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Ren C, Zhang X, Wei H, Wang S, Wang W, He L, Lu Y, Zhang K, Zhang Z, Wang G, Huang Y. Effect of Replacing Alfalfa Hay with Common Vetch Hay in Sheep Diets on Growth Performance, Rumen Fermentation and Rumen Microbiota. Animals (Basel) 2024; 14:2182. [PMID: 39123708 PMCID: PMC11310988 DOI: 10.3390/ani14152182] [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: 06/04/2024] [Revised: 07/23/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024] Open
Abstract
The aim of this study was to determine whether the inclusion of 40% of common vetch (CV) hay as a feed ingredient in place of alfalfa hay (AH) would improve performance and ruminal fermentation and microbiota in fattening lambs. Twenty lambs were equally divided into two groups: control group (fed 40% AH with 20% rice straw) and CV group (fed 40% CV hay with 20% rice straw). Concerning hay quality, CV hay had greater in vitro digestibility of dry matter and neutral detergent fiber (p < 0.05) than AH. Lambs fed the CV diet had a higher average daily gain (ADG) and efficiency of feed and economy than lambs fed the control group. The NH3-N content and estimated methane produced per unit of ADG of the CV diet group were significantly lower (p < 0.05) than control group. Multiple differential microbial genera were identified, with Prevotella being the most dominant genus and a tendency towards higher (p = 0.095) in lambs offered CV diet. The higher Ruminococcus abundance (p < 0.05) was found in animals of the CV group compared to the control group. In summary, CV can be incorporated into lamb diets as a low-cost forage alternative to AH to improve feed efficiency and animal performance and to reduce methane produced per unit of ADG.
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Affiliation(s)
- Chunhuan Ren
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; (C.R.); (X.Z.); (H.W.); (S.W.); (W.W.); (Y.L.); (K.Z.); (Z.Z.)
| | - Xiaoan Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; (C.R.); (X.Z.); (H.W.); (S.W.); (W.W.); (Y.L.); (K.Z.); (Z.Z.)
- National Agricultural Green Development Long-Term Fixed Observation Yingshang Test Station, Fuyang 236200, China
- Center of Agriculture Technology Cooperation and Promotion of Dingyuan County, Chuzhou 233200, China
| | - Huiqing Wei
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; (C.R.); (X.Z.); (H.W.); (S.W.); (W.W.); (Y.L.); (K.Z.); (Z.Z.)
| | - Sunze Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; (C.R.); (X.Z.); (H.W.); (S.W.); (W.W.); (Y.L.); (K.Z.); (Z.Z.)
| | - Wenjie Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; (C.R.); (X.Z.); (H.W.); (S.W.); (W.W.); (Y.L.); (K.Z.); (Z.Z.)
| | - Li He
- New Rural Development Research Institute, Anhui Agricultural University, Hefei 230036, China;
| | - Yuan Lu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; (C.R.); (X.Z.); (H.W.); (S.W.); (W.W.); (Y.L.); (K.Z.); (Z.Z.)
| | - Kefan Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; (C.R.); (X.Z.); (H.W.); (S.W.); (W.W.); (Y.L.); (K.Z.); (Z.Z.)
| | - Zijun Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; (C.R.); (X.Z.); (H.W.); (S.W.); (W.W.); (Y.L.); (K.Z.); (Z.Z.)
- Center of Agriculture Technology Cooperation and Promotion of Dingyuan County, Chuzhou 233200, China
| | - Guanjun Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; (C.R.); (X.Z.); (H.W.); (S.W.); (W.W.); (Y.L.); (K.Z.); (Z.Z.)
- National Agricultural Green Development Long-Term Fixed Observation Yingshang Test Station, Fuyang 236200, China
| | - Yafeng Huang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; (C.R.); (X.Z.); (H.W.); (S.W.); (W.W.); (Y.L.); (K.Z.); (Z.Z.)
- Center of Agriculture Technology Cooperation and Promotion of Dingyuan County, Chuzhou 233200, China
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Jost SM, Cardona L, Rohrbach E, Mathis A, Holliger C, Verhulst NO. Environment rather than breed or body site shapes the skin bacterial community of healthy sheep as revealed by metabarcoding. Vet Dermatol 2024; 35:273-283. [PMID: 38082464 DOI: 10.1111/vde.13223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 09/11/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024]
Abstract
BACKGROUND The skin is inhabited by a variety of micro-organisms, with bacteria representing the predominant taxon of the skin microbiome. In sheep, the skin bacterial community of healthy animals has been addressed in few studies, only with culture-based methods or sequencing of cloned amplicons. OBJECTIVES The objectives of this study were to determine the sheep skin bacterial community composition by using metabarcoding for a detailed characterisation and to determine the effect of body part, breed and environment. MATERIALS AND METHODS Overall, 267 samples were taken from 89 adult female sheep, belonging to three different breeds and kept on nine different farms in Switzerland. From every individual, one sample each was taken from belly, left ear and left leg and metabarcoding of the 16S rRNA V3-V4 hypervariable region was performed. RESULTS The main phyla identified were Actinobacteriota, Firmicutes, Proteobacteria and Bacteriodota. The alpha diversity as determined by Shannon's diversity index was significantly different between sheep from different farms. Beta diversity analysis by principal coordinate analysis (PCoA) showed clustering of the samples by farm and body site, while breed had only a marginal influence. A sparse partial least squares discriminant analysis (sPLS-DA) revealed seven main groups of operational taxonomic units (OTUs) of which groups of OTUs were specific for some farms. CONCLUSIONS AND CLINICAL RELEVANCE These findings indicate that environment has a larger influence on skin microbial variability than breed, although the sampled breeds, the most abundant ones in Switzerland, are phenotypically similar. Future studies on the sheep skin microbiome may lead to novel insights in skin diseases and prevention.
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Affiliation(s)
- Stéphanie M Jost
- Vetsuisse and Medical Faculty, Vector Entomology unit, National Centre for Vector Entomology, Institute of Parasitology, University of Zürich, Zürich, Switzerland
| | - Laëtitia Cardona
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Emmanuelle Rohrbach
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Alexander Mathis
- Vetsuisse and Medical Faculty, Vector Entomology unit, National Centre for Vector Entomology, Institute of Parasitology, University of Zürich, Zürich, Switzerland
| | - Christof Holliger
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Niels O Verhulst
- Vetsuisse and Medical Faculty, Vector Entomology unit, National Centre for Vector Entomology, Institute of Parasitology, University of Zürich, Zürich, Switzerland
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Liu H, Peng W, Mao K, Yang Y, Wu Q, Wang K, Zeng M, Han X, Han J, Zhou H. The Changes in Fecal Bacterial Communities in Goats Offered Rumen-Protected Fat. Microorganisms 2024; 12:822. [PMID: 38674767 PMCID: PMC11052158 DOI: 10.3390/microorganisms12040822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Leizhou goats are famous for their delicious meat but have inferior growth performance. There is little information on rumen-protected fat (RPF) from the Leizhou goat. Hence, we observed the effects of RPF on growth, fecal short-chain fatty acids, and bacteria community with respect to Leizhou goats. Twelve goats (13.34 ± 0.024 kg) were selected and assigned randomly to one of two treatments: (1) a control diet (CON) and (2) 2.4% RPF with a control diet (RPF). The final body weight and average daily gain (ADG) were greater (p < 0.05), and the dry matter intake (DMI): ADG was lower (p < 0.05) in the RPF group than in the CON group. There were no differences in DMI between the CON and RPF groups. The concentrations of total short-chain fatty acids, acetate, propionate, and butyrate were lower (p < 0.05) in the RPF group than in the CON group. The relative abundances of Ruminococcus, Rikenellaceae_RC9_gut_group, Treponema, norank_f__norank_o__RF39, Eubacterium_siraeum_group, and Ruminococcus_torques_group were lower (p < 0.05) in the RPF group than in the CON group. The relative abundances of Bacteroides, norank_f__norank_o__Clostridia_UCG-014, norank_f__Eubacterium_coprostanoligenes_group, Eubacterium_ruminantium_group, norank_f__Oscillospirale-UCG-010, Oscillospiraceae_UCG-002, and Family_XIII_AD3011_group were greater (p < 0.05) in the RPF group than in the CON group. It was concluded that RPF could improve the goats' growth performance by regulating their fecal bacteria communities.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jiancheng Han
- Zhanjiang Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524000, China; (H.L.); (W.P.); (K.M.); (Y.Y.); (Q.W.); (M.Z.)
| | - Hanlin Zhou
- Zhanjiang Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524000, China; (H.L.); (W.P.); (K.M.); (Y.Y.); (Q.W.); (M.Z.)
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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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Wu Y, Gao N, Sun C, Feng T, Liu Q, Chen WH. A compendium of ruminant gastrointestinal phage genomes revealed a higher proportion of lytic phages than in any other environments. MICROBIOME 2024; 12:69. [PMID: 38576042 PMCID: PMC10993611 DOI: 10.1186/s40168-024-01784-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 02/29/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND Ruminants are important livestock animals that have a unique digestive system comprising multiple stomach compartments. Despite significant progress in the study of microbiome in the gastrointestinal tract (GIT) sites of ruminants, we still lack an understanding of the viral community of ruminants. Here, we surveyed its viral ecology using 2333 samples from 10 sites along the GIT of 8 ruminant species. RESULTS We present the Unified Ruminant Phage Catalogue (URPC), a comprehensive survey of phages in the GITs of ruminants including 64,922 non-redundant phage genomes. We characterized the distributions of the phage genomes in different ruminants and GIT sites and found that most phages were organism-specific. We revealed that ~ 60% of the ruminant phages were lytic, which was the highest as compared with those in all other environments and certainly will facilitate their applications in microbial interventions. To further facilitate the future applications of the phages, we also constructed a comprehensive virus-bacteria/archaea interaction network and identified dozens of phages that may have lytic effects on methanogenic archaea. CONCLUSIONS The URPC dataset represents a useful resource for future microbial interventions to improve ruminant production and ecological environmental qualities. Phages have great potential for controlling pathogenic bacterial/archaeal species and reducing methane emissions. Our findings provide insights into the virome ecology research of the ruminant GIT and offer a starting point for future research on phage therapy in ruminants. Video Abstract.
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Affiliation(s)
- Yingjian Wu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Na Gao
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Chuqing Sun
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Tong Feng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China.
| | - Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
- Institution of Medical Artificial Intelligence, Binzhou Medical University, Yantai, 264003, China.
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Wu D, Zhang Z, Song Q, Jia Y, Qi J, Xu M. Modulating Gastrointestinal Microbiota in Preweaning Dairy Calves: Dose-Dependent Effects of Milk-Based Sodium Butyrate Supplementation. Microorganisms 2024; 12:333. [PMID: 38399737 PMCID: PMC10893347 DOI: 10.3390/microorganisms12020333] [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: 12/28/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Sodium butyrate (SB), an essential nutritional additive for livestock, has drawn notable interest for its potential for enhancing microbiota development in ruminant animals. This study aimed to assess SB's effects on ruminal and intestinal microbiota when added to milk for preweaning dairy calves nearing 45 days old. We administered SB in the calves' milk at four levels: 0 g/d (control), 4.4 g/d (low), 8.8 g/d (medium), and 17.6 g/d (high). After a six-week trial with ten replicates per group, ruminal fluid and fecal samples were collected for 16S rRNA sequencing, specifically targeting the V3-V4 regions to analyze microbiota. The results indicated an enhancement in ruminal microbiota, particularly in community richness, with low-level SB supplementation but minimal benefits from medium and high levels of supplementation. Increasing the level of SB supplementation had a negative impact on intestinal microbiota, affecting community richness and some potentially beneficial bacterial genera. However, low SB supplementation could positively adjust the communication between ruminal and intestinal microbiota. Overall, this study suggests feeding milk supplemented with a low level of SB to suckling calves close to an older age to promote ruminal microbiota development.
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Affiliation(s)
- Donglin Wu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (D.W.); (Z.Z.); (Y.J.)
| | - Zhanhe Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (D.W.); (Z.Z.); (Y.J.)
| | - Qifan Song
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (D.W.); (Z.Z.); (Y.J.)
| | - Yang Jia
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (D.W.); (Z.Z.); (Y.J.)
- National Center of Technology Innovation for Dairy, Hohhot 010080, China
| | - Jingwei Qi
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (D.W.); (Z.Z.); (Y.J.)
- National Center of Technology Innovation for Dairy, Hohhot 010080, China
| | - Ming Xu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (D.W.); (Z.Z.); (Y.J.)
- National Center of Technology Innovation for Dairy, Hohhot 010080, China
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Nezhadi J, Rezaee MA, Ozma MA, Ganbarov K, Kafil HS. Gut Microbiota Exchange in Domestic Animals and Rural-urban People Axis. Curr Pharm Biotechnol 2024; 25:825-837. [PMID: 37877143 DOI: 10.2174/0113892010261535230920062107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/13/2023] [Accepted: 08/25/2023] [Indexed: 10/26/2023]
Abstract
In recent years, one of the most critical topics in microbiology that can be addressed is microbiome and microbiota. The term microbiome contains both the microbiota and structural elements, metabolites/signal molecules, and the surrounding environmental conditions, and the microbiota consists of all living members forming the microbiome. Among; the intestinal microbiota is one of the most important microbiota, also called the gut microbiota. After colonization, the gut microbiota can have different functions, including resistance to pathogens, maintaining the intestinal epithelium, metabolizing dietary and pharmaceutical compounds, and controlling immune function. Recently, studies have shown that the gut microbiota can prevent the formation of fat in the body. In this study, we examined the gut microbiota in various animals, including dogs, cats, dairy cows, sheep, chickens, horses, and people who live in urban and rural areas. Based on the review of various studies, it has been determined that the population of microbiota in animals and humans is different, and various factors such as the environment, nutrition, and contact with animals can affect the microbiota of people living in urban and rural areas.
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Affiliation(s)
- Javad Nezhadi
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Mahdi Asghari Ozma
- Department of Microbiology, Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Khudaverdi Ganbarov
- Department of Microbiology, Research Laboratory of Microbiology and Virology, Baku State University, Baku, Azerbaijan
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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Gao H, Jiang F, Zhang J, Chi X, Song P, Li B, Cai Z, Zhang T. Effects of ex situ conservation on diversity and function of the gut microbiota of the Tibetan wild ass (Equus kiang). Integr Zool 2023; 18:1089-1104. [PMID: 37231976 DOI: 10.1111/1749-4877.12726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Ex situ conservation is the main method for the protection of endangered wildlife. To explore the effect of ex situ conservation on the gut microbiota of the kiang (Equus kiang), metagenomic sequencing combined with bioinformatics analysis was used to investigate the composition and function of the gut microbiota of the kiang. The results showed that ex situ conservation not only protected wildlife, but also affected the composition and function of gut microbiota, as well as the health of animals. In the zoo, the ratio of the relative abundance of Firmicutes to that of Bacteroidetes (F/B) is higher, clusters of potentially pathogenic bacteria (such as Catonella, Catonella, and Mycoplasma) are more numerous, the abundance of resistance genes is higher, and the abundance of metabolic functions is increased. The dynamic changes of the gut microbiota also played an important role in the nutritional absorption, energy metabolism, and environmental adaptation of the kiang. Improving the rearing environment and increasing food diversity play important roles for increasing the diversity of gut microbiota, reducing the spread of potentially pathogenic bacteria, and reducing diseases. In the wild, especially in winter and in food-deficient areas, food supplementation can enhance the gut microbial homeostasis of wild animals and reduce the impact of crises. In depth studies of the gut microbial function of wildlife have important implications for improving ex situ conservation.
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Affiliation(s)
- Hongmei Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Feng Jiang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Jingjie Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiangwen Chi
- Department of Student Affairs, Qinghai University, Xining, China
| | - Pengfei Song
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Bin Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhenyuan Cai
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Tongzuo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
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Xiao H, Yan H, Tian P, Ji S, Zhao W, Lu C, Zhang Y, Liu Y. The effect of early colonized gut microbiota on the growth performance of suckling lambs. Front Microbiol 2023; 14:1273444. [PMID: 37954254 PMCID: PMC10635232 DOI: 10.3389/fmicb.2023.1273444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/04/2023] [Indexed: 11/14/2023] Open
Abstract
The early colonized gut microbiota during the newborn period has been reported to play important roles in the health and immunity of animals; however, whether they can affect the growth performance of suckling lambs is still unclear. In this study, a total of 84 newborn lambs were assigned into LF-1 (top 15%), LF-2 (medium 70%), and LF-3 (bottom 15%) groups according to their average body weight gain at 30 days of age. Fecal samples of lambs (LF) as well as feces (MF), vagina (VAG), colostrum (COL), teat skin (TEAT) samples of ewes, and the air sediment (AIR) in the delivery room were collected 72 h after birth, and then the 16S rRNA gene was sequenced on the Illumina MiSeq platform. The results showed that the early colonized gut microbiota had a significant effect on the growth performance of suckling lambs with alpha and beta diversity (p < 0.05), and we observed that the contribution of early colonized bacteria on the growth performance of lambs increased with age (from BW30 at 25.35% to BW45 at 31.10%; from ADG30 at 33.02% to ADG45 at 39.79% by measuring the relative effects of factors that influence growth performance). The early colonized gut microbiota of suckling lambs with high growth performance was similar to that in VAG, MF, and AIR (p < 0.05). With the RandomForest machine learning algorithm, we detected 11, 11, 6, and 4 bacterial taxa at the genus level that were associated with BW30, BW45, ADG30, and ADG45 of suckling lambs, respectively, and the correlation analysis showed that Butyricicoccus, Ruminococcus_gnavus_group, Ruminococcaceae_Other, and Fusobacterium could significantly affect the growth performance (BW30, BW45, ADG30, and ADG45) of suckling lambs (p < 0.05). In conclusion, the early colonized gut microbiota could significantly affect the growth performance of suckling lambs, and targeting the early colonized gut microbiota might be an alternative strategy to improve the growth performance of suckling lambs.
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Affiliation(s)
| | | | | | - Shoukun Ji
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
| | | | | | | | - Yueqin Liu
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
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Huang Y, Jonsson NN, McLaughlin M, Burchmore R, Johnson PCD, Jones RO, McGill S, Brady N, Weidt S, Eckersall PD. Quantitative TMT-based proteomics revealing host, dietary and microbial proteins in bovine faeces including barley serpin Z4, a prominent component in the head of beer. J Proteomics 2023; 285:104941. [PMID: 37285906 DOI: 10.1016/j.jprot.2023.104941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/21/2023] [Accepted: 05/25/2023] [Indexed: 06/09/2023]
Abstract
There has been little information about the proteome of bovine faeces or about the contribution to the faecal proteome of proteins from the host, the feed or the intestinal microbiome. Here, the bovine faecal proteome and the origin of its component proteins was assessed, while also determining the effect of treating barley, the major carbohydrate in the feed, with either ammonia (ATB) or sodium propionate (PTB) preservative. Healthy continental crossbreed steers were allocated to two groups and fed on either of the barley-based diets. Five faecal samples from each group were collected on Day 81 of the trial and analysed by quantitative proteomics using nLC-ESI-MS/MS after tandem mass tag labelling. In total, 281 bovine proteins, 199 barley proteins, 176 bacterial proteins and 190 archaeal proteins were identified in the faeces. Mucosal pentraxin, albumin and digestive enzymes were among bovine proteins identified. Serpin Z4 a protease inhibitor was the most abundant barley protein identified which is also found in barley-based beer, while numerous microbial proteins were identified, many originating bacteria from Clostridium, while Methanobrevibacter was the dominant archaeal genus. Thirty-nine proteins were differentially abundant between groups, the majority being more abundant in the PTB group compared to the ATB group. SIGNIFICANCE: Proteomic examination of faeces is becoming a valuable means to assess the health of the gastro-intestinal tract in several species, but knowledge on the proteins present in bovine faeces is limited. This investigation aimed to characterise the proteome of bovine faecal extracts in order to evaluate the potential for investigations of the proteome as a means to assess the health, disease and welfare of cattle in the future. The investigation was able to identify proteins in bovine faeces that had been (i) produced by the individual cattle, (ii) present in the barley-based feed eaten by the cattle or (iii) produced by bacteria and other microbes in the rumen or intestines. Bovine proteins identified included mucosal pentraxin, serum albumin and a variety of digestive enzymes. Barley proteins found in the faeces included serpin Z4, a protease inhibitor that is also found in beer having survived the brewing process. Bacterial and archaeal proteins in the faecal extracts were related to several pathways related to the metabolism of carbohydrates. The recognition of the range of proteins that can be identified in bovine faeces raises the possibility that non-invasive sample collection of this material could provide a novel diagnostic approach to cattle health and welfare.
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Affiliation(s)
- Y Huang
- School of Biodiversity, One Health & Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G61 1QH, UK
| | - N N Jonsson
- School of Biodiversity, One Health & Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G61 1QH, UK
| | - M McLaughlin
- School of Biodiversity, One Health & Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G61 1QH, UK
| | - R Burchmore
- Institute of Infection, Immunity & Inflammation and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1BD, UK
| | - P C D Johnson
- School of Biodiversity, One Health & Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G61 1QH, UK
| | - R O Jones
- School of Biodiversity, One Health & Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G61 1QH, UK
| | - S McGill
- Institute of Infection, Immunity & Inflammation and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1BD, UK
| | - N Brady
- School of Biodiversity, One Health & Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G61 1QH, UK
| | - S Weidt
- Institute of Infection, Immunity & Inflammation and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1BD, UK
| | - P D Eckersall
- School of Biodiversity, One Health & Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G61 1QH, UK; Interdisciplinary Laboratory of Clinical Analysis of the University of Murcia (Interlab-UMU), Department of Animal Medicine and Surgery, Veterinary School, University of Murcia, Murcia 30100, Spain.
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11
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Liang J, Ali S, Lv C, Yang H, Zhao X, Ni X, Li C, Danzeng B, Wang Y, Quan G. Dietary protein levels modulate the gut microbiome composition through fecal samples derived from lactating ewes. Front Endocrinol (Lausanne) 2023; 14:1194425. [PMID: 37621652 PMCID: PMC10446493 DOI: 10.3389/fendo.2023.1194425] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/02/2023] [Indexed: 08/26/2023] Open
Abstract
In ruminants, the digestion and utilization of dietary proteins are closely linked to the bacterial populations that are present in the gastrointestinal tract. In the present study, 16S rDNA sequencing, together with a metagenomic strategy was used to characterize the fecal bacteria of ewes in the early lactation stage after feeding with three levels of dietary proteins 8.58%, 10.34%, and 13.93%, in three different groups (H_1), (H_m) and (H_h), respectively. A total of 376,278,516 clean data-points were obtained by metagenomic sequencing. Firmicutes and Bacteroidetes were the dominant phyla, regardless of the dietary protein levels. In the H_h group, the phyla Proteobacteria, Caldiserica, and Candidatus_Cryosericota were less abundant than those in the H_I group. In contrast, Lentisphaerae, Chlamydiae, and Planctomycetes were significantly more abundant in the H_h group. Some genera, such as Prevotella, Roseburia, and Firmicutes_unclassified, were less abundant in the H_h group than those in the H_I group. In contrast, Ruminococcus, Ruminococcaceae_noname, Anaerotruncus, Thermotalae, Lentisphaerae_noname, and Paraprevotella were enriched in the H_h group. The acquired microbial genes were mainly clustered into biological processes; molecular functions; cytosol; cellular components; cytoplasm; structural constituents of ribosomes; plasma membranes; translation; and catalytic activities. 205987 genes were significantly enriched in the H_h group. In contrast, 108129 genes were more abundant in the H_I group. Our findings reveal that dynamic changes in fecal bacteria and their genes are strongly influenced by the levels of dietary proteins. We discovered that differentially expressed genes mainly regulate metabolic activity and KEGG demonstrated the primary involvement of these genes in the metabolism of carbohydrates, amino acids, nucleotides, and vitamins. Additionally, genes responsible for metabolism were more abundant in the H_h group. Investigating fecal bacterial characteristics may help researchers develop a dietary formula for lactating ewes to optimize the growth and health of ewes and lambs.
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Affiliation(s)
- Jiachong Liang
- The Small Ruminant Department, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan, China
| | - Sikandar Ali
- The Small Ruminant Department, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan, China
- Zhejiang Vegamax Biotechnology Co., Ltd, Hangzhou, Zhejiang, China
| | - Chunrong Lv
- The Small Ruminant Department, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan, China
| | - Hongyuan Yang
- The Small Ruminant Department, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan, China
| | - Xiaoqi Zhao
- The Small Ruminant Department, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan, China
| | - Xiaojun Ni
- The Small Ruminant Department, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan, China
| | - Chunyan Li
- The Small Ruminant Department, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan, China
| | - Baiji Danzeng
- The Small Ruminant Department, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan, China
| | - Yajing Wang
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Guobo Quan
- The Small Ruminant Department, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan, China
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12
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Cholewińska P, Szeligowska N, Wojnarowski K, Nazar P, Greguła-Kania M, Junkuszew A, Rant W, Radzik-Rant A, Marcinkowska A, Bodkowski R. Selected bacteria in sheep stool depending on breed and physiology state. Sci Rep 2023; 13:11739. [PMID: 37474553 PMCID: PMC10359392 DOI: 10.1038/s41598-023-38785-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 07/14/2023] [Indexed: 07/22/2023] Open
Abstract
One of the important factors influencing the microbial community of ruminants, besides environment or diet, are breed and physiology. Therefore, the purpose of this study was to assess these changes in the levels of basic microbial phyla and families. For this study, qPCR analysis was performed to determine the level of bacteria (Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria clusters and Clostridiaceae, Lactobacillaceae families) in the feces of ewes of three native Polish sheep breeds (Polish Lowland Sheep (PON), Świniarka Sheep (SW), and synthetic line BCP) at different physiological periods (conception, early pregnancy, lambing, end of lactation). The animals were kept in the same environment and were at the same age (2-years). The results showed a significant effect of both breed (p = 0.038) and physiological period (p < 0.05, p < 0.01) on the levels of bacteria analyzed. The breed showed differences across physiological periods. The influence of the race factor was noted primarily between the BCP synthetic line and the other two breeds (differences in terms of all analyzed clusters and families except Actinobacteria phyla). In the case of SW and PON, however, the observed differences were only at the level of Proteobacteria cluster and Clostridiaceae family. On the other hand, the early pregnant and lambing periods were the most microbiologically diverse in terms of the analyzed clusters and families of bacteria.
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Affiliation(s)
- Paulina Cholewińska
- Chair for Fish Diseases and Fisheries Biology, Ludwig-Maximilians-University of Munich, 80539, Munich, Germany
| | - Natalia Szeligowska
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 80126, Naples, Italy
| | - Konrad Wojnarowski
- Chair for Fish Diseases and Fisheries Biology, Ludwig-Maximilians-University of Munich, 80539, Munich, Germany
| | - Paulina Nazar
- Department of Animal Breeding and Agriculture Advisory, Faculty of Animal Sciences and Bioeconomy, University of Life Sciences in Lublin, 20-950, Lublin, Poland
| | - Monika Greguła-Kania
- Department of Animal Breeding and Agriculture Advisory, Faculty of Animal Sciences and Bioeconomy, University of Life Sciences in Lublin, 20-950, Lublin, Poland
| | - Andrzej Junkuszew
- Department of Animal Breeding and Agriculture Advisory, Faculty of Animal Sciences and Bioeconomy, University of Life Sciences in Lublin, 20-950, Lublin, Poland
| | - Witold Rant
- Institute of Animal Breeding, Warsaw University of Life Sciences-SGGW, 02-786, Warsaw, Poland
| | - Aurelia Radzik-Rant
- Institute of Animal Breeding, Warsaw University of Life Sciences-SGGW, 02-786, Warsaw, Poland
| | - Anna Marcinkowska
- Institute of Animal Breeding, Wroclaw University of Environmental and Life Sciences, 51-630, Wroclaw, Poland
| | - Robert Bodkowski
- Institute of Animal Breeding, Wroclaw University of Environmental and Life Sciences, 51-630, Wroclaw, Poland.
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13
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Wang Y, Xu B, Chen H, Yang F, Huang J, Jiao X, Zhang Y. Environmental factors and gut microbiota: Toward better conservation of deer species. Front Microbiol 2023; 14:1136413. [PMID: 36960286 PMCID: PMC10027939 DOI: 10.3389/fmicb.2023.1136413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/16/2023] [Indexed: 03/09/2023] Open
Abstract
Thousands of microbial species inhabiting the animal gut, collectively known as the gut microbiota, play many specific roles related to host nutrient metabolism and absorption, immune regulation, and protection from pathogenic bacteria. Gut microbiota composition is affected by several internal and external factors, such as the host genotype, dietary intake, breeding environment, and antibiotic exposure. As deer species are important members for maintaining ecosystem balance, understanding the effects of multiple factors on the gut microbiota of deer species, particularly endangered ones, is crucial. In this review, we summarize and discuss the factors that significantly affect the gut microbiota of deer and present the impacts of these factors on microbial composition. In particular, we focused on the changes in gut microbiota due to dietary differences under different conditions, including seasonal changes, different geographical locations, and captivity, as well as weaning and pathogen disturbance. Understanding the correlations between gut microbiota composition and its driving factors is important for evaluating and improving the captive breeding environment for better conservation of endangered deer species, and reintroducing wild deer populations in the future.
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Affiliation(s)
- Yu Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Bo Xu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Huan Chen
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Fang Yang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Jinlin Huang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Xin’an Jiao
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- Xin’an Jiao,
| | - Yunzeng Zhang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- *Correspondence: Yunzeng Zhang,
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14
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Phillips CJC. Zoonotic Disease Risks of Live Export of Cattle and Sheep, with a Focus on Australian Shipments to Asia and the Middle East. Animals (Basel) 2022; 12:ani12233425. [PMID: 36496946 PMCID: PMC9738783 DOI: 10.3390/ani12233425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
The growing human and livestock populations in the world today and increased international transport of livestock is increasing the risk of both emerging and endemic zoonotic diseases. This review focuses on the potential for the live export trade to transmit zoonotic diseases. Both cattle and sheep are exposed to major stresses during the transport process, which are described, together with the impact of these stresses on the immune function of transported animals. Heat stress, overcrowding, inanition, ship and vehicle motion and accumulation of noxious gases are analysed for their ability to potentiate infectious diseases. The major zoonoses are described: pustular dermatitis, pneumonia, salmonellosis, as well as some common conditions, such as conjunctivitis, with specific reference to stressors associated with each disorder. Historical precedents exist for restriction of the trade based on disease risks. Finally, the economic and regulatory frameworks are considered to evaluate ways in which the spread of zoonotic diseases can be controlled.
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Affiliation(s)
- Clive J. C. Phillips
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51014 Tartu, Estonia;
- Curtin University Sustainability Policy (CUSP) Institute, Curtin University, Kent St., Bentley, WA 6102, Australia
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15
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Gut Microbiome Studies in Livestock: Achievements, Challenges, and Perspectives. Animals (Basel) 2022; 12:ani12233375. [PMID: 36496896 PMCID: PMC9736591 DOI: 10.3390/ani12233375] [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: 09/13/2022] [Revised: 11/16/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022] Open
Abstract
The variety and makeup of the gut microbiome are frequently regarded as the primary determinants of health and production performances in domestic animals. High-throughput DNA/RNA sequencing techniques (NGS) have recently gained popularity and permitted previously unheard-of advancements in the study of gut microbiota, particularly for determining the taxonomic composition of such complex communities. Here, we summarize the existing body of knowledge on livestock gut microbiome, discuss the state-of-the-art in sequencing techniques, and offer predictions for next research. We found that the enormous volumes of available data are biased toward a small number of globally distributed and carefully chosen varieties, while local breeds (or populations) are frequently overlooked despite their demonstrated resistance to harsh environmental circumstances. Furthermore, the bulk of this research has mostly focused on bacteria, whereas other microbial components such as protists, fungi, and viruses have received far less attention. The majority of these data were gathered utilizing traditional metabarcoding techniques that taxonomically identify the gut microbiota by analyzing small portions of their genome (less than 1000 base pairs). However, to extend the coverage of microbial genomes for a more precise and thorough characterization of microbial communities, a variety of increasingly practical and economical shotgun techniques are currently available.
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16
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Comparison of Bacterial and Fungal Community Structure and Potential Function Analysis of Yak Feces before and after Weaning. BIOMED RESEARCH INTERNATIONAL 2022; 2022:6297231. [PMID: 36082156 PMCID: PMC9448584 DOI: 10.1155/2022/6297231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/07/2022] [Accepted: 07/26/2022] [Indexed: 11/17/2022]
Abstract
Weaning is one of the most stressful periods in yak growth. However, the impact of weaning on microbial diversity, structure, and potential function of yak feces is not clear. In this study, 12 Xinjiang yaks aged 3, 4, 5, and 6 months old were selected to collect fresh feces before and after weaning. Through 16S rRNA and ITS high-throughput sequencing, the dynamic distribution and potential function of yak fecal, bacterial, and fungal communities in each month were revealed. The study found that the richness of fungi had a significant impact on weaning. At the phylum level, Firmicutes, Bacteroidetes, Ascomycota, and Basidiomycota, and at the genus level, 5-7N15, Oscillospira, Roseburia, Dorea, Preussia, Neoascochyta, Naganishia, and Sporormiella were enriched in yak feces of different months old. The abundance and proportion of bacteria Firmicutes, Bacteroidetes, 5-7N15, and fungi Mucoromyceta changed significantly before and after weaning. With the increase of months, Verrucomicrobia and Akkermansia have shown a downward trend. Through the prediction and analysis of fecal microbial function, it was found that at the level of primary pathways, weaning has a significant impact on cellular processes, environmental information processing, genetic information processing, metabolism, and organismal systems. At the level of secondary metabolic pathways, weaning has a significant impact on cell motility, signal transduction, folding, sorting and degradation, translation, amino acid metabolism, glycan biosynthesis and metabolism, metabolism of terpenoids and polyketides, and xenobiotics biodegradation and metabolism. In addition, by analyzing the differences in functional pathways and microbial composition between sample groups of different months, it was found that the differences in functional pathways were related to the abundance differences of some microorganisms. In general, the changes in the composition and structure of yak fecal microflora may reflect the adaptability of the intestinal microbiota.
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17
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Effect of whole-plant corn silage treated with lignocellulose-degrading bacteria on growth performance, rumen fermentation, and rumen microflora in sheep. Animal 2022; 16:100576. [PMID: 35777297 DOI: 10.1016/j.animal.2022.100576] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 05/26/2022] [Accepted: 06/02/2022] [Indexed: 01/11/2023] Open
Abstract
Lignification of cellulose limits the effective utilisation of fibre in plant cell wall. Lignocellulose-degrading bacteria secrete enzymes that decompose lignin and have the potential to improve fibre digestibility. Therefore, this study aimed to investigate the effect of whole-plant corn silage inoculated with lignocellulose-degrading bacteria on the growth performance, rumen fermentation, and rumen microbiome in sheep. Twelve 2-month-old male hybrid sheep (Dorper ♂ × small-tailed Han ♀) were randomly assigned into two dietary groups (n = 6): (1) untreated whole-plant corn silage (WPCS) and (2) WPCS inoculated with bacterial inoculant (WPCSB). Whole-plant corn silage inoculated with bacterial inoculant had higher in situ NDF digestibility than WPCS. Sheep in the WPCSB group had significantly higher average daily gain, DM intake, and feed conversion rate than those in the WPCS group (P < 0.05). Furthermore, higher volatile fatty acid concentrations were detected in WPCSB rumen samples, leading to lower ruminal pH (P < 0.05). The WPCSB group showed higher abundance of Bacteroidetes and lower abundance of Firmicutes in the rumen microbiome than the WPCS group (P < 0.05). Multiple differential genera were identified, with Prevotella being the most dominant genus and more abundant in WPCSB samples. Moreover, the enriched functional attributes, including those associated with glycolysis/gluconeogenesis and citrate cycle, were more actively expressed in the WPCSB samples than in the WPCS samples. Additionally, certain glucoside hydrolases that hydrolyse the side chains of hemicelluloses and pectins were also actively expressed in the WPCSB microbiome. These findings suggested that WPCSB increased NDF digestibility in three ways: (1) by increasing the relative abundance of the most abundant genera, (2) by recruiting more functional features involved in glycolysis/gluconeogenesis and citrate cycle pathways, and (3) by increasing the relative abundance and/or expression activity of the glucoside hydrolases involved in hemicellulose and pectin metabolism. Our findings provide novel insights into the microbial mechanisms underlying improvement in the growth performance of sheep/ruminants. However, the biological mechanisms cannot be fully elucidated using only metagenomics tools; therefore, a combined multi-omics approach will be used in subsequent studies.
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18
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Künzel S, Yergaliyev T, Wild KJ, Philippi H, Petursdottir AH, Gunnlaugsdottir H, Reynolds CK, Humphries DJ, Camarinha-Silva A, Rodehutscord M. Methane Reduction Potential of Brown Seaweeds and Their Influence on Nutrient Degradation and Microbiota Composition in a Rumen Simulation Technique. Front Microbiol 2022; 13:889618. [PMID: 35836418 PMCID: PMC9273974 DOI: 10.3389/fmicb.2022.889618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/17/2022] [Indexed: 12/30/2022] Open
Abstract
This study aimed to investigate the effects of two brown Icelandic seaweed samples (Ascophyllum nodosum and Fucus vesiculosus) on in vitro methane production, nutrient degradation, and microbiota composition. A total mixed ration (TMR) was incubated alone as control or together with each seaweed at two inclusion levels (2.5 and 5.0% on a dry matter basis) in a long-term rumen simulation technique (Rusitec) experiment. The incubation period lasted 14 days, with 7 days of adaptation and sampling. The methane concentration of total gas produced was decreased at the 5% inclusion level of A. nodosum and F. vesiculosus by 8.9 and 3.6%, respectively (P < 0.001). The total gas production was reduced by all seaweeds, with a greater reduction for the 5% seaweed inclusion level (P < 0.001). Feed nutrient degradation and the production of volatile fatty acids and ammonia in the effluent were also reduced, mostly with a bigger effect for the 5% inclusion level of both seaweeds, indicating a reduced overall fermentation (all P ≤ 0.001). Microbiota composition was analyzed by sequencing 16S rRNA amplicons from the rumen content of the donor cows, fermenter liquid and effluent at days 7 and 13, and feed residues at day 13. Relative abundances of the most abundant methanogens varied between the rumen fluid used for the start of incubation and the samples taken at day 7, as well as between days 7 and 13 in both fermenter liquid and effluent (P < 0.05). According to the differential abundance analysis with q2-ALDEx2, in effluent and fermenter liquid samples, archaeal and bacterial amplicon sequence variants were separated into two groups (P < 0.05). One was more abundant in samples taken from the treatment without seaweed supplementation, while the other one prevailed in seaweed supplemented treatments. This group also showed a dose-dependent response to seaweed inclusion, with a greater number of differentially abundant members between a 5% inclusion level and unsupplemented samples than between a 2.5% inclusion level and TMR. Although supplementation of both seaweeds at a 5% inclusion level decreased methane concentration in the total gas due to the high iodine content in the seaweeds tested, the application of practical feeding should be done with caution.
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Affiliation(s)
- Susanne Künzel
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
- Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
| | - Timur Yergaliyev
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
- Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
| | - Katharina J. Wild
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
- Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
| | - Hanna Philippi
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
- Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
| | | | - Helga Gunnlaugsdottir
- Matís, Reykjavík, Iceland
- Faculty of Food Science and Nutrition, School of Health Sciences, University of Iceland, Reykjavík, Iceland
| | - Chris K. Reynolds
- School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
| | - David J. Humphries
- School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
| | - Amélia Camarinha-Silva
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
- Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
| | - Markus Rodehutscord
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
- Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
- *Correspondence: Markus Rodehutscord,
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19
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Aggerbeck MR, Nielsen TK, Mosbacher JB, Schmidt NM, Hansen LH. Muskoxen homogenise soil microbial communities and affect the abundance of methanogens and methanotrophs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 827:153877. [PMID: 35218841 DOI: 10.1016/j.scitotenv.2022.153877] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
Grazing herbivores may affect soil microbial communities indirectly by impacting soil structure and vegetation composition. In high arctic environments, this impact is poorly elucidated, while having potentially wide-reaching effects on the ecosystem. This study examines how a key arctic herbivore, the muskox Ovibos moschatus, affects the soil microbial community in a high arctic fen. Environmental DNA was extracted from soil samples taken from grazed control plots and from muskox exclosures established 5 years prior. We sequenced amplicons of the 16S rRNA gene to provide insight into the microbial communities. We found that in the grazed control plots, microbial communities exhibited high evenness and displayed highly similar overall diversity. In plots where muskoxen had been excluded, microbial diversity was significantly reduced, and had more uneven intra-sample populations and overall lower ecological richness and evenness. We observed that the composition of microbial communities in grazed soils were significantly affected by the presence of muskoxen, as seen by elevated relative abundances of Bacteroides and Firmicutes, two major phyla found in muskox faeces. Furthermore, an increase in relative abundance of bacteria involved in degradation of recalcitrant carbohydrates and cycling of nitrogen was observed in grazed soil. Ungrazed soils displayed increased abundances of bacteria potentially involved in anaerobic oxidation of methane, whereas some methanogens were more abundant in grazed soils. This corroborates a previous finding that methane emissions are higher in arctic fens under muskox grazing. Our results show that the presence of large herbivores stimulates soil microbial diversity and has a homogenizing influence on the inter-species dynamics in soil microbial communities. The findings of this study, thus, improve our understanding of the effect of herbivore grazing on arctic ecosystems and the derived methane cycling.
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Affiliation(s)
| | - Tue Kjærgaard Nielsen
- Department of Plant and Environmental Science, University of Copenhagen, 1871 Copenhagen, Denmark
| | - Jesper Bruun Mosbacher
- Department of Ecoscience, Aarhus University, 4000 Roskilde, Denmark; Arctic Research Centre, Aarhus University, 8000 Aarhus, Denmark
| | - Niels Martin Schmidt
- Department of Ecoscience, Aarhus University, 4000 Roskilde, Denmark; Arctic Research Centre, Aarhus University, 8000 Aarhus, Denmark
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Science, University of Copenhagen, 1871 Copenhagen, Denmark.
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20
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The Microbiota and Cytokines Correlation between the Jejunum and Colon in Altay Sheep. Animals (Basel) 2022; 12:ani12121564. [PMID: 35739900 PMCID: PMC9219508 DOI: 10.3390/ani12121564] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Both the jejunum and the colon secrete unique immune factors that interact with the gut microbiota. Investigating the association of gut microbiota and the host immune system, we detected higher populations of Bacteroides, Fibrobacteres and Spirochetes in the colon than in the jejunum of Altay sheep, which is a unique breed in Xinjiang. Levels of IL-6 and IL-12 were lower in the colon than in the jejunum. IL-10 was positively correlated with Ruminococcus_2 in the jejunum. These results indicate a potential interaction between intestinal microbiota and the host immune system that may be considered for the prevention of sheep diseases and the screening of probiotics. Abstract Both the jejunum and colon release cytokines that interact with intestinal microbiota. However, it is largely unclear which cytokines and microbial populations are involved in the homeostasis of the intestinal ecosystem for sheep health. To address this, we collected contents for isolating microbiota and tissues for determining cytokines from the jejunum and colon of 7-month-old Altay sheep. We used the techniques of 16S rRNA sequencing and ELISA to detect microbial population and cytokine level, respectively. Correlations between microbial population and cytokines were analyzed by Spearman correlation coefficient. The correlation analysis revealed higher populations of Bacteroides, Fibrobacteres and Spirochetes in the colon than in the jejunum, and IL-6 and IL-12 levels were higher in the jejunum than in the colon. Association analysis further revealed a positive association between IL-10 level and both Ruminococcus_2 and norank_f_Bifidobacteriaceae population in the jejunum. The analysis also revealed positive associations between IL-6 level and Ruminococcaceae_UCG-014 and Ruminococcaceae_UCG-013 population, IL-10 and Prevotellaceae_UCG-004, as well as TNF-α and Prevotellaceae_UCG-003 in the colon. These results indicate a potential interaction between the intestinal microbiota and the host immune system that needs to be further clarified for considering dietary formulations to maintain animal health and disease prevention.
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Bajagai YS, Trotter M, Williams TM, Costa DFA, Whitton MM, Ren X, Wilson CS, Stanley D. The role of microbiota in animal health and productivity: misinterpretations and limitations. ANIMAL PRODUCTION SCIENCE 2022. [DOI: 10.1071/an21515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Cholewińska P, Wołoszyńska M, Michalak M, Czyż K, Rant W, Smoliński J, Wyrostek A, Wojnarowski K. Influence of selected factors on the Firmicutes, Bacteroidetes phyla and the Lactobacillaceae family in the digestive tract of sheep. Sci Rep 2021; 11:23801. [PMID: 34893656 PMCID: PMC8664831 DOI: 10.1038/s41598-021-03207-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 11/22/2021] [Indexed: 12/11/2022] Open
Abstract
In this study, we used 10 healthy sheep, which gave birth to healthy twins. Stool samples were collected from mothers and their offspring 3 times during the study (0, 28 and 56 day postpartum). Milk samples were taken from the mothers at the same time. RT PCR analysis of faeces and milk was performed in order to assess the level of bacteria from the Firmicutes and Bacteroidetes phyla including the family Lactobacillaceae (phylum Firmicutes). The composition of mother's milk was also analyzed and their BCS. The data were compiled statistically. The obtained results showed that the level of the studied groups of bacteria may change due to the change of diet. Additionally, there were significant differences between lambs and mothers in the levels of the studied groups of bacteria. Analysis also shown that in the digestive system of mothers was a smaller disproportion in the level of the studied bacterial phyla than in lambs. The results also indicated the occurrence of differences in the bacterial composition at the individual level, both in ewes and their offspring. Additionally, in the conducted experiment, there were differences in the level of Firmicutes and Bacteroidetes groups depending on the sex.
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Affiliation(s)
- Paulina Cholewińska
- Institute of Animal Breeding, Wroclaw University of Environmental and Life Sciences, 51-630, Wroclaw, Poland.
| | - Magdalena Wołoszyńska
- grid.411200.60000 0001 0694 6014Department of Genetics, Wroclaw University of Environmental and Life Sciences, 51-630 Wroclaw, Poland
| | - Marta Michalak
- grid.411200.60000 0001 0694 6014Department of Animal Nutrition and Feed Management, Wroclaw University of Environmental and Life Sciences, 51-630 Wroclaw, Poland
| | - Katarzyna Czyż
- grid.411200.60000 0001 0694 6014Institute of Animal Breeding, Wroclaw University of Environmental and Life Sciences, 51-630 Wroclaw, Poland
| | - Witold Rant
- grid.13276.310000 0001 1955 7966Institute of Animal Breeding, Warsaw University of Life Sciences – SGGW, 02-786 Warsaw, Poland
| | - Jakub Smoliński
- grid.411200.60000 0001 0694 6014Institute of Animal Breeding, Wroclaw University of Environmental and Life Sciences, 51-630 Wroclaw, Poland
| | - Anna Wyrostek
- grid.411200.60000 0001 0694 6014Institute of Animal Breeding, Wroclaw University of Environmental and Life Sciences, 51-630 Wroclaw, Poland
| | - Konrad Wojnarowski
- grid.411200.60000 0001 0694 6014Institute of Animal Breeding, Wroclaw University of Environmental and Life Sciences, 51-630 Wroclaw, Poland
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Zoelzer F, Burger AL, Dierkes PW. Unraveling differences in fecal microbiota stability in mammals: from high variable carnivores and consistently stable herbivores. Anim Microbiome 2021; 3:77. [PMID: 34736528 PMCID: PMC8567652 DOI: 10.1186/s42523-021-00141-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 10/18/2021] [Indexed: 01/04/2023] Open
Abstract
Background Through the rapid development in DNA sequencing methods and tools, microbiome studies on a various number of species were performed during the last decade. This advance makes it possible to analyze hundreds of samples from different species at the same time in order to obtain a general overview of the microbiota. However, there is still uncertainty on the variability of the microbiota of different animal orders and on whether certain bacteria within a species are subject to greater fluctuations than others. This is largely due to the fact that the analysis in most extensive comparative studies is based on only a few samples per species or per study site. In our study, we aim to close this knowledge gap by analyzing multiple individual samples per species including two carnivore suborders Canoidea and Feloidea as well as the orders of herbivore Perissodactyla and Artiodactyla held in different zoos. To assess microbial diversity, 621 fecal samples from 31 species were characterized by sequencing the V3–V4 region of the 16S rRNA gene using Illumina MiSeq. Results We found significant differences in the consistency of microbiota composition and in fecal microbial diversity between carnivore and herbivore species. Whereas the microbiota of Carnivora is highly variable and inconsistent within and between species, Perissodactyla and Ruminantia show fewer differences across species boundaries. Furthermore, low-abundance bacterial families show higher fluctuations in the fecal microbiota than high-abundance ones. Conclusions Our data suggest that microbial diversity is significantly higher in herbivores than in carnivores, whereas the microbiota in carnivores, unlike in herbivores, varies widely even within species. This high variability has methodological implications and underlines the need to analyze a minimum amount of about 10 samples per species. In our study, we found considerable differences in the occurrence of different bacterial families when looking at just three and six samples. However, from a sample number of 10 onwards, these within-species fluctuations balanced out in most cases and led to constant and more reliable results. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00141-0.
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Affiliation(s)
- Franziska Zoelzer
- Bioscience Education and Zoo Biology, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany.
| | - Anna Lena Burger
- Bioscience Education and Zoo Biology, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany
| | - Paul Wilhelm Dierkes
- Bioscience Education and Zoo Biology, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany
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24
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Graf AC, Striesow J, Pané-Farré J, Sura T, Wurster M, Lalk M, Pieper DH, Becher D, Kahl BC, Riedel K. An Innovative Protocol for Metaproteomic Analyses of Microbial Pathogens in Cystic Fibrosis Sputum. Front Cell Infect Microbiol 2021; 11:724569. [PMID: 34513734 PMCID: PMC8432295 DOI: 10.3389/fcimb.2021.724569] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 08/11/2021] [Indexed: 12/28/2022] Open
Abstract
Hallmarks of cystic fibrosis (CF) are increased viscosity of mucus and impaired mucociliary clearance within the airways due to mutations of the cystic fibrosis conductance regulator gene. This facilitates the colonization of the lung by microbial pathogens and the concomitant establishment of chronic infections leading to tissue damage, reduced lung function, and decreased life expectancy. Although the interplay between key CF pathogens plays a major role during disease progression, the pathophysiology of the microbial community in CF lungs remains poorly understood. Particular challenges in the analysis of the microbial population present in CF sputum is (I) the inhomogeneous, viscous, and slimy consistence of CF sputum, and (II) the high number of human proteins masking comparably low abundant microbial proteins. To address these challenges, we used 21 CF sputum samples to develop a reliable, reproducible and widely applicable protocol for sputum processing, microbial enrichment, cell disruption, protein extraction and subsequent metaproteomic analyses. As a proof of concept, we selected three sputum samples for detailed metaproteome analyses and complemented and validated metaproteome data by 16S sequencing, metabolomic as well as microscopic analyses. Applying our protocol, the number of bacterial proteins/protein groups increased from 199-425 to 392-868 in enriched samples compared to nonenriched controls. These early microbial metaproteome data suggest that the arginine deiminase pathway and multiple proteases and peptidases identified from various bacterial genera could so far be underappreciated in their contribution to the CF pathophysiology. By providing a standardized and effective protocol for sputum processing and microbial enrichment, our study represents an important basis for future studies investigating the physiology of microbial pathogens in CF in vivo – an important prerequisite for the development of novel antimicrobial therapies to combat chronic recurrent airway infection in CF.
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Affiliation(s)
- Alexander C Graf
- Institute of Microbiology, Department of Microbial Physiology & Molecular Biology, University of Greifswald, Greifswald, Germany
| | - Johanna Striesow
- Research Group ZIK Plasmatis, Leibniz Institute for Plasma Science and Technology, Greifswald, Germany
| | - Jan Pané-Farré
- Center for Synthetic Microbiology, Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Thomas Sura
- Institute of Microbiology, Department of Microbial Proteomics, University of Greifswald, Greifswald, Germany
| | - Martina Wurster
- Institute of Biochemistry, Department of Cellular Biochemistry & Metabolomics, University of Greifswald, Greifswald, Germany
| | - Michael Lalk
- Institute of Biochemistry, Department of Cellular Biochemistry & Metabolomics, University of Greifswald, Greifswald, Germany
| | - Dietmar H Pieper
- Research Group Microbial Interactions and Processes, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Dörte Becher
- Institute of Microbiology, Department of Microbial Proteomics, University of Greifswald, Greifswald, Germany
| | - Barbara C Kahl
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Katharina Riedel
- Institute of Microbiology, Department of Microbial Physiology & Molecular Biology, University of Greifswald, Greifswald, Germany
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Mortazavi SMH, Kaur M, Farahnaky A, Torley PJ, Osborn AM. The pathogenic and spoilage bacteria associated with red meat and application of different approaches of high CO 2 packaging to extend product shelf-life. Crit Rev Food Sci Nutr 2021; 63:1733-1754. [PMID: 34445909 DOI: 10.1080/10408398.2021.1968336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
With the fast-global development of packaging techniques, the potential antimicrobial effect of CO2, as a safe, cheap and readily available gas, makes it the integral component for packaging of meat products. The associated spoilage and/or pathogenic bacteria on raw meat may respond in different ways to elevated CO2 concentrations. The growth of some aerobic Gram-negative bacteria such as Pseudomonas spp. is significantly inhibited but some LAB bacteria may be allowed to grow faster and dominate the product. The antimicrobial efficacy of enriched CO2 packaging is attributed to the rate of CO2 solubility in the product which is itself affected by the level of headspace CO2, product pH, temperature and the ratio of headspace gas to product (G:P). This review, first, explores the varied range of beef and sheep meat spoilage and pathogenic bacteria and the intrinsic and extrinsic parameters that may influence the pattern of microbial growth and meat spoilage rate during storage. Then, the antimicrobial mechanism of elevated CO2 packaging will be discussed and the different approaches of achieving enriched CO2 packaging i.e. the traditional technique of flushing a desired gas mixture and/or using the new commercially developed CO2 emitters will then be compared in terms of their strengths, limitations and technical mode of action.
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Affiliation(s)
| | - Mandeep Kaur
- Biosciences and Food Technology Discipline, School of Science, RMIT University, Melbourne, Australia
| | - Asgar Farahnaky
- Biosciences and Food Technology Discipline, School of Science, RMIT University, Melbourne, Australia
| | - Peter J Torley
- Biosciences and Food Technology Discipline, School of Science, RMIT University, Melbourne, Australia
| | - A Mark Osborn
- Biosciences and Food Technology Discipline, School of Science, RMIT University, Melbourne, Australia
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Levels of Main Bacterial Phyla in the Gastrointestinal Tract of Sheep Depending on Parity and Age. Animals (Basel) 2021; 11:ani11082203. [PMID: 34438660 PMCID: PMC8388517 DOI: 10.3390/ani11082203] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 01/07/2023] Open
Abstract
Simple Summary The ruminant microbiome is considered a specific ecosystem found within the gastrointestinal tract. A balanced intestinal microbiota is important not only for maintaining gut homeostasis, but also for regulating immune function and has a direct impact on the gut–brain axis. Factors, such as pregnancy, age, or genetics, can influence the microbial composition of the digestive system. The results of the study suggest that the parity, as well as the age of the animals, may affect the level of microorganisms in the digestive system. Abstract During pregnancy and parturition, the homeostasis of the body is disturbed, and the immune system is undermined, which is associated with hormonal changes within the body. Recently, it has also been suggested that physiological and hormonal changes associated with pregnancy may affect the composition of the gastrointestinal microbiome. Therefore, the aim of this study was to determine the composition of the microbiome in the third month of pregnancy in sheep in their first and second parity. Eighteen females in total were selected for the experiment, and they were divided into two groups: primiparous (aged 1 year) and multiparous ones (aged 2 years). The animals were fed the same fodder, and did not show any disease symptoms. Fecal samples were collected individually from each female (n = 20), and then bacterial DNA isolation and real-time PCR were performed for the main bacterial phyla (Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria) and families (Lactobacillaceae and Clostridia). The obtained results showed the differentiation in the microbiome between the primiparous and multiparous ewes with respect to the following groups: Bacteroidetes, Proteobacteria, and Actinobacteria—the level was higher in the case of the primiparas. These results suggest that the parity and age of the females may affect the gastrointestinal microbiome, but further studies are recommended.
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Penati M, Sala G, Biscarini F, Boccardo A, Bronzo V, Castiglioni B, Cremonesi P, Moroni P, Pravettoni D, Addis MF. Feeding Pre-weaned Calves With Waste Milk Containing Antibiotic Residues Is Related to a Higher Incidence of Diarrhea and Alterations in the Fecal Microbiota. Front Vet Sci 2021; 8:650150. [PMID: 34307516 PMCID: PMC8298036 DOI: 10.3389/fvets.2021.650150] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 05/25/2021] [Indexed: 01/18/2023] Open
Abstract
The cows receiving antibiotics for intra-mammary infection (IMI) produce milk that cannot be marketed. This is considered waste milk (WM), and a convenient option for farmers is using it as calf food. However, adding to the risk of selecting resistant bacteria, residual antibiotics might interfere with the gut microbiome development and influence gastrointestinal health. We assessed the longitudinal effect of unpasteurized WM containing residual cefalexin on calf intestinal health and fecal microbiota in an 8-week trial. After 3 days of colostrum, six calves received WM and six calves received bulk tank milk (BM) for 2 weeks. For the following 6 weeks, all 12 calves received milk substitute and starter feed. Every week for the first 2 weeks and every 2 weeks for the remaining 6 weeks, we subjected all calves to clinical examination and collected rectal swabs for investigating the fecal microbiota composition. Most WM calves had diarrhea episodes in the first 2 weeks of the trial (5/6 WM and 1/6 BM), and their body weight was significantly lower than that of BM calves. Based on 16S rRNA gene analysis, WM calves had a lower fecal microbiota alpha diversity than that in BM calves, with the lowest p-value at Wk4 (p < 0.02), 2 weeks after exposure to WM. The fecal microbiota beta diversity of the two calf groups was also significantly different at Wk4 (p < 0.05). Numerous significant differences were present in the fecal microbiota taxonomy of WM and BM calves in terms of relative normalized operational taxonomic unit (OTU) levels, affecting five phyla, seven classes, eight orders, 19 families, and 47 genera. At the end of the trial, when 6 weeks had passed since exposure to WM, the phyla Bacteroidetes, Firmicutes, and Saccharibacteria were lower, while Chlamydiae were higher in WM calves. Notably, WM calves showed a decrease in beneficial taxa such as Faecalibacterium, with a concomitant increase in potential pathogens such as Campylobacter, Pseudomonas, and Chlamydophila spp. In conclusion, feeding pre-weaned calves with unpasteurized WM containing antibiotics is related to a higher incidence of neonatal diarrhea and leads to significant changes in the fecal microbiota composition, further discouraging this practice in spite of its short-term economic advantages.
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Affiliation(s)
- Martina Penati
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Lodi, Italy
| | - Giulia Sala
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Lodi, Italy
| | - Filippo Biscarini
- Institute of Agricultural Biology and Biotechnology, National Research Council (CNR), Milan, Italy
| | - Antonio Boccardo
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Lodi, Italy
| | - Valerio Bronzo
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Lodi, Italy
| | - Bianca Castiglioni
- Institute of Agricultural Biology and Biotechnology, National Research Council (CNR), Milan, Italy
| | - Paola Cremonesi
- Institute of Agricultural Biology and Biotechnology, National Research Council (CNR), Milan, Italy
| | - Paolo Moroni
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Lodi, Italy
- Quality Milk Production Services, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, United States
| | - Davide Pravettoni
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Lodi, Italy
| | - Maria Filippa Addis
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Lodi, Italy
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Szeligowska N, Cholewińska P, Czyż K, Wojnarowski K, Janczak M. Inter and intraspecies comparison of the level of selected bacterial phyla in in cattle and sheep based on feces. BMC Vet Res 2021; 17:224. [PMID: 34172061 PMCID: PMC8235250 DOI: 10.1186/s12917-021-02922-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 05/25/2021] [Indexed: 12/23/2022] Open
Abstract
Background The microbiome of the digestive tract of ruminants contains microbial ecosystem that is affected by both environmental and genetic factors. The subject of this study concerns the influence of selected genetic factors, such as species of animals and “host” individual differences on the digestive tract microbiome composition. The results show the core microbiological composition (Firmicutes and Bacteroidetes) of ruminants digestive tract (based on feces) depending on breed and “host”. The Bacteroidetes and Firmicutes phyla are the most abundant in ruminants digestive tract. The aim of the study was to determine the differences prevalence level of Bacteroidetes and Firmicutes phyla in feces of Charolaise cattle and Polish Olkuska Sheep with respect to intra- and inter-species variability. Results The research group in the experiment consisted of animals at the age of 3 months kept in the same environmental conditions – rams of Polish Olkuska Sheep (n = 10) and Charolaise bulls (n = 10). Feces were collected individually from each animal (animals without disease symptoms were selected), living on the same environmental conditions. The analysis of the results in terms of species showed differences in the Firmicutes phylum level and Lactobacillaceae family between rams and bulls. Subsequently, the analysis performed for the “host effect” showed differentiation in the levels of the Bacteroidetes and Firmicutes phyla between individuals in a group and also between the groups. Conclusion The obtained results suggest that, apart from the diet and the environment, the species and the individual host are equally important factors influencing the microbiological composition of the digestive system of ruminants.
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Affiliation(s)
- Natalia Szeligowska
- Institute of Animal Breeding, Wroclaw University of Environmental and Life Sciences, 51-630, Wroclaw, Poland
| | - Paulina Cholewińska
- Institute of Animal Breeding, Wroclaw University of Environmental and Life Sciences, 51-630, Wroclaw, Poland.
| | - Katarzyna Czyż
- Institute of Animal Breeding, Wroclaw University of Environmental and Life Sciences, 51-630, Wroclaw, Poland
| | - Konrad Wojnarowski
- Institute of Animal Breeding, Wroclaw University of Environmental and Life Sciences, 51-630, Wroclaw, Poland
| | - Marzena Janczak
- Institute of Animal Breeding, Wroclaw University of Environmental and Life Sciences, 51-630, Wroclaw, Poland
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Wu J, Buckley HL, Curry L, Stevenson BA, Schipper LA, Lear G. Livestock exclusion reduces the spillover effects of pastoral agriculture on soil bacterial communities in adjacent forest fragments. Environ Microbiol 2021; 23:2919-2936. [PMID: 33734554 DOI: 10.1111/1462-2920.15473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 03/16/2021] [Indexed: 11/29/2022]
Abstract
Forest-to-pasture conversion is known to cause global losses in plant and animal diversity, yet impacts of livestock management after such conversion on vital microbial communities in adjoining natural ecosystems remain poorly understood. We examined how pastoral land management practices impact soil microorganisms in adjacent native forest fragments, by comparing bacterial communities sampled along 21 transects bisecting pasture-forest boundaries. Our results revealed greater bacterial taxon richness in grazed pasture soils and the reduced dispersal of pasture-associated taxa into adjacent forest soils when land uses were separated by a boundary fence. Relative abundance distributions of forest-associated taxa (i.e., Proteobacteria and Nitrospirae) and a pasture-associated taxon (i.e., Firmicutes) also suggest a greater impact of pastoral land uses on forest fragment soil bacterial communities when no fence is present. Bacterial community richness and composition were most related to changes in soil physicochemical variables commonly associated with agricultural fertilization, including concentrations of Olsen P, total P, total Cd, delta 15 N and the ratio of C:P and N:P. Overall, our findings demonstrate clear, and potentially detrimental effects of agricultural disturbance on bacterial communities in forest soils adjacent to pastoral land. We provide evidence that simple land management decisions, such as livestock exclusion, can mitigate the effects of agriculture on adjacent soil microbial communities.
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Affiliation(s)
- Jieyun Wu
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1010, New Zealand.,Plant Health & Environment Laboratory, Ministry for Primary Industries, PO Box 2095, Auckland, 1140, New Zealand
| | - Hannah L Buckley
- School of Science, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
| | - Liz Curry
- Tonkin and Taylor, 711 Victoria Street, Hamilton, 3204, New Zealand
| | - Bryan A Stevenson
- Manaaki Whenua-Landcare Research, Private Bag 3127, Hamilton, 3240, New Zealand
| | - Louis A Schipper
- Environmental Research Institute, School of Science, The University of Waikato, Hamilton, 3240, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1010, New Zealand
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Abate TA, Desta AF, Love NG. Evaluating tannery wastewater treatment performance based on physicochemical and microbiological characteristics: An Ethiopian case study. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2021; 93:658-669. [PMID: 32474980 PMCID: PMC8246915 DOI: 10.1002/wer.1364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
Tanneries are an important industrial sector in Ethiopia; consequently, gaps in wastewater treatment process performance need to be identified as the country increases its emphasis on compliance. A case study was conducted to evaluate physicochemical and microbial water quality at a tannery near Addis Ababa. The treatment process was designed for the following: sulfide oxidation; biological oxygen demand reduction; and chromium removal. While some of Ethiopia's standards for industrial wastewater treatment were met through treatment, effluent COD, sulfide, total nitrogen, and total chromium guidelines were not. 16S rRNA gene analysis was used to evaluate the microbial community composition across the treatment train. The results show that common ruminant phyla were dominant throughout, with Firmicutes and Bacteroidetes comprising 77% to 82% relative abundance. The Firmicutes Clostridium increased consistently in relative abundance with treatment, comprising 39% to 61% of the total bacterial community in the effluent. Improved treatment is needed to meet environmental and public health goals. PRACTITIONER POINTS: Case Study of tannery wastewater treatment in Ethiopia shows ineffective treatment of chemical pollutants. Microbiological pollutants from tannery wastewater systems can introduce agents of importance to public health The microbiological composition of tannery influent, mixed liquor and effluent contains mostly four bacterial phyla lead by Firmicutes. Most pathogenic bacterial genera found in the tannery wastewater treatment system became a decreasing percentage of the total population. Clostridium comprises up to 61% of the effluent bacterial population and deserves further evaluation to better understand the consequences of its dominance.
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Affiliation(s)
| | - Adey F. Desta
- Molecular, Cellular and Microbial BiologyAddis Ababa UniversityAddis AbabaEthiopia
| | - Nancy G. Love
- Department of Civil and Environmental EngineeringUniversity of MichiganAnn ArborMIUSA
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Bacterial profiling of Haemonchus contortus gut microbiome infecting Dohne Merino sheep in South Africa. Sci Rep 2021; 11:5905. [PMID: 33723324 PMCID: PMC7961046 DOI: 10.1038/s41598-021-85282-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/26/2021] [Indexed: 11/09/2022] Open
Abstract
A metagenomic approach was used to study the gut microbiome of Haemonchus contortus field strains and that of its predilection site, the abomasum of Dohne Merino sheep. The abomasum contents and H. contortus were collected from 10 naturally infected Dohne Merino sheep. The H. contortus specimens were classified and sexually differentiated using morphometric characters and was further confirmed through molecular identification. We investigated differences and similarities between the bacterial composition of the adult male and female H. contortus gut microbiomes, which were both dominated by bacteria from the Escherichia, Shigella, Vibrio and Halomonas genera. Major abundance variations were identified between the shared adult male and female H. contortus microbiomes. The results also revealed that Succiniclasticum, Rikenellaceae RC9 gut group and Candidatus Saccharimonas were the predominant genera in the Dohne Merino abomasum. This study provides insight into the highly diverse bacterial composition of the H. contortus gut microbiome and the Dohne Merino abomasum which needs to be studied further to explore the complex interactions of different gastrointestinal nematode microbiomes with the host.
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Analysis of Hindgut Microbiome of Sheep and Effect of Different Husbandry Conditions. Animals (Basel) 2020; 11:ani11010004. [PMID: 33375098 PMCID: PMC7822195 DOI: 10.3390/ani11010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/11/2020] [Accepted: 12/18/2020] [Indexed: 11/17/2022] Open
Abstract
The microbiome is now seen as an important resource to understand animal health and welfare in many species. However, there are few studies aiming at identifying the association between fecal microbiome composition and husbandry conditions in sheep. A wide range of stressors associated with management and housing of animals increases the hypothalamic–pituitary axis activity, with growing evidence that the microbiome composition can be modified. Therefore, the purpose of the present study was to describe the core microbiome in sheep, characterized using 16S rRNA gene sequencing, and to explore whether exposure to stressful husbandry conditions changed sheep hindgut microbiome composition. Sheep (n = 10) were divided in two groups: isolated group (individually separated for 3 h/day) and control group (housed in the home pen for the entire trial period). Sheep core microbiome was dominated by Firmicutes (43.6%), Bacteroidetes (30.38%), Proteobacteria (10.14%), and Verrucomicrobia (7.55%). Comparative results revealed few operational taxonomic units (OTUs) with significantly different relative abundance between groups. Chao1, abundance-based coverage estimator (ACE), and Fisher’s alpha indices did not show differences between groups. OTU-based Bray–Curtis distances between groups were not significant (p-value = 0.07). In conclusion, these results describing the core microbiome of sheep do not suggest a strong effect of stressful husbandry conditions on microbial composition.
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Quijada NM, Bodas R, Lorenzo JM, Schmitz-Esser S, Rodríguez-Lázaro D, Hernández M. Dietary Supplementation with Sugar Beet Fructooligosaccharides and Garlic Residues Promotes Growth of Beneficial Bacteria and Increases Weight Gain in Neonatal Lambs. Biomolecules 2020; 10:E1179. [PMID: 32823755 PMCID: PMC7465112 DOI: 10.3390/biom10081179] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/04/2020] [Accepted: 08/08/2020] [Indexed: 11/25/2022] Open
Abstract
The proper development of the early gastrointestinal tract (GIT) microbiota is critical for newborn ruminants. This microbiota is susceptible to modification by diverse external factors (such as diet) that can lead to long-lasting results when occurring in young ruminants. Dietary supplementation with prebiotics, ingredients nondigestible and nonabsorbable by the host that stimulate the growth of beneficial GIT bacteria, has been applied worldwide as a potential approach in order to improve ruminant health and production yields. However, how prebiotics affect the GIT microbiota during ruminants' early life is still poorly understood. We investigated the effect of milk supplementation with a combination of two well-known prebiotics, fructooligosaccharides (FOS) from sugar beet and garlic residues (all together named as "additive"), exerted on preweaned lamb growth and the composition of their fecal microbiota, by using 16S rRNA gene amplicon high-throughput sequencing. The results showed a significant increase in the mean daily weight gain of lambs fed with the additive. Lamb fecal microbiota was also influenced by the additive intake, as additive-diet lambs showed lower bacterial diversity and were significantly more abundant in Bifidobacterium, Enterococcus, Lactobacillus and Veillonella. These bacteria have been previously reported to confer beneficial properties to the ruminant, including promotion of growth and health status, and our results showed that they were strongly linked to the additive intake and the increased weight gain of lambs. This study points out the combination of FOS from sugar beet and garlic residues as a potential prebiotic to be used in young ruminants' nutrition in order to improve production yields.
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Affiliation(s)
- Narciso M. Quijada
- Laboratorio de Biología Molecular y Microbiología, Instituto Tecnológico Agrario de Castilla y León (ITACyL), 47071 Valladolid, Spain; (N.M.Q.); (R.B.)
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090 Vienna, Austria
- Institute of Food Safety, Food Technology and Veterinary Public Health, Unit of Food Microbiology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Raúl Bodas
- Laboratorio de Biología Molecular y Microbiología, Instituto Tecnológico Agrario de Castilla y León (ITACyL), 47071 Valladolid, Spain; (N.M.Q.); (R.B.)
| | - Jose M. Lorenzo
- Centro Tecnológico de la Carne de Galicia, Avd. Galicia nº 4, Parque Tecnológico de Galicia, San Cibrao das Viñas, 32900 Ourense, Spain;
- Área de Tecnología de los Alimentos, Facultad de Ciencias de Ourense, Universidad de Vigo, 32004 Ourense, Spain
| | | | - David Rodríguez-Lázaro
- Microbiology Division, Department of Biotechnology and Food Science, Faculty of Sciences, University of Burgos, 09001 Burgos, Spain;
| | - Marta Hernández
- Laboratorio de Biología Molecular y Microbiología, Instituto Tecnológico Agrario de Castilla y León (ITACyL), 47071 Valladolid, Spain; (N.M.Q.); (R.B.)
- Microbiology Division, Department of Biotechnology and Food Science, Faculty of Sciences, University of Burgos, 09001 Burgos, Spain;
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Bighorn sheep gut microbiomes associate with genetic and spatial structure across a metapopulation. Sci Rep 2020; 10:6582. [PMID: 32313214 PMCID: PMC7171152 DOI: 10.1038/s41598-020-63401-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 03/28/2020] [Indexed: 12/11/2022] Open
Abstract
Studies in laboratory animals demonstrate important relationships between environment, host traits, and microbiome composition. However, host-microbiome relationships in natural systems are understudied. Here, we investigate metapopulation-scale microbiome variation in a wild mammalian host, the desert bighorn sheep (Ovis canadensis nelsoni). We sought to identify over-represented microbial clades and understand how landscape variables and host traits influence microbiome composition across the host metapopulation. To address these questions, we performed 16S sequencing on fecal DNA samples from thirty-nine bighorn sheep across seven loosely connected populations in the Mojave Desert and assessed relationships between microbiome composition, environmental variation, geographic distribution, and microsatellite-derived host population structure and heterozygosity. We first used a phylogenetically-informed algorithm to identify bacterial clades conserved across the metapopulation. Members of genus Ruminococcaceae, genus Lachnospiraceae, and family Christensenellaceae R7 group were among the clades over-represented across the metapopulation, consistent with their known roles as rumen symbionts in domestic livestock. Additionally, compositional variation among hosts correlated with individual-level geographic and genetic structure, and with population-level differences in genetic heterozygosity. This study identifies microbiome community variation across a mammalian metapopulation, potentially associated with genetic and geographic population structure. Our results imply that microbiome composition may diverge in accordance with landscape-scale environmental and host population characteristics.
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Qin W, Song P, Lin G, Huang Y, Wang L, Zhou X, Li S, Zhang T. Gut Microbiota Plasticity Influences the Adaptability of Wild and Domestic Animals in Co-inhabited Areas. Front Microbiol 2020; 11:125. [PMID: 32117147 PMCID: PMC7018712 DOI: 10.3389/fmicb.2020.00125] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 01/20/2020] [Indexed: 12/23/2022] Open
Abstract
Due to the increased economic demand for livestock, the number of livestock is increasing. Because of human interference, the survival of wild animals is threatened in the face of competition, particularly in co-inhabited grazing pastures. This may lead to differences in the adaptability between wild and domestic animals, as well as nutritional deficiencies in wild animals. The gut microbiota is closely associated with host health, nutrition, and adaptability. However, the gut microbiota diversity and functions in domestic and wild animals in co-inhabited areas are unclear. To reveal the adaptability of wild and domestic animals in co-inhabited areas based on gut microbiota, we assessed the gut microbiota diversity. This study was based on the V3–V4 region of 16S rRNA and gut microbiota functions according to the metagenome analysis of fresh fecal samples in wild goitered gazelles (Gazella subgutturosa) and domestic sheep (Ovis aries) in the Qaidam Basin. The wild and domestic species showed significant differences in alpha- and beta-diversities. Specifically, the alpha-diversity was lower in goitered gazelles. We speculated that the nutritional and habitat status of the goitered gazelles were worse. The gut microbiota functions in the gazelles were enriched in metabolism and cellular processes based on the KEGG database. In summary, we reasoned that gut microbiota can improve the adaptability of goitered gazelles through energy maintenance by the functions of gut microbiota in the face of nutritional deficiencies. These findings highlight the importance of gut microbiota diversity to improve the adaptability of goitered gazelles, laying a foundation for the conservation of wild goitered gazelles. In addition, we further provide management suggestions for domestic sheep in co-inhabited grazing pastures.
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Affiliation(s)
- Wen Qin
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Pengfei Song
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Gonghua Lin
- School of Life Sciences, Jinggangshan University, Ji'an, China
| | - YanGan Huang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Lei Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | | | - Shengqing Li
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
| | - Tongzuo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
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36
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Mamun MAA, Sandeman M, Rayment P, Brook-Carter P, Scholes E, Kasinadhuni N, Piedrafita D, Greenhill AR. Variation in gut bacterial composition is associated with Haemonchus contortus parasite infection of sheep. Anim Microbiome 2020; 2:3. [PMID: 33499986 PMCID: PMC7807447 DOI: 10.1186/s42523-020-0021-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 01/14/2020] [Indexed: 12/26/2022] Open
Abstract
Background One of the greatest impediments to global small ruminant production is infection with the gastrointestinal parasite, Haemonchus contortus. In recent years there has been considerable interest in the gut microbiota and its impact on health. Relatively little is known about interactions between the gut microbiota and gastrointestinal tract pathogens in sheep. Thus, this study was undertaken to investigate the link between the faecal microbiota of sheep, as a sample representing the gastrointestinal microbiota, and infection with H. contortus. Results Sheep (n = 28) were experimentally inoculated with 14,000 H. contortus infective larvae. Faecal samples were collected 4 weeks prior to and 4 weeks after infection. Microbial analyses were conducted using automated ribosomal intergenic spacer analysis (ARISA) and 16S rRNA gene sequencing. A comparison of pre-infection microbiota to post-infection microbiota was conducted. A high parasite burden associated with a relatively large change in community composition, including significant (p ≤ 0.001) differences in the relative abundances of Firmicutes and Bacteroidetes following infection. In comparison, low parasite burden associated with a smaller change in community composition, with the relative abundances of the most abundant phyla remaining stable. Interestingly, differences were observed in pre-infection faecal microbiota in sheep that went on to develop a high burden of H. contortus infection (n = 5) to sheep that developed a low burden of infection (n = 5). Differences observed at the community level and also at the taxa level, where significant (p ≤ 0.001) in relative abundance of Bacteroidetes (higher in high parasite burden sheep) and Firmicutes (lower in high parasite burden sheep). Conclusions This study reveals associations between faecal microbiota and high or low H. contortus infection in sheep. Further investigation is warranted to investigate causality and the impact of microbiome manipulation.
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Affiliation(s)
- Md Abdullah Al Mamun
- Monash University, Faculty of Science, Melbourne, VIC, 3800, Australia.,Animal Health, Ecology and Diagnostics Research Group, School of Health and Life Sciences, Federation University Australia, Gippsland Campus, Northways Rd, Churchill, 3842, Australia.,Dept of Parasitology, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Mark Sandeman
- Animal Health, Ecology and Diagnostics Research Group, School of Health and Life Sciences, Federation University Australia, Gippsland Campus, Northways Rd, Churchill, 3842, Australia
| | - Phil Rayment
- Animal Health, Ecology and Diagnostics Research Group, School of Health and Life Sciences, Federation University Australia, Gippsland Campus, Northways Rd, Churchill, 3842, Australia
| | - Phillip Brook-Carter
- Animal Health, Ecology and Diagnostics Research Group, School of Health and Life Sciences, Federation University Australia, Gippsland Campus, Northways Rd, Churchill, 3842, Australia
| | - Emily Scholes
- Monash University, Faculty of Science, Melbourne, VIC, 3800, Australia
| | - Naga Kasinadhuni
- Australian Genome Research Facility, Melbourne, QLD, 4072, Australia
| | - David Piedrafita
- Monash University, Faculty of Science, Melbourne, VIC, 3800, Australia.,Animal Health, Ecology and Diagnostics Research Group, School of Health and Life Sciences, Federation University Australia, Gippsland Campus, Northways Rd, Churchill, 3842, Australia
| | - Andrew R Greenhill
- Monash University, Faculty of Science, Melbourne, VIC, 3800, Australia. .,Animal Health, Ecology and Diagnostics Research Group, School of Health and Life Sciences, Federation University Australia, Gippsland Campus, Northways Rd, Churchill, 3842, Australia.
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37
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Zhu C, Song W, Tao Z, Liu H, Zhang S, Xu W, Li H. Analysis of microbial diversity and composition in small intestine during different development times in ducks. Poult Sci 2020; 99:1096-1106. [PMID: 32029146 PMCID: PMC7587750 DOI: 10.1016/j.psj.2019.12.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Indexed: 01/09/2023] Open
Abstract
We studied the microbial profiles of the duodenum, jejunum, and ileum during different developmental stages in the duck using high-throughput sequencing of the bacterial 16S rRNA gene. We also investigated the differences in the microbiota in the duodenum, jejunum, and ileum at different developmental times. A correlation analysis was performed between the most abundant bacterial genera and the development of the small intestine. An analysis of alpha diversity indicated different species richness and bacterial diversity in the different small intestinal segments and at different development times. A beta diversity analysis indicated differences in the bacterial community compositions across time. In a weighted UniFrac principal coordinates analysis, the samples clustered into two categories, 2 to 4 wk and 6 to 10 wk, in the duodenum, jejunum, and ileum. Our results show that the small intestine is predominantly populated by the phyla Firmicutes, Bacteroidetes, and Proteobacteria throughout the developmental stages of the duck. The duodenum, jejunum, and ileum shared most of the bacterial phyla and genera present, although they showed significant differences in their relative abundances in the intestinal segments and developmental stages. They shared different bacterial taxa during development times and among different segments when the intergroup differences were analyzed. The genera Bacillus, Corynebacterium 1, Lactococcus, Sphingomonas, and Haliangium correlated moderately positively with the increase in bodyweight and the lengths and weights of the duodenum, jejunum, and ileum, and these genera may be considered important markers when assessing the heath of the intestinal microbiota in ducks. This study provides a foundation upon which to extend our knowledge of the diversity and composition of the duck microbiota and a basis for further studies of the management of the small intestinal microbiota and improvements in the health and production of ducks.
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Affiliation(s)
- Chunhong Zhu
- Jiangsu Institute of Poultry Science, Jiangsu Yangzhou, 225125, China.
| | - Weitao Song
- Jiangsu Institute of Poultry Science, Jiangsu Yangzhou, 225125, China
| | - Zhiyun Tao
- Jiangsu Institute of Poultry Science, Jiangsu Yangzhou, 225125, China
| | - Hongxiang Liu
- Jiangsu Institute of Poultry Science, Jiangsu Yangzhou, 225125, China
| | - Shuangjie Zhang
- Jiangsu Institute of Poultry Science, Jiangsu Yangzhou, 225125, China
| | - Wenjuan Xu
- Jiangsu Institute of Poultry Science, Jiangsu Yangzhou, 225125, China
| | - Huifang Li
- Jiangsu Institute of Poultry Science, Jiangsu Yangzhou, 225125, China.
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38
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Mamun MAA, Sandeman M, Rayment P, Brook-Carter P, Scholes E, Kasinadhuni N, Piedrafita D, Greenhill AR. The composition and stability of the faecal microbiota of Merino sheep. J Appl Microbiol 2019; 128:280-291. [PMID: 31563150 DOI: 10.1111/jam.14468] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 08/16/2019] [Accepted: 08/27/2019] [Indexed: 12/29/2022]
Abstract
AIMS To determine the composition and temporal stability of the gut (faecal) microbiota of sheep (Ovis aries). METHODS AND RESULTS Microbial population dynamics was conducted using ARISA (28 sheep) and 16S rRNA sequencing (11 sheep). Firmicutes and Bacteroidetes were the predominant bacterial phyla, constituting ~80% of the total population. The core faecal bacterial microbiota of sheep consisted of 67 of 136 detected families and 91 of 215 detected species. Predominant microbial taxa included Ruminococcaceae, unassigned families in Bacteroidales and Clostridiales, Verrucomicrobiaceae and Paraprevotellaceae. Diversity indices and core microbiota composition demonstrated the stability of the core microbiota over 2-4 weeks. The core microbiota remained similar over ~5 months. CONCLUSIONS Temporal stability of the sheep microbiota is high over 2-4 weeks in the absence of experimental variables. The core microbiota of Merino sheep shares taxa found in other breeds of sheep and other ruminants. SIGNIFICANCE AND IMPACT OF THE STUDY Numerous studies seek to investigate the impact of experimental variables on gut microbiota composition. To do so, knowledge of the innate stability (or instability) of the microbiota over an experimental time course is required, independent of other variables. We have demonstrated high stability of the gut microbiota in sheep over 3-4 weeks, with moderate stability over ~5 months.
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Affiliation(s)
- M A A Mamun
- Faculty of Science, Monash University, Churchill, Victoria, Australia.,Federation University, Churchill, Victoria, Australia.,Department of Parasitology, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - M Sandeman
- Federation University, Churchill, Victoria, Australia
| | - P Rayment
- Federation University, Churchill, Victoria, Australia
| | | | - E Scholes
- Faculty of Science, Monash University, Churchill, Victoria, Australia
| | - N Kasinadhuni
- Australian Genome Research Facility, Saint Lucia, Queensland, Australia
| | - D Piedrafita
- Faculty of Science, Monash University, Churchill, Victoria, Australia.,Federation University, Churchill, Victoria, Australia
| | - A R Greenhill
- Faculty of Science, Monash University, Churchill, Victoria, Australia.,Federation University, Churchill, Victoria, Australia
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Sun CH, Liu HY, Liu B, Yuan BD, Lu CH. Analysis of the Gut Microbiome of Wild and Captive Père David's Deer. Front Microbiol 2019; 10:2331. [PMID: 31636626 PMCID: PMC6787558 DOI: 10.3389/fmicb.2019.02331] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 09/24/2019] [Indexed: 12/27/2022] Open
Abstract
Père David’s deer (Elaphurus davidianus or milu) is a highly endangered species originating from China, and many deer are currently being raised in captivity for gradual re-introduction to the wild. Wild and captive deer currently live in the same region but have vastly different diets. In this study, we used 16S rRNA high-throughput sequencing to identify the healthy core microbiome in the gut of wild and captive Père David’s deer and investigate how dietary factors influence the gut microbiome by comparing their differences. A core shared gut microbiome was identified in healthy Père David’s deer, which was similar to that of other ruminants, mainly comprising the phyla Firmicutes and Bacteroidetes. There were no differences in the richness or diversity of the gut microbiome between the wild and captive deer. However, PCA and ANOSIM demonstrated clear differences in the microbial community structure between the captive and wild deer, which mainly manifested as changes in the relative abundance of 39 bacterial genera. As the majority of these genera were not dominant in the deer gut, no significant difference was detected in functional modules related to the microbiome between the two groups. Therefore, the difference in dietary factors does not appear to affect the healthy core gut microbiome between captive and wild Père David’s deer, suggesting strong co-evolution and the possibility of re-establishment in the wild. These data could guide future applications of population management in Père David’s deer conservation.
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Affiliation(s)
- Cheng-He Sun
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Hong-Yi Liu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Bin Liu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China.,Jiangsu Dafeng Père David's Deer National Nature Reserve, Yancheng, China
| | - Bao-Dong Yuan
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China.,College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Chang-Hu Lu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
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Xi Y, Shuling N, Kunyuan T, Qiuyang Z, Hewen D, ChenCheng G, Tianhe Y, Liancheng L, Xin F. Characteristics of the intestinal flora of specific pathogen free chickens with age. Microb Pathog 2019; 132:325-334. [PMID: 31082529 DOI: 10.1016/j.micpath.2019.05.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 04/08/2019] [Accepted: 05/09/2019] [Indexed: 02/06/2023]
Abstract
Specific pathogen-free (SPF) experimental animals are recognized as standard laboratory animals in the fields of biomedical, animal husbandry and veterinary research and production. Intestinal flora plays a critical role in nutrient absorption, improving health and protecting the host from pathogens. We therefore explored the variation and maintenance of intestinal flora in SPF chicks in order to better understand the composition of intestinal microflorain SPF chickens, and provide reference for the study of intestinal flora of SPF experimental animals. Five chicks were randomly selected at each of 14, 28, and 42 days, and ceca were removed for DNA extraction. The Illumina Miseq platform was used for microbiome analysis of the V3-V4 region of the 16S rRNA gene. During the course of chick gut microbiome development, we observed major changes in diversity, especially between day 14 and day 28. Firmicutes, Proteobacteria, and Bacteroidetes were the main bacterial taxa, and Firmicutes increased significantly with age. The genus with the highest relative abundance was Lactobacillus, followed by Faecalibacterium. In addition, while abundance of Ruminococcaceae spp., Ruminococcus, and Blautia increased with age, Lactobacillus, Enterobacteriaceae spp., and Oscillospira decreased with age. Interestingly, the abundance of Faecalibacterium first increased and then decreased over time. The characteristics of SPF chicken gut flora at different ages establish a basis for the regulation of intestinal flora in the early stage of brooding, and also provide a theoretical foundation for controlling and preventing infections and poultry diseases in newborn chickens.
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Affiliation(s)
- Yu Xi
- College of Veterinary Medicine and College of Animal Science, Jilin University, Changchun, 130062, China
| | - Niu Shuling
- College of Animal Science and Technology, Changchun Sci-Tech University, Shuangyang, Jilin Province, 130600, China
| | - Tie Kunyuan
- College of Veterinary Medicine and College of Animal Science, Jilin University, Changchun, 130062, China
| | - Zhang Qiuyang
- College of Veterinary Medicine and College of Animal Science, Jilin University, Changchun, 130062, China
| | - Deng Hewen
- College of Veterinary Medicine and College of Animal Science, Jilin University, Changchun, 130062, China
| | - Gao ChenCheng
- College of Veterinary Medicine and College of Animal Science, Jilin University, Changchun, 130062, China
| | - Yu Tianhe
- College of Veterinary Medicine and College of Animal Science, Jilin University, Changchun, 130062, China
| | - Lei Liancheng
- College of Veterinary Medicine and College of Animal Science, Jilin University, Changchun, 130062, China
| | - Feng Xin
- College of Veterinary Medicine and College of Animal Science, Jilin University, Changchun, 130062, China.
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Bai X, Lu S, Yang J, Jin D, Pu J, Díaz Moyá S, Xiong Y, Rossello-Mora R, Xu J. Precise Fecal Microbiome of the Herbivorous Tibetan Antelope Inhabiting High-Altitude Alpine Plateau. Front Microbiol 2018; 9:2321. [PMID: 30323800 PMCID: PMC6172336 DOI: 10.3389/fmicb.2018.02321] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 09/11/2018] [Indexed: 01/16/2023] Open
Abstract
The metataxonomic approach combining 16S rRNA gene amplicon sequencing using the PacBio Technology with the application of the operational phylogenetic unit (OPU) approach, has been used to analyze the fecal microbial composition of the high-altitude and herbivorous Tibetan antelopes. The fecal samples of the antelope were collected in Hoh Xil National Nature Reserve, at an altitude over 4500 m, the largest depopulated zone in Qinghai-Tibetan Plateau, China, where non-native animals or humans may experience life-threatening acute mountain sickness. In total, 104 antelope fecal samples were enrolled in this study, and were clustered into 61,258 operational taxonomic units (OTUs) at an identity of 98.7% and affiliated with 757 OPUs, including 144 known species, 256 potentially new species, 103 potentially higher taxa within known lineages. In addition, 254 comprised sequences not affiliating with any known family, and the closest relatives were unclassified lineages of existing orders or classes. A total of 42 out of 757 OPUs conformed to the core fecal microbiome, of which four major lineages, namely, un-cultured Ruminococcaceae, Lachnospiraceae, Akkermansia, and Christensenellaceae were associated with human health or longevity. The current study reveals that the fecal core microbiome of antelope is mainly composited of uncultured bacteria. The most abundant core taxa, namely, uncultured Ruminococcaceae, uncultured Akkermansia, uncultured Bacteroides, uncultured Christensenellaceae, uncultured Mollicutes, and uncultured Lachnospiraceae, may represent new bacterial candidates at high taxa levels, and several may have beneficial roles in health promotion or anti-intestinal dysbiosis. These organisms should be further isolated and evaluated for potential effect on human health and longevity.
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Affiliation(s)
- Xiangning Bai
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shan Lu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jing Yang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dong Jin
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ji Pu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Sara Díaz Moyá
- Marine Microbiology Group, Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies, Spanish National Research Council (CSIC)-University of the Balearic Islands (UIB), Esporles, Spain
| | - Yanwen Xiong
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies, Spanish National Research Council (CSIC)-University of the Balearic Islands (UIB), Esporles, Spain
| | - Jianguo Xu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
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Multi-Omic Biogeography of the Gastrointestinal Microbiota of a Pre-Weaned Lamb. Proteomes 2017; 5:proteomes5040036. [PMID: 29258228 PMCID: PMC5748571 DOI: 10.3390/proteomes5040036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 12/12/2017] [Accepted: 12/14/2017] [Indexed: 01/23/2023] Open
Abstract
The digestive functions of the pre-weaned lamb gastrointestinal tracts (GITs) have been the subject of much research in recent years, but the microbial and host functions underlying these complex processes remain largely unknown. Here, we undertook a proof-of-principle metaproteogenomic investigation on luminal and mucosal samples collected from 10 GITs of a 30-day-old pre-weaned lamb. We demonstrate that the analysis of the diverse ecological niches along the GITs can reveal microbiota composition and metabolic functions, although low amounts of microbial proteins could be identified in the small intestinal and mucosal samples. Our data suggest that a 30-day lamb has already developed mature microbial functions in the forestomachs, while the effect of the milky diet appears to be more evident in the remaining GITs. We also report the distribution and the relative abundance of the host functions, active at the GIT level, with a special focus on those involved in digestive processes. In conclusion, this pilot study supports the suitability of a metaproteogenomic approach to the characterization of microbial and host functions of the lamb GITs, opening the way to further studies aimed at investigating the impact of early dietary interventions on the GIT microbiota of small ruminants.
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Starr AE, Deeke SA, Li L, Zhang X, Daoud R, Ryan J, Ning Z, Cheng K, Nguyen LVH, Abou-Samra E, Lavallée-Adam M, Figeys D. Proteomic and Metaproteomic Approaches to Understand Host–Microbe Interactions. Anal Chem 2017; 90:86-109. [DOI: 10.1021/acs.analchem.7b04340] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Amanda E. Starr
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Shelley A. Deeke
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Leyuan Li
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Xu Zhang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Rachid Daoud
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - James Ryan
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Zhibin Ning
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Kai Cheng
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Linh V. H. Nguyen
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Elias Abou-Samra
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Mathieu Lavallée-Adam
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
- Molecular Architecture of Life Program, Canadian Institute for Advanced Research, Toronto, Ontario, M5G 1M1, Canada
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Tanca A, Fraumene C, Manghina V, Palomba A, Abbondio M, Deligios M, Pagnozzi D, Addis MF, Uzzau S. Diversity and functions of the sheep faecal microbiota: a multi-omic characterization. Microb Biotechnol 2017; 10:541-554. [PMID: 28165194 PMCID: PMC5404191 DOI: 10.1111/1751-7915.12462] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 10/13/2016] [Accepted: 10/27/2016] [Indexed: 01/08/2023] Open
Abstract
Little is currently known on the microbial populations colonizing the sheep large intestine, despite their expected key role in host metabolism, physiology and immunity. This study reports the first characterization of the sheep faecal microbiota composition and functions, obtained through the application of a multi-omic strategy. An optimized protocol was first devised for DNA extraction and amplification from sheep stool samples. Then, 16S rDNA sequencing, shotgun metagenomics and shotgun metaproteomics were applied to unravel taxonomy, genetic potential and actively expressed functions and pathways respectively. Under a taxonomic perspective, the sheep faecal microbiota appeared globally comparable to that of other ruminants, with Firmicutes being the main phylum. In functional terms, we detected 2097 gene and 441 protein families, finding that the sheep faecal microbiota was primarily involved in catabolism. We investigated carbohydrate transport and degradation activities and identified phylum-specific pathways, such as methanogenesis for Euryarchaeota and acetogenesis for Firmicutes. Furthermore, our approach enabled the identification of proteins expressed by the eukaryotic component of the microbiota. Taken together, these findings unveil structure and role of the distal gut microbiota in sheep, and open the way to further studies aimed at elucidating its connections with management and dietary variables in sheep farming.
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Affiliation(s)
- Alessandro Tanca
- Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy
| | - Cristina Fraumene
- Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy
| | - Valeria Manghina
- Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy.,Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Antonio Palomba
- Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy.,Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Marcello Abbondio
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Massimo Deligios
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Daniela Pagnozzi
- Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy
| | - Maria Filippa Addis
- Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy
| | - Sergio Uzzau
- Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy.,Department of Biomedical Sciences, University of Sassari, Sassari, Italy
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