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Wang S, Tang W, Jiang T, Wang R, Zhang R, Ou J, Wang Q, Cheng X, Ren C, Chen J, Huang Y, Zhang Z. Effect of Dietary Concentrate-to-Forage Ratios During the Cold Season on Slaughter Performance, Meat Quality, Rumen Fermentation and Gut Microbiota of Tibetan Sheep. Animals (Basel) 2024; 14:3305. [PMID: 39595356 PMCID: PMC11591461 DOI: 10.3390/ani14223305] [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: 10/03/2024] [Revised: 11/13/2024] [Accepted: 11/14/2024] [Indexed: 11/28/2024] Open
Abstract
This study aimed to investigate the effects of different dietary concentrate-to-forage ratios on slaughter performance, meat quality, rumen fermentation, rumen microbiota and fecal microbiota in Tibetan sheep. A total of sixty male Tibetan sheep were equally allocated into three dietary groups based on concentrate-to-forage ratios, i.e., 30:70 (C30), 50:50 (C50), and 70:30 (C70). Compared with the C30 group, sheep fed the C70 diet resulted in a higher (p < 0.05) slaughter live weight (SLW), hot carcass weight (HCW), dressing percentage (DP), eye muscle area, average daily gain (ADG), and ruminal total volatile fatty acids concentration and propionate molar proportion and lower (p < 0.05) shear force and cooking loss of meat, and ruminal acetate molar proportion and acetate:propionate ratio. Sheep in the C50 group exhibited a higher (p < 0.05) SLW, HCW, ADG, and ruminal propionate molar proportion and lower (p < 0.05) shear force and cooking loss of meat, and ruminal acetate molar proportion and acetate: propionate ratio compared with the C30 group. In rumen fluid, the relative abundance of Butyrivibrio was lower (p = 0.031) in the C30 group, and that of Ruminococcus was higher (p = 0.003) in the C70 group compared with the C50 group. In feces, genus Monoglobus and UCG_002 were the most abundant in the C30 group (p < 0.05), and the relative abundance of Prevotella was significantly higher in the C70 group than in other groups (p = 0.013). Correlation analysis revealed possible links between slaughter performance and meat quality and altered microbiota composition in the rumen and feces of Tibetan sheep. Overall, feeding a C70 diet resulted in superior carcass characteristics and meat quality in Tibetan sheep, thus laying a theoretical basis for the application of short-term remote feeding during the cold season.
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Affiliation(s)
- Shijia Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; (S.W.); (W.T.); (T.J.); (R.W.); (R.Z.); (J.O.); (Q.W.); (X.C.); (C.R.); (J.C.); (Y.H.)
| | - Wenhui Tang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; (S.W.); (W.T.); (T.J.); (R.W.); (R.Z.); (J.O.); (Q.W.); (X.C.); (C.R.); (J.C.); (Y.H.)
| | - Ting Jiang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; (S.W.); (W.T.); (T.J.); (R.W.); (R.Z.); (J.O.); (Q.W.); (X.C.); (C.R.); (J.C.); (Y.H.)
| | - Ru Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; (S.W.); (W.T.); (T.J.); (R.W.); (R.Z.); (J.O.); (Q.W.); (X.C.); (C.R.); (J.C.); (Y.H.)
| | - Ruoxi Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; (S.W.); (W.T.); (T.J.); (R.W.); (R.Z.); (J.O.); (Q.W.); (X.C.); (C.R.); (J.C.); (Y.H.)
| | - Jingyu Ou
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; (S.W.); (W.T.); (T.J.); (R.W.); (R.Z.); (J.O.); (Q.W.); (X.C.); (C.R.); (J.C.); (Y.H.)
| | - Qiangjun Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; (S.W.); (W.T.); (T.J.); (R.W.); (R.Z.); (J.O.); (Q.W.); (X.C.); (C.R.); (J.C.); (Y.H.)
| | - Xiao Cheng
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; (S.W.); (W.T.); (T.J.); (R.W.); (R.Z.); (J.O.); (Q.W.); (X.C.); (C.R.); (J.C.); (Y.H.)
| | - Chunhuan Ren
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; (S.W.); (W.T.); (T.J.); (R.W.); (R.Z.); (J.O.); (Q.W.); (X.C.); (C.R.); (J.C.); (Y.H.)
| | - Jiahong Chen
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; (S.W.); (W.T.); (T.J.); (R.W.); (R.Z.); (J.O.); (Q.W.); (X.C.); (C.R.); (J.C.); (Y.H.)
- Center of Agriculture Technology Cooperation and Promotion of Dingyuan County, Dingyuan 233200, China
| | - Yafeng Huang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; (S.W.); (W.T.); (T.J.); (R.W.); (R.Z.); (J.O.); (Q.W.); (X.C.); (C.R.); (J.C.); (Y.H.)
| | - Zijun Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; (S.W.); (W.T.); (T.J.); (R.W.); (R.Z.); (J.O.); (Q.W.); (X.C.); (C.R.); (J.C.); (Y.H.)
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Lu ML, Yuan GH, Rehemujiang H, Li CC, Hu LH, Duan PP, Zhang LD, Diao QY, Deng KD, Xu GS. Effects of spent substrate of oyster mushroom ( Pleurotus ostreatus) on ruminal fermentation, microbial community and growth performance in Hu sheep. Front Microbiol 2024; 15:1425218. [PMID: 39507332 PMCID: PMC11538048 DOI: 10.3389/fmicb.2024.1425218] [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: 04/30/2024] [Accepted: 10/11/2024] [Indexed: 11/08/2024] Open
Abstract
Introduction The study aimed to evaluate the effects of Pleurotus Spent Mushroom Substrate (P.SMS) on the rumen microbiota, encompassing bacteria and fungi, as well as their interactions in Hu sheep. Methods A total of forty-five 3-month-old Hu sheep were randomly assigned to five groups. Each group was fed diets in which whole-plant corn silage (WPCS) was substituted with P.SMS at varying levels: 0% (CON), 5% (PSMS5), 10% (PSMS10), 15% (PSMS15), or 20% (PSMS20). Results The results indicated that higher proportions of P.SMS during the experimental period might have a detrimental effect on feed utilization efficiency, kidney function, and blood oxygen-carrying capacity. Notably, moderate levels of P.SMS, specifically below 15%, were associated with improvements in rumen NH3-N levels and absorption capacity. The results indicated that (1) PSMS20 exhibited a significantly higher feed-to-gain ratio compared to CON (P < 0.05); (2) PSMS15 showed a significantly higher NH3-N content than CON, PSMS5, and PSMS20. Additionally, PSMS10 and PSMS20 had elevated concentrations of NH3-N compared to CON and PSMS5 (P < 0.05); (3) The length and width of rumen papillae were significantly greater in PSMS20 compared to CON and PSMS5 (P < 0.05); (4) Creatinine levels were significantly higher in PSMS20 than in CON, PSMS5, and PSMS10 (P < 0.05); (5) By the conclusion of the experiment, hemoglobin concentration in PSMS20 showed a significant increase compared to CON (P < 0.05). Furthermore, the addition of P.SMS influenced microorganisms at both the phylum and genus levels: (1) At the phylum level, the prevalence of Patescibacteria was significantly lower in PSMS20 compared to the other groups; (2) PSMS15 exhibited significantly higher relative abundances of Basidiomycota compared to CON and PSMS10, while PSMS20 also demonstrated significantly higher relative abundances compared to CON (P < 0.05); (3) At the genus level, the prevalence of Candidatus_Saccharimonas in PSMS20 was significantly lower than in PSMS5, PSMS10, and PSMS15. Conversely, the prevalence of Phanerochaete in PSMS15 was notably higher than in CON and PSMS10, and it was also significantly elevated in PSMS20 compared to CON (P < 0.05); (4) Correlation analysis indicated no significant correlation between changes in the structure of bacterial and fungal communities. Discussion Considering these findings, a high percentage of P.SMS negatively impacted feed utilization efficiency, blood oxygen carrying capacity, and kidney function, while a moderate percentage of P.SMS promotes rumen absorption capacity, indicating that feeding 10% P.SMS is optimal.
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Affiliation(s)
- Mu-Long Lu
- College of Animal Science and Technology, Tarim University, Alar, China
| | - Guo-Hong Yuan
- College of Animal Science and Technology, Tarim University, Alar, China
| | - Halidai Rehemujiang
- College of Animal Science and Technology, Tarim University, Alar, China
- Key Laboratory of Livestock and Forage Resources Utilization around Tarim, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, China
| | - Chang-Chang Li
- College of Animal Science and Technology, Tarim University, Alar, China
| | - Li-Hong Hu
- College of Animal Science and Technology, Tarim University, Alar, China
| | - Ping-Ping Duan
- College of Animal Science and Technology, Tarim University, Alar, China
| | - Li-Dong Zhang
- College of Animal Science and Technology, Tarim University, Alar, China
| | - Qi-Yu Diao
- Institute of Feed Research/Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kai-Dong Deng
- College of Animal Science and Food Engineering, Jinling Institute of Technology, Nanjing, Jiangsu, China
| | - Gui-Shan Xu
- College of Animal Science and Technology, Tarim University, Alar, China
- Key Laboratory of Livestock and Forage Resources Utilization around Tarim, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, China
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He H, Fang C, Liu L, Li M, Liu W. Environmental Driving of Adaptation Mechanism on Rumen Microorganisms of Sheep Based on Metagenomics and Metabolomics Data Analysis. Int J Mol Sci 2024; 25:10957. [PMID: 39456741 PMCID: PMC11508146 DOI: 10.3390/ijms252010957] [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: 08/22/2024] [Revised: 10/04/2024] [Accepted: 10/05/2024] [Indexed: 10/28/2024] Open
Abstract
Natural or artificial selection causes animals to adapt to their environment. The adaptive changes generated by the rumen population and metabolism form the basis of ruminant evolution. In particular, the adaptive drive for environmental adaptation reflects the high-quality traits of sheep that have migrated from other places or have been distant from their origins for a long time. The Hu sheep is the most representative sheep breed in the humid and low-altitude environments (Tai Lake region) in East Asia and has been widely introduced into the arid and high-altitude environments (Tibetan Plateau and Hotan region), resulting in environmental adaptive changes in the Hu sheep. In this study, a joint analysis of the rumen microbial metagenome and metabolome was conducted on Hu sheep from different regions (area of origin and area of introduction) with the objective of investigating the quality traits of Hu sheep and identifying microorganisms that influence the adaptive drive of ruminants. The results demonstrated that the growth performance of Hu sheep was altered due to changes in rumen tissue and metabolism following their introduction to the arid area at relatively high altitude. Metagenomic and metabolomic analyses (five ramsper area) revealed that 3580 different microorganisms and 732 different metabolites were identified in the rumen fluid of arid sheep. Among these, the representative upregulated metabolites were 4,6-isocanedione, methanesulfonic acid and N2-succinyl-L-arginine, while the dominant microorganism was Prevotella ruminicola. The downregulated metabolites were identified as campesterol, teprenone and dihydroclavaminic acid, while the disadvantaged microorganisms were Dialister_succinatiphilus, Prevotella_sp._AGR2160, Prevotella_multisaccharivorax and Selenomonas_bovis. The results of the Pearson analysis indicated that the rumen microbiota and metabolite content of sheep were significantly altered and highly correlated following their relocation from a humid lowland to an arid upland. In particular, the observed changes in rumen microorganisms led to an acceleration of body metabolism, rendering sheep highly adaptable to environmental stress. Prevotella_ruminicola was identified as playing an important role in this process. These findings provide insights into the environmental adaptation mechanisms of sheep.
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Affiliation(s)
- Haiying He
- Department of Animal Science and Biotechnology, Xinjiang Agricultural University, Urumqi 830052, China; (H.H.); (L.L.); (M.L.)
| | - Chao Fang
- Faculte de Medecine Veterinaire, Universite de Liege, Quartier Vallee 2, Avenue de Cureghem 6 (B43), 4000 Liege, Belgium;
| | - Lingling Liu
- Department of Animal Science and Biotechnology, Xinjiang Agricultural University, Urumqi 830052, China; (H.H.); (L.L.); (M.L.)
| | - Mingming Li
- Department of Animal Science and Biotechnology, Xinjiang Agricultural University, Urumqi 830052, China; (H.H.); (L.L.); (M.L.)
| | - Wujun Liu
- Department of Animal Science and Biotechnology, Xinjiang Agricultural University, Urumqi 830052, China; (H.H.); (L.L.); (M.L.)
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Zhao X, Zhang Y, Rahman A, Chen M, Li N, Wu T, Qi Y, Zheng N, Zhao S, Wang J. Rumen microbiota succession throughout the perinatal period and its association with postpartum production traits in dairy cows: A review. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2024; 18:17-26. [PMID: 39022774 PMCID: PMC11253274 DOI: 10.1016/j.aninu.2024.04.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 02/18/2024] [Accepted: 04/24/2024] [Indexed: 07/20/2024]
Abstract
The transition period for dairy cows usually refers to the 3 weeks pre-calving to the 3 weeks post-calving. During this period, dairy cows undergo metabolic and physiological adaptations because of their susceptibility to metabolic and infectious diseases. Poor feeding management under these circumstances may adversely affect the health and subsequent production performance of the cows. Owing to long-term adaptation and evolution, the rumen has become a unique ecosystem inhabited by a complex microbial community closely associated with its natural host. Dietary components are metabolized by the rumen microbiota, and volatile fatty acids and microbial protein products can be used as precursor substances for synthesizing meat and milk components. The successful transition of perinatal dairy cows includes changes in diet, physiology, and the rumen microbiota. Rumen microbial profiles have been confirmed to be heritable and repairable; however, adverse circumstances affect rumen microbial composition, host digestion and metabolism, as well as postpartum production traits of dairy cows for a certain period. Preliminary evidence indicates a close relationship between the rumen microbiota and animal performance. Therefore, changes in rumen microbes during the transition period and the intrinsic links between the microbiota and host postpartum phenotypic traits need to be better understood to optimize production performance in ruminants.
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Affiliation(s)
- Xiaowei Zhao
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Anhui Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Xinjiang Agricultural University, Urumqi 830052, China
| | - Yangdong Zhang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ashikur Rahman
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Meiqing Chen
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ning Li
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tao Wu
- Anhui Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Yunxia Qi
- Anhui Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Nan Zheng
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Shengguo Zhao
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jiaqi Wang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Duan P, Rehemujiang H, Zhang L, Lu M, Li C, Hu L, Wang Y, Diao Q, Xu G. Lycium barbarum (Wolfberry) Branches and Leaves Enhance the Growth Performance and Improve the Rumen Microbiota in Hu Sheep. Animals (Basel) 2024; 14:1610. [PMID: 38891656 PMCID: PMC11171408 DOI: 10.3390/ani14111610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/24/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
The Lycium barbarum branches and leaves (LBL) are known to contain a range of active substances that have positive effects on animal immunity and antioxidation. This study aimed to examine how LBL impacts the growth and slaughter performance as well as rumen fermentation and microbiota in Hu sheep. A total of 50 male Hu sheep of indigenous origin, aged 3 months, were randomly divided into 5 groups of 10 sheep each. The groups were given different levels of LBL supplementation (0%, 3%, 6%, 9%, and 12%) to evaluate growth performance and nutrient apparent digestibility. Rumen fluid samples were collected for analysis of the fermentation parameters and rumen chyme was examined to study the rumen microbiota. The slaughter performance, meat quality, and organ index were evaluated at the conclusion of the experiment. The results showed that the final body weight and average daily gain of the LBL1 group were significantly higher than those of the CON group, LBL3 group, and LBL4 group (p < 0.05). The average dry matter intake of the LBL4 group was significantly lower than that of other experimental groups (p < 0.05). The apparent digestibility of CP in the LBL1 and LBL2 groups was higher than that in other experimental groups (p < 0.05). At the same time, the eye muscle area and grade-rule (GR) value of Hu sheep in the LBL1 group significantly increased and the quality of Hu sheep meat improved (p < 0.05). There was no significant difference in organ weight and organ index between the experimental groups (p > 0.05). The pH of the rumen fluid in the LBL1 group was significantly lower than that in the CON group (p < 0.05). There was no significant difference in the NH3-N content between the experimental groups (p > 0.05). The propionate and valerate in the rumen fluid of Hu sheep in the LBL2 group were significantly higher than those in other experimental groups (p < 0.05). In addition, this had no significant effect on the structure and abundance of the rumen microbiota (p > 0.05). LBL is a promising functional feed. Adding an appropriate amount of LBL to the diet can improve the feed efficiency, growth performance, and meat quality of Hu sheep but has no adverse effects on the rumen. In this experiment, the appropriate supplemental level of LBL in the diet was 3%.
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Affiliation(s)
- Pingping Duan
- College of Animal Science and Technology, Tarim University, Alar 843300, China; (P.D.); (H.R.); (L.Z.); (M.L.); (C.L.); (L.H.)
| | - Halidai Rehemujiang
- College of Animal Science and Technology, Tarim University, Alar 843300, China; (P.D.); (H.R.); (L.Z.); (M.L.); (C.L.); (L.H.)
| | - Lidong Zhang
- College of Animal Science and Technology, Tarim University, Alar 843300, China; (P.D.); (H.R.); (L.Z.); (M.L.); (C.L.); (L.H.)
| | - Mulong Lu
- College of Animal Science and Technology, Tarim University, Alar 843300, China; (P.D.); (H.R.); (L.Z.); (M.L.); (C.L.); (L.H.)
| | - Changchang Li
- College of Animal Science and Technology, Tarim University, Alar 843300, China; (P.D.); (H.R.); (L.Z.); (M.L.); (C.L.); (L.H.)
| | - Lihong Hu
- College of Animal Science and Technology, Tarim University, Alar 843300, China; (P.D.); (H.R.); (L.Z.); (M.L.); (C.L.); (L.H.)
| | - Youli Wang
- College of Animal Science and Veterinary, Southwest Minzu University, Chengdu 610041, China;
| | - Qiyu Diao
- Institute of Feed Research, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Beijing 100080, China;
| | - Guishan Xu
- College of Animal Science and Technology, Tarim University, Alar 843300, China; (P.D.); (H.R.); (L.Z.); (M.L.); (C.L.); (L.H.)
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Tarim University, Alar 843300, China
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Kang R, Lee H, Seon H, Park C, Song J, Park JK, Kim YK, Kim M, Park T. Effects of diets for three growing stages by rumen inocula donors on in vitro rumen fermentation and microbiome. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2024; 66:523-542. [PMID: 38975572 PMCID: PMC11222118 DOI: 10.5187/jast.2023.e109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/25/2023] [Accepted: 10/10/2023] [Indexed: 07/09/2024]
Abstract
Hanwoo and Jeju Black cattle (Jeju Black) are native breeds of Korean cattle. Jeju Black cattle are recognized as natural monuments and are known to exhibit slower growth rates compared to Hanwoo. While several studies have analyzed the genetic characteristics of these cattle, there has been limited research on the differences in their microbiome. In this study, rumen fluid was obtained from three Hanwoo steers and three Jeju Black steers, and three different diets (total mixed rations [TMRs] for growing, early fattening, and late fattening periods) were used as substrates for in vitro fermentation. The in vitro incubation was conducted for 3 h and 24 h following a 2 × 3 factorial arrangement. After both incubation periods, fermentation characteristics were analyzed, and ruminal microbiome analysis was performed using 16S rRNA gene sequencing, employing both QIIME2 and PICRUSt2. The results revealed significant differences in the ruminal microbiota due to the inoculum effect. At the phylum level, Patescibacteria and Synergistota were found to be enriched in the Jeju Black inoculum-treated group. Additionally, using different inocula also affected the relative abundance of major taxa, including Ruminococcus, Pseudoramibacter, Ruminococcaceae CAG-352, and the [Eubacterium] ruminantium group. These microbial differences induced by the inoculum may have originated from varying levels of domestication between the two subspecies of donor animals, which mainly influenced the fermentation and microbiome features in the early incubation stages, although this was only partially offset afterward. Furthermore, predicted commission numbers of microbial enzymes, some of which are involved in the biosynthesis of secondary metabolites, fatty acids, and alpha amylase, differed based on the inoculum effect. However, these differences may account for only a small proportion of the overall metabolic pathway. Conversely, diets were found to affect protein biosynthesis and its related metabolism, which showed differential abundance in the growing diet and were potentially linked to the growth-promoting effects in beef cattle during the growing period. In conclusion, this study demonstrated that using different inocula significantly affected in vitro fermentation characteristics and microbiome features, mainly in the early stages of incubation, with some effects persisting up to 24 h of incubation.
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Affiliation(s)
- Ryukseok Kang
- Department of Animal Science and
Technology, Chung-Ang University, Anseong 17546, Korea
| | - Huseong Lee
- Division of Animal Science, Chonnam
National University, Gwangju 61186, Korea
- Graduate School of Agricultural Science,
Tohoku University, Sendai 980-0845, Japan
| | - Hyeonsu Seon
- Division of Animal Science, Chonnam
National University, Gwangju 61186, Korea
| | - Cheolju Park
- Division of Animal Science, Chonnam
National University, Gwangju 61186, Korea
| | | | | | | | - Minseok Kim
- Division of Animal Science, Chonnam
National University, Gwangju 61186, Korea
| | - Tansol Park
- Department of Animal Science and
Technology, Chung-Ang University, Anseong 17546, Korea
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Wu Y, Gao N, Sun C, Feng T, Liu Q, Chen WH. A compendium of ruminant gastrointestinal phage genomes revealed a higher proportion of lytic phages than in any other environments. MICROBIOME 2024; 12:69. [PMID: 38576042 PMCID: PMC10993611 DOI: 10.1186/s40168-024-01784-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 02/29/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND Ruminants are important livestock animals that have a unique digestive system comprising multiple stomach compartments. Despite significant progress in the study of microbiome in the gastrointestinal tract (GIT) sites of ruminants, we still lack an understanding of the viral community of ruminants. Here, we surveyed its viral ecology using 2333 samples from 10 sites along the GIT of 8 ruminant species. RESULTS We present the Unified Ruminant Phage Catalogue (URPC), a comprehensive survey of phages in the GITs of ruminants including 64,922 non-redundant phage genomes. We characterized the distributions of the phage genomes in different ruminants and GIT sites and found that most phages were organism-specific. We revealed that ~ 60% of the ruminant phages were lytic, which was the highest as compared with those in all other environments and certainly will facilitate their applications in microbial interventions. To further facilitate the future applications of the phages, we also constructed a comprehensive virus-bacteria/archaea interaction network and identified dozens of phages that may have lytic effects on methanogenic archaea. CONCLUSIONS The URPC dataset represents a useful resource for future microbial interventions to improve ruminant production and ecological environmental qualities. Phages have great potential for controlling pathogenic bacterial/archaeal species and reducing methane emissions. Our findings provide insights into the virome ecology research of the ruminant GIT and offer a starting point for future research on phage therapy in ruminants. Video Abstract.
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Affiliation(s)
- Yingjian Wu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Na Gao
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Chuqing Sun
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Tong Feng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China.
| | - Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
- Institution of Medical Artificial Intelligence, Binzhou Medical University, Yantai, 264003, China.
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Law SR, Mathes F, Paten AM, Alexandre PA, Regmi R, Reid C, Safarchi A, Shaktivesh S, Wang Y, Wilson A, Rice SA, Gupta VVSR. Life at the borderlands: microbiomes of interfaces critical to One Health. FEMS Microbiol Rev 2024; 48:fuae008. [PMID: 38425054 PMCID: PMC10977922 DOI: 10.1093/femsre/fuae008] [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: 07/26/2023] [Revised: 02/12/2024] [Accepted: 02/27/2024] [Indexed: 03/02/2024] Open
Abstract
Microbiomes are foundational components of the environment that provide essential services relating to food security, carbon sequestration, human health, and the overall well-being of ecosystems. Microbiota exert their effects primarily through complex interactions at interfaces with their plant, animal, and human hosts, as well as within the soil environment. This review aims to explore the ecological, evolutionary, and molecular processes governing the establishment and function of microbiome-host relationships, specifically at interfaces critical to One Health-a transdisciplinary framework that recognizes that the health outcomes of people, animals, plants, and the environment are tightly interconnected. Within the context of One Health, the core principles underpinning microbiome assembly will be discussed in detail, including biofilm formation, microbial recruitment strategies, mechanisms of microbial attachment, community succession, and the effect these processes have on host function and health. Finally, this review will catalogue recent advances in microbiology and microbial ecology methods that can be used to profile microbial interfaces, with particular attention to multi-omic, advanced imaging, and modelling approaches. These technologies are essential for delineating the general and specific principles governing microbiome assembly and functions, mapping microbial interconnectivity across varying spatial and temporal scales, and for the establishment of predictive frameworks that will guide the development of targeted microbiome-interventions to deliver One Health outcomes.
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Affiliation(s)
- Simon R Law
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
| | - Falko Mathes
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Environment, Floreat, WA 6014, Australia
| | - Amy M Paten
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Environment, Canberra, ACT 2601, Australia
| | - Pamela A Alexandre
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, St Lucia, Qld 4072, Australia
| | - Roshan Regmi
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, Urrbrae, SA 5064, Australia
| | - Cameron Reid
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Environment, Urrbrae, SA 5064, Australia
| | - Azadeh Safarchi
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Health and Biosecurity, Westmead, NSW 2145, Australia
| | - Shaktivesh Shaktivesh
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Data 61, Clayton, Vic 3168, Australia
| | - Yanan Wang
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Health and Biosecurity, Adelaide SA 5000, Australia
| | - Annaleise Wilson
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Health and Biosecurity, Geelong, Vic 3220, Australia
| | - Scott A Rice
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture, and Food, Westmead, NSW 2145, Australia
| | - Vadakattu V S R Gupta
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, Urrbrae, SA 5064, Australia
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Dhakal R, Neves ALA, Sapkota R, Khanal P, Ellegaard-Jensen L, Winding A, Hansen HH. Temporal dynamics of volatile fatty acids profile, methane production, and prokaryotic community in an in vitro rumen fermentation system fed with maize silage. Front Microbiol 2024; 15:1271599. [PMID: 38444805 PMCID: PMC10912478 DOI: 10.3389/fmicb.2024.1271599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 02/01/2024] [Indexed: 03/07/2024] Open
Abstract
Anaerobic in vitro fermentation is widely used to simulate rumen kinetics and study the microbiome and metabolite profiling in a controlled lab environment. However, a better understanding of the interplay between the temporal dynamics of fermentation kinetics, metabolic profiles, and microbial composition in in vitro rumen fermentation batch systems is required. To fill that knowledge gap, we conducted three in vitro rumen fermentations with maize silage as the substrate, monitoring total gas production (TGP), dry matter degradability (dDM), and methane (CH4) concentration at 6, 12, 24, 36, and 48 h in each fermentation. At each time point, we collected rumen fluid samples for microbiome analysis and volatile fatty acid (VFA) analysis. Amplicon sequencing of 16S rRNA genes (V4 region) was used to profile the prokaryotic community structure in the rumen during the fermentation process. As the fermentation time increased, dDM, TGP, VFA concentrations, CH4 concentration, and yield (mL CH4 per g DM at standard temperature and pressure (STP)) significantly increased. For the dependent variables, CH4 concentration and yield, as well as the independent variables TGP and dDM, polynomial equations were fitted. These equations explained over 85% of the data variability (R2 > 0.85) and suggest that TGP and dDM can be used as predictors to estimate CH4 production in rumen fermentation systems. Microbiome analysis revealed a dominance of Bacteroidota, Cyanobacteria, Desulfobacterota, Euryarchaeota, Fibrobacterota, Firmicutes, Patescibacteria, Proteobacteria, Spirochaetota, and Verrucomicrobiota. Significant temporal variations in Bacteroidota, Campylobacterota, Firmicutes, Proteobacteria, and Spirochaetota were detected. Estimates of alpha diversity based on species richness and the Shannon index showed no variation between fermentation time points. This study demonstrated that the in vitro fermentation characteristics of a given feed type (e.g., maize silage) can be predicted from a few parameters (CH4 concentration and yield, tVFA, acetic acid, and propionic acid) without running the actual in vitro trial if the rumen fluid is collected from similar donor cows. Although the dynamics of the rumen prokaryotes changed remarkably over time and in accordance with the fermentation kinetics, more time points between 0 and 24 h are required to provide more details about the microbial temporal dynamics at the onset of the fermentation.
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Affiliation(s)
- Rajan Dhakal
- Department of Veterinary and Animal Sciences, Production, Nutrition and Health, University of Copenhagen, Frederiksberg, Denmark
| | - André Luis Alves Neves
- Department of Veterinary and Animal Sciences, Production, Nutrition and Health, University of Copenhagen, Frederiksberg, Denmark
| | - Rumakanta Sapkota
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Prabhat Khanal
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | | | - Anne Winding
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Hanne Helene Hansen
- Department of Veterinary and Animal Sciences, Production, Nutrition and Health, University of Copenhagen, Frederiksberg, Denmark
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Aschalew ND, Zhang L, Wang Z, Xia Y, Yin G, Dong J, Zhen Y, Zhang X, Wang T, Sun Z, Qin G. Effects of yeast culture and oxalic acid supplementation on in vitro nutrient disappearance, rumen fermentation, and bacterial community composition. Front Vet Sci 2024; 10:1330841. [PMID: 38313769 PMCID: PMC10834634 DOI: 10.3389/fvets.2023.1330841] [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: 10/31/2023] [Accepted: 12/14/2023] [Indexed: 02/06/2024] Open
Abstract
Hemicellulose is an important polysaccharide in ruminant nutrition, but it has not been studied as thoroughly as cellulose. Further research is needed to explore supplements that can improve its digestibility and ruminal buffering effects. Our previous research demonstrated the efficacy of oxalic acid (OA) as an essential nutrient in yeast culture (YC) for improving rumen fermentation performance. Consequently, we conducted in vitro rumen digestion experiments to examine the effects of YC and OA on rumen fermentation and bacterial composition. Two diets containing different levels of hemicellulose were formulated: diet 1 with 10.3% and diet 2 with 17% hemicellulose. Three levels of YC (0.00, 0.625, and 1.25 g/kg) and three doses of OA (0.0, 0.4, and 0.8 g/kg, DM) were added into each diet with a 3 × 3 factorial design. A comprehensive assessment was conducted on a total of 18 experimental treatments at fermentation periods of 0, 6, 12, 24, and 48 h. In the first experiment (diet 1), the supplementation of YC, OA, and their interaction significantly increased in vitro DM disappearance (IVDMD) and NDF disappearance (IVNDFD; p < 0.001). In the second experiment (diet 2), the supplementation of OA and the interaction between YC and OA (p < 0.001) increased IVDMD and IVCPD, but had no significant effects on IVNDFD. The interactions of YC and OA significantly increased ammonia nitrogen (p < 0.001). The production of acetic acid, propionic acid, and total volatile fatty acids (TVFA), and pH levels were significantly higher in treatments supplemented with YC and OA (p < 0.001). YC and OA in both diets significantly altered the rumen bacterial community leading to increased Shannon and Simpson diversity indices (p < 0.001). In both diets, OA supplementation significantly increased the relative abundance of the phylum Bacteroidetes and Prevotella genus. The result also showed a positive correlation between the Prevotella and Selenomonas genera with IVDMD, IVNDFD, propionic acid, and TVFA production, suggesting that these dominant bacteria enhanced nutrient disappearance in the rumen. In conclusion, adding YC and OA resulted in modifications to the bacterial community's composition and diversity, and improved nutrient disappearance. These changes indicate improved rumen fermentation efficiency, which is promising for future in vivo studies.
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Affiliation(s)
- Natnael D Aschalew
- Key Laboratory of Animal Nutrition and Feed Science of Jilin Province, Key Laboratory of Animal Production Product Quality and Security Ministry of Education, JLAU-Borui Dairy Science and Technology R&D Center, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- College of Agriculture and Environmental Science, Dilla University, Dilla, Ethiopia
| | - Longyu Zhang
- Key Laboratory of Animal Nutrition and Feed Science of Jilin Province, Key Laboratory of Animal Production Product Quality and Security Ministry of Education, JLAU-Borui Dairy Science and Technology R&D Center, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Ziyuan Wang
- Key Laboratory of Animal Nutrition and Feed Science of Jilin Province, Key Laboratory of Animal Production Product Quality and Security Ministry of Education, JLAU-Borui Dairy Science and Technology R&D Center, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Yuanhong Xia
- Key Laboratory of Animal Nutrition and Feed Science of Jilin Province, Key Laboratory of Animal Production Product Quality and Security Ministry of Education, JLAU-Borui Dairy Science and Technology R&D Center, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Guopei Yin
- Key Laboratory of Animal Nutrition and Feed Science of Jilin Province, Key Laboratory of Animal Production Product Quality and Security Ministry of Education, JLAU-Borui Dairy Science and Technology R&D Center, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Jianan Dong
- Key Laboratory of Animal Nutrition and Feed Science of Jilin Province, Key Laboratory of Animal Production Product Quality and Security Ministry of Education, JLAU-Borui Dairy Science and Technology R&D Center, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Yuguo Zhen
- Key Laboratory of Animal Nutrition and Feed Science of Jilin Province, Key Laboratory of Animal Production Product Quality and Security Ministry of Education, JLAU-Borui Dairy Science and Technology R&D Center, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- Postdoctoral Scientific Research Workstation, Feed Engineering Technology Research Center of Jilin Province, Changchun Borui Science and Technology Co., Ltd., Changchun, China
| | - Xuefeng Zhang
- Key Laboratory of Animal Nutrition and Feed Science of Jilin Province, Key Laboratory of Animal Production Product Quality and Security Ministry of Education, JLAU-Borui Dairy Science and Technology R&D Center, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- Postdoctoral Scientific Research Workstation, Feed Engineering Technology Research Center of Jilin Province, Changchun Borui Science and Technology Co., Ltd., Changchun, China
| | - Tao Wang
- Key Laboratory of Animal Nutrition and Feed Science of Jilin Province, Key Laboratory of Animal Production Product Quality and Security Ministry of Education, JLAU-Borui Dairy Science and Technology R&D Center, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- Postdoctoral Scientific Research Workstation, Feed Engineering Technology Research Center of Jilin Province, Changchun Borui Science and Technology Co., Ltd., Changchun, China
| | - Zhe Sun
- Key Laboratory of Animal Nutrition and Feed Science of Jilin Province, Key Laboratory of Animal Production Product Quality and Security Ministry of Education, JLAU-Borui Dairy Science and Technology R&D Center, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- Postdoctoral Scientific Research Workstation, Feed Engineering Technology Research Center of Jilin Province, Changchun Borui Science and Technology Co., Ltd., Changchun, China
- College of Life Sciences, Engineering Research Center of Bioreactor and Pharmaceutical Development, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Guixin Qin
- Key Laboratory of Animal Nutrition and Feed Science of Jilin Province, Key Laboratory of Animal Production Product Quality and Security Ministry of Education, JLAU-Borui Dairy Science and Technology R&D Center, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- Postdoctoral Scientific Research Workstation, Feed Engineering Technology Research Center of Jilin Province, Changchun Borui Science and Technology Co., Ltd., Changchun, China
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Gu M, Liu H, Jiang X, Qiu S, Li K, Lu J, Zhang M, Qiu Y, Wang B, Ma Z, Gan Q. Analysis of Rumen Degradation Characteristics, Attached Microbial Community, and Cellulase Activity Changes of Garlic Skin and Artemisia argyi Stalk. Animals (Basel) 2024; 14:169. [PMID: 38200900 PMCID: PMC10778316 DOI: 10.3390/ani14010169] [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: 11/28/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
The purpose of this study was to study the chemical composition, rumen degradation characteristics, surface attached microbial community and cellulase activity of garlic skin (GS) and Artemisia argyi stalk (AS), in order to explain their feeding value. Four 14-month-old healthy Min Dong male goats with permanent rumen fistula were selected as experimental animals. The rumen degradation characteristics of GS and AS were determined by using the nylon bag method, and the bacterial composition, cellulase activity and their relationship on the surface of the two groups were analyzed with high-throughput sequencing of 16S rRNA gene. The results showed that in GS and AS, the effective degradation rate (ED) values of dry matter (DM) were 42.53% and 37.12%, the ED values of crude protein (CP) were 37.19% and 43.38%, the ED values of neutral detergent fiber (NDF) were 36.83% and 36.23%, and the ED values of acid detergent fiber (ADF) were 33.81% and 34.77%. During rumen degradation, the richness and evenness of bacteria attached to the AS surface were higher. At the phylum level, Bacteroidetes and Firmicutes were always the main rumen bacteria in the two groups. At the genus level, fiber-degrading bacteria such as Prevotella, Treponema, and Ruminococcus showed higher levels in GS (p < 0.05). Compared with GS, the activity of β-glucosidase (BG enzyme), endo-β-1,4-glucanase (C1 enzyme), exo-β-1,4-glucanase (Cx enzyme) and neutral xylanase (NEX enzyme) attached to AS surface showed a higher trend. Correlation analysis showed that the relative abundance of Succinivibrio and Rikenellaceae_RC9_gut_group was positively correlated with the rumen degradability of nutrients in GS, and the relative abundance of Christensenellaceae R-7_group, Succinivibrio and Ruminococcus was positively correlated with the rumen degradability of nutrients in AS. The conclusion of this study shows that AS has more potential to become ruminant roughage than GS. In addition, this study also revealed the relationship between cellulase activity and bacteria, which provided new information for us to better analyze the effects of GS and AS on the rumen of ruminants and provided an important theoretical basis for the development and utilization of agricultural by-products.
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Affiliation(s)
- Mingming Gu
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350000, China; (M.G.); (H.L.); (X.J.); (S.Q.); (J.L.); (M.Z.); (Y.Q.); (B.W.); (Z.M.)
| | - Haoyu Liu
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350000, China; (M.G.); (H.L.); (X.J.); (S.Q.); (J.L.); (M.Z.); (Y.Q.); (B.W.); (Z.M.)
| | - Xinghui Jiang
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350000, China; (M.G.); (H.L.); (X.J.); (S.Q.); (J.L.); (M.Z.); (Y.Q.); (B.W.); (Z.M.)
| | - Shuiling Qiu
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350000, China; (M.G.); (H.L.); (X.J.); (S.Q.); (J.L.); (M.Z.); (Y.Q.); (B.W.); (Z.M.)
| | - Keyao Li
- 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;
| | - Jianing Lu
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350000, China; (M.G.); (H.L.); (X.J.); (S.Q.); (J.L.); (M.Z.); (Y.Q.); (B.W.); (Z.M.)
| | - Mingrui Zhang
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350000, China; (M.G.); (H.L.); (X.J.); (S.Q.); (J.L.); (M.Z.); (Y.Q.); (B.W.); (Z.M.)
| | - Yujun Qiu
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350000, China; (M.G.); (H.L.); (X.J.); (S.Q.); (J.L.); (M.Z.); (Y.Q.); (B.W.); (Z.M.)
| | - Benzhi Wang
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350000, China; (M.G.); (H.L.); (X.J.); (S.Q.); (J.L.); (M.Z.); (Y.Q.); (B.W.); (Z.M.)
| | - Zhiyi Ma
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350000, China; (M.G.); (H.L.); (X.J.); (S.Q.); (J.L.); (M.Z.); (Y.Q.); (B.W.); (Z.M.)
| | - Qianfu Gan
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350000, China; (M.G.); (H.L.); (X.J.); (S.Q.); (J.L.); (M.Z.); (Y.Q.); (B.W.); (Z.M.)
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12
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Pinnell LJ, Young JD, Thompson TW, Wolfe CA, Bryant TC, Nair MN, Richeson JT, Morley PS. Establishing the link between microbial communities in bovine liver abscesses and the gastrointestinal tract. Anim Microbiome 2023; 5:58. [PMID: 37986094 PMCID: PMC10662489 DOI: 10.1186/s42523-023-00278-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 10/27/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Liver abscesses (LAs) are one of the most common and important problems faced by the beef industry. The most efficacious method for the prevention of LAs in North America is through dietary inclusion of low doses of antimicrobial drugs such as tylosin, but the mechanisms by which this treatment prevents LAs are not fully understood. LAs are believed to result from mucosal barrier dysfunction in the gastrointestinal tract (GIT) allowing bacterial translocation to the liver via the portal vein, yet differences in the GIT microbiome of cattle with and without LAs have not been explored. Here, we characterized microbial communities from LAs, rumen, ileum, and colon from the same cattle for the first time. RESULTS Results demonstrate that tylosin supplementation was associated with differences in microbial community structure in the rumen and small intestine, largely because of differences in the predominance of Clostridia. Importantly, we show for the first time that microbial communities from multiple LAs in one animal's liver are highly similar, suggesting that abscesses found at different locations in the liver may originate from a localized source in the GIT (rather than disparate locations). A large portion of abscesses were dominated by microbial taxa that were most abundant in the hindgut. Further, we identified taxa throughout the GIT that were differentially abundant between animals with and without liver abscesses. Bifidobacterium spp.-a bacteria commonly associated with a healthy GIT in several species-were more abundant in the rumen and ileum of animals without LAs compared to those with LAs. CONCLUSIONS Together these results provide the first direct comparison of GIT and LA microbial communities within the same animal, add considerable evidence to the hypothesis that some LA microbial communities arise from the hindgut, and suggest that barrier dysfunction throughout the GIT may be the underlying cause of LA formation in cattle.
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Affiliation(s)
- Lee J Pinnell
- Veterinary Education, Research, and Outreach Program, Texas A&M University, Canyon, TX, 79015, USA
| | - J Daniel Young
- Department of Agricultural Sciences, West Texas A&M University, Canyon, TX, 79015, USA
| | - Tyler W Thompson
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Cory A Wolfe
- Veterinary Education, Research, and Outreach Program, Texas A&M University, Canyon, TX, 79015, USA
| | - Tony C Bryant
- Five Rivers Cattle Feeding, Johnstown, CO, 80534, USA
| | - Mahesh N Nair
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - John T Richeson
- Department of Agricultural Sciences, West Texas A&M University, Canyon, TX, 79015, USA
| | - Paul S Morley
- Veterinary Education, Research, and Outreach Program, Texas A&M University, Canyon, TX, 79015, USA.
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Mao Y, Wang F, Kong W, Wang R, Liu X, Ding H, Ma Y, Guo Y. Dynamic changes of rumen bacteria and their fermentative ability in high-producing dairy cows during the late perinatal period. Front Microbiol 2023; 14:1269123. [PMID: 37817752 PMCID: PMC10560760 DOI: 10.3389/fmicb.2023.1269123] [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: 07/29/2023] [Accepted: 08/31/2023] [Indexed: 10/12/2023] Open
Abstract
Background High-producing dairy cows face varying degrees of metabolic stress and challenges during the late perinatal period, resulting in ruminal bacteria abundance and their fermentative ability occurring as a series of changes. However, the dynamic changes are still not clear. Aims/methods Ten healthy, high-producing Holstein dairy cows with similar body conditions and the same parity were selected, and ruminal fluid from the dairy cows at postpartum 0, 7, 14, and 21 d was collected before morning feeding. 16S rRNA high-throughput sequencing, GC-MS/MS targeted metabolomics, and UPLC-MS/MS untargeted metabolomics were applied in the study to investigate the dynamic changes within 21 d postpartum. Results The results displayed that the structures of ruminal bacteria were significantly altered from 0 to 7 d postpartum (R = 0.486, P = 0.002), reflecting the significantly declining abundances of Euryarchaeota and Chloroflexi phyla and Christensenellaceae, Methanobrevibacter, and Flexilinea genera (P < 0.05) and the obviously ascending abundances of Ruminococcaceae, Moryella, Pseudobutyrivibrio, and Prevotellaceae genera at 7 d postpartum (P < 0.05). The structures of ruminal bacteria also varied significantly from 7 to 14 d postpartum (R = 0.125, P = 0.022), reflecting the reducing abundances of Christensenellaceae, Ruminococcaceae, and Moryella genera (P < 0.05), and the elevating abundances of Sharpea and Olsenella genera at 14 d postpartum (P < 0.05). The metabolic profiles of ruminal SCFAs were obviously varied from 0 to 7 d postpartum, resulting in higher levels of propionic acid, butyric acid, and valeric acid at 7 d postpartum (P < 0.05); the metabolic profiles of other ruminal metabolites were significantly shifted from 0 to 7 d postpartum, with 27 significantly elevated metabolites and 35 apparently reduced metabolites (P < 0.05). The correlation analysis indicated that propionic acid was positively correlated with Prevotellaceae and Ruminococcaceae (P < 0.05), negatively correlated with Methanobrevibacter (P < 0.01); butyric acid was positively associated with Prevotellaceae, Ruminococcaceae, and Pseudobutyrivibrio (P < 0.05), negatively associated with Christensenellaceae (P < 0.01); valeric acid was positively linked with Prevotellaceae and Ruminococcaceae (P < 0.05); pyridoxal was positively correlated with Flexilinea and Methanobrevibacter (P < 0.05) and negatively correlated with Ruminococcaceae (P < 0.01); tyramine was negatively linked with Ruminococcaceae (P < 0.01). Conclusion The findings contribute to the decision of nutritional management and prevention of metabolic diseases in high-producing dairy cows during the late perinatal period.
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Affiliation(s)
- Yongxia Mao
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Feifei Wang
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Weiyi Kong
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Ruiling Wang
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Xin Liu
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Hui Ding
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Yun Ma
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Yansheng Guo
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan, China
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Liu L, Wu P, Guo A, Yang Y, Chen F, Zhang Q. Research progress on the regulation of production traits by gastrointestinal microbiota in dairy cows. Front Vet Sci 2023; 10:1206346. [PMID: 37592942 PMCID: PMC10427726 DOI: 10.3389/fvets.2023.1206346] [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: 04/15/2023] [Accepted: 07/20/2023] [Indexed: 08/19/2023] Open
Abstract
The composition and abundance of microorganisms in the gastrointestinal tract of cows are complex and extensive, and they play a crucial role in regulating nutrient digestion, absorption, maintaining digestive tract stability, and promoting the production and health of the host. The fermentation carried out by these microorganisms in the gastrointestinal tract is fundamental to the health and productivity of cows. Rumen microorganisms produce the majority of enzymes required to break down feed substrates, such as cellulose, protein, lipids, and other plant materials, through fermentation. This process provides energy metabolism substrates that satisfy approximately 70% of the host's energy requirements for physiological activities. Gut microorganisms primarily decompose cellulose that is difficult to digest in the rumen, thereby providing heat and energy to the hosts. Additionally, they have an impact on host health and productivity through their role in immune function. Understanding the composition and function of the cow gut microbiota can help regulate dairy cattle breeding traits and improve their health status. As a result, it has become a popular research topic in dairy cattle breeding. This article provides a review of the composition, structure, physiological characteristics, and physiological effects of the cow gut microbiota, serving as a theoretical foundation for future studies that aim to utilize the gut microbiota for dairy cattle breeding or improving production traits. It may also serve as a reference for research on gut microbiota of other ruminants.
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Affiliation(s)
- Lily Liu
- College of Life Science, Southwest Forestry University, Kunming, China
| | - Peifu Wu
- College of Life Science, Southwest Forestry University, Kunming, China
| | - Aiwei Guo
- College of Life Science, Southwest Forestry University, Kunming, China
| | - Yajin Yang
- College of Life Science, Southwest Forestry University, Kunming, China
| | - Fenfen Chen
- College of Life Science, Southwest Forestry University, Kunming, China
| | - Qin Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing, China
- College of Animal Science and Technology, Shandong Agricultural University, Tai’an, China
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15
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Freetly HC, Lindholm-Perry AK. Rumen and cecum bacteria of beef cattle that differ in feed efficiency fed a forage diet. J Anim Sci 2023; 101:skad292. [PMID: 37666002 PMCID: PMC10552577 DOI: 10.1093/jas/skad292] [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: 10/14/2022] [Accepted: 08/31/2023] [Indexed: 09/06/2023] Open
Abstract
Most of the research addressing feed efficiency and the microbiota has been conducted in cattle fed grain diets, although cattle evolved to consume forage diets. Our hypothesis was that the bacteria in the rumen and cecum differed in cattle that have a common feed intake but had different ^average daily body weight gains (ADG) on a forage diet. Heifers (n = 134) were 606 ± 1 d of age and weighed 476 ± 3 kg at the start of the 84-d feeding study. Heifers were offered ad libitum access to a totally mixed ration that consisted of 86% ground brome hay, 10% wet distillers grains with solubles, and 4% mineral supplement as dry matter. Feed intake and body weight gain were measured, and gain was calculated. Heifers with the least (n = 8) and greatest (n = 8) ADG within 0.32 SD of the mean daily dry matter intake were selected for sampling. Digesta samples from the rumen and cecum were collected, and subsequent 16S analysis was conducted to identify Amplicon Sequence Variants. There were no differences in Alpha and Beta diversity between ADG classification within sample sites (P > 0.05). Both sample sites contained calculated balances of sister clades using phylogenetic isometric log ratio transferred data that differed across ADG classification. These findings suggest that bacteria did not differ at the community level, but there was structural difference at the clade level.
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Affiliation(s)
- Harvey C Freetly
- Nutrition, Growth & Physiology Research Unit, USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933
| | - Amanda K Lindholm-Perry
- Nutrition, Growth & Physiology Research Unit, USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933
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16
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Betancur-Murillo CL, Aguilar-Marín SB, Jovel J. Prevotella: A Key Player in Ruminal Metabolism. Microorganisms 2022; 11:microorganisms11010001. [PMID: 36677293 PMCID: PMC9866204 DOI: 10.3390/microorganisms11010001] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/15/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
Ruminants are foregut fermenters that have the remarkable ability of converting plant polymers that are indigestible to humans into assimilable comestibles like meat and milk, which are cornerstones of human nutrition. Ruminants establish a symbiotic relationship with their microbiome, and the latter is the workhorse of carbohydrate fermentation. On the other hand, during carbohydrate fermentation, synthesis of propionate sequesters H, thus reducing its availability for the ultimate production of methane (CH4) by methanogenic archaea. Biochemically, methane is the simplest alkane and represents a downturn in energetic efficiency in ruminants; environmentally, it constitutes a potent greenhouse gas that negatively affects climate change. Prevotella is a very versatile microbe capable of processing a wide range of proteins and polysaccharides, and one of its fermentation products is propionate, a trait that appears conspicuous in P. ruminicola strain 23. Since propionate, but not acetate or butyrate, constitutes an H sink, propionate-producing microbes have the potential to reduce methane production. Accordingly, numerous studies suggest that members of the genus Prevotella have the ability to divert the hydrogen flow in glycolysis away from methanogenesis and in favor of propionic acid production. Intended for a broad audience in microbiology, our review summarizes the biochemistry of carbohydrate fermentation and subsequently discusses the evidence supporting the essential role of Prevotella in lignocellulose processing and its association with reduced methane emissions. We hope this article will serve as an introduction to novice Prevotella researchers and as an update to others more conversant with the topic.
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Affiliation(s)
- Claudia Lorena Betancur-Murillo
- Escuela de Ciencias Básicas, Tecnología e Ingeniería, Universidad Nacional Abierta y a Distancia, UNAD, Bogotá 111511, Colombia
| | | | - Juan Jovel
- Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Dr NW, Calgary, AB T2N 4Z6, Canada
- Correspondence:
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17
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The Microbial Ecology of Liver Abscesses in Cattle. Vet Clin North Am Food Anim Pract 2022; 38:367-381. [DOI: 10.1016/j.cvfa.2022.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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18
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Klassen L, Reintjes G, Li M, Jin L, Amundsen C, Xing X, Dridi L, Castagner B, Alexander TW, Abbott DW. Fluorescence activated cell sorting and fermentation analysis to study rumen microbiome responses to administered live microbials and yeast cell wall derived prebiotics. Front Microbiol 2022; 13:1020250. [PMID: 36938132 PMCID: PMC10022430 DOI: 10.3389/fmicb.2022.1020250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 12/12/2022] [Indexed: 03/06/2023] Open
Abstract
Rapid dietary changes, such as switching from high-forage to high-grain diets, can modify the rumen microbiome and initiate gastrointestinal distress, such as bloating. In such cases, feed additives, including prebiotics and live microbials, can be used to mitigate these negative consequences. Bio-Mos® is a carbohydrate-based prebiotic derived from yeast cells that is reported to increase livestock performance. Here, the responses of rumen bacterial cells to Bio-Mos® were quantified, sorted by flow cytometry using fluorescently-labeled yeast mannan, and taxonomically characterized using fluorescence in situ hybridization and 16S rRNA sequencing. Further, to evaluate the effects of bovine-adapted Bacteroides thetaiotaomicron administration as a live microbial with and without Bio-Mos® supplementation, we analyzed microbial fermentation products, changes to carbohydrate profiles, and shifts in microbial composition of an in vitro rumen community. Bio-Mos® was shown to be an effective prebiotic that significantly altered microbial diversity, composition, and fermentation; while addition of B. thetaiotaomicron had no effect on community composition and resulted in fewer significant changes to microbial fermentation. When combined with Bio-Mos®, there were notable, although not significant, changes to major bacterial taxa, along with increased significant changes in fermentation end products. These data suggest a synergistic effect is elicited by combining Bio-Mos® and B. thetaiotaomicron. This protocol provides a new in vitro methodology that could be extended to evaluate prebiotics and probiotics in more complex artificial rumen systems and live animals.
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Affiliation(s)
- Leeann Klassen
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Greta Reintjes
- Department of Pharmacology & Therapeutics, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Meiying Li
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Long Jin
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Carolyn Amundsen
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Xiaohui Xing
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Lharbi Dridi
- Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada
| | - Bastien Castagner
- Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada
| | - Trevor W. Alexander
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - D. Wade Abbott
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
- *Correspondence: D. Wade Abbott,
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