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da Silva ÉBR, da Silva JAR, da Silva WC, Belo TS, Sousa CEL, dos Santos MRP, Neves KAL, Rodrigues TCGDC, Camargo-Júnior RNC, Lourenço-Júnior JDB. A Review of the Rumen Microbiota and the Different Molecular Techniques Used to Identify Microorganisms Found in the Rumen Fluid of Ruminants. Animals (Basel) 2024; 14:1448. [PMID: 38791665 PMCID: PMC11117383 DOI: 10.3390/ani14101448] [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: 01/24/2024] [Revised: 03/13/2024] [Accepted: 03/19/2024] [Indexed: 05/26/2024] Open
Abstract
Variations in environments, including climate, diet, and agricultural practices, significantly impact the composition and microbial activity. A profound understanding of these adaptations allows for the improvement of nutrition and ruminant production. Therefore, this review aims to compile data from the literature on the rumen microbiota and molecular techniques for identifying the different types of microorganisms from the rumen fluid of ruminants. Analyzing the literature on rumen microbiology in different ruminants is complex due to microbial interactions, influenced by the environment and nutrition of these animals. In addition, it is worth noting that the genera of protozoa and fungi most evident in the studies used in this review on the microbiology of rumen fluid were Entodinium spp. and Aspergillus spp., respectively, and Fibrobacter spp. for bacteria. About the techniques used, it can be seen that DNA extraction, amplification, and sequencing were the most cited in the studies evaluated. Therefore, this review describes what is present in the literature and provides an overview of the main microbial agents in the rumen and the molecular techniques used.
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Affiliation(s)
- Éder Bruno Rebelo da Silva
- Postgraduate Program in Animal Science (PPGCAN), Institute of Veterinary Medicine, Federal University of Para (UFPA), Castanhal 68746-360, Brazil; (W.C.d.S.); (T.C.G.d.C.R.); (R.N.C.C.-J.); (J.d.B.L.-J.)
| | | | - Welligton Conceição da Silva
- Postgraduate Program in Animal Science (PPGCAN), Institute of Veterinary Medicine, Federal University of Para (UFPA), Castanhal 68746-360, Brazil; (W.C.d.S.); (T.C.G.d.C.R.); (R.N.C.C.-J.); (J.d.B.L.-J.)
| | - Tatiane Silva Belo
- Department of Veterinary Medicine, University Center of the Amazon (UNAMA), Santarém 68010-200, Brazil; (T.S.B.); (C.E.L.S.)
| | - Carlos Eduardo Lima Sousa
- Department of Veterinary Medicine, University Center of the Amazon (UNAMA), Santarém 68010-200, Brazil; (T.S.B.); (C.E.L.S.)
| | | | | | - Thomaz Cyro Guimarães de Carvalho Rodrigues
- Postgraduate Program in Animal Science (PPGCAN), Institute of Veterinary Medicine, Federal University of Para (UFPA), Castanhal 68746-360, Brazil; (W.C.d.S.); (T.C.G.d.C.R.); (R.N.C.C.-J.); (J.d.B.L.-J.)
| | - Raimundo Nonato Colares Camargo-Júnior
- Postgraduate Program in Animal Science (PPGCAN), Institute of Veterinary Medicine, Federal University of Para (UFPA), Castanhal 68746-360, Brazil; (W.C.d.S.); (T.C.G.d.C.R.); (R.N.C.C.-J.); (J.d.B.L.-J.)
| | - José de Brito Lourenço-Júnior
- Postgraduate Program in Animal Science (PPGCAN), Institute of Veterinary Medicine, Federal University of Para (UFPA), Castanhal 68746-360, Brazil; (W.C.d.S.); (T.C.G.d.C.R.); (R.N.C.C.-J.); (J.d.B.L.-J.)
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Ma X, Li Z, Cai L, Xiao M, He F, Liu Z, Chen D, Wang Y, Shen L, Gu Y. Analysis of fungal diversity in the gut feces of wild takin ( Budorcas taxicolor). Front Microbiol 2024; 15:1364486. [PMID: 38699479 PMCID: PMC11063333 DOI: 10.3389/fmicb.2024.1364486] [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: 01/31/2024] [Accepted: 04/08/2024] [Indexed: 05/05/2024] Open
Abstract
Introduction The composition of the intestinal microbiome correlates significantly with an animal's health status. Hence, this indicator is highly important and sensitive for protecting endangered animals. However, data regarding the fungal diversity of the wild Budorcas taxicolor (takin) gut remain scarce. Therefore, this study analyzes the fungal diversity, community structure, and pathogen composition in the feces of wild B. taxicolor. Methods To ensure comprehensive data analyses, we collected 82 fecal samples from five geographical sites. Amplicon sequencing of the internal transcribed spacer (ITS) rRNA was used to assess fecal core microbiota and potential pathogens to determine whether the microflora composition is related to geographical location or diet. We further validated the ITS rRNA sequencing results via amplicon metagenomic sequencing and culturing of fecal fungi. Results and discussion The fungal diversity in the feces of wild Budorcas taxicolor primarily comprised three phyla (99.69%): Ascomycota (82.19%), Fungi_unclassified (10.37%), and Basidiomycota (7.13%). At the genus level, the predominant fungi included Thelebolus (30.93%), Functional_unclassified (15.35%), and Ascomycota_unclassified (10.37%). Within these genera, certain strains exhibit pathogenic properties, such as Thelebolus, Cryptococcus, Trichosporon, Candida, Zopfiella, and Podospora. Collectively, this study offers valuable information for evaluating the health status of B. taxicolor and formulating protective strategies.
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Affiliation(s)
- Xiaoping Ma
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zhiguo Li
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Lijun Cai
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Management Office of Tangjiahe National Nature Reserve, Qingchuan, China
| | - Mei Xiao
- Management Office of Tangjiahe National Nature Reserve, Qingchuan, China
| | - Fang He
- Management Office of Tangjiahe National Nature Reserve, Qingchuan, China
| | - Zhen Liu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Dong Chen
- Sichuan Provincial Center for Animal Disease Prevention and Control, Chengdu, China
| | - Ya Wang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Limin Shen
- Management Office of Tangjiahe National Nature Reserve, Qingchuan, China
| | - Yu Gu
- College of Life Sciences, Sichuan Agricultural University, Chengdu, China
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Yin G, Sun Z, Wang Z, Xia Y, Cheng L, Qin G, Aschalew ND, Liu H, Zhang X, Wu Q, Zhang W, Zhao W, Wang T, Zhen Y. Mechanistic insights into inositol-mediated rumen function promotion and metabolic alteration using in vitro and in vivo models. Front Vet Sci 2024; 11:1359234. [PMID: 38435365 PMCID: PMC10904589 DOI: 10.3389/fvets.2024.1359234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 02/01/2024] [Indexed: 03/05/2024] Open
Abstract
Inositol is a bioactive factor that is widely found in nature; however, there are few studies on its use in ruminant nutrition. This study investigated the effects of different inositol doses and fermentation times on rumen fermentation and microbial diversity, as well as the levels of rumen and blood metabolites in sheep. Rumen fermentation parameters, microbial diversity, and metabolites after different inositol doses were determined in vitro. According to the in vitro results, six small-tailed Han sheep fitted with permanent rumen fistulas were used in a 3 × 3 Latin square feeding experiment where inositol was injected into the rumen twice a day and rumen fluid and blood samples were collected. The in vitro results showed that inositol could increase in vitro dry matter digestibility, in vitro crude protein digestibility, NH3-N, acetic acid, propionic acid, and rumen microbial diversity and affect rumen metabolic pathways (p < 0.05). The feeding experiment results showed that inositol increased the blood concentration of high-density lipoprotein and IgG, IgM, and IL-4 levels. The rumen microbial composition was significantly affected (p < 0.05). Differential metabolites in the rumen were mainly involved in ABC transporters, biotin metabolism, and phenylalanine metabolism, whereas those in the blood were mainly involved in arginine biosynthesis and glutathione and tyrosine metabolism. In conclusion, inositol improves rumen function, affects rumen microorganisms and rumen and blood metabolites and may reduce inflammation, improving animal health.
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Affiliation(s)
- 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
| | - 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
- College of Life Sciences, Engineering Research Center of Bioreactor and Pharmaceutical Development, Ministry of Education, 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
| | - Zhanqing 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
| | - Long Cheng
- 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
| | - 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
| | - 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, Dila, Ethiopia
| | - Hongyun Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, 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
| | - Qilu Wu
- College of Life Sciences, Engineering Research Center of Bioreactor and Pharmaceutical Development, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Weigang Zhang
- Postdoctoral Scientific Research Workstation, Feed Engineering Technology Research Center of Jilin Province, Changchun Borui Science and Technology Co., Ltd., Changchun, China
| | - Wei Zhao
- 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
| | - 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
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Wu Y, Jiao C, Diao Q, Tu Y. Effect of Dietary and Age Changes on Ruminal Microbial Diversity in Holstein Calves. Microorganisms 2023; 12:12. [PMID: 38276181 PMCID: PMC10818949 DOI: 10.3390/microorganisms12010012] [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: 11/02/2023] [Revised: 12/01/2023] [Accepted: 12/03/2023] [Indexed: 01/27/2024] Open
Abstract
Ruminal microorganisms play a crucial role in the energy supply of ruminants and animal performance. We analyzed the variations in rumen bacteria and fungi at 45 d, 75 d, and 105 d by using 16SrRNA and ITS sequencing data and investigated their correlation with rumen fermentation. According to the results, rumen microflora tended to gradually mature with age, and bacterial and fungal establishment gradually stabilized. Upon comparing the three periods, the concentration of propionic acid increased significantly (p < 0.05) after weaning, and weaning accompanied by a transition in diet remarkably decreased (p < 0.05) rumen diversity in the short term and induced a corresponding change in the rumen microbiota composition. Bacteroidota, Actinobacteriota, and Firmicutes were the core bacterial phyla for all age periods. Ruminococcus, NK4A214_group, Sharpea, Rikenellaceae_RC9_gut_group, and norank_f__Butyricicoccaceae were the markedly abundant bacterial genera in pre-weaning. After weaning, the relative abundance of Erysipelotrichaceae_ UCG-002, Eubacterium_ruminantium_group, and Solobacterium significantly increased (p < 0.05). The relative abundance of Acetitomaculum increased with age with the greatest abundance noted at 105 d (37%). The dominant fungal phyla were Ascomycota and Basidiomycota, and Aspergillus and Xeromyces were the most abundant fungal genera after weaning. Trichomonascus, Phialosimplex, and Talaromyces were enriched at 105 d. However, the low abundance of Neocallimastigomycota was not detected throughout the study, which is worthy of further investigation. In addition, correlations were observed between age-related abundances of specific genera and microbiota functions and rumen fermentation-related parameters. This study revealed that rumen microbiota and rumen fermentation capacity are correlated, which contributed to a better understanding of the effects of age and diet on rumen microbiology and fermentation in calves.
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Affiliation(s)
| | | | | | - Yan Tu
- Key Laboratory for Dairy Cow Nutrition, Institute of Feed Research of Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (C.J.); (Q.D.)
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Zhou X, Ma Y, Yang C, Zhao Z, Ding Y, Zhang Y, Wang P, Zhao L, Li C, Su Z, Wang X, Ming W, Zeng L, Kang X. Rumen and Fecal Microbiota Characteristics of Qinchuan Cattle with Divergent Residual Feed Intake. Microorganisms 2023; 11:microorganisms11020358. [PMID: 36838323 PMCID: PMC9964965 DOI: 10.3390/microorganisms11020358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/18/2023] [Accepted: 01/26/2023] [Indexed: 02/04/2023] Open
Abstract
Residual feed intake (RFI) is one of the indicators of feed efficiency. To investigate the microbial characteristics and differences in the gastrointestinal tract of beef cattle with different RFI, a metagenome methodology was used to explore the characteristics of the rumen and fecal microbiota in 10 Qinchuan cattle (five in each of the extremely high and extremely low RFI groups). The results of taxonomic annotation revealed that Bacteroidetes and Firmicutes were the most dominant phyla in rumen and feces. Prevotella was identified as a potential biomarker in the rumen of the LRFI group by the LEfSe method, while Turicibacter and Prevotella might be potential biomarkers of the HRFI and LRFI group in feces, respectively. Functional annotation revealed that the microbiota in the rumen of the HRFI group had a greater ability to utilize dietary polysaccharides and dietary protein. Association analysis of rumen microbes (genus level) with host genes revealed that microbiota including Prevotella, Paraprevotella, Treponema, Oscillibacter, and Muribaculum, were significantly associated with differentially expressed genes regulating RFI. This study discovered variances in the microbial composition of rumen and feces of beef cattle with different RFIs, demonstrating that differences in microbes may play a critical role in regulating the bovine divergent RFI phenotype variations.
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de Freitas AS, Gan FC, de David DB, Wurdig Roesch LF. The microbiome shifts throughout the gastrointestinal tract of Bradford cattle in the Pampa biome. PLoS One 2022; 17:e0279386. [PMID: 36538559 PMCID: PMC9767327 DOI: 10.1371/journal.pone.0279386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
A deep understanding of the cattle gastrointestinal microbiome is crucial to selective breeding high-efficiency animals that produce more and generate less environmental damage. Here we performed the taxonomic identification of Bacterial and Archaeal communities using high throughput 16SrRNA gene sequencing from critical compartments of the gastrointestinal tract of Bradford cattle raised in a natural grassland in the Pampa biome, Brazil. We analyzed 110 samples, including saliva, ruminal fluid, and feces from 36 months old Bradford heifers (weighing on average 343 ± 30 kg by the sampling time). To reduce unexpected variation and confounders, we selected the animals from the same breed, submitted them to the same food source, and collected the samples for three consecutive years from different animals in the same season. Our main goal was to analyze the microbial shifts throughout the gastrointestinal tract to reference future works proposing management strategies and interventions to improve animal nutrition and increase production in the Pampa Biome. To accomplish our objective, we accessed the microbial community differences in groups with a high and low weight gain controlling for food ingestion and quality of grazed pasture. Few taxa were shared among the samples. About 40% of the phyla and 60% of the genera were unique from saliva samples, and 12.4% of the microbial genera were uniquely found in feces. All samples shared only 36.1% of phyla and 7.5% of genera. Differences in microbial diversity and taxa counts were observed. The ruminal fluid presented the lowest microbial richness, while saliva and feces presented the highest microbial richness. On the other hand, saliva and feces also presented more distinct communities between themselves when compared with ruminal samples. Our data showed that the saliva microbiome is not representative of the rumen microbiome and should not be used as an easy-to-collect sample for studies about the rumen microbiome.
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Affiliation(s)
| | - Flávia Caroline Gan
- Centro Interdisciplinar de Pesquisas em Biotecnologia–CIP-Biotec, Campus São Gabriel, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
| | - Diego Bittencourt de David
- Departamento de Diagnóstico e Pesquisa Agropecuária–DDPA, Secretaria Estadual da Agricultura, Pecuária e Desenvolvimento Rural–SEADPR/RS, São Gabriel, Rio Grande do Sul, Brazil
| | - Luiz Fernando Wurdig Roesch
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
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Wang Q, Zeng X, Zeng Y, Liu X, Wang Y, Wang X, Li J, Wang Y, Feng Z, Huang P, Yin J, Huang J, Zhu M, Yang H. Effects of Phragmites australis Shoot Remainder Silage on Growth Performance, Blood Biochemical Parameters, and Rumen Microbiota of Beef Cattle. Front Vet Sci 2022; 9:778654. [PMID: 35274018 PMCID: PMC8902168 DOI: 10.3389/fvets.2022.778654] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 01/03/2022] [Indexed: 11/26/2022] Open
Abstract
The objective of the present study was to assess the effects of replacing corn silage with Phragmites australis shoot remainder (PSR) silage on intake, growth performance, serum biochemical parameters, and rumen microbial diversity of growing-finishing beef. Fifteen Angus beef cattle with an average body weight of 253 ± 2.94 kg were randomly divided into three groups (five replicas vs. each group vs. Angus beef cattle). The three treatments were group A fed 60% PSR silage + 40% concentrate, group B fed 30% PSR silage + 30% corn silage + 40% concentrate, and group C fed 60% corn silage + 40% concentrate. The adaptation period was 15 days, and the trial period lasted for 45 days. Results showed that the ADG was significantly higher, and FCR was significantly lower both in groups A and B compared with group C. The results of serum biochemical parameters showed that the concentration of GLU was significantly lower in group B than both groups A and C. Microbial diversity results showed that the OTUs, Shannon, Chao1, and ACE indices were significantly lower in group A compared with groups B and C. At the phyla level, the relative abundances of Tenericutes and Melainabacteria had significant differences among the three groups, and the relative abundances of Papillibacter, Anaeroplasma, and Anaerovorax had significant differences among the three groups at the genus level. Additionally, Rikenellaceae was the unique biomarker among the three groups. Furthermore, the results of function prediction showed that the gene families associated with metabolism of cofactors and vitamins, cellular processes and signaling, metabolism, biosynthesis of other secondary metabolites, infectious diseases, signaling molecules and interaction, nervous system, and digestive system were significantly decreased, while lipid metabolism was dramatically increased from groups A to C at KEGG level 2. At KEGG level 3, 11 metabolic pathways were significantly influenced among the three groups. In summary, these findings indicated that PSR silage substituted the corn silage totally or partially improved the growth performance, and altered the rumen microbial composition and diversity and the corresponding change in prediction function of rumen bacteria in Angus beef cattle.
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Affiliation(s)
- Qiye Wang
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, China
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agro-Ecological Processes in Subtropical Region, Hunan Provincial Engineering Research Center of Healthy Livestock, Scientific Observing and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Xianglin Zeng
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Yutong Zeng
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Xiaoruowei Liu
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Yancan Wang
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Xin Wang
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Jianzhong Li
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Yiqiang Wang
- Key Lab of Non-wood Forest Nurturing and Protection of National Ministry of Education, Hunan Provincial Key Laboratory for Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, China
| | - Zhi Feng
- Key Lab of Non-wood Forest Nurturing and Protection of National Ministry of Education, Hunan Provincial Key Laboratory for Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, China
| | - Pengfei Huang
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Jia Yin
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Jing Huang
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Mingzhi Zhu
- Key Laboratory of Tea Science of Ministry of Education, National Research Center of Engineering Technology for Utilization of Functional Ingredients From Botanicals, College of Horticulture, Hunan Agricultural University, Changsha, China
- *Correspondence: Mingzhi Zhu
| | - Huansheng Yang
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, China
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agro-Ecological Processes in Subtropical Region, Hunan Provincial Engineering Research Center of Healthy Livestock, Scientific Observing and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- Huansheng Yang
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Ryu EP, Davenport ER. Host Genetic Determinants of the Microbiome Across Animals: From Caenorhabditis elegans to Cattle. Annu Rev Anim Biosci 2022; 10:203-226. [PMID: 35167316 PMCID: PMC11000414 DOI: 10.1146/annurev-animal-020420-032054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Animals harbor diverse communities of microbes within their gastrointestinal tracts. Phylogenetic relationship, diet, gut morphology, host physiology, and ecology all influence microbiome composition within and between animal clades. Emerging evidence points to host genetics as also playing a role in determining gut microbial composition within species. Here, we discuss recent advances in the study of microbiome heritability across a variety of animal species. Candidate gene and discovery-based studies in humans, mice, Drosophila, Caenorhabditis elegans, cattle, swine, poultry, and baboons reveal trends in the types of microbes that are heritable and the host genes and pathways involved in shaping the microbiome. Heritable gut microbes within a host species tend to be phylogenetically restricted. Host genetic variation in immune- and growth-related genes drives the abundances of these heritable bacteria within the gut. With only a small slice of the metazoan branch of the tree of life explored to date, this is an area rife with opportunities to shed light into the mechanisms governing host-microbe relationships.
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Affiliation(s)
- Erica P Ryu
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA; ,
| | - Emily R Davenport
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA; ,
- Huck Institutes of the Life Sciences and Institute for Computational and Data Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
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Abstract
Host-associated microbiomes contribute in many ways to the homeostasis of the metaorganism. The microbiome's contributions range from helping to provide nutrition and aiding growth, development, and behavior to protecting against pathogens and toxic compounds. Here we summarize the current knowledge of the diversity and importance of the microbiome to animals, using representative examples of wild and domesticated species. We demonstrate how the beneficial ecological roles of animal-associated microbiomes can be generally grouped into well-defined main categories and how microbe-based alternative treatments can be applied to mitigate problems for both economic and conservation purposes and to provide crucial knowledge about host-microbiota symbiotic interactions. We suggest a Customized Combination of Microbial-Based Therapies to promote animal health and contribute to the practice of sustainable husbandry. We also discuss the ecological connections and threats associated with animal biodiversity loss, microorganism extinction, and emerging diseases, such as the COVID-19 pandemic.
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Affiliation(s)
- Raquel S Peixoto
- Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil; .,Current affiliation: Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900 Saudia Arabia;
| | - Derek M Harkins
- J. Craig Venter Institute, Rockville, Maryland 20850, USA; ,
| | - Karen E Nelson
- J. Craig Venter Institute, Rockville, Maryland 20850, USA; ,
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