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Niu M, Zhao Y, Xiang L, Jia Y, Yuan J, Dai X, Chen H. 16S rRNA gene sequencing analysis of gut microbiome in a mini-pig diabetes model. Animal Model Exp Med 2022; 5:81-88. [PMID: 35213788 PMCID: PMC8879634 DOI: 10.1002/ame2.12202] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/23/2021] [Accepted: 01/05/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Currently, increasing attention is being paid to the important role of intestinal microbiome in diabetes. However, few studies have evaluated the characteristics of gut microbiome in diabetic miniature pigs, despite it being a good model animal for assessing diabetes. METHODS In this study, a mini-pig diabetes model (DM) was established by 9-month high-fat diet (HFD) combined with low-dose streptozotocin, while the animals fed standard chow diet constituted the control group. 16S ribosomal RNA (rRNA) gene sequencing was performed to assess the characteristics of the intestinal microbiome in diabetic mini-pigs. RESULTS The results showed that microbial structure in diabetic mini-pigs was altered, reflected by increases in levels of Coprococcus_3 and Clostridium_sensu_stricto_1, which were positively correlated with diabetes, and decreases in levels of the bacteria Rikenellaceae, Clostridiales_vadinBB60_group, and Bacteroidales_RF16_group, which were inversely correlated with blood glucose and insulin resistance. Moreover, PICRUSt-predicted pathways related to the glycolysis and Entner-Doudoroff superpathway, enterobactin biosynthesis, and the l-tryptophan biosynthesis were significantly elevated in the DM group. CONCLUSION These results reveal the composition and predictive functions of the intestinal microbiome in the mini-pig diabetes model, further verifying the relationship between HFD, gut microbiome, and diabetes, and providing novel insights into the application of the mini-pig diabetes model in gut microbiome research.
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Affiliation(s)
- Miaomiao Niu
- Laboratory Animal Center, Chinese PLA General Hospital, Beijing, PR China
| | - Yuqiong Zhao
- Laboratory Animal Center, Chinese PLA General Hospital, Beijing, PR China
| | - Lei Xiang
- Laboratory Animal Center, Chinese PLA General Hospital, Beijing, PR China
| | - Yunxiao Jia
- Laboratory Animal Center, Chinese PLA General Hospital, Beijing, PR China
| | - Jifang Yuan
- Laboratory Animal Center, Chinese PLA General Hospital, Beijing, PR China
| | - Xin Dai
- Laboratory Animal Center, Chinese PLA General Hospital, Beijing, PR China
| | - Hua Chen
- Laboratory Animal Center, Chinese PLA General Hospital, Beijing, PR China
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Fang S, Chen X, Ye X, Zhou L, Xue S, Gan Q. Effects of Gut Microbiome and Short-Chain Fatty Acids (SCFAs) on Finishing Weight of Meat Rabbits. Front Microbiol 2020; 11:1835. [PMID: 32849435 PMCID: PMC7431612 DOI: 10.3389/fmicb.2020.01835] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/13/2020] [Indexed: 12/12/2022] Open
Abstract
Understanding how the gut microbiome and short-chain fatty acids (SCFAs) affect finishing weight is beneficial to improve meat production in the meat rabbit industry. In this study, we identified 15 OTUs and 23 microbial species associated with finishing weight using 16S rRNA gene and metagenomic sequencing analysis, respectively. Among these, butyrate-producing bacteria of the family Ruminococcaceae were positively associated with finishing weight, whereas the microbial taxa related to intestinal damage and inflammation showed opposite effects. Furthermore, interactions of these microbial taxa were firstly found to be associated with finishing weight. Gut microbial functional capacity analysis revealed that CAZymes, such as galactosidase, xylanase, and glucosidase, could significantly affect finishing weight, given their roles in regulating nutrient digestibility. GOs related to the metabolism of several carbohydrates and amino acids also showed important effects on finishing weight. Additionally, both KOs and KEGG pathways related to the membrane transportation system and involved in aminoacyl-tRNA biosynthesis and butanoate metabolism could act as key factors in modulating finishing weight. Importantly, gut microbiome explained nearly 11% of the variation in finishing weight, and our findings revealed that a subset of metagenomic species could act as predictors of finishing weight. SCFAs levels, especially butyrate level, had critical impacts on finishing weight, and several finishing weight-associated species were potentially contributed to the shift in butyrate level. Thus, our results should give deep insights into how gut microbiome and SCFAs influence finishing weight of meat rabbits and provide essential knowledge for improving finishing weight by manipulating gut microbiome.
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Affiliation(s)
- Shaoming Fang
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuan Chen
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaoxing Ye
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liwen Zhou
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuaishuai Xue
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qianfu Gan
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, China
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Sapountzis P, Segura A, Desvaux M, Forano E. An Overview of the Elusive Passenger in the Gastrointestinal Tract of Cattle: The Shiga Toxin Producing Escherichia coli. Microorganisms 2020; 8:microorganisms8060877. [PMID: 32531983 PMCID: PMC7355788 DOI: 10.3390/microorganisms8060877] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/05/2020] [Accepted: 06/07/2020] [Indexed: 02/07/2023] Open
Abstract
For approximately 10,000 years, cattle have been our major source of meat and dairy. However, cattle are also a major reservoir for dangerous foodborne pathogens that belong to the Shiga toxin-producing Escherichia coli (STEC) group. Even though STEC infections in humans are rare, they are often lethal, as treatment options are limited. In cattle, STEC infections are typically asymptomatic and STEC is able to survive and persist in the cattle GIT by escaping the immune defenses of the host. Interactions with members of the native gut microbiota can favor or inhibit its persistence in cattle, but research in this direction is still in its infancy. Diet, temperature and season but also industrialized animal husbandry practices have a profound effect on STEC prevalence and the native gut microbiota composition. Thus, exploring the native cattle gut microbiota in depth, its interactions with STEC and the factors that affect them could offer viable solutions against STEC carriage in cattle.
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Affiliation(s)
- Panagiotis Sapountzis
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, 63000 Clermont-Ferrand, France; (A.S.); (M.D.); (E.F.)
- Correspondence:
| | - Audrey Segura
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, 63000 Clermont-Ferrand, France; (A.S.); (M.D.); (E.F.)
- Chr. Hansen Animal Health & Nutrition, 2970 Hørsholm, Denmark
| | - Mickaël Desvaux
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, 63000 Clermont-Ferrand, France; (A.S.); (M.D.); (E.F.)
| | - Evelyne Forano
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, 63000 Clermont-Ferrand, France; (A.S.); (M.D.); (E.F.)
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Holman DB, Gzyl KE. A meta-analysis of the bovine gastrointestinal tract microbiota. FEMS Microbiol Ecol 2020; 95:5497297. [PMID: 31116403 DOI: 10.1093/femsec/fiz072] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/21/2019] [Indexed: 01/04/2023] Open
Abstract
The bovine gastrointestinal (GI) tract microbiota has important influences on animal health and production. Presently, a large number of studies have used high-throughput sequencing of the archaeal and bacteria 16S rRNA gene to characterize these microbiota under various experimental parameters. By aggregating publically available archaeal and bacterial 16S rRNA gene datasets from 52 studies we were able to determine taxa that are common to nearly all microbiota samples from the bovine GI tract as well as taxa that are strongly linked to either the rumen or feces. The methanogenic genera Methanobrevibacter and Methanosphaera were identified in nearly all fecal and rumen samples (> 99.1%), as were the bacterial genera Prevotella and Ruminococcus (≥ 92.9%). Bacterial genera such as Alistipes, Bacteroides, Clostridium, Faecalibacterium and Escherichia/Shigella were associated with feces and Fibrobacter, Prevotella, Ruminococcus and Succiniclasticum with the rumen. As expected, individual study strongly affected the bacterial community structure, however, fecal and rumen samples did appear separated from each other. This meta-analysis provides the first comparison of high-throughput sequencing 16S rRNA gene datasets generated from the bovine GI tract by multiple studies and may serve as a foundation for improving future microbial community research with cattle.
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Affiliation(s)
- Devin B Holman
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, 6000 C & E Trail, Lacombe, AB, Canada, T4L 1W1
| | - Katherine E Gzyl
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, 6000 C & E Trail, Lacombe, AB, Canada, T4L 1W1
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Fang S, Chen X, Pan J, Chen Q, Zhou L, Wang C, Xiao T, Gan QF. Dynamic distribution of gut microbiota in meat rabbits at different growth stages and relationship with average daily gain (ADG). BMC Microbiol 2020; 20:116. [PMID: 32410629 PMCID: PMC7227296 DOI: 10.1186/s12866-020-01797-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 04/21/2020] [Indexed: 02/07/2023] Open
Abstract
Background The mammalian intestinal tract harbors diverse and dynamic microbial communities that play pivotal roles in host health, metabolism, immunity, and development. Average daily gain (ADG) is an important growth trait in meat rabbit industry. The effects of gut microbiota on ADG in meat rabbits are still unknown. Results In this study, we investigated the dynamic distribution of gut microbiota in commercial Ira rabbits from weaning to finishing and uncover the relationship between the microbiota and average daily gain (ADG) via 16S rRNA gene sequencing. The results indicated that the richness and diversity of gut microbiota significantly increased with age. Gut microbial structure was less variable among finishing rabbits than among weaning rabbits. The relative abundances of the dominant phyla Firmicutes, Bacteroidetes, Verrucomicrobia and Cyanobacteria, and the 15 predominant genera significantly varied with age. Metagenomic prediction analysis showed that both KOs and KEGG pathways related to the metabolism of monosaccharides and vitamins were enriched in the weaning rabbits, while those related to the metabolism of amino acids and polysaccharides were more abundant in the finishing rabbits. We identified 34 OTUs, 125 KOs, and 25 KEGG pathways that were significantly associated with ADG. OTUs annotation suggested that butyrate producing bacteria belong to the family Ruminococcaceae and Bacteroidales_S24-7_group were positively associated with ADG. Conversely, Eubacterium_coprostanoligenes_group, Christensenellaceae_R-7_group, and opportunistic pathogens were negatively associated with ADG. Both KOs and KEGG pathways correlated with the metabolism of vitamins, basic amino acids, and short chain fatty acids (SCFAs) showed positive correlations with ADG, while those correlated with aromatic amino acids metabolism and immune response exhibited negative correlations with ADG. In addition, our results suggested that 10.42% of the variation in weaning weight could be explained by the gut microbiome. Conclusions Our findings give a glimpse into the dynamic shifts in gut microbiota of meat rabbits and provide a theoretical basis for gut microbiota modulation to improve ADG in the meat rabbit industry.
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Affiliation(s)
- Shaoming Fang
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xuan Chen
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiahua Pan
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qiaohui Chen
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liwen Zhou
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chongchong Wang
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Tianfang Xiao
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Qian Fu Gan
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Fang S, Chen X, Zhou L, Wang C, Chen Q, Lin R, Xiao T, Gan Q. Faecal microbiota and functional capacity associated with weaning weight in meat rabbits. Microb Biotechnol 2019; 12:1441-1452. [PMID: 31571427 PMCID: PMC6801154 DOI: 10.1111/1751-7915.13485] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 05/15/2019] [Accepted: 08/15/2019] [Indexed: 12/18/2022] Open
Abstract
Weaning weight is an important economic trait in the meat rabbit industry. Evidence has linked the gut microbiota to health and production performance in rabbits. However, the effect of gut microbiota on meat rabbit weaning weight remains unclear. In this study, we performed 16S rRNA gene sequencing analysis of 135 faecal samples from commercial Ira rabbits. We detected 50 OTUs significantly associated with weaning weight. OTUs that showed positive associations with weaning weight were mostly members of the family Ruminococcaceae which are important in degrading dietary fibres and producing butyrate. On the contrary, OTUs annotated to genera Blautia, Lachnoclostridium and Butyricicoccus correlated with fat deposition were negatively associated with weaning weight. Predicted functional capacity analysis revealed that 91 KOs and 26 KEGG pathways exhibited potential correlations with weaning weight. We found that gut microbiota involved in the metabolism of amino acids, butanoate, energy and monosaccharides affected weaning weight. Additionally, cross-validation analysis indicated that 16.16% of the variation in weaning weight was explained by the gut microbiome. Our findings provide important information to improve weaning weight of meat rabbits by modulating their gut microbiome.
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Affiliation(s)
- Shaoming Fang
- College of Animal ScienceFujian Agriculture and Forestry UniversityFuzhouChina
| | - Xuan Chen
- College of Life ScienceFujian Agriculture and Forestry UniversityFuzhouChina
| | - Liwen Zhou
- College of Animal ScienceFujian Agriculture and Forestry UniversityFuzhouChina
| | - Chongchong Wang
- College of Animal ScienceFujian Agriculture and Forestry UniversityFuzhouChina
| | - Qiaohui Chen
- College of Animal ScienceFujian Agriculture and Forestry UniversityFuzhouChina
| | - Ruiyi Lin
- College of Animal ScienceFujian Agriculture and Forestry UniversityFuzhouChina
| | - Tianfang Xiao
- College of Animal ScienceFujian Agriculture and Forestry UniversityFuzhouChina
| | - QianFu Gan
- College of Animal ScienceFujian Agriculture and Forestry UniversityFuzhouChina
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Du R, Jiao S, Dai Y, An J, Lv J, Yan X, Wang J, Han B. Probiotic Bacillus amyloliquefaciens C-1 Improves Growth Performance, Stimulates GH/IGF-1, and Regulates the Gut Microbiota of Growth-Retarded Beef Calves. Front Microbiol 2018; 9:2006. [PMID: 30210477 PMCID: PMC6120984 DOI: 10.3389/fmicb.2018.02006] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 08/08/2018] [Indexed: 01/08/2023] Open
Abstract
Growth retardation of calves is defined as a symptom of impaired growth and development, probably due to growth hormone disorder as well as natural and environmental factors in livestock. The growth-promoting effects of probiotics were determined in 50 growth-retarded growth calves. They were supplied with Bacillus amyloliquefaciens C-1 (Ba, 4 × 1010CFU/d, n = 16), B. subtilis (Bs, 4 × 1010CFU/d, n = 18), and negative control (NC, n = 16) for 30 days. Pre- and post-intervention, the growth performance (weight gain rate, feed intake and feed conversion rate) was analyzed, the serum GH, IGH-1 and immunoglobulin levels were assayed, and the fecal microbiota was detected. Calves in Ba and Bs groups demonstrated increased body weight gain, feed intake and GH/IGF-1 levels, as well as a more efficient feed conversion rate, compared with NC group (P < 0.05). Additionally, the abundances of bacteria contributing to the production of energy and SCFAs (short chain fatty acids), including Proteobacteria, Rhodospirillaceae, Campylobacterales, and Butyricimonas were increased compared with NC group (P < 0.05, FDR < 0.1); and the suspected pathogens, which included Anaeroplasma and Acholeplasma were decreased (P < 0.05, FDR < 0.1) in both the Bs and Ba groups. Akkermansia, which is involved in the intestinal mucosal immune response, was increased in Bs group after intervention (P < 0.05, FDR < 0.1), but exhibited no obvious difference in Ba group. The increased bacterial genera in Ba group were Sphaerochaeta and Treponema (P < 0.05, FDR < 0.1). These results indicate that the probiotics B. amyloliquefaciens and B. subtilis exhibited similar therapeutic potential in terms of growth performance by regulating hormones, and improving the intestinal and rumen development in growth-retarded animals.
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Affiliation(s)
- Renjia Du
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Shengyin Jiao
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yue Dai
- Institute of Food and Agriculture, China National Institute of Standardization, Beijing, China
| | - Jianbo An
- Xi'an Center for Disease Control and Prevention, Xi'an, China
| | - Jia Lv
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Xiaoni Yan
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Juan Wang
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Bei Han
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
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Nesengani LT, Wang J, Yang Y, Yang L, Lu W. Unravelling vaginal microbial genetic diversity and abundance between Holstein and Fleckvieh cattle. RSC Adv 2017. [DOI: 10.1039/c7ra10553c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The breed effect could determine the vaginal microbial genetic diversity and abundance between Holstein and Fleckvieh cattle.
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Affiliation(s)
- Lucky T. Nesengani
- College of Animal Science and Technology
- Jilin Agricultural University
- Changchun
- China
| | - Jun Wang
- College of Animal Science and Technology
- Jilin Agricultural University
- Changchun
- China
| | - Yujiang Yang
- College of Animal Science and Technology
- Jilin Agricultural University
- Changchun
- China
| | - Lianyu Yang
- College of Animal Science and Technology
- Jilin Agricultural University
- Changchun
- China
| | - Wenfa Lu
- College of Animal Science and Technology
- Jilin Agricultural University
- Changchun
- China
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