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Li S, Mu R, Zhu Y, Zhao F, Qiu Q, Si H, Wright ADG, Li Z. Shifts in the microbial community and metabolome in rumen ecological niches during antler growth. Comput Struct Biotechnol J 2024; 23:1608-1618. [PMID: 38680874 PMCID: PMC11047195 DOI: 10.1016/j.csbj.2024.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/29/2024] [Accepted: 04/07/2024] [Indexed: 05/01/2024] Open
Abstract
Antlers are hallmark organ of deer, exhibiting a relatively high growth rate among mammals, and requiring large amounts of nutrients to meet its development. The rumen microbiota plays key roles in nutrient metabolism. However, changes in the microbiota and metabolome in the rumen during antler growth are largely unknown. We investigated rumen microbiota (liquid, solid, ventral epithelium, and dorsal epithelium) and metabolic profiles of sika deer at the early (EG), metaphase (MG) and fast growth (FG) stages. Our data showed greater concentrations of acetate and propionate in the rumens of sika deer from the MG and FG groups than in those of the EG group. However, microbial diversity decreased during antler growth, and was negatively correlated with short-chain fatty acid (SCFA) levels. Prevotella, Ruminococcus, Schaedlerella and Stenotrophomonas were the dominant bacteria in the liquid, solid, ventral epithelium, and dorsal epithelium fractions. The proportions of Stomatobaculum, Succiniclasticum, Comamonas and Anaerotruncus increased significantly in the liquid or dorsal epithelium fractions. Untargeted metabolomics analysis revealed that the metabolites also changed significantly, revealing 237 significantly different metabolites, among which the concentrations of γ-aminobutyrate and creatine increased during antler growth. Arginine and proline metabolism and alanine, aspartate and glutamate metabolism were enhanced. The co-occurrence network results showed that the associations between the rumen microbiota and metabolites different among the three groups. Our results revealed that the different rumen ecological niches were characterized by distinct microbiota compositions, and the production of SCFAs and the metabolism of specific amino acids were significantly changed during antler growth.
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Affiliation(s)
- Songze Li
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Ruina Mu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Yuhang Zhu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Fei Zhao
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an 710100, China
| | - Huazhe Si
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
- Key Lab of Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- Jilin Provincial Engineering Research Center for Efficient Breeding and Product Development of Sika Deer, Jilin Agricultural University, Changchun 130118, China
| | | | - Zhipeng Li
- Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
- Key Lab of Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- Jilin Provincial Engineering Research Center for Efficient Breeding and Product Development of Sika Deer, Jilin Agricultural University, Changchun 130118, China
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Abdullah HM, Mohammed OB, Sheikh A, Almathen F, Khalid AM, Bakhiet AO, Abdelrahman MM. Molecular detection of ruminal micro-flora and micro-fauna in Saudi Arabian camels: Effects of season and region. Saudi J Biol Sci 2024; 31:103982. [PMID: 38600912 PMCID: PMC11004988 DOI: 10.1016/j.sjbs.2024.103982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/12/2024] [Accepted: 03/22/2024] [Indexed: 04/12/2024] Open
Abstract
This study investigated and explored the availability of micro-flora and micro-fauna in the ruminal contents of Arabian camel (Camelus dromedarius) from three different regions in Saudi Arabia along with two seasons. Samples were prepared and tested by conventional polymerase chain reaction (PCR). This study confirmed that the bacterial flora were dominating over other microbes. Different results of the availability of each microbe in each region and season were statistically analyzed and discussed. There was no significant effect of season on the micro-flora or micro-fauna however, the location revealed a positive effect with Ruminococcus flavefaciens (p < 0 0.03) in the eastern region. This study was the first to investigate the abundance of micro-flora and micro-fauna in the ruminal contents of camels of Saudi Arabia. This study underscores the significance of camel ruminal micro-flora and micro-fauna abundance, highlighting their correlation with both seasonality and geographic location. This exploration enhances our comprehension of camel rumination and digestion processes. The initial identification of these microbial communities serves as a foundational step, laying the groundwork for future in-depth investigations into camel digestibility and nutritional requirements.
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Affiliation(s)
- Hashim M. Abdullah
- Camel Research Center, King Faisal University, P.O. Box 400, Al-Hofuf 31982, Al-Ahsa, Saudi Arabia
| | - Osama B. Mohammed
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah Sheikh
- Camel Research Center, King Faisal University, P.O. Box 400, Al-Hofuf 31982, Al-Ahsa, Saudi Arabia
| | - Faisal Almathen
- Camel Research Center, King Faisal University, P.O. Box 400, Al-Hofuf 31982, Al-Ahsa, Saudi Arabia
- Department of Veterinary Public Health, College of Veterinary Medicine, King Faisal University, P.O. Box 400, Al-Hofuf 31982, Al-Ahsa, Saudi Arabia
| | - Ahmed M. Khalid
- Department of Veterinary Public Health, College of Veterinary Medicine, King Faisal University, P.O. Box 400, Al-Hofuf 31982, Al-Ahsa, Saudi Arabia
- Department of Genetics and Animal Breeding, Faculty of Animal Production, University of Khartoum, Shambat 13314, Sudan
| | - Amel O. Bakhiet
- Deanship of Scientific Research, Sudan University of Science and Technology, P.O. Box 407, Khartoum, Sudan
| | - Mutassim M. Abdelrahman
- Department of Animal Production, College of Food and Agriculture Science, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
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Qiu S, Li K, He X, Gu M, Jiang X, Lu J, Ma Z, Liang X, Gan Q. The Effects of Composite Alkali-Stored Spent Hypsizygus marmoreus Substrate on Carcass Quality, Rumen Fermentation, and Rumen Microbial Diversity in Goats. Animals (Basel) 2024; 14:166. [PMID: 38200897 PMCID: PMC10778354 DOI: 10.3390/ani14010166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 12/21/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
The objective of this study was to investigate the effects of composite alkali-stored spent Hypsizygus marmoreus substrate (SHMS) on carcass quality, rumen fermentation, and rumen microbial diversity in goats. Twenty-four 6-month-old Chuanzhong black goats with similar body weights (20 ± 5 kg) were selected and randomly divided into four groups (n = 6 per group) and received four treatments: 0% (control group, CG); 20% (low-addition group, LG); 30% (moderate-addition group, MG); and 40% (high-addition group, HG) of SHMS-replaced silage corn and oat hay. The experiment lasted for 74 days (including a 14 d adaptation period and a 60 d treatment period). The results of this study showed that MG and HG significantly improved the marble score of goat meat (p < 0.05). The flesh color score significantly increased in each group (p < 0.05). The fat color scores significantly increased in LG and MG (p < 0.05). There were no significant effects on the pH value or shear force of the longissimus dorsi in each group (p > 0.05). The cooking loss in MG was higher than that in CG (p < 0.05). The histidine and tyrosine contents in each group of muscles significantly increased (p < 0.05), with no significant effect on fatty acids (p > 0.05). The rumen pH of MG significantly decreased (p < 0.05), while the total volatile fatty acids (TVFAs) and ammoniacal nitrogen (NH3-N) increased by 44.63% and 54.50%, respectively. The addition of the SHMS altered both the alpha and beta diversities of the rumen microbiota and significant differences in the composition and structure of the four microbial communities. The dominant bacterial phylum in each group were Firmicutes and Bacteroidetes, with Prevotella 1 as the dominant bacterial genus. Correlation analysis revealed that rumen bacteria are closely related to the animal carcass quality and rumen fermentation. In the PICRUSt prediction, 21 significantly different pathways were found, and the correlation network showed a positive correlation between the Prevotella 1 and 7 metabolic pathways, while the C5-branched dibasic acid metabolism was positively correlated with nine bacteria. In summary, feeding goats with an SHMS diet can improve the carcass quality, promote rumen fermentation, and alter the microbial structure. The research results can provide a scientific reference for the utilization of SHMS as feed in the goat industry.
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Affiliation(s)
- Shuiling Qiu
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.Q.); (K.L.); (X.H.); (M.G.); (X.J.); (J.L.); (Z.M.)
| | - Keyao Li
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.Q.); (K.L.); (X.H.); (M.G.); (X.J.); (J.L.); (Z.M.)
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Xiangbo He
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.Q.); (K.L.); (X.H.); (M.G.); (X.J.); (J.L.); (Z.M.)
| | - Mingming Gu
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.Q.); (K.L.); (X.H.); (M.G.); (X.J.); (J.L.); (Z.M.)
| | - Xinghui Jiang
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.Q.); (K.L.); (X.H.); (M.G.); (X.J.); (J.L.); (Z.M.)
| | - Jianing Lu
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.Q.); (K.L.); (X.H.); (M.G.); (X.J.); (J.L.); (Z.M.)
| | - Zhiyi Ma
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.Q.); (K.L.); (X.H.); (M.G.); (X.J.); (J.L.); (Z.M.)
| | - Xuewu Liang
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.Q.); (K.L.); (X.H.); (M.G.); (X.J.); (J.L.); (Z.M.)
| | - Qianfu Gan
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.Q.); (K.L.); (X.H.); (M.G.); (X.J.); (J.L.); (Z.M.)
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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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Liu X, Yang Z, Yang J, Wang D, Niu J, Bai B, Sun W, Ma S, Cheng Y, Hao L. A Comparative Study of Growth Performance, Blood Biochemistry, Rumen Fermentation, and Ruminal and Fecal Bacterial Structure between Yaks and Cattle Raised under High Concentrate Feeding Conditions. Microorganisms 2023; 11:2399. [PMID: 37894057 PMCID: PMC10609059 DOI: 10.3390/microorganisms11102399] [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: 09/08/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
This study compared the growth performance, serum biochemical indicators, rumen fermentation parameters, rumen bacterial structure, and fecal bacterial structure of cattle and yaks fed for two months and given a feed containing concentrate of a roughage ratio of 7:3 on a dry matter basis. Compared with cattle, yak showed better growth performance. The serum biochemical results showed that the albumin/globulin ratio in yak serum was significantly higher than that in cattle. Aspartate aminotransferase, indirect bilirubin, creatine kinase, lactate dehydrogenase, and total cholesterol were significantly lower in yaks than in cattle. The rumen pH, acetate to propionate ratio, and acetate were lower in yaks than in cattle, whereas the lactate in yaks was higher than in cattle. There were significant differences in the structure of ruminal as well as fecal bacteria between cattle and yaks. The prediction of rumen bacterial function showed that there was a metabolic difference between cattle and yaks. In general, the metabolic pathway of cattle was mainly riched in a de novo synthesis of nucleotides, whereas that of yaks was mainly riched in the metabolic utilization of nutrients. This study provides a basis for understanding a rumen ecology under the condition of a high concentrate diet.
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Affiliation(s)
- Xiaojing Liu
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, Qinghai Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining 810016, China; (X.L.); (Z.Y.); (J.Y.); (J.N.); (B.B.); (W.S.); (S.M.)
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China;
| | - Zhanming Yang
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, Qinghai Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining 810016, China; (X.L.); (Z.Y.); (J.Y.); (J.N.); (B.B.); (W.S.); (S.M.)
| | - Jinfen Yang
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, Qinghai Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining 810016, China; (X.L.); (Z.Y.); (J.Y.); (J.N.); (B.B.); (W.S.); (S.M.)
| | - Dongyang Wang
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China;
| | - Jianzhang Niu
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, Qinghai Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining 810016, China; (X.L.); (Z.Y.); (J.Y.); (J.N.); (B.B.); (W.S.); (S.M.)
| | - Binqiang Bai
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, Qinghai Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining 810016, China; (X.L.); (Z.Y.); (J.Y.); (J.N.); (B.B.); (W.S.); (S.M.)
| | - Wu Sun
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, Qinghai Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining 810016, China; (X.L.); (Z.Y.); (J.Y.); (J.N.); (B.B.); (W.S.); (S.M.)
| | - Shike Ma
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, Qinghai Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining 810016, China; (X.L.); (Z.Y.); (J.Y.); (J.N.); (B.B.); (W.S.); (S.M.)
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China;
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
| | - Lizhuang Hao
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, Qinghai Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining 810016, China; (X.L.); (Z.Y.); (J.Y.); (J.N.); (B.B.); (W.S.); (S.M.)
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Forwood DL, Innes DJ, Parra MC, Stark T, de Souza DP, Chaves AV, Meale SJ. Feeding an unsalable carrot total-mixed ration altered bacterial amino acid degradation in the rumen of lambs. Sci Rep 2023; 13:6942. [PMID: 37117259 PMCID: PMC10147942 DOI: 10.1038/s41598-023-34181-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 04/25/2023] [Indexed: 04/30/2023] Open
Abstract
The objective of this study was to determine the influence of a total-mixed ration including unsalable carrots at 45% DM on the rumen microbiome; and the plasma, rumen and liver metabolomes. Carrots discarded at processing were investigated as an energy-dense substitute for barley grain in a conventional feedlot diet, and improved feed conversion efficiency by 25%. Here, rumen fluid was collected from 34 Merino lambs at slaughter (n = 16 control; n = 18 carrot) after a feeding period of 11-weeks. The V4 region of the 16S rRNA gene was sequenced to profile archaeal and bacterial microbe communities. Further, a comprehensive, targeted profile of known metabolites was constructed for blood plasma, rumen fluid and biopsied liver metabolites using a gas chromatography mass spectrometry (GC-MS) metabolomics approach. An in vitro batch culture was used to characterise ruminal fermentation including gas and methane (CH4) production. In vivo rumen microbial community structure of carrot fed lambs was dissimilar (P < 0.01; PERMANOVA), and all measures of alpha diversity were greater (P < 0.01), compared to those fed the control diet. Unclassified genera in Bacteroidales (15.9 ± 6.74% relative abundance; RA) were more abundant (P < 0.01) in the rumen fluid of carrot-fed lambs, while unclassified taxa in the Succinivibrionaceae family (11.1 ± 3.85% RA) were greater (P < 0.01) in the control. The carrot diet improved in vitro ruminal fermentation evidenced as an 8% increase (P < 0.01) in DM digestibility and a 13.8% reduction (P = 0.01) in CH4 on a mg/ g DM basis, while the control diet increased (P = 0.04) percentage of propionate within total VFA by 20%. Fourteen rumen fluid metabolites and 27 liver metabolites were influenced (P ≤ 0.05) by diet, while no effect (P ≥ 0.05) was observed in plasma metabolites. The carrot diet enriched (impact value = 0.13; P = 0.01) the tyrosine metabolism pathway (acetoacetic acid, dopamine and pyruvate), while the control diet enriched (impact value = 0.42; P ≤ 0.02) starch and sucrose metabolism (trehalose and glucose) in rumen fluid. This study demonstrated that feeding 45% DM unsalable carrots diversified bacterial communities in the rumen. These dietary changes influenced pathways of tyrosine degradation, such that previous improvements in feed conversion efficiency in lambs could be explained.
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Affiliation(s)
- Daniel L Forwood
- School of Agriculture and Food Sciences, Faculty of Science, The University of Queensland, Gatton, Australia
| | - David J Innes
- School of Agriculture and Food Sciences, Faculty of Science, The University of Queensland, Gatton, Australia
| | - Mariano C Parra
- School of Agriculture and Food Sciences, Faculty of Science, The University of Queensland, Gatton, Australia
| | - Terra Stark
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
| | - David P de Souza
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Parkville, Australia
| | - Alex V Chaves
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camperdown, Australia
| | - Sarah J Meale
- School of Agriculture and Food Sciences, Faculty of Science, The University of Queensland, Gatton, Australia.
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Guo W, Bi SS, Wang WW, Zhou M, Neves ALA, Degen AA, Guan LL, Long RJ. Maternal rumen and milk microbiota shape the establishment of early-life rumen microbiota in grazing yak calves. J Dairy Sci 2023; 106:2054-2070. [PMID: 36710176 DOI: 10.3168/jds.2022-22655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/05/2022] [Indexed: 01/30/2023]
Abstract
Early-life gut microbial colonization and development exert a profound impact on the health and metabolism of the host throughout the life span. The transmission of microbes from the mother to the offspring affects the succession and establishment of the early-life rumen microbiome in newborns, but the contributions of different maternal sites to the rumen microbial establishment remain unclear. In the present study, samples from different dam sites (namely, oral, rumen fluid, milk, and teat skin) and rumen fluid of yak calves were collected at 6 time points between d 7 and 180 postpartum to determine the contributions of the different maternal sites to the establishment of the bacterial and archaeal communities in the rumen during early life. Our analysis demonstrated that the dam's microbial communities clustered according to the sites, and the calves' rumen microbiota resembled that of the dam consistently regardless of fluctuations at d 7 and 14. The dam's rumen microbiota was the major source of the calves' rumen bacteria (7.9%) and archaea (49.7%) compared with the other sites, whereas the potential sources of the calf rumen microbiota from other sites varied according to the age. The contribution of dam's rumen bacteria increased with age from 0.36% at d 7 to 14.8% at d 180, whereas the contribution of the milk microbiota showed the opposite trend, with its contribution reduced from 2.7% at d 7 to 0.2% at d 180. Maternal oral archaea were the main sources of the calves' rumen archaea at d 14 (50.4%), but maternal rumen archaea became the main source gradually and reached 66.2% at d 180. These findings demonstrated the potential microbial transfer from the dam to the offspring that could influence the rumen microbiota colonization and establishment in yak calves raised under grazing regimens, providing the basis for future microbiota manipulation strategies during their early life.
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Affiliation(s)
- W Guo
- State Key Laboratory of Grassland Agro-ecosystems, International Centre of Tibetan Plateau Ecosystem Management, School of Life Sciences, Lanzhou University, Lanzhou 730000, China; Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang 550025, China; Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - S S Bi
- State Key Laboratory of Grassland Agro-ecosystems, International Centre of Tibetan Plateau Ecosystem Management, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - W W Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang 550025, China
| | - M Zhou
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - A L A Neves
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 3, DK-1870, Frederiksberg C, Denmark
| | - A A Degen
- Desert Animal Adaptations and Husbandry, Wyler Department of Dryland Agriculture, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer Sheva 8410500, Israel
| | - L L Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada.
| | - R J Long
- State Key Laboratory of Grassland Agro-ecosystems, International Centre of Tibetan Plateau Ecosystem Management, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
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8
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Breed and ruminal fraction effects on bacterial and archaeal community composition in sheep. Sci Rep 2023; 13:3336. [PMID: 36849493 PMCID: PMC9971215 DOI: 10.1038/s41598-023-28909-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/27/2023] [Indexed: 03/01/2023] Open
Abstract
While the breed of cattle can impact on the composition and structure of microbial communities in the rumen, breed-specific effects on rumen microbial communities have rarely been examined in sheep. In addition, rumen microbial composition can differ between ruminal fractions, and be associated with ruminant feed efficiency and methane emissions. In this study, 16S rRNA amplicon sequencing was used to investigate the effects of breed and ruminal fraction on bacterial and archaeal communities in sheep. Solid, liquid and epithelial rumen samples were obtained from a total of 36 lambs, across 4 different sheep breeds (Cheviot (n = 10), Connemara (n = 6), Lanark (n = 10) and Perth (n = 10)), undergoing detailed measurements of feed efficiency, who were offered a nut based cereal diet ad-libitum supplemented with grass silage. Our results demonstrate that the feed conversion ratio (FCR) was lowest for the Cheviot (most efficient), and highest for the Connemara breed (least efficient). In the solid fraction, bacterial community richness was lowest in the Cheviot breed, while Sharpea azabuensis was most abundant in the Perth breed. Lanark, Cheviot and Perth breeds exhibited a significantly higher abundance of epithelial associated Succiniclasticum compared to the Connemara breed. When comparing ruminal fractions, Campylobacter, Family XIII, Mogibacterium, and Lachnospiraceae UCG-008 were most abundant in the epithelial fraction. Our findings indicate that breed can impact the abundance of specific bacterial taxa in sheep while having little effect on the overall composition of the microbial community. This finding has implications for genetic selection breeding programs aimed at improving feed conversion efficiency of sheep. Furthermore, the variations in the distribution of bacterial species identified between ruminal fractions, notably between solid and epithelial fractions, reveals a rumen fraction bias, which has implications for sheep rumen sampling techniques.
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In Vitro Modulation of Rumen Fermentation by Microbiota from the Recombination of Rumen Fluid and Solid Phases. Microbiol Spectr 2023; 11:e0338722. [PMID: 36475888 PMCID: PMC9927485 DOI: 10.1128/spectrum.03387-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Rumen microbiota transplantation (RMT) can improve rumen fermentation and ruminant performance. However, due to the microbial distinction in the fluid and solid phases, the current understanding of their specific roles in RMT is insufficient. Thus, this study was conducted to determine the effects of the microbiota from the recombination of the rumen fluid and solid phases on in vitro fermentation. The rumen fresh fluid (FF) and fresh solid (FS) phases were collected, and FS was washed for the fresh solid washing solution (FW). The fractions of FF, FS, and FW were autoclaved to obtain autoclaved fluid (AF), solid (AS), and washing solution (AW). Then, these phases were recombined to form eight treatments: FFFS, FFAS, FFFW, FFAW, AFFS, AFAS, AFFW, and AFAW. After 24 h of fermentation, the gas production in AFFS, FFFS, and FFAS was significantly higher than that of other groups. AFAS and AFAW had significantly lower alpha diversity than did other groups. The solid phase was enriched with fiber-degrading bacteria, including Treponema, Succinivibrio, and Ruminococcus. The fluid phase was dominated by Prevotella, Christensenellaceae R-7 group, and Rikenellaceae RC9 gut group. The washing solution had more Ruminobacter, Lachnospiraceae, and Fibrobacter. Moreover, the double-autoclaved phases displayed increased abundances of harmful bacteria, as AFAS and AFAW had higher Streptococcus and Prevotellaceae YAB2003 group abundances. A network analysis showed that the signature microbiota in AFAS and AFAW were negatively associated with the keystone microbiota in the other groups. In summary, the recombination of the solid phase and the autoclaved fluid phase had the best in vitro fermentation result, which provided certain references for RMT. IMPORTANCE This is the first study to systematically evaluate the in vitro fermentation efficiency of diets by bacteria harvested and recombined from the fluid and solid phases of rumen contents, and it took into account the effect of washing the rumen solid phase. Using "reconstituted rumen content", this study confirmed that bacteria from different fractions of the rumen digesta resulted in different fermentation production of diets and found the characteristic bacteria in each phase of rumen contents. Our data reveal that the bacteria in the solid phase have more positive effects on the in vitro fermentation parameters, that the combination of the autoclaved fluid phase and the fresh solid phase have the most ideal fermentation effect, and that the autoclave process significantly influenced the microbial composition and increased the abundance of harmful bacteria. This study provides a landmark reference for the future use of rumen microbiota transplantation to improve animal feed utilization and growth performance.
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Loublier C, Taminiau B, Heinen J, Lecoq L, Amory H, Daube G, Cesarini C. Evaluation of Bacterial Composition and Viability of Equine Feces after Processing for Transplantation. Microorganisms 2023; 11:microorganisms11020231. [PMID: 36838196 PMCID: PMC9966902 DOI: 10.3390/microorganisms11020231] [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: 12/15/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Fecal microbiota transplantation (FMT) has been used empirically for decades in equine medicine to treat intestinal dysbiosis but evidence-based information is scarce. This in vitro study aimed at assessing the effect of a commonly used pre-FMT processing method on the bacterial composition and viability of the fecal filtrate. Three samples of fresh equine manure (T0) were processed identically: the initial manure was mixed with 1 L of lukewarm water and chopped using an immersion blender to obtain a mixture (T1), which was left uncovered during 30 min (T2) and percolated through a sieve to obtain a fecal filtrate (T3). Samples were taken throughout the procedure (Tn) and immediately stored at 4 °C until processing. The 16S rDNA amplicon profiling associated with propidium monoazide treatment was performed on each sample to select live bacteria. Analyses of α and β diversity and main bacterial populations and quantitative (qPCR) analysis were performed and statistically compared (significance p < 0.05) between time points (T0-T3). No significant differences in ecological indices or mean estimated total living bacteria were found in the final fecal filtrate (T3) in regard to the original manure (T0); however, relative abundances of some minor genera (Fibrobacter, WCHB1-41_ge and Akkermansia) were significantly different in the final filtrate. In conclusion, the results support the viability of the major bacterial populations in equine feces when using the described pre-FMT protocol.
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Affiliation(s)
- Clémence Loublier
- Equine Clinical Department, Faculty of Veterinary Medicine, University of Liège, Bât. B41, 4000 Liège, Belgium
- Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Bernard Taminiau
- Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
- Department of Food Sciences—Microbiology, Faculty of Veterinary Medicine, University of Liege, Avenue de Cureghem 10, Bât. B43b, 4000 Liège, Belgium
| | - Julia Heinen
- Equine Clinical Department, Faculty of Veterinary Medicine, University of Liège, Bât. B41, 4000 Liège, Belgium
- Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Laureline Lecoq
- Equine Clinical Department, Faculty of Veterinary Medicine, University of Liège, Bât. B41, 4000 Liège, Belgium
- Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Hélène Amory
- Equine Clinical Department, Faculty of Veterinary Medicine, University of Liège, Bât. B41, 4000 Liège, Belgium
- Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Georges Daube
- Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
- Department of Food Sciences—Microbiology, Faculty of Veterinary Medicine, University of Liege, Avenue de Cureghem 10, Bât. B43b, 4000 Liège, Belgium
| | - Carla Cesarini
- Equine Clinical Department, Faculty of Veterinary Medicine, University of Liège, Bât. B41, 4000 Liège, Belgium
- Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
- Correspondence:
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11
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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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Liu X, Gao J, Liu S, Cheng Y, Hao L, Liu S, Zhu W. The uniqueness and superiority of energy utilization in yaks compared with cattle in the highlands: A review. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2022; 12:138-144. [PMID: 36683881 PMCID: PMC9841238 DOI: 10.1016/j.aninu.2022.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 11/05/2022]
Abstract
Yaks living on the Qinghai-Tibetan Plateau for a long time have evolved a series of mechanisms to adapt to the unique geographical environment and climate characteristics of the plateau. Compared with other ruminants, yaks have higher energy utilization and metabolic efficiency. This paper presents possible mechanisms responsible for the efficient energy utilization, absorption and metabolism resulting from the unique evolutionary process of yaks. It is hoped that the information discussed in this review will give a better insight into the uniqueness and superiority of yaks in regards to energy metabolism and utilization compared with cattle and open new avenues for the targeted regulation of energy utilization pathways of other ruminants.
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Affiliation(s)
- Xiaojing Liu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Jian Gao
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Suozhu Liu
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, China
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China,Corresponding authors.
| | - Lizhuang Hao
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Plateau Yak Research Center, Qinghai Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining 810016, China,Corresponding authors.
| | - Shujie Liu
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Plateau Yak Research Center, Qinghai Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining 810016, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
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13
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Collinet A, Grimm P, Jacotot E, Julliand V. Biomarkers for monitoring the equine large intestinal inflammatory response to stress-induced dysbiosis and probiotic supplementation. J Anim Sci 2022; 100:skac268. [PMID: 35980768 PMCID: PMC9576022 DOI: 10.1093/jas/skac268] [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: 05/11/2022] [Accepted: 08/16/2022] [Indexed: 11/14/2022] Open
Abstract
Large intestine barrier disturbances can have serious consequences for the health of horses. The loss of mucosal integrity that leads to increased intestinal permeability may result from a local inflammatory immune response following alterations of the microbiota, known as dysbiosis. Therefore, our research aimed to identify noninvasive biomarkers for studying the intestinal permeability and the local inflammatory immune response in horses. Regarding the biomarkers used in other mammalian species, we measured the concentrations of lipopolysaccharides (LPS), reflected by 3-OH C14, C16, and C18 fatty acids, in blood, and fecal secretory immunoglobulin-A (SIgA). These biomarkers were evaluated in two trials including 9 and 12 healthy horses, which developed large intestinal dysbiosis experimentally induced by 5 d of antibiotic administration (trimethoprim sulfadiazine [TMS]) or 5 d of abrupt introduction of high starch levels (barley) into the diet. Horses were either control or supplemented with Lactobacillus acidophilus, Ligilactobacillus salivarius, and Bifidobacterium lactis. Correlations were performed between biomarkers and fecal bacterial diversity, composition, and function. No significant interaction between day and supplementation, or supplementation effect were observed for each biomarker. However, with the dietary stressor, a significant increase in blood concentrations of 3-OH C16 (P = 0.0125) and C14 (P = 0.0252) fatty acids was measured 2 d after the cessation of barley administration. Furthermore, with the antibiotic stressor, blood levels of 3-OH C16 progressively increased (P = 0.0114) from the first day to 2 d after the end of TMS administration. No significant day effect was observed for fecal SIgA concentrations for both stressors. These results indicate that both antibiotic- and diet-induced dysbiosis resulted in a local translocation of LPS 2 d after the cessation of the stressor treatments, suggesting an impairment of intestinal permeability, without detectable local inflammation. Blood LPS and fecal SIgA concentrations were significantly correlated with several bacterial variations in the large intestine, which are features of antibiotic- and diet-induced dysbiosis. These findings support the hypothesis that a relationship exists between dysbiosis and the loss of mucosal integrity in the large intestine of horses.
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Affiliation(s)
- Axelle Collinet
- Lab To Field, 21000 Dijon, France
- Univ. Bourgogne Franche–Comté, L’Institut Agro Dijon, PAM UMR A 02.102, 21000 Dijon, France
| | | | - Emmanuel Jacotot
- Univ. Bourgogne Franche–Comté, L’Institut Agro Dijon, PAM UMR A 02.102, 21000 Dijon, France
| | - Véronique Julliand
- Univ. Bourgogne Franche–Comté, L’Institut Agro Dijon, PAM UMR A 02.102, 21000 Dijon, France
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14
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Adding dried distillers grains with solubles influences the rumen microbiome of meat goats fed lespedeza or alfalfa-based diets. Small Rumin Res 2022. [DOI: 10.1016/j.smallrumres.2022.106747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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15
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Weinert-Nelson JR, Biddle AS, Williams CA. Fecal microbiome of horses transitioning between warm-season and cool-season grass pasture within integrated rotational grazing systems. Anim Microbiome 2022; 4:41. [PMID: 35729677 PMCID: PMC9210719 DOI: 10.1186/s42523-022-00192-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/10/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Diet is a key driver of equine hindgut microbial community structure and composition. The aim of this study was to characterize shifts in the fecal microbiota of grazing horses during transitions between forage types within integrated warm- (WSG) and cool-season grass (CSG) rotational grazing systems (IRS). Eight mares were randomly assigned to two IRS containing mixed cool-season grass and one of two warm-season grasses: bermudagrass [Cynodon dactylon (L.) Pers.] or crabgrass [Digitaria sanguinalis (L.) Scop.]. Fecal samples were collected during transitions from CSG to WSG pasture sections (C-W) and WSG to CSG (W-C) on days 0, 2, 4, and 6 following pasture rotation and compared using 16S rRNA gene sequencing. RESULTS Regardless of IRS or transition (C-W vs. W-C), species richness was greater on day 4 and 6 in comparison to day 0 (P < 0.05). Evenness, however, did not differ by day. Weighted UniFrac also did not differ by day, and the most influential factor impacting β-diversity was the individual horse (R2 ≥ 0.24; P = 0.0001). Random forest modeling was unable to accurately predict days within C-W and W-C, but could predict the individual horse based on microbial composition (accuracy: 0.92 ± 0.05). Only three differentially abundant bacterial co-abundance groups (BCG) were identified across days within all C-W and W-C for both IRS (W ≥ 126). The BCG differing by day for all transitions included amplicon sequence variants (ASV) assigned to bacterial groups with known fibrolytic and butyrate-producing functions including members of Lachnospiraceae, Clostridium sensu stricto 1, Anaerovorax the NK4A214 group of Oscillospiraceae, and Sarcina maxima. In comparison, 38 BCG were identified as differentially abundant by horse (W ≥ 704). The ASV in these groups were most commonly assigned to genera associated with degradation of structural carbohydrates included Rikenellaceae RC9 gut group, Treponema, Christensenellaceae R-7 group, and the NK4A214 group of Oscillospiraceae. Fecal pH also did not differ by day. CONCLUSIONS Overall, these results demonstrated a strong influence of individual horse on the fecal microbial community, particularly on the specific composition of fiber-degraders. The equine fecal microbiota were largely stable across transitions between forages within IRS suggesting that the equine gut microbiota adjusted at the individual level to the subtle dietary changes imposed by these transitions. This adaptive capacity indicates that horses can be managed in IRS without inducing gastrointestinal dysfunction.
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Affiliation(s)
- Jennifer R. Weinert-Nelson
- grid.430387.b0000 0004 1936 8796Department of Animal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901 USA
| | - Amy S. Biddle
- grid.33489.350000 0001 0454 4791Department of Animal and Food Sciences, College of Agriculture and Natural Resources, University of Delaware, Newark, DE 19711 USA
| | - Carey A. Williams
- grid.430387.b0000 0004 1936 8796Department of Animal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901 USA
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16
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Silva LHP, Reis SF, Melo ATO, Jackson BP, Brito AF. Supplementation of Ascophyllum nodosum meal and monensin: Effects on diversity and relative abundance of ruminal bacterial taxa and the metabolism of iodine and arsenic in lactating dairy cows. J Dairy Sci 2022; 105:4083-4098. [PMID: 35221070 DOI: 10.3168/jds.2021-21107] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 01/05/2022] [Indexed: 01/10/2024]
Abstract
Previous research has shown that the brown seaweed Ascophyllum nodosum (ASCO) has antimicrobial and antioxidant properties and also increases milk I concentration. We aimed to investigate the effects of supplementing ASCO meal or monensin (MON) on ruminal fermentation, diversity and relative abundance of ruminal bacterial taxa, metabolism of I and As, and blood concentrations of thyroid hormones, antioxidant enzymes, and cortisol in lactating dairy cows. Five multiparous ruminally cannulated Jersey cows averaging (mean ± standard deviation) 102 ± 15 d in milk and 450 ± 33 kg of body weight at the beginning of the study were used in a Latin square design with 28-d periods (21 d for diet adaptation and 7 d for data and sample collection). Cows were fed ad libitum a basal diet containing (dry matter basis) 65% forage as haylage and corn silage and 35% concentrate and were randomly assigned to 1 of the following 5 dietary treatments: 0, 57, 113, or 170 g/d of ASCO meal, or 300 mg/d of MON. Supplements were placed directly into the rumen once daily after the morning feeding. Diets had no effect on ruminal pH and NH3-N concentration, which averaged 6.02 and 6.86 mg/dL, respectively. Total volatile fatty acid concentration decreased linearly in cows fed incremental amounts of ASCO meal. Supplementation with ASCO meal did not change the ruminal molar proportions of volatile fatty acids apart from butyrate, which responded quadratically with the lowest values observed at 56 and 113 g/d of ASCO supplementation. Compared with the control diet or diets containing ASCO meal, cows fed MON showed greater molar proportion of propionate. Diets did not affect the α diversity indices Shannon, Simpson, and Fisher for ruminal bacteria. However, feeding incremental levels of ASCO meal linearly decreased the relative abundance of Tenericutes in ruminal fluid. Monensin increased the relative abundance of the CAG:352 bacterial genus in ruminal fluid compared with the control diet. Linear increases in response to ASCO meal supplementation were observed for the concentrations and output of I in serum, milk, urine, and feces. Fecal excretion of As increased linearly in cows fed varying amounts of ASCO meal, but ASCO did not affect the concentration and secretion of As in milk. The plasma activities of the antioxidant enzymes and the serum concentrations of thyroid hormones did not change. In contrast, circulating cortisol decreased linearly in diets containing ASCO meal. The apparent total-tract digestibilities of dry matter, organic matter, and crude protein increased linearly with ASCO meal, but those of neutral and acid detergent fiber were not affected. In summary, feeding incremental amounts of ASCO meal decreased serum cortisol concentration, and increased I concentrations and output in serum, milk, feces, and urine.
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Affiliation(s)
- L H P Silva
- Department of Agriculture, Nutrition and Food Systems, University of New Hampshire, Durham 03824
| | - S F Reis
- Department of Agriculture, Nutrition and Food Systems, University of New Hampshire, Durham 03824
| | - A T O Melo
- Department of Agriculture, Nutrition and Food Systems, University of New Hampshire, Durham 03824
| | - B P Jackson
- Department of Earth Sciences, Dartmouth College, Hanover, NH 03755
| | - A F Brito
- Department of Agriculture, Nutrition and Food Systems, University of New Hampshire, Durham 03824.
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17
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Responsive changes of rumen microbiome and metabolome in dairy cows with different susceptibility to subacute ruminal acidosis. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2022; 8:331-340. [PMID: 35024470 PMCID: PMC8718735 DOI: 10.1016/j.aninu.2021.10.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 09/29/2021] [Accepted: 10/11/2021] [Indexed: 12/19/2022]
Abstract
Subacute ruminal acidosis (SARA) represents one of the most important digestive disorders in intensive dairy farms, and dairy cows are individually different in the severity of SARA risk. The objectives of the current study were to investigate differences in the ruminal bacterial community and metabolome in dairy cattle with different susceptibility to SARA. In the present study, 12 cows were initially enrolled in the experiment. Based on average ruminal pH, 4 cows with the lowest ruminal pH were assigned to the susceptible group (SUS, pH = 5.76, n = 4) and 4 cows with the highest ruminal pH assigned to the tolerant group (TOL, pH = 6.10, n = 4). Rumen contents from susceptible (SUS, n = 4) and tolerant (TOL, n = 4) dairy cows were collected through rumen fistula to systematically reveal the rumen microbial and metabolic alterations of dairy cows with different susceptibility to SARA using multi-omics approaches (16S and 18S rRNA gene sequencing and metabolome). The results showed that despite being fed the same diet, SUS cows had lower ruminal pH and higher concentrations of total volatile fatty acids (VFA) and propionate than TOL cows (P < 0.05). No significant differences were observed in dry matter intake, milk yield, and other milk compositions between the SUS and TOL groups (P > 0.05). The principal coordinates analysis based on the analysis of molecular variance indicated a significant difference in bacterial composition between the two groups (P = 0.01). More specifically, the relative abundance of starch-degrading bacteria (Prevotella spp.) was greater (P < 0.05), while the proportion of fiber-degrading bacteria (unclassified Ruminococcaceae spp., Ruminococcus spp., Papillibacter, and unclassified Family_XIII) was lower in the rumen of SUS cows compared with TOL cows (P < 0.05). Community analysis of protozoa showed that there were no significant differences in the diversity, richness, and community structure (P > 0.05). Metabolomics analysis revealed that the concentrations of organic acids (such as lactic acid), biogenic amines (such as histamine), and bacterial degradation products (such as hypoxanthine) were significantly higher in the SUS group compared to the TOL group (P < 0.05). These findings revealed that the higher proportion of starch-degrading bacteria/lower fiber-degrading bacteria in the rumen of SUS cows resulted in higher VFA-producing capacity, in particular propionate. This caused a disruption in metabolic homeostasis in the rumen which might be the reason for the higher susceptibility to SARA. Overall, these findings enhanced our understanding of the ruminal microbiome and metabolic changes in cows susceptible to SARA.
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Li J, Tang X, Chen S, Zhao J, Shao T. Ensiling pretreatment with two novel microbial consortia enhances bioethanol production in sterile rice straw. BIORESOURCE TECHNOLOGY 2021; 339:125507. [PMID: 34303101 DOI: 10.1016/j.biortech.2021.125507] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 06/13/2023]
Abstract
The present study extracts and enriches cellulolytic microbial consortia from yak (Bos grunniens) and evaluates their effects on the fermentation profile and bioethanol yield in rice straw silage. Two microbial consortia (CF and PY) with high cellulolytic activity were isolated and observed to be prone to utilize natural carbon sources. Two consortia were introduced with and without combined lactic acid bacteria (CLAB) to rice straw for up to 60 days of ensiling, and their application notably decreased the levels of structural carbohydrates and pH values of rice straw silages. Treatments that combining microbial consortia and CLAB resulted in the highest levels of lactic acid, water soluble carbohydrates, mono- and disaccharides, and lignocellulose degradation, with PY + CLAB group yielding the highest bioethanol production. The microbial consortia identified herein exhibit great potential for degrading fibrous substrates, and their combination with CLAB provides a feasible way to efficiently use rice straw for bioethanol production.
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Affiliation(s)
- Junfeng Li
- Institute of Ensiling and Processing of Grass, College of Agro-grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoyue Tang
- Institute of Ensiling and Processing of Grass, College of Agro-grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Sifan Chen
- Institute of Ensiling and Processing of Grass, College of Agro-grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Jie Zhao
- Institute of Ensiling and Processing of Grass, College of Agro-grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Tao Shao
- Institute of Ensiling and Processing of Grass, College of Agro-grassland Science, Nanjing Agricultural University, Nanjing 210095, China.
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19
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Xu C, Liu W, Sun B, Zhang S, Zhang S, Yang Y, Lei Y, Chang L, Xie P, Suo H. Multi-Omics Analysis Reveals a Dependent Relationship Between Rumen Bacteria and Diet of Grass- and Grain-Fed Yaks. Front Microbiol 2021; 12:642959. [PMID: 34421832 PMCID: PMC8377600 DOI: 10.3389/fmicb.2021.642959] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
Current information on the differences between rumen bacteria and metabolites of the grass-fed and grain-fed yaks is limited. Understanding the composition and alterations of rumen microbial metabolites is important to clarify its potential role in grass-fed and grain-fed systems. The aim of this research was to explore the influence of different production systems on the functional attributes and metabolites in the rumen microbiota of yak using genomics (Illumina MiSeq sequencing of the 16S rRNA gene) and untargeted metabolomics (UHPLC-QTOF-MS). Rumen samples were obtained from grass-fed (C), grain-fed for 3-month (G3), and grain-fed for 6-month yaks (G6). Results showed that the grain-fed yaks presented a lower rumen bacterial richness and diversity when compared to grass-fed yaks. Bacteroidota, Firmicutes, and Fibrobacterota were the main bacterial phyla. At the phylum and genus level, the grass-fed yaks significantly increased the abundance of Fibrobacterota and Fibrobacter (p < 0.05), respectively. The metabolomics analysis revealed that the metabolite profiles differed among the three groups. Compared with the grass-fed group, grain feeding significantly increased azelaic acid, hypoxanthine, uridine, L-phenylalanine, anserine, and decreased alpha-linolenic acid, adenine. Pathway enrichment analysis showed significant differences in metabolic pathways among all comparison groups, but the glycerophospholipid metabolism and alpha-linolenic acid metabolism pathway were common key metabolic pathways. This study showed that the combined analysis of microbiota and metabolites could distinguish different production systems and the fattening time of yaks, providing novel insights for us to understand the function of the rumen bacteria.
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Affiliation(s)
- Chenchen Xu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenwen Liu
- College of Food Science, Southwest University, Chongqing, China
| | - Baozhong Sun
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Songshan Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shou Zhang
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Yuanli Yang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuanhua Lei
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lan Chang
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Peng Xie
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huayi Suo
- College of Food Science, Southwest University, Chongqing, China
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20
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Effects of rumen-protected methionine and lysine supplementation on milk yields and components, rumen fermentation, and the rumen microbiome in lactating yaks (Bos grunniens). Anim Feed Sci Technol 2021. [DOI: 10.1016/j.anifeedsci.2021.114972] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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21
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Ahmad AA, Zhang JB, Liang Z, Yang C, Kalwar Q, Shah T, Du M, Muhammad I, Zheng J, Yan P, Ding XZ, Long R. Dynamics of rumen bacterial composition of yak ( Bos grunniens) in response to dietary supplements during the cold season. PeerJ 2021; 9:e11520. [PMID: 34178446 PMCID: PMC8216167 DOI: 10.7717/peerj.11520] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 05/05/2021] [Indexed: 11/20/2022] Open
Abstract
This study aimed to explore the rumen bacterial community of yak in response to dietary supplements during the cold season. In addition, the rumen fermentation products were also analyzed. Twenty-one female domestic yaks were randomly divided into three groups i.e., pure grazing (GG) group, grazing plus oats hay supplement (OG) group, and grazing plus concentrate supplement group (CG). Rumen contents were collected after 90 days to assess rumen fermentation parameters and bacterial community. The GC group presented higher concentrations of ammonia nitrogen (P < 0.001), and total volatile fatty acids (TVFA) (P < 0.001), and lower rumen pH (P < 0.001) compared to other experimental groups. The CG group displayed higher proportions of propionate, butyrate, isobutyrate, and isovalerate while lower A/P ratio compared to other experimental groups. Shannon, Chao1, and ACE values were significantly lower in the OG group compared to GG and CG groups. Anosim test showed significant differences in bacterial community structure between groups but the PCA plot was not very informative to see these differences. Bacteroidetes, Proteobacteria, and Firmicutes were the three dominant phyla in all groups. The genera Oscillospira was more abundant in GG and OG groups. Higher relative abundance of Ruminococcus and Clostridium was observed in the GG group, while Ruminobacter, Corynebacterium, and Selenomonas were more abundant in the CG group. These findings will help in improving our understanding of rumen bacteria in yaks in response to changes in diet.
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Affiliation(s)
- Anum Ali Ahmad
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jian Bo Zhang
- Key Laboratory of yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Zeyi Liang
- Key Laboratory of yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Chao Yang
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan, Provincial Engineering Research Center for Healthy Livestock and Poultry Production, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
| | - Qudratullah Kalwar
- Key Laboratory of yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Tariq Shah
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Mei Du
- Key Laboratory of yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ishaq Muhammad
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Juanshan Zheng
- Key Laboratory of yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ping Yan
- Key Laboratory of yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xue-Zhi Ding
- Key Laboratory of yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ruijun Long
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, China
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22
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Liu W, Wang Q, Song J, Xin J, Zhang S, Lei Y, Yang Y, Xie P, Suo H. Comparison of Gut Microbiota of Yaks From Different Geographical Regions. Front Microbiol 2021; 12:666940. [PMID: 34163445 PMCID: PMC8216380 DOI: 10.3389/fmicb.2021.666940] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/12/2021] [Indexed: 11/17/2022] Open
Abstract
Gut microbiota are closely linked to host health and adaptability to different geographical environments. However, information on the influence of different geographical conditions on the intestinal microbiota of yaks is limited. In this study, 18 yak fecal samples were collected from three regions of China, namely Shangri-la, Lhasa, and Yushu, and were analyzed via high-throughput sequencing. The alpha diversity, as measured by the Shannon, ACE, and Chao indices, was the highest in the Shangri-la samples. Principal coordinate analysis detected significant differences in the composition of the intestinal microbiota of yaks from different regions. A total of six phyla, 21 families, and 29 genera were identified in the fecal samples. The dominant phyla in the samples were Firmicutes and Bacteroidetes, and the most abundant family was Ruminococcaceae. In addition, Ruminococcaceae_UCG-005 was the predominant genus and was more abundant in Yushu samples than in other samples. However, the predicted functional gene composition of the gut microbiota of yaks from different regions was similar. Our results revealed that geographical conditions influence the diversity and composition of the intestinal microbiota of yaks.
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Affiliation(s)
- Wenwen Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Food Science, Southwest University, Chongqing, China
| | - Qiang Wang
- College of Food Science, Southwest University, Chongqing, China
| | - Jiajia Song
- College of Food Science, Southwest University, Chongqing, China
| | - Jinwei Xin
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Songshan Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuanhua Lei
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuanli Yang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Peng Xie
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huayi Suo
- College of Food Science, Southwest University, Chongqing, China
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23
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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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24
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Collinet A, Grimm P, Julliand S, Julliand V. Multidimensional Approach for Investigating the Effects of an Antibiotic-Probiotic Combination on the Equine Hindgut Ecosystem and Microbial Fibrolysis. Front Microbiol 2021; 12:646294. [PMID: 33841371 PMCID: PMC8027512 DOI: 10.3389/fmicb.2021.646294] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 02/16/2021] [Indexed: 12/11/2022] Open
Abstract
The equine hindgut ecosystem is specialized in dietary fibers' fermentation to provide horses' energy and contribute to its health. Nevertheless, antibiotics are known to disrupt the hindgut microbiota, affecting the fibrolytic activity of bacteria and the intestinal immune balance, leading to diseases. This in vivo study used a general and comprehensive approach for characterizing the hindgut ecosystem of 9 healthy horses over 28 days in response to a 5-day challenge with oral trimethoprim-sulfadiazine (TMS), with a special emphasis on microbial fibrolytic activity and the host immune response. Horses were supplemented with two doses of Lactobacillus acidophilus, Ligilactobacillus salivarius (formerly L. salivarius), and Bifidobacterium lactis blend or a placebo in a 3 × 3 Latin square design. Changes in fecal microbiota were investigated using 16S rRNA sequencing. Clostridioides difficile was quantified in feces using quantitative polymerase chain reaction. Anaerobic microbiological culture was used to enumerate functional bacterial groups (cellulolytic, amylolytic, and lactic acid-utilizing). The environmental dimensions were assessed by measuring the concentrations of volatile fatty acids (VFAs) and lactic acid using biochemical methods, and changes in pH and dry matter weight. Systemic and local inflammation was evaluated by determination of cytokine and immunoglobulin (Ig)A concentrations in the serum and secretory IgA (SIgA) concentrations in the feces using immuno-enzymatic methods. Oral TMS treatment strongly altered the whole hindgut ecosystem by 2 days after the first administration. Bacterial diversity decreased in proportion to the relative abundance of fibrolytic genera, which coincided with the decrease in the concentration of cellulolytic bacteria. At the same time, the composition of microbiota members was reorganized in terms of relative abundances, probably to support the alteration in fibrolysis. C. difficile DNA was not found in these horses, but the relative abundances of several potential pathobiont genera increased. 2 days after the first TMS administration, fecal concentrations of VFAs and SIgA increased in parallel with fecal water content, suggesting an alteration of the integrity of the hindgut mucosa. Recovery in bacterial composition, functions, and immune biomarkers took 2-9 days after the end of TMS administration. Supplementation with this bacterial blend did not limit bacterial alteration but might have interesting mucosal immunomodulatory effects.
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Affiliation(s)
- Axelle Collinet
- Lab To Field, Dijon, France.,Univ. Bourgogne Franche-Comté, AgroSup Dijon, PAM UMR A 02.102, Dijon, France
| | | | | | - Véronique Julliand
- Univ. Bourgogne Franche-Comté, AgroSup Dijon, PAM UMR A 02.102, Dijon, France
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25
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Anderson CJ, Koester LR, Schmitz-Esser S. Rumen Epithelial Communities Share a Core Bacterial Microbiota: A Meta-Analysis of 16S rRNA Gene Illumina MiSeq Sequencing Datasets. Front Microbiol 2021; 12:625400. [PMID: 33790876 PMCID: PMC8005654 DOI: 10.3389/fmicb.2021.625400] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/22/2021] [Indexed: 01/11/2023] Open
Abstract
In this meta-analysis, 17 rumen epithelial 16S rRNA gene Illumina MiSeq amplicon sequencing data sets were analyzed to identify a core rumen epithelial microbiota and core rumen epithelial OTUs shared between the different studies included. Sequences were quality-filtered and screened for chimeric sequences before performing closed-reference 97% OTU clustering, and de novo 97% OTU clustering. Closed-reference OTU clustering identified the core rumen epithelial OTUs, defined as any OTU present in ≥ 80% of the samples, while the de novo data was randomly subsampled to 10,000 reads per sample to generate phylum- and genus-level distributions and beta diversity metrics. 57 core rumen epithelial OTUs were identified including metabolically important taxa such as Ruminococcus, Butyrivibrio, and other Lachnospiraceae, as well as sulfate-reducing bacteria Desulfobulbus and Desulfovibrio. Two Betaproteobacteria OTUs (Neisseriaceae and Burkholderiaceae) were core rumen epithelial OTUs, in contrast to rumen content where previous literature indicates they are rarely found. Two core OTUs were identified as the methanogenic archaea Methanobrevibacter and Methanomethylophilaceae. These core OTUs are consistently present across the many variables between studies which include different host species, geographic region, diet, age, farm management practice, time of year, hypervariable region sequenced, and more. When considering only cattle samples, the number of core rumen epithelial OTUs expands to 147, highlighting the increased similarity within host species despite geographical location and other variables. De novo OTU clustering revealed highly similar rumen epithelial communities, predominated by Firmicutes, Bacteroidetes, and Proteobacteria at the phylum level which comprised 79.7% of subsampled sequences. The 15 most abundant genera represented an average of 54.5% of sequences in each individual study. These abundant taxa broadly overlap with the core rumen epithelial OTUs, with the exception of Prevotellaceae which were abundant, but not identified within the core OTUs. Our results describe the core and abundant bacteria found in the rumen epithelial environment and will serve as a basis to better understand the composition and function of rumen epithelial communities.
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Affiliation(s)
- Chiron J Anderson
- Department of Animal Science, Iowa State University, Ames, IA, United States.,Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
| | - Lucas R Koester
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States.,Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, United States
| | - Stephan Schmitz-Esser
- Department of Animal Science, Iowa State University, Ames, IA, United States.,Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
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26
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Rabee AE, Forster R, Elekwachi C, Sabra E, Lamara M. Comparative analysis of the metabolically active microbial communities in the rumen of dromedary camels under different feeding systems using total rRNA sequencing. PeerJ 2020; 8:e10184. [PMID: 33194403 PMCID: PMC7603790 DOI: 10.7717/peerj.10184] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 09/23/2020] [Indexed: 11/20/2022] Open
Abstract
Breakdown of plant biomass in rumen depends on interactions between bacteria, archaea, fungi, and protozoa; however, the majority of studies of the microbiome of ruminants, including the few studies of the rumen of camels, only studied one of these microbial groups. In this study, we applied total rRNA sequencing to identify active microbial communities in 22 solid and liquid rumen samples from 11 camels. These camels were reared at three stations that use different feeding systems: clover, hay and wheat straw (G1), fresh clover (G2), and wheat straw (G3). Bacteria dominated the libraries of sequence reads generated from all rumen samples, followed by protozoa, archaea, and fungi respectively. Firmicutes, Thermoplasmatales, Diplodinium, and Neocallimastix dominated bacterial, archaeal, protozoal and fungal communities, respectively in all samples. Libraries generated from camels reared at facility G2, where they were fed fresh clover, showed the highest alpha diversity. Principal co-ordinate analysis and linear discriminate analysis showed clusters associated with facility/feed and the relative abundance of microbes varied between liquid and solid fractions. This provides preliminary evidence that bacteria dominate the microbial communities of the camel rumen and these communities differ significantly between populations of domesticated camels.
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Affiliation(s)
- Alaa Emara Rabee
- Animal and Poultry Nutrition Department, Desert Research Center, Cairo, Cairo, Egypt
| | - Robert Forster
- Lethbridge Research and Development Centre, Agriculture and Agrifood Canada, Lethbridge, AB, Canada
| | - Chijioke Elekwachi
- Lethbridge Research and Development Centre, Agriculture and Agrifood Canada, Lethbridge, AB, Canada
| | - Ebrahim Sabra
- Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Menoufia, Egypt
| | - Mebarek Lamara
- Institut de Recherche sur les Forêts, Université du Québec en Abitibi-Témiscamingue, Rouyn-Noranda, QC, Canada
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27
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Shen J, Li Z, Yu Z, Zhu W. Effects of dietary replacement of soybean meal with dried distillers grains with solubles on the microbiota occupying different ecological niches in the rumen of growing Hu lambs. J Anim Sci Biotechnol 2020; 11:93. [PMID: 32939263 PMCID: PMC7487462 DOI: 10.1186/s40104-020-00499-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 07/16/2020] [Indexed: 11/11/2022] Open
Abstract
Background Diet has a profound impact on the rumen microbiota, and the impact can vary among the different rumen ecological niches (REN). This study investigated the effects of dietary replacement of soybean meal (SBM) with dried distillers grains with solubles (DDGS) on the rumen microbiota occupying different REN of growing Hu lambs. After a 9-week feeding trial, 6 lambs from each dietary treatment (SBM vs. DDGS-based diets) were slaughtered for sample collection. The microbiota of the rumen solid, liquid, and epithelium fractions was examined using amplicon sequencing analysis of bacterial 16S rRNA gene, functional prediction, and qPCR. Results No interaction of dietary protein source (PS) and REN were detected for virtually all the measurements made in this study. The DDGS substitution resulted in very limited influence on bacterial community structure. However, the metabolic pathways predicted from 16S rRNA gene sequences varied greatly between SBM- and DDGS-based diets. The populations of rumen total bacteria, fungi, sulfate-reducing bacteria (SRB), and methanogens were not influenced by DDGS substitution, but the population of protozoa was reduced. The bacterial communities in rumen solid (RS) and liquid (RL) were similar in taxonomic composition but were different in relative abundance of some taxa. In contrast, the bacterial composition and relative abundance of rumen epithelium (RE) were greatly distinct from those of the RS and the RL. In alignment with the bacterial relative abundance, the metabolic pathways predicted from 16S rRNA genes also varied greatly among the different REN. The populations of total bacteria, protozoa, and methanogens attached to the RE were smaller than those in the RS and RL, and the fungal population on the rumen epithelium was smaller than that in the RS but similar to that in the RL. On the contrary, the SRB population on the RE was greater than that in the RS and RL. Conclusions Substitution of SBM with DDGS had greater impact to the protozoa than to the other microbes, and the microbial community structure and functions at different REN are distinct and niche-adapted.
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Affiliation(s)
- Junshi Shen
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China.,National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095 China
| | - Zhipeng Li
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China.,Department of Special Animal Nutrition and Feed Science, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112 China
| | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State University, Columbus, OH 43210 USA
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China.,National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095 China
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28
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Yang C, Tsedan G, Liu Y, Hou F. Shrub coverage alters the rumen bacterial community of yaks ( Bos grunniens) grazing in alpine meadows. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2020; 62:504-520. [PMID: 32803183 PMCID: PMC7416157 DOI: 10.5187/jast.2020.62.4.504] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 05/20/2020] [Accepted: 05/26/2020] [Indexed: 12/17/2022]
Abstract
Proliferation of shrubs at the expense of native forage in pastures has been
associated with large changes in dry-matter intake and dietary components for
grazing ruminants. These changes can also affect the animals’ physiology
and metabolism. However, little information is available concerning the effect
of pastoral-shrub grazing on the rumen bacterial community. To explore rumen
bacteria composition in grazing yaks and the response of rumen bacteria to
increasing shrub coverage in alpine meadows, 48 yak steers were randomly
assigned to four pastures with shrub coverage of 0%, 5.4%, 11.3%, and 20.1%
(referred as control, low, middle, and high, respectively), and ruminal fluid
was collected from four yaks from each pasture group after 85 days. Rumen
fermentation products were measured and microbiota composition determined using
Ion S5TM XL sequencing of the 16S rRNA gene. Principal coordinates
analysis (PCoA) and similarity analysis indicated that the degree of shrub
coverage correlated with altered rumen bacterial composition of yaks grazing in
alpine shrub meadows. At the phyla level, the relative abundance of
Firmicutes in rumen increased with increasing shrub
coverage, whereas the proportions of Bacteroidetes,
Cyanobacteria and Verrucomicrobia
decreased. Yaks grazing in the high shrub-coverage pasture had decreased species
of the genus Prevotellaceae UCG-001,
Lachnospiraceae XPB1014 group,
Lachnospiraceae AC2044 group,
Lachnospiraceae FCS020 group and
Fretibacterium, but increased species of
Christensenellaceae R-7 group,
Ruminococcaceae NK4A214 group,
Ruminococcus 1, Ruminococcaceae UCG-002,
Ruminococcaceae UCG-005 and
Lachnospiraceae UCG-008. These variations can enhance the
animals’ utilization efficiencies of cellulose and hemicellulose from
native forage. Meanwhile, yaks grazed in the high shrub-coverage pasture had
increased concentrations of ammonia nitrogen (NH3-N) and
branched-chain volatile fatty acids (isobutyrate and isovalerate) in rumen
compared with yaks grazing in the pasture without shrubs. These results indicate
that yaks grazing in a high shrub-coverage pasture may have improved dietary
energy utilization and enhanced resistance to cold stress during the winter. Our
findings provide evidence for the influence of shrub coverage on the rumen
bacterial community of yaks grazing in alpine meadows as well as insights into
the sustainable production of grazing yaks on lands with increasing shrub
coverage on the Qinghai-Tibet Plateau.
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Affiliation(s)
- Chuntao Yang
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Guru Tsedan
- Animal Husbandry Science and Technology Demonstration Park of Maqu County, Gannan 743000, China
| | - Yang Liu
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Fujiang Hou
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
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29
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Li Z, Mu C, Xu Y, Shen J, Zhu W. Changes in the Solid-, Liquid-, and Epithelium-Associated Bacterial Communities in the Rumen of Hu Lambs in Response to Dietary Urea Supplementation. Front Microbiol 2020; 11:244. [PMID: 32153533 PMCID: PMC7046558 DOI: 10.3389/fmicb.2020.00244] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 01/31/2020] [Indexed: 01/10/2023] Open
Abstract
The rumen bacteria in the solid, liquid, and epithelial fractions are distinct and play important roles in the degradation of urea nitrogen. However, the effects of urea on rumen bacteria from the three fractions remain unclear. In this study, 42 Hu lambs were fed a total mixed ration based on concentrate and roughage (55:45, dry matter basis) and randomly assigned to one of three experimental diets: a basal diet with no urea (UC, 0 g/kg), a basal diet supplemented with low urea levels (LU, 10 g/kg DM), and a basal diet supplemented with high urea levels (HU, 30 g/kg DM). After an 11-week feeding trial, six animals from each treatment were harvested. Rumen metabolites levels were measured, and bacteria of the rumen solid, liquid, and epithelial fractions were examined based on 16S rRNA gene sequencing. Under urea supplementation, the concentrations of ammonia and butyrate in the rumen increased, whereas the concentration of propionate decreased. The population of total protozoa was the highest in the LU treatment. Prevotella 1 was the most abundant genus in all samples. The unclassified Muribaculaceae, bacteria within the families Lachnospiraceae and Ruminococcaceae, and Christensenellaceae R7 were abundant in the solid and liquid fractions. Butyrivibrio 2 and Treponema 2 were the abundant bacteria in the epithelial fraction. Principal coordinate analysis showed separation of the solid, liquid and epithelial bacteria regardless of diet, suggesting that rumen fraction had stronger influences on the bacterial community than did urea supplementation. However, the influences on the bacterial community differed among the three fractions. In the solid and liquid fractions, Succinivibrionaceae UCG 001 and Prevotella 1 showed decreased abundance with dietary urea supplementation, whereas the abundance of Oscillospira spp. was increased. Howardella spp. and Desulfobulbus spp. were higher in the epithelial fraction of the UC and LU treatments relative to HU treatment. Comparisons of predictive function in the rumen solid, liquid, and epithelial fractions among the three treatments also revealed differences. Collectively, these results reveal the change of the rumen bacterial community to dietary urea supplementation.
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Affiliation(s)
- Zhipeng Li
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.,Department of Special Animal Nutrition and Feed Science, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Chunlong Mu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.,National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Yixuan Xu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Junshi Shen
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.,National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.,National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
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Ren Q, Si H, Yan X, Liu C, Ding L, Long R, Li Z, Qiu Q. Bacterial communities in the solid, liquid, dorsal, and ventral epithelium fractions of yak (Bos grunniens) rumen. Microbiologyopen 2019; 9:e963. [PMID: 31701637 PMCID: PMC7002109 DOI: 10.1002/mbo3.963] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/18/2019] [Accepted: 10/18/2019] [Indexed: 12/03/2022] Open
Abstract
Yak (Bos grunniens) is an important and dominant livestock species in the challenging environment of the Qinghai–Tibetan Plateau. Rumen microbiota of the solid, liquid, and epithelium fractions play key roles in nutrient metabolism and contribute to host adaptation in ruminants. However, there is a little knowledge of the microbiota in these rumen fractions of yak. Therefore, we collected samples of solid, liquid, dorsal, and ventral epithelium fractions from five female yaks, then amplified bacterial 16S rRNA gene V4 regions and sequenced them using an Illumina MiSeq platform. Principal coordinates analysis detected significant differences in bacterial communities between the liquid, solid, and epithelium fractions, and between dorsal and ventral epithelium fractions. Rikenellaceae RC9, the families Lachnospiraceae and Ruminococcaceae, and Fibrobacter spp. were the abundant and enriched bacteria in solid fraction, while the genera Prevotella and Prevotellaceae UCG 003 were higher in the liquid fraction. Campylobacter spp., Comamonas spp., Desulfovibrio spp., and Solobacterium spp. were significantly higher in dorsal epithelium, while Howardella spp., Prevotellaceae UCG 001, Ruminococcaceae UCG 005, and Treponema 2 were enriched in the ventral epithelium. Comparison of predictive functional profiles among the solid, liquid, and dorsal, and ventral epithelium fractions also revealed significant differences. Microbiota in the ventral fraction of yak rumen also significantly differ from reported microbiota of cattle. In conclusion, our results improve our knowledge of the taxonomic composition and roles of yak rumen microbiota.
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Affiliation(s)
- Qingmiao Ren
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Huazhe Si
- Department of Special Animal Nutrition and Feed Science, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Xiaoting Yan
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Chang Liu
- Research Center for Ecology and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Luming Ding
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Ruijun Long
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Zhipeng Li
- Department of Special Animal Nutrition and Feed Science, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Qiang Qiu
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, China
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