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Lv S, Zhang Y, Zhang Z, Meng S, Pu Y, Liu X, Liu L, Ma Y, Liu W, Jiang L. Diversity of the fecal microbiota in Chinese ponies. Front Vet Sci 2023; 10:1102186. [PMID: 36777669 PMCID: PMC9909481 DOI: 10.3389/fvets.2023.1102186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/09/2023] [Indexed: 01/27/2023] Open
Abstract
Introduction The gut microbiomes of equine are plentiful and intricate, which plays an important part in the growth. However, there is a relative lack of information on the microbial diversity in the pony's gut. Methods In this article, 118 fecal samples from DeBa pony, NiQi pony and GuZh horse were studied by 16S rRNA amplicon sequencing. Results Diversity analysis was used to determine the difference of gut microbiota composition among different breeds. Alpha diversity analysis showed that the gut microbiota of NiQi ponies were abundant and various. Beta diversity analysis showed that the microorganisms constitution of DeBa ponies was more similar to that of NiQi ponies. LDA Effect Size (LEfSe) analysis result that the microorganism biomarkers for NiQi pony at the genus level were Phascolarctobacterium, Paludibacter, and Fibrobacter; the bacterial biomarker for DeBa pony was Streptococcus and Prevotella; and the bacterial biomarkers for GuZh horses was Treponema, Treponema Mogibacterium, Adlercreutzia, and Blautia. The correlation analysis between genera with >1% abundance and horse height found that Streptococcus (P < 0.01), Treponema (P < 0.01), Coprococcus (P < 0.01), Prevotella (P < 0.01), Phascolarctobacterium (P < 0.01), and Mogibacterium (P < 0.01) were significantly associated with horses' height. The functional prediction results indicated that DeBa pony have a microbiota functional more similar to NiQi pony. Discussion For the first time, our results announce the species composition and structure of the gut microbiota in Chinese ponies. At the same time, our results can provide theoretical reference for further understanding the healthy breeding, feeding management and disease prevention of horses.
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Affiliation(s)
- Shipeng Lv
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China,Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yanli Zhang
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Zhengkai Zhang
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Sihan Meng
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yabin Pu
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Xuexue Liu
- Centre d'Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Lingling Liu
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Yuehui Ma
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Wujun Liu
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China,*Correspondence: Wujun Liu ✉
| | - Lin Jiang
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China,Lin Jiang ✉
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Ritt L, Orso C, Silveira A, Frazzon J, de Vargas D, Wagner R, de Oliveira F, Nörnberg J, Fischer V. Oregano extract fed to pre-weaned dairy calves. Part 1: effects on intake, digestibility, body weight, and rumen and intestinal bacteria microbiota. Livest Sci 2023. [DOI: 10.1016/j.livsci.2023.105165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Mahayri TM, Fliegerová KO, Mattiello S, Celozzi S, Mrázek J, Mekadim C, Sechovcová H, Kvasnová S, Atallah E, Moniello G. Host Species Affects Bacterial Evenness, but Not Diversity: Comparison of Fecal Bacteria of Cows and Goats Offered the Same Diet. Animals (Basel) 2022; 12:ani12162011. [PMID: 36009603 PMCID: PMC9404439 DOI: 10.3390/ani12162011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/29/2022] [Accepted: 08/05/2022] [Indexed: 12/19/2022] Open
Abstract
Simple Summary Comparison of bacterial diversity and composition of feces from cows and goats offered the same pasture-based diet revealed that the animal species had no effect on bacterial species richness and diversity, but significantly affected species evenness. Both diet and host species influence the gut microbiome. Abstract The aim of this study was to compare the diversity and composition of fecal bacteria in goats and cows offered the same diet and to evaluate the influence of animal species on the gut microbiome. A total of 17 female goats (Blond Adamellan) and 16 female cows (Brown Swiss) kept on an organic farm were fed pasture and hay. Bacterial structure in feces was examined by high-throughput sequencing using the V4–V5 region of the 16S rRNA gene. The Alpha diversity measurements of the bacterial community showed no statistical differences in species richness and diversity between the two groups of ruminants. However, the Pielou evenness index revealed a significant difference and showed higher species evenness in cows compared to goats. Beta diversity measurements showed statistical dissimilarities and significant clustering of bacterial composition between goats and cows. Firmicutes were the dominant phylum in both goats and cows, followed by Bacteroidetes, Proteobacteria, and Spirochaetes. Linear discriminant analysis with effect size (LEfSe) showed a total of 36 significantly different taxa between goats and cows. Notably, the relative abundance of Ruminococcaceae UCG-005, Christensenellaceae R-7 group, Ruminococcaceae UCG-010, Ruminococcaceae UCG-009, Ruminococcaceae UCG-013, Ruminococcaceae UCG-014, Ruminococcus 1, Ruminococcaceae UCG-002, Lachnospiraceae NK4A136 group, Treponema 2, Lachnospiraceae AC2044 group, and Bacillus was higher in goats compared to cows. In contrast, the relative abundance of Turicibacter, Solibacillus, Alloprevotella, Prevotellaceae UCG-001, Negativibacillus, Lachnospiraceae UCG-006, and Eubacterium hallii group was higher in cows compared with goats. Our results suggest that diet shapes the bacterial community in feces, but the host species has a significant impact on community structure, as reflected primarily in the relative abundance of certain taxa.
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Affiliation(s)
- Tiziana Maria Mahayri
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, Czech Academy of Science, 14220 Prague, Czech Republic
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Kateřina Olša Fliegerová
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, Czech Academy of Science, 14220 Prague, Czech Republic
- Correspondence: ; Tel.: +420-267-090-504
| | - Silvana Mattiello
- Department of Agricultural and Environmental Sciences—Production, Landscape, Agroenergy, University of Milan, 20133 Milan, Italy
| | - Stefania Celozzi
- Department of Agricultural and Environmental Sciences—Production, Landscape, Agroenergy, University of Milan, 20133 Milan, Italy
| | - Jakub Mrázek
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, Czech Academy of Science, 14220 Prague, Czech Republic
| | - Chahrazed Mekadim
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, Czech Academy of Science, 14220 Prague, Czech Republic
| | - Hana Sechovcová
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, Czech Academy of Science, 14220 Prague, Czech Republic
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences in Prague, 16500 Prague, Czech Republic
| | - Simona Kvasnová
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, Czech Academy of Science, 14220 Prague, Czech Republic
| | - Elie Atallah
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Giuseppe Moniello
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
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Rumen sampling methods bias bacterial communities observed. PLoS One 2022; 17:e0258176. [PMID: 35511785 PMCID: PMC9070869 DOI: 10.1371/journal.pone.0258176] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 04/10/2022] [Indexed: 01/04/2023] Open
Abstract
The rumen is a complex ecosystem that plays a critical role in our efforts to improve feed efficiency of cattle and reduce their environmental impacts. Sequencing of the 16S rRNA gene provides a powerful tool to survey the bacterial and some archaeal. Oral stomach tubing a cow to collect a rumen sample is a rapid, cost-effective alternative to rumen cannulation for acquiring rumen samples. In this study, we determined how sampling method (oral stomach tubing vs cannulated grab sample), as well as rumen fraction type (liquid vs solid), bias the bacterial and archaeal communities observed. Liquid samples were further divided into liquid strained through cheesecloth and unstrained. Fecal samples were also collected to determine how these differed from the rumen sample types. The abundance of major archaeal communities was not different at the family level in samples acquired via rumen cannula or stomach tube. In contrast to the stable archaeal communities across sample type, the bacterial order WCHB1-41 (phylum Kiritimatiellaeota) was enriched in both liquid strained and unstrained samples as well as the family Prevotellaceae as compared to grab samples. However, these liquid samples had significantly lower abundance of Lachnospiraceae compared with grab samples. Solid samples strained of rumen liquid most closely resembled the grab samples containing both rumen liquid and solid particles obtained directly from the rumen cannula; therefore, inclusion of particulate matter is important for an accurate representation of the rumen bacteria. Stomach tube samples were the most variable and were most representative of the liquid phase. In comparison with a grab sample, stomach tube samples had significantly lower abundance of Lachnospiraceae, Fibrobacter and Treponema. Fecal samples did not reflect the community composition of the rumen, as fecal samples had significantly higher relative abundance of Ruminococcaceae and significantly lower relative abundance of Lachnospiraceae compared with grab samples.
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Palumbo F, Squartini A, Barcaccia G, Macolino S, Pornaro C, Pindo M, Sturaro E, Ramanzin M. A multi-kingdom metabarcoding study on cattle grazing Alpine pastures discloses intra-seasonal shifts in plant selection and faecal microbiota. Sci Rep 2021; 11:889. [PMID: 33441587 PMCID: PMC7806629 DOI: 10.1038/s41598-020-79474-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 12/09/2020] [Indexed: 12/15/2022] Open
Abstract
Diet selection by grazing livestock may affect animal performance as well as the biodiversity of grazed areas. Recent DNA barcoding techniques allow to assess dietary plant composition in faecal samples, which may be additionally integrated by the description of gut microbiota. In this high throughput metabarcoding study, we investigated the diversity of plant, fungal and bacterial taxa in faecal samples of lactating cows of two breeds grazing an Alpine semi-natural grassland during summer. The estimated plant composition of the diet comprised 67 genera and 39 species, which varied remarkably during summer, suggesting a decline of the diet forage value with the advancing of the vegetative season. The fungal community included Neocallimastigomycota gut symbionts, but also Ascomycota and Basidiomycota plant parasite and coprophilous taxa, likely ingested during grazing. The proportion of ingested fungi was remarkably higher than in other studies, and varied during summer, although less than that observed for plants. Some variation related to breed was also detected. The gut bacterial taxa remained stable through the summer but displayed a breed-specific composition. The study provided insights in the reciprocal organisms' interactions affecting, and being affected by, the foraging behaviour: plants showed a high temporal variation, fungi a smaller one, while bacteria had practically none; conversely, the same kingdoms showed the opposite gradient of variation as respect to the animal host breed, as bacteria revealed to be the group mostly characterized by host-specificity.
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Affiliation(s)
- Fabio Palumbo
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, Viale dell'Università 16, 35020, Legnaro, Padova, Italy
| | - Andrea Squartini
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, Viale dell'Università 16, 35020, Legnaro, Padova, Italy.
| | - Gianni Barcaccia
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, Viale dell'Università 16, 35020, Legnaro, Padova, Italy
| | - Stefano Macolino
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, Viale dell'Università 16, 35020, Legnaro, Padova, Italy
| | - Cristina Pornaro
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, Viale dell'Università 16, 35020, Legnaro, Padova, Italy
| | - Massimo Pindo
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via Mach 1, S. Michele All'Adige, 38010, Trento, Italy
| | - Enrico Sturaro
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, Viale dell'Università 16, 35020, Legnaro, Padova, Italy
| | - Maurizio Ramanzin
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, Viale dell'Università 16, 35020, Legnaro, Padova, Italy
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Ebeid HM, Hassan FU, Li M, Peng L, Peng K, Liang X, Yang C. Camelina sativa L. Oil Mitigates Enteric in vitro Methane Production, Modulates Ruminal Fermentation, and Ruminal Bacterial Diversity in Buffaloes. Front Vet Sci 2020; 7:550. [PMID: 33005640 PMCID: PMC7479821 DOI: 10.3389/fvets.2020.00550] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/13/2020] [Indexed: 12/13/2022] Open
Abstract
This study was aimed to evaluate the effects of Camelina sativa oil (CO) on fermentation kinetics and methane (CH4) production in rations with different roughage (R) to concentrate (C) ratios. Three total mixed rations (TMRs) were used as substrates (R70:C30, R50:C50, and R30:C70) supplemented with different levels of CO (0, 2, 4, 6, and 8% on dry matter basis) in an in vitro batch culture system. The enteric CH4 production was determined at different times of incubation while fermentation parameters were measured at the end of incubation. Results revealed that CO significantly decreased (P < 0.05) CH4 production at 48 h in medium (R50:C50) and low- (R30:C70) roughage diets than control. Camelina oil at all levels significantly (P < 0.05) affected ammonia nitrogen (NH3-N) and microbial protein (MCP) in all rations. Propionate concentration was increased by supplementing 8% CO to R70:C30 TMR, but it decreased with increasing levels of CO for low- and medium-roughage diets. Acetate concentration was significantly (P < 0.05) higher at 4% CO supplementation, but it decreased with 8% CO level in R30:C70 TMR. For all rations, CO decreased (P < 0.001) total bacteria, protozoa, and methanogens. Total fungi counts were affected by CO in all rations, especially with a 6% level in two rations (R30:C70 and R50:C50) and 8% level with high-roughage ration (R70:C30). Supplementation of CO in medium-roughage ration (R50:C50) showed a linear (P < 0.05) decrease in bacterial richness and evenness indices along with Shannon diversity as compared to the control. Moreover, CO also increased Firmicutes to Bacteroidetes ratio in all TMRs more effectively at higher levels. Camelina oil also affected the relative abundance of Prevotella in both low- and medium-roughage diets while increasing the abundance of Ruminobacter and Pseudobutyrivibrio. The present study concluded that CO enhanced fermentation kinetics while decreasing enteric in vitro CH4 production from fibrous diets. Thus, it may be considered as a potentially effective and environmentally friendly way of mitigating CH4 emission from livestock.
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Affiliation(s)
- Hossam M Ebeid
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China.,Dairy Science Department, National Research Centre, Giza, Egypt
| | - Faiz-Ul Hassan
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China.,Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Mengwei Li
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Lijuan Peng
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Kaiping Peng
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Xin Liang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Chengjian Yang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
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Ebeid HM, Mengwei L, Kholif AE, Hassan FU, Lijuan P, Xin L, Chengjian Y. Moringa Oleifera Oil Modulates Rumen Microflora to Mediate In Vitro Fermentation Kinetics and Methanogenesis in Total Mix Rations. Curr Microbiol 2020; 77:1271-1282. [PMID: 32130505 DOI: 10.1007/s00284-020-01935-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 02/24/2020] [Indexed: 01/16/2023]
Abstract
This study was conducted to evaluate potential of Moringa oleifera seed oil (MOSO) to modulate rumen microflora to mitigate methane (CH4) production in different total mixed rations (TMRs). Three TMRs with different roughage (R) to concentrate (C) ratio were used as substrates (R70:C30, R50:C50 and R30:C70) for in vitro fermentation study using batch culture technique. Results revealed that supplementation of MOSO in different rations with variable roughage to concentrates ratio altered (P < 0.05) CH4 production and fermentation parameters. M. oleifera seed oil at 3 and 4% increased (P < 0.01) microbial protein (MCP) and propionate concentration for all rations but decreased acetate concentration in R70:C30 TMR. Two levels of MOSO (3 and 4%) quadratically increased (P = 0.001) MCP and decreased acetate in R30:C70 while all levels increased propionate. For R30:C70 and R50:C50 rations, MOSO linearly and quadratically decreased (P < 0.001) protozoa and methanogen counts; however, protozoa, methanogens and bacteria were significantly increased in R70:C30 ration without any change in fungal counts. Supplementation of higher level of MOSO (4%) in high roughage ration (R70:C30) showed negative effects on diversity (Shannon index) and evenness of bacterial species as compared to control and lower oil level. Moreover, it also decreased Firmicutes to Bacteroidetes ratio in high roughage rations more obviously at lower levels. Moringa oil also stimulated Prevotella in both high and low roughages diets that indicates its potential to mediate rumen acidosis. Conclusively, MOSO enhanced fermentation kinetics and decreased CH4 production through effective modulation of rumen microbiome.
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Affiliation(s)
- Hossam M Ebeid
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, 530001, China
- Dairy Science Department, National Research Centre, 33 Bohouth St. Dokki, Giza, 12622, Egypt
| | - Li Mengwei
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, 530001, China
| | - Ahmed E Kholif
- Dairy Science Department, National Research Centre, 33 Bohouth St. Dokki, Giza, 12622, Egypt
| | - Faiz-Ul Hassan
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, 530001, China
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Peng Lijuan
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, 530001, China
| | - Liang Xin
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, 530001, China
| | - Yang Chengjian
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, 530001, China.
- Animal Nutrition and Feed Science, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, 24-1 Yongwu Road, Nanning, 530001, Guangxi, People's Republic of China.
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Cui X, Wang Z, Yan T, Chang S, Wang H, Hou F. Rumen bacterial diversity of Tibetan sheep ( Ovis aries) associated with different forage types on the Qinghai-Tibetan Plateau. Can J Microbiol 2019; 65:859-869. [PMID: 31386822 DOI: 10.1139/cjm-2019-0154] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Diet is the great determinant of bacterial composition in the rumen. However, little is known about the rumen bacterial community of Tibetan sheep living in the special ecological environment of the Qinghai-Tibetan Plateau (QTP) of China. In the present study, we used high-throughput sequencing to investigate the rumen bacterial community of Tibetan sheep associated with two primary diets: alpine pasture diet (a continuation of the sheep's natural grazing diet) and oat (Avena sativa) hay diet on the QTP. The results showed that bacterial community richness and species diversity of the oat hay diet group were significantly greater than that of the native pasture diet group (p < 0.05). Principal co-ordinate analysis and analysis of similarities revealed that the bacterial community of the oat hay diet group was distinctly different from that of the native pasture diet group (p < 0.05). Bacteroidetes and Firmicutes were the predominant microbial phyla in the rumen. The rumen of oat-hay-fed sheep had higher proportions of Proteobacteria and novel bacteria species than the rumen of native-pasture-fed sheep. Actinobacteria, an uncommon bacterial phylum, occurred only in the oat-hay-fed group. At the genus level, Komagataeibacter, Ruminococcaceae_UCG-014, and Ruminococcaceae_NK4A214 showed significantly higher relative abundance in the oat-hay-fed sheep than in the native-pasture-fed sheep (p < 0.05). This study is the first of the QTP to employ high-throughput sequencing to examine the influence of diet on the rumen microbiome of Tibetan sheep.
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Affiliation(s)
- Xiongxiong Cui
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu Province, China
| | - Zhaofeng Wang
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu Province, China
| | - Tianhai Yan
- Agri-Food and Biosciences Institute, Belfast, Northern Ireland, UK
| | - Shenghua Chang
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu Province, China
| | - Hong Wang
- Animal Husbandry Science and Technology Demonstration Park of Maqu County, Gannan, Gansu Province, China
| | - Fujiang Hou
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu Province, China
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Effect of Dietary Supplementation of Moringa Oleifera on the Production Performance and Fecal Methanogenic Community of Lactating Dairy Cows. Animals (Basel) 2019; 9:ani9050262. [PMID: 31121857 PMCID: PMC6562924 DOI: 10.3390/ani9050262] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/09/2019] [Accepted: 05/20/2019] [Indexed: 11/18/2022] Open
Abstract
Simple Summary High-quality forages such as protein-rich ingredients are essential to maximize production performance in dairy production. However, enteric methane produced by methanogenesis represents a substantial waste of feed energy for ruminants. Thus, it is important to evaluate the environmental effect when such feed ingredients are used to provide necessary nutrients. The aim of the present study was to examine the effects of dietary supplementation of Moringa oleifera on the production performance and fecal methanogenic community in lactating cows. The study’s main results suggest that inclusion of Moringa oleifera improved milk fat content and changed the composition and diversity of methanogens. This study indicates that secondary metabolites from Moringa oleifera may regulate fermentation conditions and associations between some methanogens and other microbes. These findings provide basic information on the utilization of alternative forage resources for dairy cows and can help to better understand the regulation of microbial metabolic function and methane emissions. Abstract Development of alternative forage resources is of great importance to provide necessary nutrients and minimize greenhouse gas emissions in ruminant production. The aim of this study was to examine the effects of dietary supplementation of Moringa oleifera on the production performance and fecal methanogenic community in dairy cows using methyl-coenzyme M reductase α-subunit gene. Sixty-four cows were allocated to one of four treatments: basal diet without M. oleifera (control) or low (3% w/w, M3), medium (6%, M6), or high (9%, M9) supplementation with M. oleifera. This study demonstrated that different supplementation levels of Moringa oleifera in the diet achieved similar feed intake and milk production, but adding 6% of Moringa oleifera improved milk fat content. Two families, two phyla, three genera, and three species in total were identified among the four treatments. The fecal archaeal community in the control treatment was predominated by Methanobrevibacter (39.1% of the total sequence reads) followed by Methanosphaera and Methanocorpusculum at the genus level. The increased abundance of the Methanosphaera genus and Methanosphaera sp. ISO3-F5 species was induced by secondary metabolites of Moringa oleifera in the diet. Results indicated that Moringa oleifera supplementation not only improved dairy product quality but could also potentially reduce methane emissions.
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10
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Wang L, Liu K, Wang Z, Bai X, Peng Q, Jin L. Bacterial Community Diversity Associated With Different Utilization Efficiencies of Nitrogen in the Gastrointestinal Tract of Goats. Front Microbiol 2019; 10:239. [PMID: 30873128 PMCID: PMC6401623 DOI: 10.3389/fmicb.2019.00239] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/28/2019] [Indexed: 01/17/2023] Open
Abstract
The objective of this study was to examine the association between bacterial community structure and the utilization efficiency of nitrogen (UEN) phenotypes by determining the bacterial community in the gastrointestinal tract (GIT) of goats that differ in UEN using high-throughput 16S rRNA gene sequencing. Thirty Nubian goats were selected as experimental animals, and their UEN was determined in a metabolic experiment. Subsequently, eight individuals were grouped into the high nitrogen utilization (HNU) phenotype, and seven were grouped into the low nitrogen utilization (LNU) phenotype. The bacterial 16S rRNA gene amplicons from the rumen, abomasum, jejunum, cecum and colon contents of these animals were sequenced using next-generation high-throughput sequencing technology. Two hundred thirty-nine genera belonging to 23 phyla in the rumen, 319 genera belonging to 30 phyla in the abomasum, 248 genera belonging to 36 phyla in the jejunum, 248 genera belonging to 25 phyla in the colon and 246 genera belonging to 23 phyla in the cecum were detected, with Bacteroidetes and Firmicutes predominating. In addition, a significant correlation was observed between the UEN and the genera Succiniclasticum, Bacteroides, Ruminobacter, Methanimicrococcus, Mogibacterium, Eubacterium_hallii_group and Ruminococcus_1 in the rumen; Bacteroidales_S24-7_group, Bacteroidales_RF16_group, Bacteroidales_UCG-001 and Anaerovibrio in the abomasum; Ruminococcus_2, Candidatus_Saccharimonas, Candidatus_Arthromitus and Coprococcus_1 in the jejunum; Erysipelotrichaceae_UCG-004, Akkermansia, Senegalimassilia, Candidatus_Soleaferrea and Methanocorpusculum in the colon; and Ruminococcaceae_UCG-002, Anaerovibrio and Ruminococcaceae_UCG-007 in the cecum. Furthermore, the real-time PCR results showed that the ruminal copies of Fibrobacter_succinogenes, Butyrivibrio_fibrisolvens, Ruminococcus_sp._HUN007, Prevotella ruminicola and Streptococcus bovis in the HNU animals were significantly higher than those in the LNU animals. This study suggests an association of GIT microbial communities as a factor that influences UEN in goats.
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Affiliation(s)
- Lizhi Wang
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
| | - Kaizhen Liu
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
| | - Zhisheng Wang
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
| | - Xue Bai
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
| | - Quanhui Peng
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
| | - Lei Jin
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
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ELMASRY AMA, MENDOZA GD, MIRANDA LA, MARTÍNEZ JA, VÁZQUEZ G, PLATA FX. In vitro gas production of high forage diets incubated with two live yeast (Biosaf SC47 and Procreatin 7). THE INDIAN JOURNAL OF ANIMAL SCIENCES 2018. [DOI: 10.56093/ijans.v88i12.85808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Chen X, Liu X, Du Y, Wang B, Zhao N, Geng Z. Green forage and fattening duration differentially modulate cecal microbiome of Wanxi white geese. PLoS One 2018; 13:e0204210. [PMID: 30252869 PMCID: PMC6155509 DOI: 10.1371/journal.pone.0204210] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 09/05/2018] [Indexed: 12/31/2022] Open
Abstract
Gut microbial ecology is responsible for fatty acid metabolism in ruminants. The cecal microbiota composition of geese and their adaptation to fiber inclusion and feeding timeswere investigated in this study. A total of 116 Wanxi white geese were randomly selected at 70 days old. Eight geese were subjected to cecal sampling at 70 d of age, and the remaining 108 geese were divided into four groups with three replicates each (9 geese in each replicate). The geese in the four groups were fed 0, 15, 30, and 45% green forage (relative to dry matter), respectively. Three birds from each replicate were selected for cecal sampling at 80, 90, and 100 days old. All samples were subjected to 16S rRNA gene sequencing using the Illumina Ion Personal Genome Machine platform. Bacterial abundance was analyzed using two-way ANOVA analysis, and the relationship between the relative abundance of bacteria (phylum level) and fatty acids was analyzed using acanonical correspondence analysis. Cecal microbiota in geese were mainly composed of Bacteroidetes (68.46%), Firmicutes (20.04%), and Proteobacteria (7.89%). Dietary treatments had no significant effect on the α-diversity indices of the cecal bacterial community (P > 0.05), but a numerical increase occurred with increased fattening duration and green forage inclusion. The Selenomonadales order (P = 0.024), Negativicutes class (P = 0.026), and Megamonas (P = 0.012) and Oscillospira (P = 0.042) genera were affected by green forageinclusion level, and microflora abundance was mainly influenced by the fattening duration. Bacteria phyla were mostly set along the line of linolenic acid and oleic acid. Finally, Bacteroidales might be an intestinal promoter that improves unsaturated fatty acid synthesis in geese.
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Affiliation(s)
- Xingyong Chen
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, P.R. China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, P.R. China
| | - Xue Liu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, P.R. China
| | - Yeye Du
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, P.R. China
| | - Bin Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, P.R. China
- Department of Primary Education, Tongcheng Teachers College, Tongcheng, P.R. China
| | - Ning Zhao
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, P.R. China
| | - Zhaoyu Geng
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, P.R. China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, P.R. China
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Liu K, Wang L, Yan T, Wang Z, Xue B, Peng Q. Relationship between the structure and composition of rumen microorganisms and the digestibility of neutral detergent fibre in goats. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2018; 32:82-91. [PMID: 30056683 PMCID: PMC6325412 DOI: 10.5713/ajas.18.0043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 06/07/2018] [Indexed: 11/27/2022]
Abstract
OBJECTIVE This experiment was conducted to compare the structure and composition of ruminal microorganisms in goats with high and low neutral detergent fibre (NDF) digestibility. METHODS Nineteen crossbred goats were used as experimental animals and fed the same total mixed rations during the 30-day pre-treatment and 6-day digestion trialperiods. All faeces were collected during the digestion period for measuring the NDF digestibility. Then, high and the low NDF digestibility individuals were chosen for the high NDF digestibility group (HFD) and low NDF digestibility group (LFD), respectively. Rumen contents were collected for total microbial DNA extraction. The V4 region of the bacterial 16S rRNA gene was amplified using universal primers of bacteria and sequenced using high-throughput sequencer. The sequences were mainly analysed by QIIME 1.8.0. RESULTS A total of 18,694 operational taxonomic units were obtained, within 81.98% belonged to bacteria, 6.64% belonged to archaea and 11.38% was unassigned microorganisms. Bacteroidetes, Firmicutes, and Proteobacteria were the predominant microbial phyla in both groups. At the genus level, the relative abundance of fifteen microorganisms were significantly higher (p<0.05) and six microorganisms were extremely significantly higher (p<0.01) in LFD than HFD. Overall, 176 core shared genera were identified in the two groups. The relative abundance of 2 phyla, 5 classes, 10 orders, 13 families and 15 genera had a negative correlation with NDF digestibility, but only the relative abundance of Pyramidobacter had a positive correlation with NDF digestibility. CONCLUSION There were substantial differences in NDF digestibility among the individual goats, and the NDF digestibility had significant correlation with the relative abundance of some ruminal microorganisms.
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Affiliation(s)
- Kaizhen Liu
- Animal Nutrition Institute, Key Laboratory of Bovine Low-Carbon Farming and Safe Production, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Lizhi Wang
- Animal Nutrition Institute, Key Laboratory of Bovine Low-Carbon Farming and Safe Production, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Tianhai Yan
- Animal Nutrition Institute, Key Laboratory of Bovine Low-Carbon Farming and Safe Production, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.,Agri - Food and Biosciences Institute, Hillsborough, Co. Down, BT26 6DR, UK
| | - Zhisheng Wang
- Animal Nutrition Institute, Key Laboratory of Bovine Low-Carbon Farming and Safe Production, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Bai Xue
- Animal Nutrition Institute, Key Laboratory of Bovine Low-Carbon Farming and Safe Production, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Quanhui Peng
- Animal Nutrition Institute, Key Laboratory of Bovine Low-Carbon Farming and Safe Production, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
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Shen H, Lu Z, Xu Z, Chen Z, Shen Z. Associations among dietary non-fiber carbohydrate, ruminal microbiota and epithelium G-protein-coupled receptor, and histone deacetylase regulations in goats. MICROBIOME 2017; 5:123. [PMID: 28927467 PMCID: PMC5606034 DOI: 10.1186/s40168-017-0341-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 09/12/2017] [Indexed: 05/26/2023]
Abstract
BACKGROUND Diet-derived short-chain fatty acids (SCFAs) in the rumen have broad effects on the health and growth of ruminants. The microbe-G-protein-coupled receptor (GPR) and microbe-histone deacetylase (HDAC) axes might be the major pathway mediating these effects. Here, an integrated approach of transcriptome sequencing and 16S rRNA gene sequencing was applied to investigate the synergetic responses of rumen epithelium and rumen microbiota to the increased intake of dietary non-fiber carbohydrate (NFC) from 15 to 30% in the goat model. In addition to the analysis of the microbial composition and identification of the genes and signaling pathways related to the differentially expressed GPRs and HDACs, the combined data including the expression of HDACs and GPRs, the relative abundance of the bacteria, and the molar proportions of the individual SCFAs were used to identify the significant co-variation of the SCFAs, clades, and transcripts. RESULTS The major bacterial clades promoted by the 30% NFC diet were related to lactate metabolism and cellulose degradation in the rumen. The predominant functions of the GPR and HDAC regulation network, under the 30% NFC diet, were related to the maintenance of epithelium integrity and the promotion of animal growth. In addition, the molar proportion of butyrate was inversely correlated with the expression of HDAC1, and the relative abundance of the bacteria belonging to Clostridum_IV was positively correlated with the expression of GPR1. CONCLUSIONS This study revealed that the effects of rumen microbiota-derived SCFA on epithelium growth and metabolism were mediated by the GPR and HDAC regulation network. An understanding of these mechanisms and their relationships to dietary components provides better insights into the modulation of ruminal fermentation and metabolism in the promotion of livestock production.
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Affiliation(s)
- Hong Shen
- College of Life Science, Nanjing Agricultural University, Nanjing, Jiangsu, China
- Bioinformatics Center, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Zhongyan Lu
- Key Lab of Animal Physiology and Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China.
| | - Zhihui Xu
- College of Life Science, Nanjing Agricultural University, Nanjing, Jiangsu, China
- Bioinformatics Center, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Zhan Chen
- College of Life Science, Nanjing Agricultural University, Nanjing, Jiangsu, China
- Bioinformatics Center, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Zanming Shen
- Key Lab of Animal Physiology and Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China
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Liu K, Xu Q, Wang L, Wang J, Guo W, Zhou M. The impact of diet on the composition and relative abundance of rumen microbes in goat. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 30:531-537. [PMID: 27507180 PMCID: PMC5394839 DOI: 10.5713/ajas.16.0353] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 07/11/2016] [Accepted: 08/08/2016] [Indexed: 11/30/2022]
Abstract
Objective This experiment was conducted to explore the impact of diet on the ruminal microbial community in goats. Methods Twelve goats were divided into two groups and fed complete feed (CF) or all forage (AF) diet. The total microbial DNAs in the rumen liquid were extracted. The V4 region of microbial 16S rRNA genes was amplified and sequenced using high-throughput. Information of sequences was mainly analyzed by QIIME 1.8.0. Results The results showed that Bacteroidetes and Firmicutes were the most predominant microbial phyla in the rumen of all goats. At genus level, the abundance of fiber-digesting bacteria such as Ruminococcus and Lachnospiracea incertae sedis was significantly higher in AF than that in CF, while the levels of fat-degrading bacterium Anaerovibrio and protein-degrading bacterium Pseudomonas were opposite. The core shared genera, Prevotella and Butyrivibrio were widespread in the rumen of goats and no significant difference was observed in relative abundance between groups. Conclusion We concluded that the richness of fiber-, protein-, and fat-digesting bacteria was affected by diet and tended to increase with the rise of their corresponding substrate contents in the ration; some bacteria shared by all goats maintained stable despite the difference in the ration, and they might be essential in maintaining the normal function of rumen.
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Affiliation(s)
- Kaizhen Liu
- Institute of Animal Nutrition, Sichuan Agricultural University, Ya'an 625014, China
| | - Qin Xu
- Institute of Animal Nutrition, Sichuan Agricultural University, Ya'an 625014, China
| | - Lizhi Wang
- Institute of Animal Nutrition, Sichuan Agricultural University, Ya'an 625014, China
| | - Jiwen Wang
- Institute of Animal Nutrition, Sichuan Agricultural University, Ya'an 625014, China
| | - Wei Guo
- Institute of Animal Nutrition, Sichuan Agricultural University, Ya'an 625014, China
| | - Meili Zhou
- Institute of Animal Nutrition, Sichuan Agricultural University, Ya'an 625014, China
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Zeitz J, Ineichen S, Soliva C, Leiber F, Tschuor A, Braun U, Kreuzer M, Clauss M. Variability in microbial population and fermentation traits at various sites within the forestomach and along the digestive tract as assessed in goats fed either grass or browse. Small Rumin Res 2016. [DOI: 10.1016/j.smallrumres.2015.12.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Insam H, Podmirseg SM, Wagner AO, Simunek J. No oxygen-still vigorous: 8th International Symposium on Anaerobic Microbiology (ISAM 8) Innsbruck, Austria. Anaerobe 2014; 29:1-2. [DOI: 10.1016/j.anaerobe.2014.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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