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Pei J, Guan Y, Xiao W, Ge J, Feng L, Yang H. The comparison of gut microbiota between wild and captive Asian badgers (Meles leucurus) under different seasons. Sci Rep 2024; 14:18199. [PMID: 39107422 PMCID: PMC11303745 DOI: 10.1038/s41598-024-69277-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 08/02/2024] [Indexed: 08/10/2024] Open
Abstract
The gut microbiota plays an important role in the immunology, physiology and growth and development of animals. However, currently, there is a lack of available sequencing data on the gut microbiota of Asian badgers. Studying the gut microbiota of Asian badgers could provide fundamental data for enhancing productivity and immunity of badgers' breeding, as well as for the protection of wild animals. In this study, we first characterized the composition and structure of the gut microbiota in the large intestines of wild and captive Asian badgers during summer and winter by sequencing the V3-V4 region of the 16S ribosomal RNA gene. A total of 9 dominant phyla and 12 genera among the bacterial communities of the large intestines exhibited significant differences. Our results showed that Firmicutes and Proteobacteria were the most predominant in both wild and captive badgers, regardless of the season. Romboutsia, Streptococcus and Enterococcus may represent potential sources of zoonoses, warranting further attention and study. Our findings indicated that the diversity and availability of food resources were the most important influencing factors on the gut microbiota of Asian badgers, providing fundamental data for the protection and conservation of wild animals. Variation in the gut microbiota due to season, age and sex in both wild and captive Asian badgers should be considered in future research directions. Furthermore, combined multi-omics studies could provide more information for wild animal conservation, and enhancing our understanding of the molecular mechanism between the microbiota and host.
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Affiliation(s)
- Jianchi Pei
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Forestry and Grassland Administration Key Laboratory for Northeast Tiger and Leopard National Park Conservation Ecology, Northeast Tiger and Leopard Biodiversity National Observation and Research Station, National Forestry and Grassland Administration Amur Tiger and Amur Leopard Monitoring and Research Center, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yu Guan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Forestry and Grassland Administration Key Laboratory for Northeast Tiger and Leopard National Park Conservation Ecology, Northeast Tiger and Leopard Biodiversity National Observation and Research Station, National Forestry and Grassland Administration Amur Tiger and Amur Leopard Monitoring and Research Center, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
| | - Wenhong Xiao
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jianping Ge
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Forestry and Grassland Administration Key Laboratory for Northeast Tiger and Leopard National Park Conservation Ecology, Northeast Tiger and Leopard Biodiversity National Observation and Research Station, National Forestry and Grassland Administration Amur Tiger and Amur Leopard Monitoring and Research Center, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Limin Feng
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Forestry and Grassland Administration Key Laboratory for Northeast Tiger and Leopard National Park Conservation Ecology, Northeast Tiger and Leopard Biodiversity National Observation and Research Station, National Forestry and Grassland Administration Amur Tiger and Amur Leopard Monitoring and Research Center, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Haitao Yang
- Institute of Remote Sensing and Geographic Information System, School of Earth and Space Sciences, Peking University, Beijing, 100871, China.
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Ren J, Yu D, Li N, Liu S, Xu H, Li J, He F, Zou L, Cao Z, Wen J. Biological Characterization and Whole-Genome Analysis of Bacillus subtilis MG-1 Isolated from Mink Fecal Samples. Microorganisms 2023; 11:2821. [PMID: 38137965 PMCID: PMC10745379 DOI: 10.3390/microorganisms11122821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/12/2023] [Accepted: 11/15/2023] [Indexed: 12/24/2023] Open
Abstract
Bacillus subtilis is an important part of the gut microbiota and a commonly used probiotic. In the present study, to assess the biological characteristics and probiotic properties of B. subtilis derived from mink, we isolated B. subtilis MG-1 isolate from mink fecal samples, characterized its biological characteristics, optimized the hydrolysis of casein by its crude extract, and comprehensively analyzed its potential as a probiotic in combination with whole-genome sequencing. Biological characteristics indicate that, under low-pH conditions (pH 2), B. subtilis MG-1 can still maintain a survival rate of 64.75%; under the conditions of intestinal fluid, gastric acid, and a temperature of 70 °C, the survival rate was increased by 3, 1.15 and 1.17 times compared with the control group, respectively. This shows that it can tolerate severe environments. The results of hydrolyzed casein in vitro showed that the crude bacterial extract of isolate MG-1 exhibited casein hydrolyzing activity (21.56 U/mL); the enzyme activity increased to 32.04 U/mL under optimized reaction conditions. The complete genome sequencing of B. subtilis MG-1 was performed using the PacBio third-generation sequencing platform. Gene annotation analysis results revealed that B. subtilis MG-1 was enriched in several Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways, and most genes were related to Brite hierarchy pathways (1485-35.31%) and metabolism pathways (1395-33.17%). The egg-NOG annotation revealed that most genes were related to energy production and conversion (185-4.10%), amino acid transport and metabolism (288-6.38%), carbohydrate transport and metabolism (269-5.96%), transcription (294-6.52%), and cell wall/membrane/envelope biogenesis (231-5.12%). Gene Ontology (GO) annotation elucidated that most genes were related to biological processes (8230-45.62%), cellular processes (3582-19.86%), and molecular processes (6228-34.52%). Moreover, the genome of B. subtilis MG-1 was predicted to possess 77 transporter-related genes. This study demonstrates that B. subtilis MG-1 has potential for use as a probiotic, and further studies should be performed to develop it as a probiotic additive in animal feed to promote animal health.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Jianxin Wen
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China; (J.R.); (D.Y.); (N.L.); (S.L.); (H.X.); (J.L.); (F.H.); (L.Z.); (Z.C.)
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Iatrou AM, Michailidou S, Papadopoulos GA, Afaloniati H, Lagou MK, Kiritsi M, Argiriou A, Angelopoulou K, Poutahidis T, Fortomaris P. Effects of Dietary Supplementation of Spirulina platensis on the Immune System, Intestinal Bacterial Microbiome and Skin Traits of Mink. Animals (Basel) 2023; 13:ani13020190. [PMID: 36670730 PMCID: PMC9854837 DOI: 10.3390/ani13020190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 01/06/2023] Open
Abstract
The impact of dietary inclusion of Spirulina platensis on the immune system, intestinal microbiome and skin of mink was investigated. Forty-eight animals were equally separated into four groups. Groups B and D were control animals, while groups A and C had their feed supplemented daily with 100 mg/kg of body weight Spirulina. Mink in groups A and B were descended from dams supplemented with spirulina during their reproductive period, while those in groups C and D were descended from dams fed the control diets. Fur growth rate and quality were graded semi-quantitatively. Fecal microbiome analysis, skin thickness histomorphometry, immunohistochemical labeling and counts of immune cells in the colon, mesenteric lymph nodes and spleen and quantitative gene expression analysis of cytokines in the colon were performed. Skin thickness, fur growth rate and skin quality were similar among groups (p > 0.05). However, differences were observed among groups concerning the relative and differential abundance of bacterial species. Tgf-β expression was lower in group A, whereas IL-β1 was lower in group C compared to group B (p < 0.05). Group D had significantly lower numbers of inflammatory cells in the colon and mesenteric lymph nodes. The results revealed that Spirulina decreased indices of subclinical inflammation in mink gut, while differences in the bacterial communities among groups were observed.
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Affiliation(s)
- Anna Maria Iatrou
- Laboratory of Animal Husbandry, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
- Correspondence: ; Tel.: +30-2310999958
| | - Sofia Michailidou
- Center for Research and Technology, Hellas Institute of Applied Biosciences, Thermi, 57001 Thessaloniki, Greece
| | - Georgios A. Papadopoulos
- Laboratory of Animal Husbandry, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Hara Afaloniati
- Laboratory of Biochemistry and Toxicology, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Maria K. Lagou
- Laboratory of Pathology, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Maria Kiritsi
- Center for Research and Technology, Hellas Institute of Applied Biosciences, Thermi, 57001 Thessaloniki, Greece
| | - Anagnostis Argiriou
- Center for Research and Technology, Hellas Institute of Applied Biosciences, Thermi, 57001 Thessaloniki, Greece
- Department of Food Science and Nutrition, University of the Aegean, 81400 Lemnos, Greece
| | - Katerina Angelopoulou
- Laboratory of Biochemistry and Toxicology, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Theofilos Poutahidis
- Laboratory of Pathology, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Paschalis Fortomaris
- Laboratory of Animal Husbandry, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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Guo G, Eccles KM, McMillan M, Thomas PJ, Chan HM, Poulain AJ. The Gut Microbial Community Structure of the North American River Otter (Lontra canadensis) in the Alberta Oil Sands Region in Canada: Relationship with Local Environmental Variables and Metal Body Burden. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2020; 39:2516-2526. [PMID: 32946150 DOI: 10.1002/etc.4876] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/23/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
The Alberta Oil Sands Region in Canada is home to one of the largest oil bitumen deposits in the world. The North American river otter (Lontra canadensis) is a top predator with a small home range and is sensitive to disturbances; it has been designated as a sentinel species for the potential impacts of the natural resource exploitation on freshwater ecosystems in the Alberta Oil Sands Region. With an increasing interest in noninvasive biomarkers, recent studies suggest that gut microbiota can be used as a potential biomarker of early biological effects on aquatic wildlife. The goal of the present study was to determine the river otter gut microbial structure related to environmental variables characterizing mining activities and metal body burden. We obtained 18 trapped animals from and surrounding the surface mineable area of the Alberta Oil Sands Region. The gut microbial community structure was characterized using high-throughput sequencing of 16S rRNA gene amplicon analyses. Trace metal concentrations in the liver were measured by inductively coupled plasma-mass spectrometry. Our study revealed that the gut bacteria of river otters in the Alberta Oil Sands Region clustered in 4 groups dominated by Peptostreptococcaceae, Carnobacteriaceae, Enterobacteriaceae, Clostridiaceae, and Nostocaceae. We show that arsenic, barium, rubidium, liver-body weight ratio, and δ15 N were associated with each cluster. When comparing affected versus less affected sites, we show that river otter gut bacterial community and structure are significantly related to trophic level of the river otter but not to Alberta Oil Sands Region mining activities. Our study reveals that the gut bacterial dynamics can provide insights into the diet and habitat use of river otters but that more work is needed to use it as a pollution biomarker. Environ Toxicol Chem 2020;39:2516-2526. © 2020 SETAC.
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Affiliation(s)
- Galen Guo
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Kristin M Eccles
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Morgan McMillan
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Philippe J Thomas
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
- Science and Technology Branch, Environment and Climate Change Canada, National Wildlife Research Center, Ottawa, Ontario, Canada
| | - Hing Man Chan
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
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Compo NR, Gomez DE, Tapscott B, Weese JS, Turner PV. Fecal bacterial microbiota of Canadian commercial mink (Neovison vison): Yearly, life stage, and seasonal comparisons. PLoS One 2018; 13:e0207111. [PMID: 30419047 PMCID: PMC6231641 DOI: 10.1371/journal.pone.0207111] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 10/25/2018] [Indexed: 01/01/2023] Open
Abstract
The gastrointestinal microbiome is known to play a critical role in animal health but has been relatively poorly characterized in commercial mink, an obligate carnivore. Whether the microbiota can be manipulated in mink to improve pelt quality, health, and well-being is unknown. The objectives of this study were to characterize the fecal microbiota of commercial mink, and to evaluate potential changes due to year (2014 vs 2015), life stage (adult female vs weaned kit), season (summer vs winter), and between Canadian farms. Pooled fecal samples were collected from adult females and weaned kits in the summers of 2014 (n = 173) and 2015 (n = 168), and from females in the winter of 2016 (n = 39), a time when females undergo marked calorie restriction, from 49 mink farms in Ontario. Bacterial DNA was extracted and the V4 region of the 16S rRNA gene was amplified. Approximately 22 million sequences were identified following quality control filtering. A total of 31 bacterial phyla were identified; however, only 3 comprised >1% of the total sequences identified, with Firmicutes and Proteobacteria together comprising 95% of the total sequences. Comparisons were made by life stage, season and year; no differences were found in the relative abundance of any taxa between samples collected from adult females and weaned kits from the same year and the greatest number of differences at each taxonomic level were noted between 2014 and 2015. Significantly more operational taxonomic units (OTUs) were found in 2014 than 2015 or 2016 (p<0.05) and samples from 2014 were more even, but less diverse than in 2015 (p = 0.002 and 0.001, respectively). There were significant differences in community population and structure by year and season (all p-values <0.001). The predominant phyla and genera at the farm level were similar from year to year. Together, these indicate that mink environment, season, and time are important factors in the stability of gastrointestinal microbiota, once mink reach maturity.
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Affiliation(s)
- Nicole R. Compo
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
| | - Diego E. Gomez
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
| | - Brian Tapscott
- Ontario Ministry of Agriculture, Food, and Rural Affairs, Elora, Ontario, Canada
| | - J. Scott Weese
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
| | - Patricia V. Turner
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
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Birch JM, Ullman K, Struve T, Agger JF, Hammer AS, Leijon M, Jensen HE. Investigation of the viral and bacterial microbiota in intestinal samples from mink (Neovison vison) with pre-weaning diarrhea syndrome using next generation sequencing. PLoS One 2018; 13:e0205890. [PMID: 30335814 PMCID: PMC6193705 DOI: 10.1371/journal.pone.0205890] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 10/03/2018] [Indexed: 01/21/2023] Open
Abstract
Pre-weaning diarrhea (PWD) in mink kits is a common multifactorial syndrome on commercial mink farms. Several potential pathogens such as astroviruses, caliciviruses, Escherichia coli and Staphylococcus delphini have been studied, but the etiology of the syndrome seems complex. In pooled samples from 38 diarrheic and 42 non-diarrheic litters, each comprising of intestinal contents from 2-3 mink kits from the same litter, the bacterial populations were studied using Illumina Next Generation Sequencing technology and targeted 16S amplicon sequencing. In addition, we used deep sequencing to determine and compare the viral intestinal content in 31 healthy non-diarrheic and 30 diarrheic pooled samples (2-3 mink kits from the same litter per pool). The results showed high variations in composition of the bacterial species between the pools. Enterococci, staphylococci and streptococci dominated in both diarrheic and non-diarrheic pools. However, enterococci accounted for 70% of the reads in the diarrheic group compared to 50% in the non-diarrheic group and this increase was at the expense of staphylococci and streptococci which together accounted for 45% and 17% of the reads in the non-diarrheic and diarrheic group, respectively. Moreover, in the diarrheic pools there were more reads assigned to Clostridia, Escherichia-Shigella and Enterobacter compared to the non-diarrheic pools. The taxonomically categorized sequences from the virome showed that the most prevalent viruses in all pools were caliciviruses and mamastroviruses (almost exclusively type 10). However, the numbers of reads assigned to caliciviruses were almost 3 times higher in the diarrheic pools compared the non-diarrheic pools and Sapporo-like caliciviruses were more abundant than the Norwalk-like caliciviruses. The results from this study have contributed to the insight into the changes in the intestinal microbiota associated with the PWD syndrome of mink.
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Affiliation(s)
- Julie Melsted Birch
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Karin Ullman
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden
| | - Tina Struve
- Kopenhagen Fur Diagnostics, Kopenhagen Fur, Glostrup, Denmark
| | - Jens Frederik Agger
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Anne Sofie Hammer
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Mikael Leijon
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden
| | - Henrik Elvang Jensen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
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Xie XT, Kropinski AM, Tapscott B, Weese JS, Turner PV. Prevalence of fecal viruses and bacteriophage in Canadian farmed mink (Neovison vison). Microbiologyopen 2018; 8:e00622. [PMID: 29635866 PMCID: PMC6341152 DOI: 10.1002/mbo3.622] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 12/18/2017] [Accepted: 01/05/2018] [Indexed: 01/01/2023] Open
Abstract
Recent viral metagenomic studies have demonstrated the diversity of eukaryotic viruses and bacteriophage shed in the feces of domestic species. Although enteric disease is a major concern in the commercial mink farming industry, few etiologic agents have been well characterized. This study aimed to identify viruses shed in the fecal matter of clinically healthy commercial mink from 40 southern Ontario farms. Viral RNA was extracted from 67 pooled fecal samples (30 adult female mink and 37 kit) and amplified for Illumina sequencing on the NextSeq platform, and the resulting contigs were trimmed and assembled using Trimmomatic 0.36.0 and Spades 3.8.0 in iVirus (CyVerse, AZ, USA) and SeqMan NGen 12 (DNAStar, WI, USA). Identification of assembled sequences >100 bp (Geneious 10.1.3) showed an abundance of bacteriophage sequences, mainly from families Siphoviridae (53%), Podoviridae (22%), Myoviridae (20%), Inoviridae (1%), Leviviridae (0.04%), Tectiviridae (0.01%), and Microviridae (0.01%). A diverse range of vertebrate viruses were detected, of which posavirus 3, mink bocavirus, gyroviruses, and avian‐associated viruses were most abundant. Additionally, sequences from nonvertebrate viruses with water and soil‐associated amebal and algal hosts were also highly prevalent. The results of this study show that viruses shed in the fecal matter of healthy commercial mink are highly diverse and could be closely associated with diet, and that more research is necessary to determine how the detected viruses may impact mink health.
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Affiliation(s)
- Xiao-Ting Xie
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
| | | | - Brian Tapscott
- Ontario Ministry of Agriculture, Food and Rural Affairs (OMAFRA), Elora, ON, Canada
| | - J Scott Weese
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
| | - Patricia V Turner
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
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