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Han C, Cao H, Tan H, Li X, Yang W. Distribution and community structure of antibiotic resistance genes in the Three Gorges Reservoir Area. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:50952-50966. [PMID: 39103584 DOI: 10.1007/s11356-024-34590-2] [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: 03/19/2024] [Accepted: 07/29/2024] [Indexed: 08/07/2024]
Abstract
Antibiotic resistance genes (ARG) are widespread across various regions. While several studies have investigated the distribution of antibiotic resistance in natural environments, the occurrence and diversity of ARGs in the Three Gorges Reservoir have not been fully elucidated. In this study, we employed metagenomic sequencing techniques to investigate the abundance, diversity, and influencing factors of ARGs in the ecosystem of the Three Gorges Reservoir. A total of 874 ARGs, 20 antibiotic classes, and 6 resistance mechanisms were detected. The dominant ARG is the macB, the dominant antibiotic class is multidrug resistance (MDR), and the dominant resistance mechanism is antibiotic efflux. The microorganisms with the highest contribution to ARGs are Betaproteobacteria and Gammaproteobacteria. In this region, pH and NH4+ concentration were significantly negatively correlated with the relative abundance of most ARGs, while NO3- concentration and TN were significantly positively correlated with the relative abundance of most ARGs. The results indicate that the Three Gorges Reservoir constitutes a significant reservoir of ARGs. By studying the distribution of ARGs in the sediments of the Three Gorges Reservoir Area and the relationship between environmental factors and ARGs, we can more comprehensively understand the pollution status of ARGs in this area, and provide theoretical support for subsequent treatment.
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Affiliation(s)
- Chang Han
- College of Water Conservancy and Hydropower Engineering, Hohai University, Nanjing, 210024, China
| | - Huiqun Cao
- Changjiang River Scientific Research Institute, Wuhan, 430010, China
| | - Haoyue Tan
- Changjiang River Scientific Research Institute, Wuhan, 430010, China
| | - Xiaomeng Li
- Changjiang River Scientific Research Institute, Wuhan, 430010, China
| | - Wenjun Yang
- Changjiang River Scientific Research Institute, Wuhan, 430010, China.
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2
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Deb S, Wild MA, LeClair T, Shah DH. Discovery of novel treponemes associated with pododermatitis in elk ( Cervus canadensis). Appl Environ Microbiol 2024; 90:e0010524. [PMID: 38742897 PMCID: PMC11218636 DOI: 10.1128/aem.00105-24] [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: 01/17/2024] [Accepted: 04/16/2024] [Indexed: 05/16/2024] Open
Abstract
Pododermatitis, also known as treponeme-associated hoof disease (TAHD), presents a significant challenge to elk (Cervus canadensis) populations in the northwestern USA, with Treponema spp. consistently implicated in the lesion development. However, identifying species-specific Treponema strains from these lesions is hindered by its culture recalcitrance and limited genomic information. This study utilized shotgun sequencing, in silico genome reconstruction, and comparative genomics as a culture-independent approach to identify metagenome-assembled Treponema genomes (MATGs) from skin scraping samples collected from captive elk experimentally challenged with TAHD. The genomic analysis revealed 10 new MATGs, with 6 representing novel genomospecies associated with pododermatitis in elk and 4 corresponding to previously identified species-Treponema pedis and Treponema phagedenis. Importantly, genomic signatures of novel genomospecies identified in this study were consistently detected in biopsy samples of free-ranging elk diagnosed with TAHD, indicating a potential etiologic association. Comparative metabolic profiling of the MATGs against other Treponema genomes showed a distinct metabolic profile, suggesting potential host adaptation or geographic uniqueness of these newly identified genomospecies. The discovery of novel Treponema genomospecies enhances our understanding of the pathogenesis of pododermatitis and lays the foundation for the development of improved molecular surveillance tools to monitor and manage the disease in free-ranging elk.IMPORTANCETreponema spp. play an important role in the development of pododermatitis in free-ranging elk; however, the species-specific detection of Treponema from pododermatitis lesions is challenging due to culture recalcitrance and limited genomic information. The study utilized shotgun sequencing and in silico genome reconstruction to identify novel Treponema genomospecies from elk with pododermatitis. The discovery of the novel Treponema species opens new avenues to develop molecular diagnostic and epidemiologic tools for the surveillance of pododermatitis in elk. These findings significantly enhance our understanding of the genomic landscape of the Treponemataceae consortium while offering valuable insights into the etiology and pathogenesis of emerging pododermatitis in elk populations.
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Affiliation(s)
- Sushanta Deb
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Margaret A. Wild
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Thomas LeClair
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Devendra H. Shah
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
- School of Veterinary Medicine, Texas Tech University, Amarillo, Texas, USA
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Crosby-Durrani HE, Carter SD, Blowey RW, Evans NJ. Molecular Screening for Digital Dermatitis-Associated Treponemes in Bovine Ischaemic Teat Necrosis Lesions and Milk in Dairy Cattle. Pathogens 2024; 13:427. [PMID: 38787279 PMCID: PMC11123857 DOI: 10.3390/pathogens13050427] [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: 03/18/2024] [Revised: 04/30/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024] Open
Abstract
Bovine ischaemic teat necrosis (ITN) is a disease affecting the skin of the teats of dairy cows with an unknown aetiopathogenesis. Digital dermatitis (DD)-associated treponemes have previously been suggested as a potential aetiological agent in ITN, although the sample size was small. The current study, using established PCR techniques, aimed to examine the association with the presence of DD-associated treponemes in a large number of ITN samples from a wider geographical area, and surveyed the potential of milk as an infection reservoir. From 95 ITN lesions, 35.8% (n = 34) were positive for at least one DD-associated treponeme compared with only 5.6% (n = 1) of 18 non-lesioned teats from cows with ITN lesions on a different teat using a nested PCR approach. All 10 age- and production-matched control cows were negative for DD-associated treponemes via PCR. No DD-associated treponemes could be detected from foremilk of cows with (n = 19) and without (n = 31) a DD lesion on the hind feet. DD-associated treponemes could be detected via PCR after incubation in milk for up to 2 h. Therefore, milk does not appear to be a competent reservoir for transmission of DD-associated treponemes. Moreover, in the current study DD-associated treponemes were only detected in a subset of ITN samples, so it is unlikely these opportunistic skin-associated pathogens are the major or sole agent of ITN.
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Affiliation(s)
- Hayley E. Crosby-Durrani
- Institute of Infection, Veterinary, and Ecological Sciences, University of Liverpool, Leahurst Campus, Chester High Road, Neston CH64 7TE, UK
| | - Stuart D. Carter
- Institute of Infection, Veterinary, and Ecological Sciences, University of Liverpool, Leahurst Campus, Chester High Road, Neston CH64 7TE, UK
| | | | - Nicholas J. Evans
- Institute of Infection, Veterinary, and Ecological Sciences, University of Liverpool, Leahurst Campus, Chester High Road, Neston CH64 7TE, UK
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Wilson-Welder JH, Han S, Bayles DO, Alt DP, Kanipe C, Garrison K, Mansfield KG, Olsen SC. Correlation of lesion severity with bacterial changes in Treponeme-Associated Hoof Disease from free-roaming wild elk (Cervus canadensis). Anim Microbiome 2024; 6:20. [PMID: 38650043 PMCID: PMC11036743 DOI: 10.1186/s42523-024-00304-9] [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: 09/15/2023] [Accepted: 03/25/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Treponeme-Associated Hoof Disease (TAHD) is a polybacterial, multifactorial disease affecting free-ranging wild elk (Cervus canadensis) in the Pacific Northwest. Previous studies have indicated a bacterial etiology similar to digital dermatitis in livestock, including isolation of Treponema species from lesions. The lesions appear to progress rapidly from ulcerative areas in the interdigital space or along the coronary band to severe, ulcerative, necrotic, proliferative lesions under-running the hoof wall, perforating the sole, and contributing to hoof elongation, deformity, and overgrowth. Eventually the lesions undermine the laminal structure leading to sloughing of the hoof horn capsule. The objective of this study was to characterize the bacterial communities associated with hoof lesions, which were categorized into 5 stages or disease grade severities, with 0 being unaffected tissue and 4 being sloughed hoof capsule. We also wanted to determine if the etiology of TAHD through morphological changes was dominated by Treponema, as observed in hoof diseases in livestock. RESULTS The bacterial 16S rRNA gene was sequenced from 66 hoof skin biopsy samples representing 5 lesion grades from samples collected by Washington Department of Fish and Wildlife as part of a voluntary hunter program. Analysis of the relative abundance of bacterial sequences showed that lesions were dominated by members of the bacterial phyla Proteobacteria, Firmicutes, Spirochaetes, Bacteroidetes and Actinobacteria. In lesion samples, members of the genus Treponema, Porphyromonas, and Mycoplasma increased with lesion severity. Association analysis indicated frequent identification of Treponema with Porphyromonas, Bacteroides and other anaerobic Gram-positive cocci. CONCLUSIONS The bacterial 16S rRNA gene sequencing confirmed the presence of Treponema species at all stages of TAHD lesions, treponeme specie-specific PCR and histopathology, indicating that the morphological changes are a continual progression of disease severity with similar bacterial communities. Association and abundance of these other pathogenic genera within lesions may mean synergistic role with Treponema in hoof disease pathogenesis. Characterizing bacteria involved in lesion development, and their persistence during disease progression, provides evidence for science-based management decisions in TAHD infected elk populations.
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Affiliation(s)
- Jennifer H Wilson-Welder
- Infectious Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service- USDA, 1920 Dayton Ave, 50010, Ames, IA, USA.
| | - Sushan Han
- Colorado State University Diagnostic Medicine Center, Fort Collins, CO, USA
| | - Darrell O Bayles
- Infectious Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service- USDA, 1920 Dayton Ave, 50010, Ames, IA, USA
| | - David P Alt
- Infectious Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service- USDA, 1920 Dayton Ave, 50010, Ames, IA, USA
| | - Carly Kanipe
- Infectious Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service- USDA, 1920 Dayton Ave, 50010, Ames, IA, USA
| | - Kyle Garrison
- Washington Department of Fish and Wildlife, Olympia, WA, USA
| | | | - Steven C Olsen
- Infectious Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service- USDA, 1920 Dayton Ave, 50010, Ames, IA, USA
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Erickson S, Booker C, Song J, Janzen E, Jelinski M, Schwartzkopf-Genswein K. Epidemiology of Digital Dermatitis in Western Canadian Feedlot Cattle. Animals (Basel) 2024; 14:1040. [PMID: 38612279 PMCID: PMC11011063 DOI: 10.3390/ani14071040] [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: 02/28/2024] [Revised: 03/20/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024] Open
Abstract
Digital dermatitis (DD) is an emerging disease in feedlot cattle. Our objective was to identify animal- and feedlot-level risk factors for DD by analyzing individual animal health records (n = 1,209,883) and feedlot-level records from western Canadian feedlots (n = 28) between 2014 and 2018, inclusive. The risk of a DD diagnosis was higher (incidence rate ratio (IRR) = 2.08, 95% CI 1.52 to 2.86) in cattle sourced from confined background operations (CB) versus cattle sourced from auction markets (AM). Conversely, ranch direct (RD) cattle were (IRR = 0.02, 95% CI 0.04 to 0.30) lower risk than AM cattle of being diagnosed with DD. The risk of being diagnosed with DD was higher in females than in males. The magnitude of the risk in females over males was influenced by annual DD incidence in low morbidity years (2014, 2017, and 2018) (IRR = 2.02, 95% CI 1.27 to 3.19), medium morbidity years (2016) (IRR = 2.95, 95% CI 1.64 to 5.33), and high morbidity years (2015) (IRR = 5.41, 95% CI 3.27 to 8.95). At the feedlot-level, the risk of a diagnosis of DD was lower in small capacity (SCF) versus large capacity feedlots (LCF) (IRR = 0.24, 95% CI 0.05 to 0.76). Future research should focus on identifying factors that may propagate disease transmission between cattle of different sexes and from different acquisition sources.
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Affiliation(s)
- Sarah Erickson
- TELUS Agriculture and Consumer Goods, Okotoks, AB T1S 2A2, Canada; (S.E.); (C.B.); (J.S.); (E.J.)
| | - Calvin Booker
- TELUS Agriculture and Consumer Goods, Okotoks, AB T1S 2A2, Canada; (S.E.); (C.B.); (J.S.); (E.J.)
| | - Jiming Song
- TELUS Agriculture and Consumer Goods, Okotoks, AB T1S 2A2, Canada; (S.E.); (C.B.); (J.S.); (E.J.)
| | - Eugene Janzen
- TELUS Agriculture and Consumer Goods, Okotoks, AB T1S 2A2, Canada; (S.E.); (C.B.); (J.S.); (E.J.)
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4Z6, Canada
| | - Murray Jelinski
- Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Karen Schwartzkopf-Genswein
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada;
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Ramoneda J, Fan K, Lucas JM, Chu H, Bissett A, Strickland MS, Fierer N. Ecological relevance of flagellar motility in soil bacterial communities. THE ISME JOURNAL 2024; 18:wrae067. [PMID: 38648266 PMCID: PMC11095265 DOI: 10.1093/ismejo/wrae067] [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: 01/30/2024] [Revised: 03/27/2024] [Accepted: 04/18/2024] [Indexed: 04/25/2024]
Abstract
Flagellar motility is a key bacterial trait as it allows bacteria to navigate their immediate surroundings. Not all bacteria are capable of flagellar motility, and the distribution of this trait, its ecological associations, and the life history strategies of flagellated taxa remain poorly characterized. We developed and validated a genome-based approach to infer the potential for flagellar motility across 12 bacterial phyla (26 192 unique genomes). The capacity for flagellar motility was associated with a higher prevalence of genes for carbohydrate metabolism and higher maximum potential growth rates, suggesting that flagellar motility is more prevalent in environments with higher carbon availability. To test this hypothesis, we applied a method to infer the prevalence of flagellar motility in whole bacterial communities from metagenomic data and quantified the prevalence of flagellar motility across four independent field studies that each captured putative gradients in soil carbon availability (148 metagenomes). We observed a positive relationship between the prevalence of bacterial flagellar motility and soil carbon availability in all datasets. Since soil carbon availability is often correlated with other factors that could influence the prevalence of flagellar motility, we validated these observations using metagenomic data from a soil incubation experiment where carbon availability was directly manipulated with glucose amendments. This confirmed that the prevalence of bacterial flagellar motility is consistently associated with soil carbon availability over other potential confounding factors. This work highlights the value of combining predictive genomic and metagenomic approaches to expand our understanding of microbial phenotypic traits and reveal their general environmental associations.
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Affiliation(s)
- Josep Ramoneda
- Cooperative Institute for Research in Environmental Sciences (CIRES), University of Colorado, 80309 Boulder, CO, United States
- Spanish Research Council (CSIC), Center for Advanced Studies of Blanes (CEAB), 17300 Blanes, Spain
| | - Kunkun Fan
- Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 210008 Nanjing, China
| | - Jane M Lucas
- Cary Institute of Ecosystem Studies, 12545 Millbrook, NY, United States
| | - Haiyan Chu
- Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 210008 Nanjing, China
- University of Chinese Academy of Sciences, 101408 Beijing, China
| | | | - Michael S Strickland
- Department of Soil and Water Systems, University of Idaho, 83843 Moscow, ID, United States
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences (CIRES), University of Colorado, 80309 Boulder, CO, United States
- Department of Ecology and Evolutionary Biology, University of Colorado, 80309 Boulder, CO, United States
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7
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Çömlekcioğlu U, Jezierska S, Opsomer G, Pascottini OB. Uterine microbial ecology and disease in cattle: A review. Theriogenology 2024; 213:66-78. [PMID: 37804686 DOI: 10.1016/j.theriogenology.2023.09.016] [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: 08/06/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/09/2023]
Abstract
Due to the critical contribution of the uterine-associated microbiota in reproductive health, physiology, and performance, culture-independent methods have been increasingly employed to unravel key aspects of microbial ecology in the uterus of cattle. Nowadays, we know that bacterial diversity is crucial to maintain uterine health, however, there is still no consensus on the exact composition of a healthy uterine microbiota (or eubiosis). Generally, loss of bacterial diversity (or dysbiosis) contributes to the development of uterine infections, associated with increased relative abundances of Bacteroides, Fusobacterium, Trueperella, and Porphyromonas. Uterine infections are highly prevalent and gravely influence the profitability of cattle operations, animal welfare, and public health. Thus, understanding the dynamics of uterine microbial ecology is essential to develop effective strategies focused on preventing and mitigating the adverse effects of uterine dysbiosis as well as assisting in the process of restoring the core, healthy uterine microbiota. The aim of this review is to summarize research conducted in the microbial ecology of bovine uteri. We discuss the origin of the uterine microflora of healthy cows and the factors influencing its composition. In addition, we review the biology of specific pathogens that are known to increase in abundance during the occurrence of uterine disease. Lastly, we provide an overview of the bacterial biofilm in the bovine endometrium, and we briefly summarize the rationale for the use of probiotics to prevent uterine disease in cattle.
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Affiliation(s)
- Uğur Çömlekcioğlu
- Department of Biology, Osmaniye Korkut Ata University, 8000, Osmaniye, Turkiye; Department of Internal Medicine, Reproduction and Population Medicine, Ghent University, 9820, Merelbeke, Belgium.
| | | | - Geert Opsomer
- Department of Internal Medicine, Reproduction and Population Medicine, Ghent University, 9820, Merelbeke, Belgium
| | - Osvaldo Bogado Pascottini
- Department of Internal Medicine, Reproduction and Population Medicine, Ghent University, 9820, Merelbeke, Belgium.
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8
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Dixit S, Kumar S, Sharma R, Banakar PS, Singh M, Keshri A, Tyagi AK. Rumen multi-omics addressing diet-host-microbiome interplay in farm animals: a review. Anim Biotechnol 2023; 34:3187-3205. [PMID: 35713100 DOI: 10.1080/10495398.2022.2078979] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Continuous improvement in the living standards of developing countries, calls for an urgent need of high quality meat and dairy products. The farm animals have a micro-ecosystem in gastro-intestinal tract, comprising of a wide variety of flora and fauna which converts roughages and agricultural byproducts as well as nutrient rich concentrate sources into the useful products such as volatile fatty acids and microbial crude proteins. The microbial diversity changes according to composition of the feed, host species/breed and host's individual genetic makeup. From culture methods to next-generation sequencing technologies, the knowledge has emerged a lot to know-how of microbial world viz. their identification, enzymatic activities and metabolites which are the keys of ruminant's successful existence. The structural composition of ruminal community revealed through metagenomics can be elaborated by metatranscriptomics and metabolomics through deciphering their functional role in metabolism and their responses to the external and internal stimuli. These highly sophisticated analytical tools have made possible to correlate the differences in the feed efficiency, nutrients utilization and methane emissions to their rumen microbiome. The comprehensively understood rumen microbiome will enhance the knowledge in the fields of animal nutrition, biotechnology and climatology through deciphering the significance of each and every domain of residing microbial entity. The present review undertakes the recent investigations regarding rumen multi-omics viz. taxonomic and functional potential of microbial populations, host-diet-microbiome interactions and correlation with metabolic dynamics.
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Affiliation(s)
- Sonam Dixit
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - Sachin Kumar
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - Ritu Sharma
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - P S Banakar
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - Manvendra Singh
- Krishi Vigyan Kendra, Banda University of Agriculture and Technology, Banda, India
| | - Anchal Keshri
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - A K Tyagi
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
- Animal Nutrition and Physiology, Indian Council of Agricultural Research, New Delhi, India
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Aminu S, Ascandari A, Laamarti M, Safdi NEH, El Allali A, Daoud R. Exploring microbial worlds: a review of whole genome sequencing and its application in characterizing the microbial communities. Crit Rev Microbiol 2023:1-25. [PMID: 38006569 DOI: 10.1080/1040841x.2023.2282447] [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: 05/22/2023] [Accepted: 11/06/2023] [Indexed: 11/27/2023]
Abstract
The classical microbiology techniques have inherent limitations in unraveling the complexity of microbial communities, necessitating the pivotal role of sequencing in studying the diversity of microbial communities. Whole genome sequencing (WGS) enables researchers to uncover the metabolic capabilities of the microbial community, providing valuable insights into the microbiome. Herein, we present an overview of the rapid advancements achieved thus far in the use of WGS in microbiome research. There was an upsurge in publications, particularly in 2021 and 2022 with the United States, China, and India leading the metagenomics research landscape. The Illumina platform has emerged as the widely adopted sequencing technology, whereas a significant focus of metagenomics has been on understanding the relationship between the gut microbiome and human health where distinct bacterial species have been linked to various diseases. Additionally, studies have explored the impact of human activities on microbial communities, including the potential spread of pathogenic bacteria and antimicrobial resistance genes in different ecosystems. Furthermore, WGS is used in investigating the microbiome of various animal species and plant tissues such as the rhizosphere microbiome. Overall, this review reflects the importance of WGS in metagenomics studies and underscores its remarkable power in illuminating the variety and intricacy of the microbiome in different environments.
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Affiliation(s)
- Suleiman Aminu
- Chemical and Biochemical Sciences-Green Process Engineering, University Mohammed VI Polytechnic, Ben Guerir, Morocco
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria
| | - AbdulAziz Ascandari
- Chemical and Biochemical Sciences-Green Process Engineering, University Mohammed VI Polytechnic, Ben Guerir, Morocco
| | - Meriem Laamarti
- Faculty of Medical Sciences, University Mohammed VI Polytechnic, Ben Guerir, Morocco
| | - Nour El Houda Safdi
- AgroBioSciences Program, College for Sustainable Agriculture and Environmental Science, University Mohammed VI Polytechnic, Ben Guerir, Morocco
| | - Achraf El Allali
- Bioinformatics Laboratory, College of Computing, University Mohammed VI Polytechnic, Ben Guerir, Morocco
| | - Rachid Daoud
- Chemical and Biochemical Sciences-Green Process Engineering, University Mohammed VI Polytechnic, Ben Guerir, Morocco
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10
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Bay V, Gillespie A, Ganda E, Evans NJ, Carter SD, Lenzi L, Lucaci A, Haldenby S, Barden M, Griffiths BE, Sánchez-Molano E, Bicalho R, Banos G, Darby A, Oikonomou G. The bovine foot skin microbiota is associated with host genotype and the development of infectious digital dermatitis lesions. MICROBIOME 2023; 11:4. [PMID: 36624507 PMCID: PMC9830885 DOI: 10.1186/s40168-022-01440-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Bovine Digital Dermatitis (BDD) is a prevalent infectious disease, causing painful foot skin lesions and lameness in cattle. We describe herein the bovine foot skin microbiota and its associations with BDD using 16S rRNA gene amplicon and shotgun metagenomic sequencing on samples from 259 dairy cows from three UK dairy farms. RESULTS We show evidence of dysbiosis, and differences in taxonomy and functional profiles in the bovine foot skin microbiome of clinically healthy animals that subsequently develop BDD lesions, compared to those that do not. Our results suggest that taxonomical and functional differences together with alterations in ecological interactions between bacteria in the normal foot skin microbiome may predispose an animal to develop BDD lesions. Using genome-wide association and regional heritability mapping approaches, we provide first evidence for interactions between host genotype and certain members of the foot skin microbiota. We show the existence of significant genetic variation in the relative abundance of Treponema spp. and Peptoclostridium spp. and identify regions in the bovine genome that explain a significant proportion of this variation. CONCLUSIONS Collectively this work shows early changes in taxonomic and functional profiles of the bovine foot-skin microbiota in clinically healthy animals which are associated with subsequent development of BDD and could be relevant to prevention of disease. The description of host genetic control of members of the foot skin microbiota, combined with the association of the latter with BDD development offer new insights into a complex relationship that can be exploited in selective breeding programmes. Video Abstract.
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Affiliation(s)
- V Bay
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Faculty of Agriculture, Ege University, İzmir, Turkey
| | - A Gillespie
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - E Ganda
- Department of Animal Science, Penn State University, State College, PA, USA
| | - N J Evans
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - S D Carter
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - L Lenzi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - A Lucaci
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - S Haldenby
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - M Barden
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - B E Griffiths
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | | | - R Bicalho
- FERA Diagnostics and Biologicals, College Station, TX, USA
| | - G Banos
- Scotland's Rural College (SRUC), Easter Bush, Midlothian, UK
| | - A Darby
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - G Oikonomou
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.
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11
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Jucker S, Alsaaod M, Steiner A, Zingre T, Kaessmeyer S, Gurtner C, Friker B, Brandt S, Jensen TK, Hoby S. Treatment of digital dermatitis using salicylic acid in European bison (Bison bonasus) reveals promising results. Front Vet Sci 2022; 9:1012226. [DOI: 10.3389/fvets.2022.1012226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 11/15/2022] [Indexed: 12/04/2022] Open
Abstract
Digital dermatitis (DD) associated with the presence of multiple Treponema spp. was recently described for the first time in European bison (Bison bonasus). DD is characterized by skin inflammation in the distal foot area in various ungulates. The objective of this proof of concept study was to test a treatment protocol adopted from cattle for its applicability in this wildlife species using five animals. Keratolytic salicylic acid paste was administered topically under bandages for seven days to enable removal of the affected skin. All interventions were performed under general anesthesia. To evaluate the treatment efficacy, photographs and biopsies were taken pre- and post-treatment. The biopsies were examined histologically, by PCR for the presence of different bacterial species, by Treponema-specific fluorescent in situ hybridization (FISH), and by transmission electron microscopy. Based on photographs, complete clinical healing of the 15 feet with macroscopical DD lesions was achieved. Histological examination showed mild to moderate dermatitis in 17/20 feet before, and in 12/20 feet after treatment. 17/20 feet were Treponema spp. PCR positive before, and none was positive after treatment. Dichelobacter nodosus, Fusobacterium necrophorum, and Porphyromonas levii could not be detected in any of the samples. By FISH and electron microscopy, Treponema spp. could be visualized in the stratum corneum before, but not after treatment. These results suggest that this treatment method can be applied as standard practice prior to transporting DD affected European bison to prevent the spread of this contagious disease.
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12
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Thomas AD, Pajor EA, Caddey B, Goldhawk C, Martins L, Orsel K. An experimental model to induce digital dermatitis in beef calves. BMC Vet Res 2022; 18:238. [PMID: 35739561 PMCID: PMC9219410 DOI: 10.1186/s12917-022-03345-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/14/2022] [Indexed: 11/10/2022] Open
Abstract
Background Digital dermatitis (DD) is a multifactorial infectious disease affecting the skin on feet of cattle causing erosion and inflammation above the heel bulbs. Some cases of DD cause lameness and significantly impact animal welfare and productivity. While DD has emerged as a concern for the beef industry, key information regarding early detection and its impact on cattle behaviour is lacking. The primary objective of this study was to determine if an established DD experimental model for dairy calves could be used to induce DD lesions in beef calves. A secondary objective was to describe changes in behaviour and pain associated with induction of DD lesions. Eight beef calves acquired from a single cow-calf operator were enrolled in the study. Upon enrolment, calves were evaluated and determined to be free of foot lesions. Within the experimental environment, calves were housed in individual pens and assigned to two groups (mock-inoculated and inoculated). Both hind feet of each calf were enrolled. Within calf, inoculation protocol was consistent, and a 28-day experimental protocol was employed. Two days prior to inoculation, both hind feet of each calf were abraded (area above the heel bulbs and below the dewclaws), moistened, and wrapped to facilitate an anaerobic condition. Feet were inoculated with macerated DD lesion material or mock inoculum and remained wrapped until clinical signs of DD or protocol endpoint. Results After a period of 14 to 18 days post inoculation, three of five inoculated calves developed clinical signs (lameness), and upon close inspection, DD lesions were present on at least one hind foot. Two of five inoculated calves did not develop lesions within 28 days. Zero of three mock-inoculated calves developed DD. Treponema spp. were detected by quantitative polymerase chain reaction from biopsies of induced lesions. Measurements of behaviour prior to disease induction were numerically different between DD affected and mock-inoculated calves. Conclusions An experimental infection model established for dairy cattle was used to successfully induce acute DD lesions in three of five inoculated beef calves. This model can provide a framework to study intervention protocols and to evaluate the impact of DD on behaviour and pain.
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Affiliation(s)
- Anice D Thomas
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada
| | - Edmond A Pajor
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada
| | - Benjamin Caddey
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada
| | - Christy Goldhawk
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada
| | - Larissa Martins
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada
| | - Karin Orsel
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada.
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13
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Wilson-Welder JH, Mansfield K, Han S, Bayles DO, Alt DP, Olsen SC. Lesion Material From Treponema-Associated Hoof Disease of Wild Elk Induces Disease Pathology in the Sheep Digital Dermatitis Model. Front Vet Sci 2022; 8:782149. [PMID: 35097043 PMCID: PMC8790030 DOI: 10.3389/fvets.2021.782149] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/29/2021] [Indexed: 12/26/2022] Open
Abstract
A hoof disease among wild elk (Cervus elaphus) in the western United States has been reported since 2008. Now present in Washington, Oregon, Idaho, and California, this hoof disease continues to spread among elk herds suggesting an infectious etiology. Causing severe lesions at the hoof-skin junction, lesions can penetrate the hoof-horn structure causing severe lameness, misshapen hooves, and in some cases, sloughed hooves leaving the elk prone to infection, malnutrition, and premature death. Isolated to the feet, this disease has been termed treponeme-associated hoof disease due to the numerous Treponema spp. found within lesions. In addition to the Treponema spp., treponeme-associated hoof disease shares many similarities with digital dermatitis of cattle and livestock including association with several groups of anaerobic bacteria such as Bacteroides, Clostridia, and Fusobacterium, neutrophilic inflammatory infiltrate, and restriction of the disease to the foot and hoof tissues. To determine if there was a transmissible infectious component to this disease syndrome, elk lesion homogenate was used in a sheep model of digital dermatitis. Ten animals were inoculated with lesion material and lesion development was followed over 7 weeks. Most inoculated feet developed moderate to severe lesions at 2- or 4-weeks post-inoculation timepoints, with 16 of 18 feet at 4 weeks also had spirochetes associated within the lesions. Histopathology demonstrated spirochetes at the invading edge of the lesions along with other hallmarks of elk hoof disease, neutrophilic inflammatory infiltrates, and keratinocyte erosion. Treponema-specific PCR demonstrated three phylotypes associated with elk hoof disease and digital dermatitis were present. Serum of infected sheep had increased anti-Treponema IgG when compared to negative control sheep and pre-exposure samples. Analysis of the bacterial microbiome by sequencing of the bacterial 16S rRNA gene showed a community structure in sheep lesions that was highly similar to the elk lesion homogenate used as inoculum. Bacteroidies, Fusobacterium, and Clostridia were among the bacterial taxa overrepresented in infected samples as compared to negative control samples. In conclusion, there is a highly transmissible, infectious bacterial component to elk treponeme-associated hoof disease which includes several species of Treponema as well as other bacteria previously associated with digital dermatitis.
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Affiliation(s)
- Jennifer H. Wilson-Welder
- Infectious Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture (USDA), Ames, IA, United States
- *Correspondence: Jennifer H. Wilson-Welder
| | - Kristin Mansfield
- Washington Department of Fish and Wildlife, Spokane Valley, WA, United States
| | - Sushan Han
- Colorado State University Diagnostic Medicine Center, Fort Collins, CO, United States
| | - Darrell O. Bayles
- Infectious Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture (USDA), Ames, IA, United States
| | - David P. Alt
- Infectious Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture (USDA), Ames, IA, United States
| | - Steven C. Olsen
- Infectious Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture (USDA), Ames, IA, United States
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14
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Selberherr E, Penz T, König L, Conrady B, Siegl A, Horn M, Schmitz-Esser S. The life cycle-dependent transcriptional profile of the obligate intracellular amoeba symbiont Amoebophilus asiaticus. FEMS Microbiol Ecol 2022; 98:6499296. [PMID: 34999767 PMCID: PMC8831229 DOI: 10.1093/femsec/fiac001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/22/2021] [Accepted: 01/04/2022] [Indexed: 12/04/2022] Open
Abstract
Free-living amoebae often harbor obligate intracellular bacterial symbionts. Amoebophilus (A.) asiaticus is a representative of a lineage of amoeba symbionts in the phylum Bacteroidota. Here, we analyse the transcriptome of A. asiaticus strain 5a2 at four time points during its infection cycle and replication within the Acanthamoeba host using RNA sequencing. Our results reveal a dynamic transcriptional landscape throughout different A. asiaticus life cycle stages. Many intracellular bacteria and pathogens utilize eukaryotic-like proteins (ELPs) for host cell interaction and the A. asiaticus 5a2 genome shows a particularly high abundance of ELPs. We show the expression of all genes encoding ELPs and found many ELPs to be differentially expressed. At the replicative stage of A. asiaticus, ankyrin repeat proteins and tetratricopeptide/Sel1-like repeat proteins were upregulated. At the later time points, high expression levels of a type 6 secretion system that likely prepares for a new infection cycle after lysing its host, were found. This study reveals comprehensive insights into the intracellular lifestyle of A. asiaticus and highlights candidate genes for host cell interaction. The results from this study have implications for other intracellular bacteria such as other amoeba-associated bacteria and the arthropod symbionts Cardinium forming the sister lineage of A. asiaticus.
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Affiliation(s)
- E Selberherr
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Austria
| | - T Penz
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.,current affiliation: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - L König
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - B Conrady
- Department of Veterinary and Animal Science, University of Copenhagen, Denmark
| | - A Siegl
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - M Horn
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - S Schmitz-Esser
- Department of Animal Science, Iowa State University, Ames, USA
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15
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Blanchard AM, Staley CE, Shaw L, Wattegedera SR, Baumbach CM, Michler JK, Rutland C, Back C, Newbold N, Entrican G, Tötemeyer S. A Trifecta of New Insights into Ovine Footrot for Infection Drivers, Immune Response, and Host-Pathogen Interactions. Infect Immun 2021; 89:e0027021. [PMID: 34227837 PMCID: PMC8445190 DOI: 10.1128/iai.00270-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/16/2021] [Indexed: 12/02/2022] Open
Abstract
Footrot is a polymicrobial infectious disease in sheep causing severe lameness, leading to one of the industry's largest welfare problems. The complex etiology of footrot makes in situ or in vitro investigations difficult. Computational methods offer a solution to understanding the bacteria involved and how they may interact with the host, ultimately providing a way to identify targets for future hypothesis-driven investigative work. Here, we present the first combined global analysis of bacterial community transcripts together with the host immune response in healthy and diseased ovine feet during a natural polymicrobial infection state using metatranscriptomics. The intratissue and surface bacterial populations and the most abundant bacterial transcriptomes were analyzed, demonstrating that footrot-affected skin has reduced diversity and increased abundances of not only the causative bacterium Dichelobacter nodosus but also other species such as Mycoplasma fermentans and Porphyromonas asaccharolytica. Host transcriptomics reveals the suppression of biological processes related to skin barrier function, vascular functions, and immunosurveillance in unhealthy interdigital skin, supported by histological findings that type I collagen (associated with scar tissue formation) is significantly increased in footrot-affected interdigital skin compared to outwardly healthy skin. Finally, we provide some interesting indications of host and pathogen interactions associated with virulence genes and the host spliceosome, which could lead to the identification of future therapeutic targets.
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Affiliation(s)
- Adam M. Blanchard
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, Leicestershire, United Kingdom
| | - Ceri E. Staley
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, Leicestershire, United Kingdom
| | - Laurence Shaw
- School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
| | - Sean R. Wattegedera
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Midlothian, Scotland
| | - Christina-Marie Baumbach
- Institute of Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
| | - Jule K. Michler
- Institute of Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
| | - Catrin Rutland
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, Leicestershire, United Kingdom
| | - Charlotte Back
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, Leicestershire, United Kingdom
| | - Nerissa Newbold
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, Leicestershire, United Kingdom
| | - Gary Entrican
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Midlothian, Scotland
| | - Sabine Tötemeyer
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, Leicestershire, United Kingdom
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16
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Caddey B, De Buck J. Meta-Analysis of Bovine Digital Dermatitis Microbiota Reveals Distinct Microbial Community Structures Associated With Lesions. Front Cell Infect Microbiol 2021; 11:685861. [PMID: 34336713 PMCID: PMC8322762 DOI: 10.3389/fcimb.2021.685861] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/16/2021] [Indexed: 01/04/2023] Open
Abstract
Bovine digital dermatitis (DD) is a significant cause of infectious lameness and economic losses in cattle production across the world. There is a lack of a consensus across different 16S metagenomic studies on DD-associated bacteria that may be potential pathogens of the disease. The goal of this meta-analysis was to identify a consistent group of DD-associated bacteria in individual DD lesions across studies, regardless of experimental design choices including sample collection and preparation, hypervariable region sequenced, and sequencing platform. A total of 6 studies were included in this meta-analysis. Raw sequences and metadata were identified on the NCBI sequence read archive and European nucleotide archive. Bacterial community structures were investigated between normal skin and DD skin samples. Random forest models were generated to classify DD status based on microbial composition, and to identify taxa that best differentiate DD status. Among all samples, members of Treponema, Mycoplasma, Porphyromonas, and Fusobacterium were consistently identified in the majority of DD lesions, and were the best genera at differentiating DD lesions from normal skin. Individual study and 16S hypervariable region sequenced had significant influence on final DD lesion microbial composition (P < 0.05). These findings indicate that members of Treponema, Mycoplasma, Porphyromonas, and/or Fusobacterium may have significant roles in DD pathogenesis, and should be studied further in respect to elucidating DD etiopathogenic mechanisms and developing more effective treatment and mitigation strategies.
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Affiliation(s)
- Ben Caddey
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Jeroen De Buck
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
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17
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Tracking Reservoirs of Antimicrobial Resistance Genes in a Complex Microbial Community Using Metagenomic Hi-C: The Case of Bovine Digital Dermatitis. Antibiotics (Basel) 2021; 10:antibiotics10020221. [PMID: 33672258 PMCID: PMC7926801 DOI: 10.3390/antibiotics10020221] [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: 01/22/2021] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 02/08/2023] Open
Abstract
Bovine digital dermatitis (DD) is a contagious infectious cause of lameness in cattle with unknown definitive etiologies. Many of the bacterial species detected in metagenomic analyses of DD lesions are difficult to culture, and their antimicrobial resistance status is largely unknown. Recently, a novel proximity ligation-guided metagenomic approach (Hi-C ProxiMeta) has been used to identify bacterial reservoirs of antimicrobial resistance genes (ARGs) directly from microbial communities, without the need to culture individual bacteria. The objective of this study was to track tetracycline resistance determinants in bacteria involved in DD pathogenesis using Hi-C. A pooled sample of macerated tissues from clinical DD lesions was used for this purpose. Metagenome deconvolution using ProxiMeta resulted in the creation of 40 metagenome-assembled genomes with ≥80% complete genomes, classified into five phyla. Further, 1959 tetracycline resistance genes and ARGs conferring resistance to aminoglycoside, beta-lactams, sulfonamide, phenicol, lincosamide, and erythromycin were identified along with their bacterial hosts. In conclusion, the widespread distribution of genes conferring resistance against tetracycline and other antimicrobials in bacteria of DD lesions is reported for the first time. Use of proximity ligation to identify microorganisms hosting specific ARGs holds promise for tracking ARGs transmission in complex microbial communities.
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18
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Newbrook K, Carter SD, Crosby-Durrani H, Evans NJ. Challenge of Bovine Foot Skin Fibroblasts With Digital Dermatitis Treponemes Identifies Distinct Pathogenic Mechanisms. Front Cell Infect Microbiol 2021; 10:538591. [PMID: 33489929 PMCID: PMC7820575 DOI: 10.3389/fcimb.2020.538591] [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: 04/14/2020] [Accepted: 11/24/2020] [Indexed: 11/13/2022] Open
Abstract
Bovine digital dermatitis (BDD) is a common infectious disease of digital skin in cattle and an important cause of lameness worldwide, with limited treatment options. It is of increasing global concern for both animal welfare and food security, imposing a large economic burden on cattle farming industries each year. A polytreponemal etiology has been consistently identified, with three key phylogroups implicated globally: Treponema medium, Treponema phagedenis, and Treponema pedis. Pathogenic mechanisms which might enable targeted treatment/therapeutic development are poorly defined. This study used RNA sequencing to determine global differential mRNA expression in primary bovine foot skin fibroblasts following challenge with three representative BDD treponemes and a commensal treponeme, Treponema ruminis. A pro-inflammatory response was elicited by the BDD treponemes, mediated through IL-8/IL-17 signaling. Unexpectedly, the three BDD treponemes elicited distinct mechanisms of pathogenesis. T. phagedenis and T. pedis increased abundance of mRNA transcripts associated with apoptosis, while T. medium and T. pedis increased transcripts involved in actin rearrangement and loss of cell adhesion, likely promoting tissue invasion. The upregulation of antimicrobial peptide precursor, DEFB123, by T. phagedenis spirochaetes may present a microbial ecological advantage to all treponemes within BDD infected tissue, explaining their dominance within lesions. A commensal, T. ruminis, significantly dysregulated over three times the number of host mRNA transcripts compared to BDD treponemes, implying BDD treponemes, akin to the syphilis pathogen (Treponema pallidum), have evolved as "stealth pathogens" which avoid triggering substantial host immune/inflammatory responses to enable persistence and tissue invasion. Immunohistochemistry demonstrated increased IL-6, IL-8, RND1, and CFB protein expression in BDD lesions, confirming in vitro fibroblast observations and highlighting the system's value in modeling BDD pathogenesis. Several unique shared gene targets were identified, particularly RGS16, GRO1, MAFF, and ZC3H12A. The three key BDD Treponema phylogroups elicited both distinct and shared pathogenic mechanisms in bovine foot skin; upregulating inflammation whilst simultaneously suppressing adaptive immunity. The novel gene targets identified here should enable future vaccine/therapeutic approaches.
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Affiliation(s)
- Kerry Newbrook
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Stuart D Carter
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Hayley Crosby-Durrani
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Nicholas J Evans
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
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19
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20
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Espiritu HM, Mamuad LL, Kim SH, Jin SJ, Lee SS, Kwon SW, Cho YI. Microbiome Shift, Diversity, and Overabundance of Opportunistic Pathogens in Bovine Digital Dermatitis Revealed by 16S rRNA Amplicon Sequencing. Animals (Basel) 2020; 10:ani10101798. [PMID: 33022998 PMCID: PMC7599724 DOI: 10.3390/ani10101798] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/22/2020] [Accepted: 09/30/2020] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Bovine digital dermatitis (BDD) is a foot infection known as the primary cause of lameness in cattle due to painful lesions, posing serious impacts on the productivity and welfare of affected animals. Members of the bacterial group Treponema have long been considered as the main causative agents because previous investigations by bacterial isolation, tissue analyses, and high molecular sequencing have persistently identified this group in BDD. However, other studies indicated that the presence of several bacteria on the lesion due to the slurry environment the cattle foot are exposed to, suggests an interdependent polybacterial nature which could also play a role in disease development and progression. Therefore, we analyzed the diversity and relationship of the diverse microbiome in BDD lesions compared to normal skin from cattle foot by using next-generation high throughput sequencing. Based on the results obtained, we concluded that the shift in microbial composition which leads to richer diversity in BDD, and the overabundance of opportunistic bacterial pathogens could be associated with BDD pathogenesis. Abstract This study analyzed the diversity and phylogenetic relationship of the microbiome of bovine digital dermatitis (BDD) lesions and normal skin from cattle foot by using 16S rRNA amplicon sequencing. Three BDD samples and a normal skin sample were pre-assessed for analysis. The Illumina Miseq platform was used for sequencing and sequences were assembled and were categorized to operational taxonomic units (OTUs) based on similarity, then the core microbiome was visualized. The phylogeny was inferred using MEGA7 (Molecular evolutionary genetics analysis version 7.0). A total of 129 and 185 OTUs were uniquely observed in normal and in BDD samples, respectively. Of the 47 shared OTUs, 15 species presented increased abundance in BDD. In BDD and normal samples, Spirochetes and Proteobacteria showed the most abundant phyla, respectively, suggesting the close association of observed species in each sample group. The phylogeny revealed the evolutionary relationship of OTUs and the Euclidean distance suggested a high sequence divergence between OTUs. We concluded that a shift in the microbiome leads to richer diversity in BDD lesions, and the overabundance of opportunistic pathogens and its synergistic relationship with commensal bacteria could serve as factors in disease development. The influence of these factors should be thoroughly investigated in future studies to provide deeper insights on the pathogenesis of BDD.
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Affiliation(s)
- Hector M. Espiritu
- Department of Animal Science and Technology, Sunchon National University, Suncheon, Jeonnam 57922, Korea; (H.M.E.); (L.L.M.); (S.-h.K.); (S.-j.J.); (S.-s.L.)
| | - Lovelia L. Mamuad
- Department of Animal Science and Technology, Sunchon National University, Suncheon, Jeonnam 57922, Korea; (H.M.E.); (L.L.M.); (S.-h.K.); (S.-j.J.); (S.-s.L.)
| | - Seon-ho Kim
- Department of Animal Science and Technology, Sunchon National University, Suncheon, Jeonnam 57922, Korea; (H.M.E.); (L.L.M.); (S.-h.K.); (S.-j.J.); (S.-s.L.)
| | - Su-jeong Jin
- Department of Animal Science and Technology, Sunchon National University, Suncheon, Jeonnam 57922, Korea; (H.M.E.); (L.L.M.); (S.-h.K.); (S.-j.J.); (S.-s.L.)
| | - Sang-suk Lee
- Department of Animal Science and Technology, Sunchon National University, Suncheon, Jeonnam 57922, Korea; (H.M.E.); (L.L.M.); (S.-h.K.); (S.-j.J.); (S.-s.L.)
| | - Seok-won Kwon
- Woosarang Animal Hospital, Yongin, Gyeonggi 17026, Korea;
| | - Yong-il Cho
- Department of Animal Science and Technology, Sunchon National University, Suncheon, Jeonnam 57922, Korea; (H.M.E.); (L.L.M.); (S.-h.K.); (S.-j.J.); (S.-s.L.)
- Correspondence: ; Tel.: +82-61-750-3234
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21
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Tegtmeyer PC, Staton GJ, Evans NJ, Rohde J, Punsmann TM, Ganter M. First cases of contagious ovine digital dermatitis in Germany. Acta Vet Scand 2020; 62:46. [PMID: 32854737 PMCID: PMC7457254 DOI: 10.1186/s13028-020-00544-0] [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: 01/02/2020] [Accepted: 08/20/2020] [Indexed: 12/24/2022] Open
Abstract
Contagious ovine digital dermatitis (CODD) is a significant disease of the ovine foot characterised by severe lameness and progressive separation of the hoof horn capsule from the underlying tissue. Similar to bovine digital dermatitis (BDD), pathogenic members of the genus Treponema including the Treponema medium phylogroup, Treponema phagedenis phylogroup and Treponema pedis are frequently found together in CODD lesions. To date, CODD was only described in Ireland and the United Kingdom. In northern Germany, cases of an unusually severe lameness presented in a sheep flock that had been affected by footrot for several years. These cases were non-responsive to conventional footrot therapies, with some sheep exhibiting substantial lesions of the claw horn that resulted in horn detachment. Lesion swab samples were collected from both clinically affected and asymptomatic animals. In all clinically affected sheep, CODD-associated Treponema phylogroups were detected by polymerase chain reaction. This is the first report of CODD in Germany and mainland Europe, indicating a wider geographic spread than previously considered. In cases of severe lameness attributed to claw lesions in sheep that fail to respond to footrot treatment, CODD should be considered irrespective of geographic location.
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22
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Jo J, Oh J, Park C. Microbial community analysis using high-throughput sequencing technology: a beginner's guide for microbiologists. J Microbiol 2020; 58:176-192. [PMID: 32108314 DOI: 10.1007/s12275-020-9525-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/11/2019] [Accepted: 12/16/2019] [Indexed: 12/19/2022]
Abstract
Microbial communities present in diverse environments from deep seas to human body niches play significant roles in the complex ecosystem and human health. Characterizing their structural and functional diversities is indispensable, and many approaches, such as microscopic observation, DNA fingerprinting, and PCR-based marker gene analysis, have been successfully applied to identify microorganisms. Since the revolutionary improvement of DNA sequencing technologies, direct and high-throughput analysis of genomic DNA from a whole environmental community without prior cultivation has become the mainstream approach, overcoming the constraints of the classical approaches. Here, we first briefly review the history of environmental DNA analysis applications with a focus on profiling the taxonomic composition and functional potentials of microbial communities. To this end, we aim to introduce the shotgun metagenomic sequencing (SMS) approach, which is used for the untargeted ("shotgun") sequencing of all ("meta") microbial genomes ("genomic") present in a sample. SMS data analyses are performed in silico using various software programs; however, in silico analysis is typically regarded as a burden on wet-lab experimental microbiologists. Therefore, in this review, we present microbiologists who are unfamiliar with in silico analyses with a basic and practical SMS data analysis protocol. This protocol covers all the bioinformatics processes of the SMS analysis in terms of data preprocessing, taxonomic profiling, functional annotation, and visualization.
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Affiliation(s)
- Jihoon Jo
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Jooseong Oh
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Chungoo Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea.
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23
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Mahmood T, Guo Y. Dietary fiber and chicken microbiome interaction: Where will it lead to? ACTA ACUST UNITED AC 2019; 6:1-8. [PMID: 32211522 PMCID: PMC7082689 DOI: 10.1016/j.aninu.2019.11.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 10/25/2019] [Accepted: 11/13/2019] [Indexed: 12/18/2022]
Abstract
The last few decades have been marked by a rapid genetic improvement in chicken growth rates. The modern-day chicken is more efficient in converting feed into muscle mass than their predecessors. This enhanced efficiency emanates from better nutrient digestion, absorption, and metabolism. The gut has therefore become a research focus especially after the ban on the use of antibiotics as growth promoters (AGP) in poultry. In pursuance of better gut health in the post-AGP era, many different strategies are being continuously sought and tested. The gut is inhabited by more than 900 bacterial species along with fungi and archaea, and they play an important role to maintain a conducive milieu for the host. A beneficial shift in the microbial ecosystem of the chicken can be promoted by many dietary and non-dietary interventions, however, diet is ranked as one of the most important and potent regulators of gut microbiota composition. Therefore, the constituents of the diet warrant special attention in the modulation of the gut ecosystem. Among dietary constituents, fiber possesses a significant ability to modulate the microbiota. In this review, we will highlight the importance of fiber in poultry nutrition and will also discuss the effects of fiber on gut microbiota and its resultant ramifications on the liver and brain.
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24
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Hesseling J, Legione AR, Stevenson MA, McCowan CI, Pyman MF, Finochio C, Nguyen D, Roic CL, Thiris OL, Zhang AJ, van Schaik G, Coombe JE. Bovine digital dermatitis in Victoria, Australia. Aust Vet J 2019; 97:404-413. [PMID: 31286478 DOI: 10.1111/avj.12859] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 06/12/2019] [Accepted: 06/17/2019] [Indexed: 12/24/2022]
Abstract
AIMS The objectives of this study were to estimate the prevalence of digital dermatitis (DD) in Victoria, Australia, and to investigate which organisms are consistent with typical DD lesions. The prevalence and causative pathogens of DD are not clear yet in Australia and this paper is one of the first to explore these questions in this country. METHODS Examination and sampling of limbs was undertaken at three knackeries in Victoria, Australia. Limbs were classified as normal (N), active DD-lesion (A), dried or chronic DD-lesion (D) or suspected case of DD (S). A total of 823 cows were examined. Six skin biopsies were taken at each knackery, from which DNA was extracted for diversity profiling. Histochemical staining of samples was performed on eight of the skin biopsies. RESULTS DD was detected in 29.8% of all cows. The prevalence of DD was significantly higher in dairy cows (32.2%) than in beef cows (10.8%). The differential abundance of Treponema-species was significantly increased in dried lesions, compared with the normal skin biopsies. Actinobacteria, Proteobacteria, Firmicutes and Tenericutes were found to be significantly different in abundance in the DD lesions compared with normal skin biopsies. Silver staining of samples showed only mild inflammation and in two samples organisms with morphology consistent with Spirochaetes were detected. CONCLUSIONS The calculated prevalence indicates that DD is present in Victoria, Australia. The results of diversity profiling showed that the presence of Treponema-species was significantly different between the samples of DD lesions and normal skin.
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Affiliation(s)
- J Hesseling
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands
| | - A R Legione
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, 250 Princes Highway, Werribee, Victoria, 3030, Australia
| | - M A Stevenson
- Asia Pacific Centre for Animal Health, University of Melbourne, Parkville, Victoria, 3052, Australia
| | - C I McCowan
- Agriculture Victoria, Veterinary Diagnostics, AgriBio, 5 Ring Road, Bundoora, Victoria, 3083, Australia
| | - M F Pyman
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, 250 Princes Highway, Werribee, Victoria, 3030, Australia
| | - C Finochio
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, 250 Princes Highway, Werribee, Victoria, 3030, Australia
| | - D Nguyen
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, 250 Princes Highway, Werribee, Victoria, 3030, Australia
| | - C L Roic
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, 250 Princes Highway, Werribee, Victoria, 3030, Australia
| | - O L Thiris
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, 250 Princes Highway, Werribee, Victoria, 3030, Australia
| | - A J Zhang
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, 250 Princes Highway, Werribee, Victoria, 3030, Australia
| | - G van Schaik
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands
| | - J E Coombe
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, 250 Princes Highway, Werribee, Victoria, 3030, Australia
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25
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Zhao H, Yan B, Mo X, Li P, Li B, Li Q, Li N, Mo S, Ou Q, Shen P, Wu B, Jiang C. Prevalence and proliferation of antibiotic resistance genes in the subtropical mangrove wetland ecosystem of South China Sea. Microbiologyopen 2019; 8:e871. [PMID: 31251470 PMCID: PMC6855136 DOI: 10.1002/mbo3.871] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/28/2019] [Accepted: 04/30/2019] [Indexed: 12/14/2022] Open
Abstract
The emerging pollutants antibiotic resistance genes (ARGs) are prevalent in aquatic environments such as estuary. Coastal mangrove ecosystems always serve as natural wetlands for receiving sewage which always carry ARGs. Currently, the research considering ARG distribution in mangrove ecosystems gains more interest. In this work, we investigated the diversity of ARGs in an urban estuary containing mangrove and nonmangrove areas of the South China Sea. A total of 163 ARGs that classified into 22 resistance types and six resistance mechanisms were found. ARG abundance of the samples in the estuary is between 0.144 and 0.203. This is within the general range of Chinese estuaries. The difference analysis showed that abundances of total ARGs, six most abundant ARGs (mtrA, rpoB, rpoC, rpsL, ef‐Tu, and parY), the most abundant resistance types (elfamycin, multidrug, and peptide), and the most abundant resistance mechanism (target alteration) were significantly lower in mangrove sediment than that in nonmangrove sediment (p < 0.05). Network and partial redundancy analysis showed that sediment properties and mobile genetic elements were the most influential factors impacting ARG distribution rather than microbial community. The two factors collectively explain 51.22% of the differences of ARG distribution. Our study indicated that mangrove sediments have the capacity to remove ARGs. This work provides a research paradigm for analysis of ARG prevalence and proliferation in the subtropical marine coastal mangrove ecosystem.
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Affiliation(s)
- Huaxian Zhao
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Guangxi Academy of Sciences, Beihai, China.,Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Bing Yan
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Guangxi Academy of Sciences, Beihai, China.,Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning, China
| | - Xueyan Mo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Pu Li
- PFOMIC Bioinformatics Company, Nanning, China
| | - Baoqin Li
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou, China
| | - Quanwen Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Nan Li
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education (Nanning Normal University), Nanning, China
| | - Shuming Mo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Qian Ou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Peihong Shen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Bo Wu
- Department of chemical and biological engineering, Guangxi Normal University for Nationalities, Chongzuo, China
| | - Chengjian Jiang
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Guangxi Academy of Sciences, Beihai, China.,Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, China
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26
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Shaw LM, Blanchard A, Chen Q, An X, Davies P, Tötemeyer S, Zhu YG, Stekel DJ. DirtyGenes: testing for significant changes in gene or bacterial population compositions from a small number of samples. Sci Rep 2019; 9:2373. [PMID: 30787410 PMCID: PMC6382752 DOI: 10.1038/s41598-019-38873-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 12/21/2018] [Indexed: 12/31/2022] Open
Abstract
High throughput genomics technologies are applied widely to microbiomes in humans, animals, soil and water, to detect changes in bacterial communities or the genes they carry, between different environments or treatments. We describe a method to test the statistical significance of differences in bacterial population or gene composition, applicable to metagenomic or quantitative polymerase chain reaction data. Our method goes beyond previous published work in being universally most powerful, thus better able to detect statistically significant differences, and through being more reliable for smaller sample sizes. It can also be used for experimental design, to estimate how many samples to use in future experiments, again with the advantage of being universally most powerful. We present three example analyses in the area of antimicrobial resistance. The first is to published data on bacterial communities and antimicrobial resistance genes (ARGs) in the environment; we show that there are significant changes in both ARG and community composition. The second is to new data on seasonality in bacterial communities and ARGs in hooves from four sheep. While the observed differences are not significant, we show that a minimum group size of eight sheep would provide sufficient power to observe significance of similar changes in further experiments. The third is to published data on bacterial communities surrounding rice crops. This is a much larger data set and is used to verify the new method. Our method has broad uses for statistical testing and experimental design in research on changing microbiomes, including studies on antimicrobial resistance.
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Affiliation(s)
- Laurence M Shaw
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK.,School of Science and Technology, Nottingham Trent University, Nottingham, NG11 8NS, UK
| | - Adam Blanchard
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, LE12 5RD, UK.,School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Brackenhurst, NG25 0FQ, UK
| | - Qinglin Chen
- Chinese Academy of Sciences, Institute of Urban Environment, Xiamen, 361021, China
| | - Xinli An
- Chinese Academy of Sciences, Institute of Urban Environment, Xiamen, 361021, China
| | - Peers Davies
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, LE12 5RD, UK.,Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK
| | - Sabine Tötemeyer
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Yong-Guan Zhu
- Chinese Academy of Sciences, Institute of Urban Environment, Xiamen, 361021, China
| | - Dov J Stekel
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK.
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27
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Kikuchi Y, Kimizuka R, Kato T, Okuda K, Kokubu E, Ishihara K. Treponema denticola Induces Epithelial Barrier Dysfunction in Polarized Epithelial Cells. THE BULLETIN OF TOKYO DENTAL COLLEGE 2018; 59:265-275. [PMID: 30333370 DOI: 10.2209/tdcpublication.2017-0052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Treponema denticola, an anaerobic spirochete found mainly in the oral cavity, is associated with periodontal disease and has a variety of virulence factors. Although in vitro studies have shown that T. denticola is able to penetrate epithelial cell monolayers, its effect on the epithelial barrier junction is not known. Human gingival epithelial cells are closely associated with adjacent membranes, forming barriers in the presence of tight junction proteins, including zonula occludens-1 (ZO-1), claudin-1, and occludin. Tight junction proteins are also expressed by Madin-Darby canine kidney (MDCK) cells in culture. In this study, the MDCK cell profile was investigated following infection with T. denticola (ATCC 35405) wild-type, as well as with its dentilisin-deficient mutant, K1. Basolateral exposure of MDCK cell monolayers to T. denticola at a multiplicity of infection (MOI) of 104 resulted in a decrease in transepithelial electrical resistance (TER). Transepithelial electrical resistance in MDCK cell monolayers also decreased following apical exposure to T. denticola (MOI=104), although this took longer with basolateral exposure. The effect on the TER was time-dependent and required the presence of live bacteria. Meanwhile, MDCK cell viability showed a decrease with either basolateral or apical exposure. Immunofluorescence analysis demonstrated decreases in the amounts of immunoreactive ZO-1 and claudin-1 in association with disruption of cell-cell junctions in MDCK cells exposed apically or basolaterally to T. denticola. Western blot analysis demonstrated degradation of ZO-1 and claudin-1 in culture lysates derived from T. denticola-exposed MDCK cells, suggesting a bacteria-induced protease capable of cleaving these tight junction proteins.
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Affiliation(s)
- Yuichiro Kikuchi
- Department of Microbiology, Tokyo Dental College.,Oral Health Science Center, Tokyo Dental College
| | | | - Tetsuo Kato
- Laboratory of Chemistry, Tokyo Dental College
| | | | - Eitoyo Kokubu
- Department of Microbiology, Tokyo Dental College.,Oral Health Science Center, Tokyo Dental College
| | - Kazuyuki Ishihara
- Department of Microbiology, Tokyo Dental College.,Oral Health Science Center, Tokyo Dental College
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28
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Ogunade I, Schweickart H, Andries K, Lay J, Adeyemi J. Monensin Alters the Functional and Metabolomic Profile of Rumen Microbiota in Beef Cattle. Animals (Basel) 2018; 8:ani8110211. [PMID: 30453603 PMCID: PMC6262558 DOI: 10.3390/ani8110211] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/13/2018] [Accepted: 11/14/2018] [Indexed: 01/10/2023] Open
Abstract
Simple Summary Monensin can enhance the efficiency of feed utilization by modulating rumen fermentation; however, its effects on rumen function has not been fully described. Thus, this study integrated metagenomics and metabolomics analysis to identify differences in functional attributes and metabolites of rumen microbiota in beef steers fed no or 200 mg/d of monensin. Our results showed differences in relative abundance of functional genes involved in lipid metabolism and amino acid metabolism as well as changes in rumen fluid metabolites and their metabolic pathways. This study revealed a better understanding of the effects of monensin, which may enable more effective use of this additive for beef cattle production. Abstract To identify differences in rumen function as a result of feeding monensin to beef cattle, rumen fluid metagenomics and metabolomics analyses were used to evaluate the functional attributes and metabolites of rumen microbiota in beef steers fed no or 200 mg/d of monensin. Eight rumen-fistulated steers were used in the study for a period of 53 days. Rumen fluid samples were collected on the last day of the experiment. Monensin increased the relative abundance of Selenomonas sp. ND2010, Prevotella dentalis, Hallella seregens, Parabacteroides distasonis, Propionispira raffinosivorans, and Prevotella brevis, but reduced the relative abundance of Robinsoniella sp. KNHs210, Butyrivibrio proteoclasticus, Clostridium botulinum, Clostridium symbiosum, Burkholderia sp. LMG29324, and Clostridium butyricum. Monensin increased the relative abundance of functional genes involved in amino acid metabolism and lipid metabolism. A total of 245 metabolites were identified. Thirty-one metabolites were found to be differentially expressed. Pathway analysis of the differentially expressed metabolites revealed upregulated metabolic pathways associated with metabolism of linoleic acid and some amino acids. These findings confirm that monensin affects rumen fermentation of forage-fed beef cattle by modulating the rumen microbiome, and by reducing amino acid degradation and biohydrogenation of linoleic acid in the rumen.
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Affiliation(s)
- Ibukun Ogunade
- College of Agriculture, Communities, and the Environment, Kentucky State University, Frankfort, KY 40601, USA.
| | - Hank Schweickart
- College of Agriculture, Communities, and the Environment, Kentucky State University, Frankfort, KY 40601, USA.
| | - Kenneth Andries
- College of Agriculture, Communities, and the Environment, Kentucky State University, Frankfort, KY 40601, USA.
| | - Jerusha Lay
- College of Agriculture, Communities, and the Environment, Kentucky State University, Frankfort, KY 40601, USA.
| | - James Adeyemi
- College of Agriculture, Communities, and the Environment, Kentucky State University, Frankfort, KY 40601, USA.
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29
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Shang Y, Kumar S, Oakley B, Kim WK. Chicken Gut Microbiota: Importance and Detection Technology. Front Vet Sci 2018; 5:254. [PMID: 30406117 PMCID: PMC6206279 DOI: 10.3389/fvets.2018.00254] [Citation(s) in RCA: 219] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 09/24/2018] [Indexed: 12/29/2022] Open
Abstract
Sustainable poultry meat and egg production is important to provide safe and quality protein sources in human nutrition worldwide. The gastrointestinal (GI) tract of chickens harbor a diverse and complex microbiota that plays a vital role in digestion and absorption of nutrients, immune system development and pathogen exclusion. However, the integrity, functionality, and health of the chicken gut depends on many factors including the environment, feed, and the GI microbiota. The symbiotic interactions between host and microbe is fundamental to poultry health and production. The diversity of the chicken GI microbiota is largely influenced by the age of the birds, location in the digestive tract and diet. Until recently, research on the poultry GI microbiota relied on conventional microbiological techniques that can only culture a small proportion of the complex community comprising the GI microbiota. 16S rRNA based next generation sequencing is a powerful tool to investigate the biological and ecological roles of the GI microbiota in chicken. Although several challenges remain in understanding the chicken GI microbiome, optimizing the taxonomic composition and biochemical functions of the GI microbiome is an attainable goal in the post-genomic era. This article reviews the current knowledge on the chicken GI function and factors that influence the diversity of gut microbiota. Further, this review compares past and current approaches that are used in chicken GI microbiota research. A better understanding of the chicken gut function and microbiology will provide us new opportunities for the improvement of poultry health and production.
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Affiliation(s)
- Yue Shang
- St. Boniface Hospital Research Centre, Winnipeg, MB, Canada
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
| | - Sanjay Kumar
- Department of Poultry Science, University of Georgia, Athens, GA, United States
| | - Brian Oakley
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA, United States
| | - Woo Kyun Kim
- Department of Poultry Science, University of Georgia, Athens, GA, United States
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30
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Bay V, Griffiths B, Carter S, Evans NJ, Lenzi L, Bicalho RC, Oikonomou G. 16S rRNA amplicon sequencing reveals a polymicrobial nature of complicated claw horn disruption lesions and interdigital phlegmon in dairy cattle. Sci Rep 2018; 8:15529. [PMID: 30341326 PMCID: PMC6195575 DOI: 10.1038/s41598-018-33993-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 10/08/2018] [Indexed: 11/08/2022] Open
Abstract
Lameness represents an intractable problem for the dairy industry. Complicated claw horn disruption lesions, interdigital hyperplasia, and interdigital phlegmon are important lameness causing foot lesions. Their aetiology is multifactorial, but infectious processes are likely implicated in disease pathogenesis. Our aim was to investigate the bacterial profiles of these lesions using 16S rRNA gene sequencing of samples obtained from 51 cattle across ten farms in the UK. In this study, interdigital hyperplasia, interdigital hyperplasia with signs of interdigital dermatitis, interdigital phlegmon, complicated sole ulcers, complicated toe ulcers lesions, and complicated white line lesions were investigated; corresponding healthy skin control samples were also analysed. All diseased tissues displayed reduced microbial richness and diversity (as described by Chao1, Shannon, and Simpson alpha-diversity indices) compared to their healthy skin control samples. Our results confirm the association of Treponema spp with some of these disorders. Other anaerobic bacteria including Fusobacterium spp., Fastidiosipila spp. and Porphyromonas spp. were implicated in the aetiology of all these lesions with the exception of interdigital hyperplasia. Complicated claw horn disruption lesions, and interdigital phlegmon were found to have similar bacterial profiles. Such sharing of bacterial genera suggests many of the infectious agents detected in these foot lesions are acting opportunistically; this finding could contribute towards future treatment and control strategies.
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Affiliation(s)
- V Bay
- Department of Epidemiology and Population Health, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - B Griffiths
- Department of Livestock Health and Welfare, Institute of Veterinary Sciences, University of Liverpool, Liverpool, UK
| | - S Carter
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - N J Evans
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - L Lenzi
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - R C Bicalho
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, USA
| | - G Oikonomou
- Department of Epidemiology and Population Health, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
- Department of Livestock Health and Welfare, Institute of Veterinary Sciences, University of Liverpool, Liverpool, UK.
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31
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Berkelmann D, Schneider D, Engelhaupt M, Heinemann M, Christel S, Wijayanti M, Meryandini A, Daniel R. How Rainforest Conversion to Agricultural Systems in Sumatra (Indonesia) Affects Active Soil Bacterial Communities. Front Microbiol 2018; 9:2381. [PMID: 30364106 PMCID: PMC6191527 DOI: 10.3389/fmicb.2018.02381] [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: 05/19/2018] [Accepted: 09/18/2018] [Indexed: 11/13/2022] Open
Abstract
Palm oil production in Indonesia increased constantly over the last decades, which led to massive deforestation, especially on Sumatra island. The ongoing conversion of rainforest to agricultural systems results in high biodiversity loss. Here, we present the first RNA-based study on the effects of rainforest transformation to rubber and oil palm plantations in Indonesia for the active soil bacterial communities. For this purpose, bacterial communities of three different converted systems (jungle rubber, rubber plantation, and oil palm plantation) were studied in two landscapes with rainforest as reference by RT-PCR amplicon-based analysis of 16S rRNA gene transcripts. Active soil bacterial communities were dominated by Frankiales (Actinobacteria), subgroup 2 of the Acidobacteria and Alphaproteobacteria (mainly Rhizobiales and Rhodospirillales). Community composition differed significantly between the converted land use systems and rainforest reference sites. Alphaproteobacteria decreased significantly in oil palm samples compared to rainforest samples. In contrast, relative abundances of taxa within the Acidobacteria increased. Most important abiotic drivers for shaping soil bacterial communities were pH, calcium concentration, base saturation and C:N ratio. Indicator species analysis showed distinct association patterns for the analyzed land use systems. Nitrogen-fixing taxa including members of Rhizobiales and Rhodospirillales were associated with rainforest soils while nitrifiers and heat-resistant taxa including members of Actinobacteria were associated with oil palm soils. Predicted metabolic profiles revealed that the relative abundances of genes associated with fixation of nitrogen significantly decreased in plantation soils. Furthermore, predicted gene abundances regarding motility, competition or gene transfer ability indicated rainforest conversion-induced changes as well.
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Affiliation(s)
- Dirk Berkelmann
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Dominik Schneider
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Martin Engelhaupt
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Melanie Heinemann
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Stephan Christel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Marini Wijayanti
- Department of Biology, Faculty of Mathematics and Natural Sciences IPB, Bogor Agricultural University, Bogor, Indonesia
| | - Anja Meryandini
- Department of Biology, Faculty of Mathematics and Natural Sciences IPB, Bogor Agricultural University, Bogor, Indonesia
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
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32
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Han S, Mansfield KG, Bradway DS, Besser TE, Read DH, Haldorson GJ, Alt DP, Wilson-Welder JH. Treponeme-Associated Hoof Disease of Free-Ranging Elk ( Cervus elaphus) in Southwestern Washington State, USA. Vet Pathol 2018; 56:118-132. [PMID: 30244661 DOI: 10.1177/0300985818798108] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A novel foot disease in free-ranging elk ( Cervus elaphus) in southwestern Washington State emerged in 2008 and spread throughout the region. Initial studies showed adult elk had chronic hoof overgrowth, sole ulcers, and sloughed hoof capsules, but no cause was determined. To identify possible causes and characterize the earliest lesions, 9-, 7-, and 3-month-old elk were collected. Nine-month-old elk had sole ulcers (3/9 elk) and sloughed/overgrown hoof capsules (4/9 elk) similar to adults. Histologically, lesions consisted of coronary, heel bulb, and interdigital ulcers with suppurative inflammation, epithelial hyperplasia, deeply invasive spirochetes, and underrunning of the hoof capsule and heel-sole junction. Spirochetes were identified as Treponema via immunohistochemistry and polymerase chain reaction (PCR). Seven-month-old elk had similar underrunning foot ulcers (6/8 elk) with Treponema identified in all lesions but no chronic overgrowth or sloughed hoof capsules. Three-month-old calves had superficial coronary erosions with no inflammation or identifiable spirochetes (3/5 elk) but were culture/PCR positive for Treponema, suggesting possible early lesions. Lesions from 9- and 7-month-old elk included aerobic and anaerobic bacteria, many of which are associated with infectious foot disease in livestock. Antibody enzyme-linked immunosorbent assay of 7- and 3-month-old elk from the enzootic region showed a trend toward increased Treponema antibody titers compared to normal control elk from outside the region, further supporting the significance of Treponema in the pathogenesis of foot disease. Treponeme-associated hoof disease (TAHD) in elk, a debilitating and progressive condition, shares similarities to bovine digital dermatitis and contagious ovine digital dermatitis.
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Affiliation(s)
- Sushan Han
- 1 Colorado State University Diagnostic Medicine Center, Fort Collins, CO, USA
| | | | - Dan S Bradway
- 3 Washington State University Washington Animal Disease and Diagnostic Laboratory, Pullman, WA, USA
| | - Thomas E Besser
- 3 Washington State University Washington Animal Disease and Diagnostic Laboratory, Pullman, WA, USA
| | - Deryck H Read
- 4 California Animal Health and Food Safety Laboratory System, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Gary J Haldorson
- 3 Washington State University Washington Animal Disease and Diagnostic Laboratory, Pullman, WA, USA
| | - David P Alt
- 5 Infectious Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service, USDA, Ames, IA, USA
| | - Jennifer H Wilson-Welder
- 5 Infectious Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service, USDA, Ames, IA, USA
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33
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Nagar P, Hasija Y. Metagenomic approach in study and treatment of various skin diseases: a brief review. BIOMEDICAL DERMATOLOGY 2018. [DOI: 10.1186/s41702-018-0029-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Wilson-Welder JH, Nally JE, Alt DP, Palmer MV, Coatney J, Plummer P. Experimental Transmission of Bovine Digital Dermatitis to Sheep: Development of an Infection Model. Vet Pathol 2017; 55:245-257. [PMID: 29145798 DOI: 10.1177/0300985817736572] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Digital dermatitis is an infectious cause of lameness primarily affecting cattle but also described in sheep, goats, and wild elk. Digital dermatitis is a polymicrobial infection, involving several Treponema species and other anaerobic bacteria. Although the exact etiology has not been demonstrated, a number of bacterial, host, and environmental factors are thought to contribute to disease development. To study host-bacterial interactions, a reproducible laboratory model of infection is required. The objective of this study was to demonstrate key aspects of bovine digital dermatitis lesions in an easy-to-handle sheep model. Crossbred sheep were obtained from a flock free of hoof disease. Skin between the heel bulb and dewclaw was abraded before wrapping to emulate a moist, anaerobic environment. After 3 days, abraded areas were inoculated with macerated lesion material from active bovine digital dermatitis and remained wrapped. By 2 weeks postinoculation, experimentally inoculated feet developed erosive, erythematous lesions. At 4 weeks postinoculation, microscopic changes in the dermis and epidermis were consistent with those described for bovine digital dermatitis, including erosion, ulceration, hyperkeratosis, ballooning degeneration of keratinocytes, and the presence of neutrophilic infiltrates. Silver staining of lesion biopsy sections confirmed that spirochetes had penetrated the host epidermis. The model was then perpetuated by passaging lesion material from experimentally infected sheep into naïve sheep. This model of bovine digital dermatitis will allow for future novel insights into pathogenic mechanisms of infection, as well as the development of improved diagnostic methods and therapeutics for all affected ruminants.
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Affiliation(s)
- Jennifer H Wilson-Welder
- 1 Infectious Bacterial Diseases, National Animal Disease Center, Agriculture Research Service, United States Department of Agriculture, Ames, IA, USA
| | - Jarlath E Nally
- 1 Infectious Bacterial Diseases, National Animal Disease Center, Agriculture Research Service, United States Department of Agriculture, Ames, IA, USA
| | - David P Alt
- 1 Infectious Bacterial Diseases, National Animal Disease Center, Agriculture Research Service, United States Department of Agriculture, Ames, IA, USA
| | - Mitchell V Palmer
- 1 Infectious Bacterial Diseases, National Animal Disease Center, Agriculture Research Service, United States Department of Agriculture, Ames, IA, USA
| | - John Coatney
- 2 Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Paul Plummer
- 2 Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.,3 Veterinary Diagnostic and Production Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
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Orsel K, Plummer P, Shearer J, De Buck J, Carter SD, Guatteo R, Barkema HW. Missing pieces of the puzzle to effectively control digital dermatitis. Transbound Emerg Dis 2017; 65 Suppl 1:186-198. [PMID: 29124910 DOI: 10.1111/tbed.12729] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Indexed: 12/14/2022]
Abstract
Since the first report of bovine digital dermatitis (DD) in 1974, there is a large body of the literature published; however, effective prevention and control of the disease remain elusive. Although many aspects of the pathogenesis of DD have been investigated, even some of the most basic questions such as the aetiology of this disease remain under debate. Treponema spp. have been strongly associated with DD lesions and occur in abundance in advanced lesions; however, efforts to induce disease with pure cultures of these organisms have been largely underwhelming and inconsistent. Furthermore, although the disease has been presented for several decades, there is limited scientific evidence regarding effective treatment of DD. Apparent discrepancies between effectiveness in vitro and in vivo have challenged the scientific community to identify new potential treatment options. With no treatment resulting in a 100% cure rate, the current expectation is manageable control, but prospects for the eradication of the disease are unlikely using current approaches. In order to develop more effective approaches to control DD on-farm, there is a critical need for a deeper understanding regarding the causation, ecology, transmission and treatment of this disease. In this article, we attempt to provide insights into specific research needs related to DD in order to assist the industry, researchers, pharmaceutical companies and research sponsors with decision-making and identified research gaps.
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Affiliation(s)
- K Orsel
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - P Plummer
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University College of Veterinary Medicine, Ames, IA, USA.,Department of Veterinary Microbiology and Preventative Medicine, Iowa State University College of Veterinary Medicine, Ames, IA, USA
| | - J Shearer
- Department of Veterinary Microbiology and Preventative Medicine, Iowa State University College of Veterinary Medicine, Ames, IA, USA
| | - J De Buck
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - S D Carter
- Department of Infection Biology, Institute of Veterinary Science, University of Liverpool, Liverpool, UK
| | - R Guatteo
- BIOEPAR, INRA, Oniris, Nantes, France
| | - H W Barkema
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
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Thomas M, Webb M, Ghimire S, Blair A, Olson K, Fenske GJ, Fonder AT, Christopher-Hennings J, Brake D, Scaria J. Metagenomic characterization of the effect of feed additives on the gut microbiome and antibiotic resistome of feedlot cattle. Sci Rep 2017; 7:12257. [PMID: 28947833 PMCID: PMC5612972 DOI: 10.1038/s41598-017-12481-6] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 09/06/2017] [Indexed: 01/28/2023] Open
Abstract
In North America, antibiotic feed additives such as monensin and tylosin are added to the finishing diets of feedlot cattle to counter the ill-effects of feeding diets with rapidly digestible carbohydrates. While these feed additives have been proven to improve feed efficiency and reduce liver abscess incidence, how these products impact the gastrointestinal microbiota is not completely understood. In this study, we analyzed the impact of providing antibiotic feed additives to feedlot cattle using metagenome sequencing of treated and control animals. Our results indicate that use of antibiotic feed additives does not produce discernable changes at the phylum level. However, treated cattle had reduced abundance of gram-positive bacteria at the genus level. The abundance of Ruminococcus, Erysipelotrichaceae and Lachnospiraceae in the gut of treated steers was reduced. Functional analysis of the data indicates that there was only minimal impact due to the treatment in the rumen. Genes involved in detoxification were significantly increased in the rumen of AB steers. But the relative abundance of these genes was < 0.3%. However, our results did not show any correlation between the presence of antimicrobial resistance genes in the gut microbiota and the administration of antibiotic feed additives.
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Affiliation(s)
- Milton Thomas
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA.,South Dakota Center for Biologics Research and Commercialization, Brookings, South Dakota, USA
| | - Megan Webb
- Department of Animal Science, South Dakota State University, Brookings, South Dakota, USA
| | - Sudeep Ghimire
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA.,South Dakota Center for Biologics Research and Commercialization, Brookings, South Dakota, USA
| | - Amanda Blair
- Department of Animal Science, South Dakota State University, Brookings, South Dakota, USA
| | - Kenneth Olson
- Department of Animal Science, South Dakota State University, Brookings, South Dakota, USA
| | - Gavin John Fenske
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA.,South Dakota Center for Biologics Research and Commercialization, Brookings, South Dakota, USA
| | - Alex Thomas Fonder
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA.,South Dakota Center for Biologics Research and Commercialization, Brookings, South Dakota, USA
| | - Jane Christopher-Hennings
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA.,South Dakota Center for Biologics Research and Commercialization, Brookings, South Dakota, USA
| | - Derek Brake
- Department of Animal Science, South Dakota State University, Brookings, South Dakota, USA
| | - Joy Scaria
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA. .,South Dakota Center for Biologics Research and Commercialization, Brookings, South Dakota, USA.
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Ariza JM, Relun A, Bareille N, Oberle K, Guatteo R. Effectiveness of collective treatments in the prevention and treatment of bovine digital dermatitis lesions: A systematic review. J Dairy Sci 2017; 100:7401-7418. [DOI: 10.3168/jds.2016-11875] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 05/12/2017] [Indexed: 11/19/2022]
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Rodrigues Hoffmann A. The cutaneous ecosystem: the roles of the skin microbiome in health and its association with inflammatory skin conditions in humans and animals. Vet Dermatol 2017; 28:60-e15. [DOI: 10.1111/vde.12408] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Aline Rodrigues Hoffmann
- Dermatopathology Specialty Service; Department of Veterinary Pathobiology; College of Veterinary Medicine and Biomedical Sciences; Texas A&M University; 4467 TAMU College Station TX 77843 USA
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Xiang L, Poźniak B, Cheng TY. Bacteriological analysis of saliva from partially or fully engorged female adult Rhipicephalus microplus by next-generation sequencing. Antonie van Leeuwenhoek 2016; 110:105-113. [PMID: 27744637 DOI: 10.1007/s10482-016-0780-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 10/04/2016] [Indexed: 11/24/2022]
Abstract
Tick-borne diseases are a major epidemiological problem worldwide. The aim of this study was to investigate the bacterial composition of saliva obtained from engorged adult Rhipicephalus microplus females. Saliva samples collected from partially or fully engorged adult female ticks were analysed using an ultra-high-throughput Illumina HiSeq 2500 sequencing system. To elucidate the possible routes of bacterial transmission, the bacterial flora from whole ticks were also investigated. Proteobacteria, Firmicutes, and Actinobacteria were the predominant phyla in all samples, and Acinetobacter, Rickettsia, Escherichia and Coxiella were the major genera. Microbial diversity in saliva samples from partially engorged ticks was more complex than that of samples from fully engorged individuals. The comparison of saliva and whole-tick samples suggests that bacteria in saliva also colonize the tick's body. We believe that some bacterial genera, such as Dermacoccus, Achromia, SMB53, Sutterella, Providencia, Mycoplana, Oscillospira, and Agrobacterium, were found and reported in ticks for the first time. The Coxiella and Rickettsia detected in this study might be tick-borne pathogens, suggesting health risks associated with exposure to R. microplus in humans and animals. These findings may serve as the basis for developing strategies to control ticks and tick-borne diseases.
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Affiliation(s)
- Liangliang Xiang
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan, China
| | - Błażej Poźniak
- Department of Biochemistry, Pharmacology and Toxicology, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, ul. Norwida 25, 50-307, Wroclaw, Poland
| | - Tian-Yin Cheng
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan, China.
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Wilson-Welder JH, Alt DP, Nally JE. Digital Dermatitis in Cattle: Current Bacterial and Immunological Findings. Animals (Basel) 2015; 5:1114-35. [PMID: 26569318 PMCID: PMC4693204 DOI: 10.3390/ani5040400] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 10/16/2015] [Accepted: 10/23/2015] [Indexed: 02/08/2023] Open
Abstract
Globally; digital dermatitis is a leading form of lameness observed in production dairy cattle. While the precise etiology remains to be determined; the disease is clearly associated with infection by numerous species of treponemes; in addition to other anaerobic bacteria. The goal of this review article is to provide an overview of the current literature; focusing on discussion of the polybacterial nature of the digital dermatitis disease complex and host immune response. Several phylotypes of treponemes have been identified; some of which correlate with location in the lesion and some with stages of lesion development. Local innate immune responses may contribute to the proliferative, inflammatory conditions that perpetuate digital dermatitis lesions. While serum antibody is produced to bacterial antigens in the lesions, little is known about cellular-based immunity. Studies are still required to delineate the pathogenic traits of treponemes associated with digital dermatitis; and other host factors that mediate pathology and protection of digital dermatitis lesions.
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Affiliation(s)
- Jennifer H Wilson-Welder
- Infectious Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA 50010, USA.
| | - David P Alt
- Infectious Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA 50010, USA.
| | - Jarlath E Nally
- Infectious Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA 50010, USA.
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