determine any GIT microbiota changes due to these stressful procedures and the FLU treatment. Dehorning was performed using an electrocautery dehorner applied to the horn for 10 seconds, and surgical castration was used as the castration method. Our analysis showed that the Shannon diversity index was significantly higher in animals that were not dehorned compared to dehorned animals. Castration stress also resulted in a significant decrease in Shannon diversity index, which was more pronounced in lower weight calves. Body weight and stress had significant effects on the taxonomic profiles of the GIT microbiota. There was a significant difference in the GIT bacterial community structure between heavy- and light-weight calves at Day 3 after castration but not at Day 0 (prior to castration). Our results indicate that dehorning and castration stress reduced microbial diversity of the GIT microbiota, but only in light-weight calves. This work is important for elucidating biological effects of stress on dairy calves and identifying potential modulation points in the microbiota of these food-producing animals to improve animal health and production.
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Affiliation(s)
- Raies A Mir
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, U S Department of Agriculture, Ames, Iowa.,Oak Ridge Institute for Science and Education (ORISE), ARS Research Participation Program, Oak Ridge, Tennessee
| | - Michael D Kleinhenz
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa.,Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas
| | - Johann F Coetzee
- Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas
| | - Heather K Allen
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, U S Department of Agriculture, Ames, Iowa
| | - Indira T Kudva
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, U S Department of Agriculture, Ames, Iowa
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Indugu N, Vecchiarelli B, Baker LD, Ferguson JD, Vanamala JKP, Pitta DW. Comparison of rumen bacterial communities in dairy herds of different production. BMC Microbiol 2017; 17:190. [PMID: 28854878 PMCID: PMC5577838 DOI: 10.1186/s12866-017-1098-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 08/22/2017] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The purpose of this study was to compare the rumen bacterial composition in high and low yielding dairy cows within and between two dairy herds. Eighty five Holstein dairy cows in mid-lactation (79-179 days in milk) were selected from two farms: Farm 12 (M305 = 12,300 kg; n = 47; 24 primiparous cows, 23 multiparous cows) and Farm 9 (M305 = 9700 kg; n = 38; 19 primiparous cows, 19 multiparous cows). Each study cow was sampled once using the stomach tube method and processed for 16S rRNA gene amplicon sequencing using the Ion Torrent (PGM) platform. RESULTS Differences in bacterial communities between farms were greater (Adonis: R2 = 0.16; p < 0.001) than within farm. Five bacterial lineages, namely Prevotella (48-52%), unclassified Bacteroidales (10-12%), unclassified bacteria (5-8%), unclassified Succinivibrionaceae (1-7%) and unclassified Prevotellaceae (4-5%) were observed to differentiate the community clustering patterns among the two farms. A notable finding is the greater (p < 0.05) contribution of Succinivibrionaceae lineages in Farm 12 compared to Farm 9. Furthermore, in Farm 12, Succinivibrionaceae lineages were higher (p < 0.05) in the high yielding cows compared to the low yielding cows in both primiparous and multiparous groups. Prevotella, S24-7 and Succinivibrionaceae lineages were found in greater abundance on Farm 12 and were positively correlated with milk yield. CONCLUSIONS Differences in rumen bacterial populations observed between the two farms can be attributed to dietary composition, particularly differences in forage type and proportion in the diets. A combination of corn silage and alfalfa silage may have contributed to the increased proportion of Proteobacteria in Farm 12. It was concluded that Farm 12 had a greater proportion of specialist bacteria that have the potential to enhance rumen fermentative digestion of feedstuffs to support higher milk yields.
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Affiliation(s)
- Nagaraju Indugu
- Department of Clinical Studies, School of Veterinary Medicine, New Bolton Center, University of Pennsylvania, Kennett Square, PA, 19348, USA
| | - Bonnie Vecchiarelli
- Department of Clinical Studies, School of Veterinary Medicine, New Bolton Center, University of Pennsylvania, Kennett Square, PA, 19348, USA
| | - Linda D Baker
- Department of Clinical Studies, School of Veterinary Medicine, New Bolton Center, University of Pennsylvania, Kennett Square, PA, 19348, USA
| | - James D Ferguson
- Department of Clinical Studies, School of Veterinary Medicine, New Bolton Center, University of Pennsylvania, Kennett Square, PA, 19348, USA
| | - Jairam K P Vanamala
- Department of Food Science, Pennsylvania State University, University Park, State College, PA, 16802, USA.,Penn State Hershey Cancer Institute, Hershey, PA, 17033, USA
| | - Dipti W Pitta
- Department of Clinical Studies, School of Veterinary Medicine, New Bolton Center, University of Pennsylvania, Kennett Square, PA, 19348, USA.
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12
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Bergmann GT. Microbial community composition along the digestive tract in forage- and grain-fed bison. BMC Vet Res 2017; 13:253. [PMID: 28818110 PMCID: PMC5561592 DOI: 10.1186/s12917-017-1161-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 08/07/2017] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Diversity and composition of microbial communities was compared across the 13 major sections of the digestive tract (esophagus, reticulum, rumen, omasum, abomasum, duodenum, jejunum, ileum, cecum, ascending colon, transverse colon, descending colon, and rectum) in two captive populations of American bison (Bison bison), one of which was finished on forage, the other on grain. RESULTS Microbial diversity fell to its lowest levels in the small intestine, with Bacteroidetes reaching their lowest relative abundance in that region, while Firmicutes and Euryarchaeota attained their highest relative abundances there. Gammaproteobacteria were most abundant in the esophagus, small intestine, and colon. The forage-finished bison population exhibited higher overall levels of diversity, as well as a higher relative abundance of Bacteroidetes in most gut sections. The grain-finished bison population exhibited elevated levels of Firmicutes and Gammaproteobacteria. Within each population, different sections of the digestive tract exhibited divergent microbial community composition, although it was essentially the same among sections within a given region of the digestive tract. Shannon diversity was lowest in the midgut. For each section of the digestive tract, the two bison populations differed significantly in microbial community composition. CONCLUSIONS Similarities among sections indicate that the esophagus, reticulum, rumen, omasum, and abomasum may all be considered to house the foregut microbiota; the duodenum, jejunum, and ileum may all be considered to house the small intestine or midgut microbiota; and the cecum, ascending colon, transverse colon, descending colon, and rectum may all be considered to house the hindgut microbiota. Acid from the stomach, bile from the gall bladder, digestive enzymes from the pancreas, and the relatively low retention time of the small intestine may have caused the midgut's low microbial diversity. Differences in microbial community composition between populations may have been most strongly influenced by differences in diet (forage or grain). The clinical condition of the animals used in the present study was not evaluated, so further research is needed to establish whether the microbial profiles of some bison in this study are indeed indicative of dysbiosis, a predisposing factor to ruminal acidosis and its sequelae.
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Affiliation(s)
- Gaddy T Bergmann
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Ramaley N122, Campus Box 334, Boulder, Colorado, 80309-0334, USA. .,Cooperative Institute for Research in Environmental Science, University of Colorado, Boulder, Box 216 UCB, Boulder, Colorado, 80309-0216, USA.
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13
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Yahya M, Blanch AR, Meijer WG, Antoniou K, Hmaied F, Ballesté E. Comparison of the Performance of Different Microbial Source Tracking Markers among European and North African Regions. JOURNAL OF ENVIRONMENTAL QUALITY 2017; 46:760-766. [PMID: 28783792 DOI: 10.2134/jeq2016.11.0432] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Microbial source tracking (MST) has been extensively used to detect the sources of fecal pollution in water. The inclusion of MST in water management strategies improves the ecological status of the ecosystem and human and animal health under interdisciplinary analysis in all aspects of health care for humans, animals, and the environment (One Health approach). In this study, the performance of MST markers targeting host-specific Bacteroidales (HF183 and Rum-2-Bac) and species (HMBif and CWBif) were evaluated in raw sewage collected from human, ruminant, swine, and poultry sources in Tunisia, Cyprus, Ireland, and Spain. In addition, the ratio between somatic coliphages and bacteriophages infecting GA17 (SOMCPH/GA17PH) was measured in Tunisia and Spain. The obtained results showed variability of the bacterial markers between the four countries, suggesting that their usefulness could be affected by several conditions (dietary habits, agricultural practices, and climatic conditions) that differ between countries. The Rum-2-Bac marker stood out as a valid MST tool, particularly in Ireland, whereas CWBif was the best option in Tunisia, Spain, and Cyprus. The human-specific HMBif marker showed good sensitivity and specificity in Tunisia, Spain, and Ireland, whereas HF183 showed a low specificity. However, HF183 was suggested as a good human marker in Ireland and Cyprus because of its higher concentration than HMBif. Regarding viral markers, the ratio of SOMCPH/GA17PH showed a clear discrimination between human and nonhuman samples. The combined use of molecular bacterial markers and the ratio of SOMCPH/GA17PH may improve the success of MST.
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Duarte AC, Holman DB, Alexander TW, Kiri K, Breves G, Chaves AV. Incubation Temperature, But Not Pequi Oil Supplementation, Affects Methane Production, and the Ruminal Microbiota in a Rumen Simulation Technique (Rusitec) System. Front Microbiol 2017; 8:1076. [PMID: 28701999 PMCID: PMC5487375 DOI: 10.3389/fmicb.2017.01076] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 05/29/2017] [Indexed: 01/05/2023] Open
Abstract
Lipid supplementation is a promising strategy for methane mitigation in cattle and has been evaluated using several different lipid sources. However, limited studies have assessed the effect of temperature on methane emissions from cattle and changes in incubation temperature have also not been extensively evaluated. The aim of this study was to evaluate the combined effect of pequi oil (high in unsaturated fatty acids) and incubation temperature on fermentation characteristics and microbial communities using the rumen simulation technique. A completely randomized experiment was conducted over a 28-day period using a Rusitec system. The experiment was divided into four periods of 7 days each, the first of which was a 7-day adaptation period followed by three experimental periods. The two treatments consisted of a control diet (no pequi oil inclusion) and a diet supplemented with pequi oil (1.5 mL/day) which increased the dietary fat content to 6% (dry matter, DM-basis). Three fermenter vessels (i.e., replicates) were allocated to each treatment. In the first experimental period, the incubation temperature was maintained at 39°C, decreased to 35°C in the second experimental period and then increased again to 39°C in the third. Pequi oil was continuously supplemented during the experiment. Microbial communities were assessed using high-throughput sequencing of the archaeal and bacterial 16S rRNA gene. Methane production was reduced by 57% following a 4°C decrease in incubation temperature. Supplementation with pequi oil increased the dietary fat content to 6% (DM-basis) but did not affect methane production. Analysis of the microbiota revealed that decreasing incubation temperature to 35°C affected the archaeal and bacterial diversity and richness of liquid-associated microbes, but lipid supplementation did not change microbial diversity.
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Affiliation(s)
- Andrea C Duarte
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, SydneyNSW, Australia
| | - Devin B Holman
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, LethbridgeAB, Canada
| | - Trevor W Alexander
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, LethbridgeAB, Canada
| | - Kerstin Kiri
- Department of Physiology, University of Veterinary MedicineHannover, Germany
| | - Gerhard Breves
- Department of Physiology, University of Veterinary MedicineHannover, Germany
| | - Alexandre V Chaves
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, SydneyNSW, Australia
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15
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Kerwin AH, Nyholm SV. Symbiotic bacteria associated with a bobtail squid reproductive system are detectable in the environment, and stable in the host and developing eggs. Environ Microbiol 2017; 19:1463-1475. [DOI: 10.1111/1462-2920.13665] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 12/07/2016] [Accepted: 01/02/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Allison H. Kerwin
- Department of Molecular and Cell Biology; University of Connecticut; CT 06269 USA
| | - Spencer V. Nyholm
- Department of Molecular and Cell Biology; University of Connecticut; CT 06269 USA
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16
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Ruminal methanogens and bacteria populations in sheep are modified by a tropical environment. Anim Feed Sci Technol 2016. [DOI: 10.1016/j.anifeedsci.2016.08.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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17
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Tapio I, Shingfield KJ, McKain N, Bonin A, Fischer D, Bayat AR, Vilkki J, Taberlet P, Snelling TJ, Wallace RJ. Oral Samples as Non-Invasive Proxies for Assessing the Composition of the Rumen Microbial Community. PLoS One 2016; 11:e0151220. [PMID: 26986467 PMCID: PMC4795602 DOI: 10.1371/journal.pone.0151220] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 02/23/2016] [Indexed: 11/19/2022] Open
Abstract
Microbial community analysis was carried out on ruminal digesta obtained directly via rumen fistula and buccal fluid, regurgitated digesta (bolus) and faeces of dairy cattle to assess if non-invasive samples could be used as proxies for ruminal digesta. Samples were collected from five cows receiving grass silage based diets containing no additional lipid or four different lipid supplements in a 5 x 5 Latin square design. Extracted DNA was analysed by qPCR and by sequencing 16S and 18S rRNA genes or the fungal ITS1 amplicons. Faeces contained few protozoa, and bacterial, fungal and archaeal communities were substantially different to ruminal digesta. Buccal and bolus samples gave much more similar profiles to ruminal digesta, although fewer archaea were detected in buccal and bolus samples. Bolus samples overall were most similar to ruminal samples. The differences between both buccal and bolus samples and ruminal digesta were consistent across all treatments. It can be concluded that either proxy sample type could be used as a predictor of the rumen microbial community, thereby enabling more convenient large-scale animal sampling for phenotyping and possible use in future animal breeding programs aimed at selecting cattle with a lower environmental footprint.
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Affiliation(s)
- Ilma Tapio
- Green Technology, Natural Resources Institute Finland, Jokioinen, Finland
| | | | - Nest McKain
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Aurélie Bonin
- Laboratoire d'Ecologie Alpine, CNRS, Grenoble, France
| | - Daniel Fischer
- Green Technology, Natural Resources Institute Finland, Jokioinen, Finland
| | - Ali R. Bayat
- Green Technology, Natural Resources Institute Finland, Jokioinen, Finland
| | - Johanna Vilkki
- Green Technology, Natural Resources Institute Finland, Jokioinen, Finland
| | | | - Timothy J. Snelling
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - R. John Wallace
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
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18
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Zeitz J, Ineichen S, Soliva C, Leiber F, Tschuor A, Braun U, Kreuzer M, Clauss M. Variability in microbial population and fermentation traits at various sites within the forestomach and along the digestive tract as assessed in goats fed either grass or browse. Small Rumin Res 2016. [DOI: 10.1016/j.smallrumres.2015.12.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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19
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The effect of a high-roughage diet on the metabolism of aromatic compounds by rumen microbes: a metagenomic study using Mehsani buffalo (Bubalus bubalis). Appl Microbiol Biotechnol 2015; 100:1319-1331. [PMID: 26711277 DOI: 10.1007/s00253-015-7239-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 12/06/2015] [Accepted: 12/09/2015] [Indexed: 01/18/2023]
Abstract
In developing countries, livestock are often fed a high-lignin, low-nutrient diet that is rich in aromatic compounds. It is therefore important to understand the structure of the microbial community responsible for the metabolism of these substances. A metagenomic analysis was therefore carried out to assess the microbial communities associated with the liquid and solid fractions of rumen biomaterial from domestic Mehsani buffalo (Bubalus bubalis) fed with varying proportions of roughage. The experimental design consisted of three feeding regimes (50, 75 and 100 % roughage) and two roughage types (green and dry). Genes associated with aromatic compound degradation were assessed via high-throughput DNA sequencing. A total of 3914.94 Mb data were generated from all treatment groups. Genes coding for functional responses associated with aromatic compound metabolism were more prevalent in the liquid fraction of rumen samples than solid fractions. Statistically significant differences (p < 0.05) were also observed between treatment groups. These differences were dependent on the proportion of roughage fed to the animal, with the type of roughage having little effect. The genes present in the highest abundance in all treatment groups were those related to aromatic compound catabolism. At the phylum level, Bacteroidetes were dominant in all treatments closely followed by the Firmicutes. This study demonstrates the use of feed type to selectively enrich microbial communities capable of metabolizing aromatic compounds in the rumen of domestic buffalo. The results may help to improve nutrient utilization efficiency in livestock and are thus of interest to farming industries, particularly in developing countries, worldwide.
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20
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Seasonal Shifts in Diet and Gut Microbiota of the American Bison (Bison bison). PLoS One 2015; 10:e0142409. [PMID: 26562019 PMCID: PMC4642958 DOI: 10.1371/journal.pone.0142409] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 10/21/2015] [Indexed: 01/23/2023] Open
Abstract
North American bison (Bison bison) are becoming increasingly important to both grassland management and commercial ranching. However, a lack of quantitative data on their diet constrains conservation efforts and the ability to predict bison effects on grasslands. In particular, we know little about the seasonality of the bison diet, the degree to which bison supplement their diet with eudicots, and how changes in diet influence gut microbial communities, all of which play important roles in ungulate performance. To address these knowledge gaps, we quantified seasonal patterns in bison diet and gut microbial community composition for a bison herd in Kansas using DNA sequencing-based analyses of both chloroplast and microbial DNA contained in fecal matter. Across the 11 sampling dates that spanned 166 days, we found that diet shifted continuously over the growing season, allowing bison to take advantage of the seasonal availability of high-protein plant species. Bison consumed more woody shrubs in spring and fall than in summer, when forb and grass intake predominated. In examining gut microbiota, the bacterial phylum Tenericutes shifted significantly in relative abundance over the growing season. This work suggests that North American bison can continuously adjust their diet with a high reliance on non-grasses throughout the year. In addition, we find evidence for seasonal patterns in gut community composition that are likely driven by the observed dietary changes.
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21
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Evaluation of composition and individual variability of rumen microbiota in yaks by 16S rRNA high-throughput sequencing technology. Anaerobe 2015; 34:74-9. [PMID: 25911445 DOI: 10.1016/j.anaerobe.2015.04.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 04/13/2015] [Accepted: 04/19/2015] [Indexed: 12/26/2022]
Abstract
The Yak (Bos grunniens) is a unique species of ruminant animals that is important to agriculture of the Tibetan plateau, and has a complex intestinal microbial community. The objective of the present study was to characterize the composition and individual variability of microbiota in the rumen of yaks using 16S rRNA gene high-throughput sequencing technique. Rumen samples used in the present study were obtained from grazing adult male yaks (n = 6) in a commercial farm in Ganzi Autonomous Prefecture of Sichuan Province, China. Universal prokaryote primers were used to target the V4-V5 hypervariable region of 16S rRNA gene. A total of 7200 operational taxonomic units (OTUs) were obtained after sequence filtering and chimera removal. Within these OTUs, 0.56% belonged to Archaea (40 OTUs), 7.19% to unassigned species (518 OTUs), and the remaining OTUs (6642) in all samples were of bacterial origin. When examining the community structure of bacteria, we identified 23 phyla within 159 families after taxonomic summarization. Bacteroidetes and Firmicutes were the predominant phyla accounting for 39.68% (SD = 0.05) and 45.90% (SD = 0.06), respectively. Moreover, 3764 OTUs were identified as shared OTUs (i.e. represented in all yaks) and belonged to 35 genera, exhibiting highly variable abundance across individual samples. Phylogenetic placement of these genera across individual samples was examined. In addition, we evaluated the distance among the 6 rumen samples by adding taxon phylogeny using UniFrac, representing 24.1% of average distance. In summary, the current study reveals a shared rumen microbiome and phylogenetic lineage and presents novel information on composition and individual variability of the bacterial community in the rumen of yaks.
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22
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Barnett MC, McFarlane J.R, Hegarty RS. Low ambient temperature elevates plasma triiodothyronine concentrations while reducing digesta mean retention time and methane yield in sheep. J Anim Physiol Anim Nutr (Berl) 2014; 99:483-91. [DOI: 10.1111/jpn.12252] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 08/23/2014] [Indexed: 10/24/2022]
Affiliation(s)
- M. C. Barnett
- School of Environmental and Rural Science; University of New England; Armidale NSW Australia
| | - J .R. McFarlane
- Centre for Bioactive Discovery in Health and Ageing; University of New England; Armidale NSW Australia
| | - R. S. Hegarty
- School of Environmental and Rural Science; University of New England; Armidale NSW Australia
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23
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Reddy B, Singh KM, Patel AK, Antony A, Panchasara HJ, Joshi CG. Insights into resistome and stress responses genes in Bubalus bubalis rumen through metagenomic analysis. Mol Biol Rep 2014; 41:6405-17. [DOI: 10.1007/s11033-014-3521-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 06/19/2014] [Indexed: 01/05/2023]
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24
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High-grain feeding alters caecal bacterial microbiota composition and fermentation and results in caecal mucosal injury in goats. Br J Nutr 2014; 112:416-27. [PMID: 24846282 DOI: 10.1017/s0007114514000993] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The effect of high-grain (HG) feeding on caecal bacterial microbiota composition and fermentation and mucosa health is largely unknown. In the present study, ten male goats were randomly assigned to either a group fed a hay diet (0 % grain; n 5) or a group fed a HG diet (65 % grain; n 5) to characterise the changes in the composition of the bacterial community and mucosal morphology in the caecum. After 7 weeks of feeding, the HG diet decreased the caecal pH (P< 0·001) and increased (P< 0·001 to P< 0·004) the caecal digesta concentrations of total volatile fatty acids and lipopolysaccharide (LPS). Pyrosequencing of the 16S ribosomal RNA gene revealed that HG feeding increased (P= 0·001 to P= 0·009) the abundance of predominant genera Turicibacter and Clostridium in the caecal lumen and in the caecal mucosa and decreased (P< 0·001 to P< 0·009) the proportion of Bacteroides in the lumen and Mucispirillum in the mucosa compared with the hay diet. Furthermore, the HG diet-fed goats exhibited intense epithelial damage and up-regulation (P< 0·001 to P< 0·025) of the relative mRNA expression of IL-1β, IL-6, IL-12 and interferon-γ (IFN-γ) in the caecal mucosa. The correlation analysis revealed that alterations in caecal pH, LPS concentration and mucosa-associated microbiota abundance during HG feeding might partly contribute to local inflammation. Collectively, these results provide insight into the adaptive response of caecal bacterial populations to HG feeding in goats and reveal that the fermentable substrates that flow into the caecum may cause dramatic alterations in microbial compositions and play a significant role in caecal dysfunction.
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25
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Singh KM, Reddy B, Patel AK, Panchasara H, Parmar N, Patel AB, Shah TM, Bhatt VD, Joshi CG. Metagenomic analysis of buffalo rumen microbiome: Effect of roughage diet on Dormancy and Sporulation genes. Meta Gene 2014; 2:252-68. [PMID: 25606408 PMCID: PMC4287859 DOI: 10.1016/j.mgene.2014.01.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 01/06/2014] [Accepted: 01/16/2014] [Indexed: 11/16/2022] Open
Abstract
Buffalo rumen microbiome experiences a variety of diet stress and represents reservoir of Dormancy and Sporulation genes. However, the information on genomic responses to such conditions is very limited. The Ion Torrent PGM next generation sequencing technology was used to characterize general microbial diversity and the repertoire of microbial genes present, including genes associated with Dormancy and Sporulation in Mehsani buffalo rumen metagenome. The research findings revealed the abundance of bacteria at the domain level and presence of Dormancy and Sporulation genes which were predominantly associated with the Clostridia and Bacilli taxa belonging to the phyla Firmicutes. Genes associated with Sporulation cluster and Sporulation orphans were increased from 50% to 100% roughage treatment, thereby promoting sporulation all along the treatments. The spore germination is observed to be the highest in the 75% roughage treatment both in the liquid and solid rumen fraction samples with respect to the decrease in the values of the genes associated with spore core dehydration, thereby facilitating spore core hydration which is necessary for spore germination.
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Affiliation(s)
- K M Singh
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - B Reddy
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - A K Patel
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - H Panchasara
- Livestock Research Station, Sardar Krushinagar Agricultural University, India
| | - N Parmar
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - A B Patel
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - T M Shah
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - V D Bhatt
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - C G Joshi
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
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26
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Pitta D, Kumar S, Veiccharelli B, Parmar N, Reddy B, Joshi C. Bacterial diversity associated with feeding dry forage at different dietary concentrations in the rumen contents of Mehshana buffalo (Bubalus bubalis) using 16S pyrotags. Anaerobe 2014; 25:31-41. [DOI: 10.1016/j.anaerobe.2013.11.008] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 11/12/2013] [Accepted: 11/22/2013] [Indexed: 12/14/2022]
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27
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The use of direct-fed microbials for mitigation of ruminant methane emissions: a review. Animal 2014; 8:250-61. [DOI: 10.1017/s1751731113002085] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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28
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Zhao L, Tyler PJ, Starnes J, Rankins D, McCaskey TA, Wang L. Evaluation of the effects of weaning diets on Escherichia coli O157 shedding, body weight, and fecal bacterial communities in beef calves. Foodborne Pathog Dis 2013; 11:55-60. [PMID: 24138032 DOI: 10.1089/fpd.2013.1587] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cattle are considered to be one of the primary reservoirs of Escherichia coli O157. In this study, the effects of weaning diets on E. coli O157 shedding, body weight, and fecal bacterial communities in beef calves were evaluated. A total of 60 calves (28 heifers and 32 steers) were weaned and randomly assigned into two groups. A peanut/soy hull-based diet (Dry Feed, DF) and a corn silage-based diet (High Moisture, HM) were fed to the two groups, respectively, during the weaning and preconditioning period. Calf body weight was measured before weaning (BW) and 14 days after weaning (AW14), and a fecal sample was collected from each calf at BW, AW14, as well as 56 days after weaning (AW56). The prevalence of O157 in feces was determined by CHROMagar(™) O157 and polymerase chain reaction (PCR). Denaturing gradient gel electrophoresis (DGGE) was employed to analyze fecal bacterial communities. A significant decrease in body weight was observed during weaning, regardless of the calf diet (p<0.05). Calves fed the HM diet lost more weight than the DF-fed calves determined at 14 days after weaning (p<0.05). Both the CHROMagar(™) and PCR results showed that the overall prevalence of O157 increased significantly during weaning. Based on the CHROMagar(™) method, O157 increased from 16.6% at BW to 38.3% at AW14 (p<0.05) and stayed at the higher level during the preconditioning period (AW56). The increase in O157 prevalence was observed in HM-fed calves during weaning but not in DF-fed ones. Weaning also changed the profile of fecal bacterial communities (p<0.05). These results showed that weaning is a critical step in beef cattle production, not only because of its effects on body weight but also due to its impact on O157 shedding and gastrointestinal tract bacterial community establishment.
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Affiliation(s)
- Liang Zhao
- 1 Food Microbiology and Safety Lab, Department of Animal Sciences, Auburn University , Auburn, Alabama
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Methanogens and methanogenesis in the rumens and ceca of lambs fed two different high-grain-content diets. Appl Environ Microbiol 2012; 79:1777-86. [PMID: 23241983 DOI: 10.1128/aem.03115-12] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The amount and nature of dietary starch are known to influence the extent and site of feed digestion in ruminants. However, how starch degradability may affect methanogenesis and methanogens along the ruminant's digestive tract is poorly understood. This study examined the diversity and metabolic activity of methanogens in the rumen and cecum of lambs receiving wheat or corn high-grain-content diets. Methane production in vivo and ex situ was also monitored. In vivo daily methane emissions (CH(4) g/day) were 36% (P < 0.05) lower in corn-fed lambs than in wheat-fed lambs. Ex situ methane production (μmol/h) was 4-fold higher for ruminal contents than for cecal contents (P < 0.01), while methanogens were 10-fold higher in the rumen than in the cecum (mcrA copy numbers; P < 0.01). Clone library analysis indicated that Methanobrevibacter was the dominant genus in both sites. Diet induced changes at the species level, as the Methanobrevibacter millerae-M. gottschalkii-M. smithii clade represented 78% of the sequences from the rumen of wheat-fed lambs and just about 52% of the sequences from the rumen of the corn-fed lambs. Diet did not affect mcrA expression in the rumen. In the cecum, however, expression was 4-fold and 2-fold lower than in the rumen for wheat- and corn-fed lambs, respectively. Though we had no direct evidence for compensation of reduced rumen methane production with higher cecum methanogenesis, the ecology of methanogens in the cecum should be better considered.
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Diversity and partitioning of bacterial populations within the accessory nidamental gland of the squid Euprymna scolopes. Appl Environ Microbiol 2012; 78:4200-8. [PMID: 22504817 DOI: 10.1128/aem.07437-11] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Microbial consortia confer important benefits to animal and plant hosts, and model associations are necessary to examine these types of host/microbe interactions. The accessory nidamental gland (ANG) is a female reproductive organ found among cephalopod mollusks that contains a consortium of bacteria, the exact function of which is unknown. To begin to understand the role of this organ, the bacterial consortium was characterized in the Hawaiian bobtail squid, Euprymna scolopes, a well-studied model organism for symbiosis research. Transmission electron microscopy (TEM) analysis of the ANG revealed dense bacterial assemblages of rod- and coccus-shaped cells segregated by morphology into separate, epithelium-lined tubules. The host epithelium was morphologically heterogeneous, containing ciliated and nonciliated cells with various brush border thicknesses. Hemocytes of the host's innate immune system were also found in close proximity to the bacteria within the tubules. A census of 16S rRNA genes suggested that Rhodobacterales, Rhizobiales, and Verrucomicrobia bacteria were prevalent, with members of the genus Phaeobacter dominating the consortium. Analysis of 454-shotgun sequencing data confirmed the presence of members of these taxa and revealed members of a fourth, Flavobacteria of the Bacteroidetes phylum. 16S rRNA fluorescent in situ hybridization (FISH) revealed that many ANG tubules were dominated by members of specific taxa, namely, Rhodobacterales, Verrucomicrobia, or Cytophaga-Flavobacteria-Bacteroidetes, suggesting symbiont partitioning to specific host tubules. In addition, FISH revealed that bacteria, including Phaeobacter species from the ANG, are likely deposited into the jelly coat of freshly laid eggs. This report establishes the ANG of the invertebrate E. scolopes as a model to examine interactions between a bacterial consortium and its host.
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Impact of feed efficiency and diet on adaptive variations in the bacterial community in the rumen fluid of cattle. Appl Environ Microbiol 2011; 78:1203-14. [PMID: 22156428 DOI: 10.1128/aem.05114-11] [Citation(s) in RCA: 134] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Limited knowledge of the structure and activities of the ruminal bacterial community prevents the understanding of the effect of population dynamics on functional bacterial groups and on host productivity. This study aimed to identify particular bacteria associated with host feed efficiency in steers with differing diets and residual feed intake (RFI) using culture-independent methods: PCR-denaturing gradient gel electrophoresis (DGGE) and quantitative real-time PCR analysis. PCR-DGGE profiles were generated from the ruminal fluid of 55 steers fed a low-energy-density diet and then switched to a high-energy-density diet. Bacterial profile comparisons by multivariate statistical analysis showed a trend only for RFI-related clusters on the high-energy diet. When steers (n = 19) belonging to the same RFI group under both diets were used to identify specific bacterial phylotypes related to feed efficiency traits, correlations were detected between dry matter intake, average daily gain, and copy numbers of the 16S rRNA gene of Succinivibrio sp. in low-RFI (efficient) steers, whereas correlations between Robinsoniella sp. and RFI (P < 0.05) were observed for high-RFI (inefficient) animals. Eubacterium sp. differed significantly (P < 0.05) between RFI groups that were only on the high-energy diet. Our work provides a comprehensive framework to understand how particular bacterial phylotypes contribute to differences in feed efficiency and ultimately influence host productivity, which may either depend on or be independent from diet factors.
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