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Kumari K, Sharma PK, Singh RP. The transcriptome response of Enterobacter sp. S-33 is modulated by low pH-stress. Genes Genomics 2024; 46:671-687. [PMID: 38687436 DOI: 10.1007/s13258-024-01513-x] [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: 06/13/2023] [Accepted: 03/26/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND Acidic environments naturally occur worldwide and uncontrolled use of agricultural practices may also cause acidification of soils. The development of acidic conditions disturbs the establishment of efficient microbial populations in their natural niches. The survival of Enterobacter species under acidic stress remains poorly understood. OBJECTIVE This study aimed to investigate the survival of an environmental isolate Enterobacter sp. S-33 under acidic stress and to identify the various genes involved in stress protection at the global gene transcription level. The obtained results provide new targets that will allow understanding the in-depth mechanisms involved in the adaptation of bacteria to environmental pH changes. METHODS We used the next-generation sequencing (NGS) method to analyze the expression (up-regulation & down-regulation) of genes under varying pH conditions. RESULTS A total of 4214 genes were differentially expressed under acidic conditions (pH 5.0), with 294 up-regulated and 167 down-regulated. At pH 6.0, 50 genes were significantly expressed, of which 34 and 16 were identified as up-regulated and down-regulated, respectively. Many of the up-regulated genes were involved in carbohydrate metabolism, amino acid transport & metabolism, and the most down-regulated genes were related to post-translational modification, lipid transport & metabolism, etc. The observed transcriptomic regulation of genes and pathways identified that Enterobacter reduced its post-translational modification, lipid transport & metabolism, and increased carbohydrate metabolism, amino acid metabolism & transport, energy production & conversion to adapt and grow in acidic stress. CONCLUSIONS The present work provides in-depth information on the characterization of genes associated with tolerance or adaptation to acidic stress of Enterobacter bacterium.
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Affiliation(s)
- Kiran Kumari
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Parva Kumar Sharma
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Rajnish Prakash Singh
- Department of Biotechnlogy, Jaypee Insttute of Information Technology, Noida, 201309, India.
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Yao R, Ai B, Wang Z, Shen B, Xue G, Yu D. Uncovering Microbial Composition of the Tissue Microenvironment in Bladder Cancer using RNA Sequencing Data. J Cancer 2024; 15:2431-2441. [PMID: 38495492 PMCID: PMC10937280 DOI: 10.7150/jca.93055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 01/27/2024] [Indexed: 03/19/2024] Open
Abstract
Purpose: Bladder cancer (BC) is one of the top 10 common tumors in the world. It has been reported that microbiota can colonize tissues and play important roles in tumorigenesis and progression. However, the current understanding of microorganisms in the BC tissue microenvironment remains unclear. Methods: In this study, we integrated the RNA-seq data of 479 BC tissue samples from seven datasets combined with a range of bioinformatics tools to explore the landscape of microbiome in the BC tissue microenvironment. Results: The pan-microbiome was estimated to surpass 1,400 genera. A total of seven core microbiota (Bacillus, Corynebacterium, Cutibacterium, Escherichia, Halomonas, Pasteurella, and Streptomyces) were identified. Among them, Bacillus was widely distributed in all datasets with a high relative abundance (10.11% of all samples on average). Moreover, some biological factors, including tissue source and tumor grade, were found significant effects on the microbial composition of the bladder tissue. Pseudomonas, Porphyrobacter, and Acinetobacter were enriched in tumor tissues, while Mycolicibacterium and Streptomyces were enriched in patients who showed durable response to BCG therapy. In addition, we established microbial co-occurrence networks and found that the BCG therapy may attenuate the microbiological interactions. Conclusions: This study clearly provided a microbial landscape of the BC tissue microenvironment, which was important for exploring the interactions between microorganisms and BC tissues. The identified specific taxa might be potential biomarkers for BC.
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Affiliation(s)
- Ruiqian Yao
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
- Department of Medical Genetics, Naval Medical University, Xiang-Yin Road, 800, Shanghai 200433, China
| | - Bin Ai
- Department of Precision Medicine, Translational Medicine Research Center, Naval Medical University, Xiang-Yin Road, 800, Shanghai 200433, China
- Shanghai Key Laboratory of Cell Engineering, Shanghai, China
| | - Zeyi Wang
- Department of Urology, Huadong Hospital, Fudan University, Shanghai, China
| | - Bing Shen
- Department of Urology, Shanghai General Hospital Affiliated to Nanjing Medical University, Shanghai, 200080, China
- Department of Urology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200080, China
| | - Geng Xue
- Department of Medical Genetics, Naval Medical University, Xiang-Yin Road, 800, Shanghai 200433, China
| | - Dong Yu
- Department of Precision Medicine, Translational Medicine Research Center, Naval Medical University, Xiang-Yin Road, 800, Shanghai 200433, China
- Shanghai Key Laboratory of Cell Engineering, Shanghai, China
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Hill MS, Gilbert JA. Microbiology of the built environment: harnessing human-associated built environment research to inform the study and design of animal nests and enclosures. Microbiol Mol Biol Rev 2023; 87:e0012121. [PMID: 38047636 PMCID: PMC10732082 DOI: 10.1128/mmbr.00121-21] [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] [Indexed: 12/05/2023] Open
Abstract
SUMMARYOver the past decade, hundreds of studies have characterized the microbial communities found in human-associated built environments (BEs). These have focused primarily on how the design and use of our built spaces have shaped human-microbe interactions and how the differential selection of certain taxa or genetic traits has influenced health outcomes. It is now known that the more removed humans are from the natural environment, the greater the risk for the development of autoimmune and allergic diseases, and that indoor spaces can be harsh, selective environments that can increase the emergence of antimicrobial-resistant and virulent phenotypes in surface-bound communities. However, despite the abundance of research that now points to the importance of BEs in determining human-microbe interactions, only a fraction of non-human animal structures have been comparatively explored. It is here, in the context of human-associated BE research, that we consider the microbial ecology of animal-built natural nests and burrows, as well as artificial enclosures, and point to areas of primary interest for future research.
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Affiliation(s)
- Megan S. Hill
- Department of Pediatrics, University of California San Diego School of Medicine, San Diego, California, USA
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Jack A. Gilbert
- Department of Pediatrics, University of California San Diego School of Medicine, San Diego, California, USA
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
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Das BK, Kumar V, Das P, Nayak KK. De novo whole transcriptome analysis of Aeromonas hydrophila isolated from the gut of an infected Labeo rohita. Front Microbiol 2023; 14:1247652. [PMID: 37779727 PMCID: PMC10539578 DOI: 10.3389/fmicb.2023.1247652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 08/28/2023] [Indexed: 10/03/2023] Open
Abstract
Aeromonas hydrophila is a major generalist bacterial pathogen causing severe infections and mortalities in aquatic animals. Its genome, which was the first to be sequenced from the Aeromonas genus, may serve as a model for studying pathogenic mechanisms. To explore the pathogen-host fitness mechanism of bacterium, a comprehensive comparative transcriptome ecotype analysis of A. hydrophila isolated from the gut of Labeo rohita during infection was performed. Special characteristics in gene expression, gene ontology terms and expression of pathogenesis-associated genes, including genes encoding secreted proteins, candidate effectors, hydrolases, and proteins involved in secondary metabolite production were revealed. Among the database, 6,533 were gene ontology (GO) annotated, while 1,480 were not allocated in any GO terms. Investigation on GO illustrated that the articulated genes were improved with molecular function, cellular components, and biological processes. Further bioinformatics analysis identified the outer membrane protein genes (ompA, ompts, ompw, omp38, and omp48), cytotoxin, amylase, and lipase genes. Overall, this work allowed to designate, for the first time, a global view on the pathogenicity of Aeromonas hydrophila during infection. Furthermore, the study provides information on the fitness of A. hydrophila, a severe pathogen with a wide host range.
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Affiliation(s)
- Basanta Kumar Das
- Aquatic Environmental Biotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, West Bengal, India
| | - Vikash Kumar
- Aquatic Environmental Biotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, West Bengal, India
| | - Priyanka Das
- Aquatic Environmental Biotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, West Bengal, India
| | - Kausalya K. Nayak
- Department of Zoology, K.B.D.A.V. College, Nirakarpur, Odisha, India
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Lapid R, Motro Y, Craddock H, Khalfin B, King R, Bar-Gal GK, Moran-Gilad J. Fecal microbiota of the synanthropic golden jackal (Canis aureus). Anim Microbiome 2023; 5:37. [PMID: 37542305 PMCID: PMC10403885 DOI: 10.1186/s42523-023-00259-3] [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: 03/25/2023] [Accepted: 07/26/2023] [Indexed: 08/06/2023] Open
Abstract
The golden jackal (Canis aureus), is a medium canid carnivore widespread throughout the Mediterranean region and expanding into Europe. This species thrives near human settlements and is implicated in zoonoses such as rabies. This study explores for the first time, the golden jackal fecal microbiota. We analyzed 111 fecal samples of wild golden jackals using 16S rRNA amplicon sequencing the connection of the microbiome to animal characteristics, burden of pathogens and geographic and climate characteristics. We further compared the fecal microbiota of the golden jackal to the black-backed jackal and domestic dog. We found that the golden jackal fecal microbiota is dominated by the phyla Bacteroidota, Fusobacteriota and Firmicutes. The golden jackal fecal microbiota was associated with different variables, including geographic region, age-class, exposure to rabies oral vaccine, fecal parasites and toxoplasmosis. A remarkable variation in the relative abundance of different taxa was also found associated with different variables, such as age-class. Linear discriminant analysis effect size (LEfSe) analysis found abundance of specific taxons in each region, Megasphaera genus in group 1, Megamonas genus in group 2 and Bacteroides coprocola species in group 3. We also found a different composition between the fecal microbiota of the golden jackal, blacked-backed jackal and the domestic dog. Furthermore, LEfSe analysis found abundance of Fusobacterium and Bacteroides genera in the golden jackal, Clostridia class in blacked-backed jackal and Megamonas genus in domestic dog. The golden jackal fecal microbiota is influenced by multiple factors including host traits and pathogen burden. The characterization of the microbiota of this thriving species may aid in mapping its spread and proximity to human settlements. Moreover, understanding the jackal microbiota could inform the study of potential animal and human health risks and inform control measures.
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Affiliation(s)
- Roi Lapid
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, P.O.B. 12, 7610001, Rehovot, Israel
| | - Yair Motro
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
| | - Hillary Craddock
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
| | - Boris Khalfin
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
| | - Roni King
- Science and Conservation Division, Israel Nature and Parks Authority, 3 Am Ve'Olamo St., 95463, Jerusalem, Israel
| | - Gila Kahila Bar-Gal
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, P.O.B. 12, 7610001, Rehovot, Israel
| | - Jacob Moran-Gilad
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel.
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Pittino F, Zawierucha K, Poniecka E, Buda J, Rosatelli A, Zordan S, Azzoni RS, Diolaiuti G, Ambrosini R, Franzetti A. Functional and Taxonomic Diversity of Anaerobes in Supraglacial Microbial Communities. Microbiol Spectr 2023; 11:e0100422. [PMID: 36939373 PMCID: PMC10100660 DOI: 10.1128/spectrum.01004-22] [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: 03/20/2022] [Accepted: 02/16/2023] [Indexed: 03/21/2023] Open
Abstract
Cryoconite holes are small ponds present on the surface of most glaciers filled with meltwater and sediment at the bottom. Although they are characterized by extreme conditions, they host bacterial communities with high taxonomic and functional biodiversity. Despite that evidence for a potential niche for anaerobic microorganisms and anaerobic processes has recently emerged, the composition of the microbial communities of the cryoconite reported so far has not shown the relevant presence of anaerobic taxa. We hypothesize that this is due to the lower growth yield of anaerobes compared to aerobic microorganisms. In this work, we aim at evaluating whether the anaerobic bacterial community represents a relevant fraction of the biodiversity of the cryoconite and at describing its structure and functions. We collected sediment samples from cryoconite holes on the Forni Glacier (Italy) and sequenced both 16S rRNA amplicon genes and 16S rRNA amplicon transcripts at different times of the day along a clear summer day. Results showed that a relevant fraction of taxa has been detected only by 16S rRNA transcripts and was undetectable in 16S rRNA gene amplicons. Furthermore, in the transcript approach, anaerobic taxa were overrepresented compared with DNA sequencing. The metatranscriptomics approach was used also to investigate the expression of the main metabolic functions. Results showed the occurrence of syntrophic and commensalism relationships among fermentative bacteria, hydrogenothrophs, and consumers of fermentation end products, which have never been reported so far in cryoconite. IMPORTANCE Recent evidence disclosed the presence of a potential niche for anaerobic microorganisms and anaerobic processes in supraglacial sediments (cryoconite), but a detailed description of the structure and functions of the anaerobic population is still lacking. This work used rRNA and mRNA sequencing and demonstrated that anaerobes are very active in these environments and represent a relevant albeit neglected part of the ecosystem functions in these environments.
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Affiliation(s)
- Francesca Pittino
- Department of Earth and Environmental Sciences (DISAT)–University of Milano-Bicocca, Milano, Italy
- Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Krzysztof Zawierucha
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Ewa Poniecka
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Jakub Buda
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Asia Rosatelli
- Department of Earth and Environmental Sciences (DISAT)–University of Milano-Bicocca, Milano, Italy
| | - Simone Zordan
- Department of Earth and Environmental Sciences (DISAT)–University of Milano-Bicocca, Milano, Italy
| | - Roberto S. Azzoni
- Department of Earth Science “Ardito Desio,” University of Milan, Milano, Italy
| | - Guglielmina Diolaiuti
- Department of Environmental Science and Policy (ESP), University of Milan, Milano, Italy
| | - Roberto Ambrosini
- Department of Environmental Science and Policy (ESP), University of Milan, Milano, Italy
| | - Andrea Franzetti
- Department of Earth and Environmental Sciences (DISAT)–University of Milano-Bicocca, Milano, Italy
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7
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Rey-Campos M, Ríos-Castro R, Gallardo-Escárate C, Novoa B, Figueras A. Exploring the Potential of Metatranscriptomics to Describe Microbial Communities and Their Effects in Molluscs. Int J Mol Sci 2022; 23:ijms232416029. [PMID: 36555669 PMCID: PMC9784687 DOI: 10.3390/ijms232416029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/01/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Metatranscriptomics has emerged as a very useful technology for the study of microbiomes from RNA-seq reads. This method provides additional information compared to the sequencing of ribosomal genes because the gene expression can also be analysed. In this work, we used the metatranscriptomic approach to study the whole microbiome of mussels, including bacteria, viruses, fungi, and protozoans, by mapping the RNA-seq reads to custom assembly databases (including the genomes of microorganisms publicly available). This strategy allowed us not only to describe the diversity of microorganisms but also to relate the host transcriptome and microbiome, finding the genes more affected by the pathogen load. Although some bacteria abundant in the metatranscriptomic analysis were undetectable by 16S rRNA sequencing, a common core of the taxa was detected by both methodologies (62% of the metatranscriptomic detections were also identified by 16S rRNA sequencing, the Oceanospirillales, Flavobacteriales and Vibrionales orders being the most relevant). However, the differences in the microbiome composition were observed among different tissues of Mytilus galloprovincialis, with the fungal kingdom being especially diverse, or among molluscan species. These results confirm the potential of a meta-analysis of transcriptome data to obtain new information on the molluscs' microbiome.
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Affiliation(s)
- Magalí Rey-Campos
- Institute of Marine Research (IIM), National Research Council (CSIC), Eduardo Cabello 6, 36208 Vigo, Spain
| | - Raquel Ríos-Castro
- Institute of Marine Research (IIM), National Research Council (CSIC), Eduardo Cabello 6, 36208 Vigo, Spain
| | - Cristian Gallardo-Escárate
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepción P.O. Box 160-C, Chile
| | - Beatriz Novoa
- Institute of Marine Research (IIM), National Research Council (CSIC), Eduardo Cabello 6, 36208 Vigo, Spain
| | - Antonio Figueras
- Institute of Marine Research (IIM), National Research Council (CSIC), Eduardo Cabello 6, 36208 Vigo, Spain
- Correspondence:
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de Cock M, Fonville M, de Vries A, Bossers A, van den Bogert B, Hakze-van der Honing R, Koets A, Sprong H, van der Poel W, Maas M. Screen the unforeseen: Microbiome-profiling for detection of zoonotic pathogens in wild rats. Transbound Emerg Dis 2022; 69:3881-3895. [PMID: 36404584 PMCID: PMC10099244 DOI: 10.1111/tbed.14759] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/30/2022] [Accepted: 11/01/2022] [Indexed: 11/22/2022]
Abstract
Wild rats can host various zoonotic pathogens. Detection of these pathogens is commonly performed using molecular techniques targeting one or a few specific pathogens. However, this specific way of surveillance could lead to (emerging) zoonotic pathogens staying unnoticed. This problem may be overcome by using broader microbiome-profiling techniques, which enable broad screening of a sample's bacterial or viral composition. In this study, we investigated if 16S rRNA gene amplicon sequencing would be a suitable tool for the detection of zoonotic bacteria in wild rats. Moreover, we used virome-enriched (VirCapSeq) sequencing to detect zoonotic viruses. DNA from kidney samples of 147 wild brown rats (Rattus norvegicus) and 42 black rats (Rattus rattus) was used for 16S rRNA gene amplicon sequencing of the V3-V4 hypervariable region. Blocking primers were developed to reduce the amplification of rat host DNA. The kidney bacterial composition was studied using alpha- and beta-diversity metrics and statistically assessed using PERMANOVA and SIMPER analyses. From the sequencing data, 14 potentially zoonotic bacterial genera were identified from which the presence of zoonotic Leptospira spp. and Bartonella tribocorum was confirmed by (q)PCR or Sanger sequencing. In addition, more than 65% of all samples were dominated (>50% reads) by one of three bacterial taxa: Streptococcus (n = 59), Mycoplasma (n = 39) and Leptospira (n = 25). These taxa also showed the highest contribution to the observed differences in beta diversity. VirCapSeq sequencing in rat liver samples detected the potentially zoonotic rat hepatitis E virus in three rats. Although 16S rRNA gene amplicon sequencing was limited in its capacity for species level identifications and can be more difficult to interpret due to the influence of contaminating sequences in these low microbial biomass samples, we believe it has potential to be a suitable pre-screening method in the future to get a better overview of potentially zoonotic bacteria that are circulating in wildlife.
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Affiliation(s)
- Marieke de Cock
- Centre for Infectious Diseases Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Manoj Fonville
- Centre for Infectious Diseases Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Ankje de Vries
- Centre for Infectious Diseases Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Alex Bossers
- Wageningen Bioveterinary Research (WBVR), Lelystad, The Netherlands.,Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | | | | | - Ad Koets
- Wageningen Bioveterinary Research (WBVR), Lelystad, The Netherlands.,Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Hein Sprong
- Centre for Infectious Diseases Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Wim van der Poel
- Wageningen Bioveterinary Research (WBVR), Lelystad, The Netherlands
| | - Miriam Maas
- Centre for Infectious Diseases Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
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Blahove MR, Carter JR. Flavivirus Persistence in Wildlife Populations. Viruses 2021; 13:v13102099. [PMID: 34696529 PMCID: PMC8541186 DOI: 10.3390/v13102099] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/01/2021] [Accepted: 10/08/2021] [Indexed: 12/14/2022] Open
Abstract
A substantial number of humans are at risk for infection by vector-borne flaviviruses, resulting in considerable morbidity and mortality worldwide. These viruses also infect wildlife at a considerable rate, persistently cycling between ticks/mosquitoes and small mammals and reptiles and non-human primates and humans. Substantially increasing evidence of viral persistence in wildlife continues to be reported. In addition to in humans, viral persistence has been shown to establish in mammalian, reptile, arachnid, and mosquito systems, as well as insect cell lines. Although a considerable amount of research has centered on the potential roles of defective virus particles, autophagy and/or apoptosis-induced evasion of the immune response, and the precise mechanism of these features in flavivirus persistence have yet to be elucidated. In this review, we present findings that aid in understanding how vector-borne flavivirus persistence is established in wildlife. Research studies to be discussed include determining the critical roles universal flavivirus non-structural proteins played in flaviviral persistence, the advancement of animal models of viral persistence, and studying host factors that allow vector-borne flavivirus replication without destructive effects on infected cells. These findings underscore the viral–host relationships in wildlife animals and could be used to elucidate the underlying mechanisms responsible for the establishment of viral persistence in these animals.
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Liyai R, Kimita G, Masakhwe C, Abuom D, Mutai B, Onyango DM, Waitumbi J. The spleen bacteriome of wild rodents and shrews from Marigat, Baringo County, Kenya. PeerJ 2021; 9:e12067. [PMID: 34557350 PMCID: PMC8418798 DOI: 10.7717/peerj.12067] [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: 12/13/2020] [Accepted: 08/05/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND There is a global increase in reports of emerging diseases, some of which have emerged as spillover events from wild animals. The spleen is a major phagocytic organ and can therefore be probed for systemic microbiome. This study assessed bacterial diversity in the spleen of wild caught small mammals so as to evaluate their utility as surveillance tools for monitoring bacteria in an ecosystem shared with humans. METHODS Fifty-four small mammals (rodents and shrews) were trapped from different sites in Marigat, Baringo County, Kenya. To characterize their bacteriome, DNA was extracted from their spleens and the V3-V4 regions of the 16S rRNA amplified and then sequenced on Illumina MiSeq. A non-target control sample was used to track laboratory contaminants. Sequence data was analyzed with Mothur v1.35, and taxomy determined using the SILVA database. The Shannon diversity index was used to estimate bacterial diversity in each animal and then aggregated to genus level before computing the means. Animal species within the rodents and shrews were identified by amplification of mitochondrial cytochrome b (cytb) gene followed by Sanger sequencing. CLC workbench was used to assemble the cytb gene sequences, after which their phylogenetic placements were determined by querying them against the GenBank nucleotide database. RESULTS cytb gene sequences were generated for 49/54 mammalian samples: 38 rodents (Rodentia) and 11 shrews (Eulipotyphyla). Within the order Rodentia, 21 Acomys, eight Mastomys, six Arvicanthis and three Rattus were identified. In the order Eulipotyphyla, 11 Crucidura were identified. Bacteria characterization revealed 17 phyla that grouped into 182 genera. Of the phyla, Proteobacteria was the most abundant (67.9%). Other phyla included Actinobacteria (16.5%), Firmicutes (5.5%), Chlamydiae (3.8%), Chloroflexi (2.6%) and Bacteroidetes (1.3%) among others. Of the potentially pathogenic bacteria, Bartonella was the most abundant (45.6%), followed by Anaplasma (8.0%), Methylobacterium (3.5%), Delftia (3.8%), Coxiella (2.6%), Bradyrhizobium (1.6%) and Acinetobacter (1.1%). Other less abundant (<1%) and potentially pathogenic included Ehrlichia, Rickettsia, Leptospira, Borrelia, Brucella, Chlamydia and Streptococcus. By Shannon diversity index, Acomys spleens carried more diverse bacteria (mean Shannon diversity index of 2.86, p = 0.008) compared to 1.77 for Crocidura, 1.44 for Rattus, 1.40 for Arvicathis and 0.60 for Mastomys. CONCLUSION This study examined systemic bacteria that are filtered by the spleen and the findings underscore the utility of 16S rRNA deep sequencing in characterizing complex microbiota that are potentially relevant to one health issues. An inherent problem with the V3-V4 region of 16S rRNA is the inability to classify bacteria reliably beyond the genera. Future studies should utilize the newer long read methods of 16S rRNA analysis that can delimit the species composition.
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Affiliation(s)
- Rehema Liyai
- Department of Zoology, Maseno University College, Kisumu, Kenya
- Basic Science Laboratory, United States Army Medical Research Directorate-Africa, Kisumu, Kenya
| | - Gathii Kimita
- Basic Science Laboratory, United States Army Medical Research Directorate-Africa, Kisumu, Kenya
| | - Clement Masakhwe
- Basic Science Laboratory, United States Army Medical Research Directorate-Africa, Kisumu, Kenya
| | - David Abuom
- Entomology Section, United States Medical Research Directorate-Africa, Kisumu, Kenya
| | - Beth Mutai
- Basic Science Laboratory, United States Army Medical Research Directorate-Africa, Kisumu, Kenya
| | | | - John Waitumbi
- Basic Science Laboratory, United States Army Medical Research Directorate-Africa, Kisumu, Kenya
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11
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Tsvetkov N, MacPhail VJ, Colla SR, Zayed A. Conservation genomics reveals pesticide and pathogen exposure in the declining bumble bee Bombus terricola. Mol Ecol 2021; 30:4220-4230. [PMID: 34181797 PMCID: PMC8457087 DOI: 10.1111/mec.16049] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/21/2021] [Accepted: 06/24/2021] [Indexed: 12/13/2022]
Abstract
In recent years, many pollinators have experienced large population declines, which threaten food security and the stability of natural ecosystems. Bumble bees are particularly important because their ability to “buzz” pollinate and tolerate cooler conditions make them critical pollinators for certain plants and regions. Here, we apply a conservation genomics approach to study the vulnerable Bombus terricola. We sequenced RNA from 30 worker abdomens, 18 of which were collected from agricultural sites and 12 of which were collected from nonagricultural sites. We found transcriptional signatures associated with exposure to insecticides, with gene expression patterns suggesting that bumble bees were exposed to neonicotinoids and/or fipronil—two compounds known to negatively impact bees. We also found transcriptional signatures associated with pathogen infections. In addition to the transcriptomic analysis, we carried out a metatranscriptomic analysis and detected five pathogens in the abdomens of workers, three of which are common in managed honey bee and bumble bee colonies. Our conservation genomics study provides functional support for the role of pesticides and pathogen spillover in the decline of B. terricola. We demonstrate that conservation genomics is an invaluable tool which allows researchers to quantify the effects of multiple stressors that impact pollinator populations in the wild.
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Affiliation(s)
| | - Victoria J MacPhail
- Faculty of Environmental and Urban Change, York University, Toronto, ON, Canada
| | - Sheila R Colla
- Faculty of Environmental and Urban Change, York University, Toronto, ON, Canada
| | - Amro Zayed
- Department of Biology, York University, Toronto, ON, Canada
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12
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Kryukov AA, Gorbunova AO, Machs EM, Mikhaylova YV, Rodionov AV, Zhurbenko PM, Yurkov AP. Perspectives of using Illumina MiSeq for identification of arbuscular mycorrhizal fungi. Vavilovskii Zhurnal Genet Selektsii 2021; 24:158-167. [PMID: 33659795 PMCID: PMC7716513 DOI: 10.18699/vj19.38-o] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Arbuscular mycorrhiza fungi (AMF) form one of the most common symbiosis with the majority of land
plants. AMF supply the plant with various mineral elements, primarily phosphorus, and improve the water supply.
The search for the most effective AMF strains for symbiosis and the creation of microbial preparations on that basis
is an important task for modern biology. Owing to the difficulties of cultivation without a host plant and their
high genetic polymorphism, identifying AMF is very difficult. A high number of cryptic species often makes morphological
identification unreliable. Recent years have seen a growth in the number of AMF biodiversity studies
performed by modern NGS-based methods, Illumina MiSeq in particular. Currently, there are still many questions
that remain for the identification of AМF. The most important are whether conservative or variable sequences
should be used to select a marker for barcoding and whether universal primers or those specific to AMF should be
used. In our work, we have successfully used universal primers ITS3 and ITS4 for the sequencing in Illumina MiSeq
of the 5.8S rDNA – ITS2 region of the 35S rRNA genes, which contain both a conservative and variable regions. The
molecular genetic approach for AMF identification was quite effective and allowed us to reliably identify eight of
nine isolates to the species level: five isolates of Rhizophagus irregularis, and one isolate of R. invermaius, Paraglomus
laccatum, and Claroideoglomus etunicatum, respectively. For all five R. irregularis isolates, high variability in
the ITS region and the absence of ecotopic-related molecular characters in the ITS2 region were demonstrated.
The NCBI data is still insufficient for accurate AMF identification of Acaulospora sp. isolates from the genus to the
species level.
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Affiliation(s)
- A A Kryukov
- All-Russian Research Institute for Agricultural Microbiology, St. Petersburg, Russia
| | - A O Gorbunova
- All-Russian Research Institute for Agricultural Microbiology, St. Petersburg, Russia Saint Petersburg State University, Biological Faculty, St. Petersburg, Russia
| | - E M Machs
- Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Y V Mikhaylova
- Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - A V Rodionov
- Saint Petersburg State University, Biological Faculty, St. Petersburg, Russia Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - P M Zhurbenko
- Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - A P Yurkov
- All-Russian Research Institute for Agricultural Microbiology, St. Petersburg, Russia
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13
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Salihoğlu R, Önal-Süzek T. Tissue Microbiome Associated With Human Diseases by Whole Transcriptome Sequencing and 16S Metagenomics. Front Genet 2021; 12:585556. [PMID: 33747035 PMCID: PMC7970108 DOI: 10.3389/fgene.2021.585556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 02/12/2021] [Indexed: 11/25/2022] Open
Abstract
In recent years, a substantial number of tissue microbiome studies have been published, mainly due to the recent improvements in the minimization of microbial contamination during whole transcriptome analysis. Another reason for this trend is due to the capability of next-generation sequencing (NGS) to detect microbiome composition even in low biomass samples. Several recent studies demonstrate a significant role for the tissue microbiome in the development and progression of cancer and other diseases. For example, the increase of the abundance of Proteobacteria in tumor tissues of the breast has been revealed by gene expression analysis. The link between human papillomavirus infection and cervical cancer has been known for some time, but the relationship between the microbiome and breast cancer (BC) is more novel. There are also recent attempts to investigate the possible link between the brain microbiome and the cognitive dysfunction caused by neurological diseases. Such studies pointing to the role of the brain microbiome in Huntington’s disease (HD) and Alzheimer’s disease (AD) suggest that microbial colonization is a risk factor. In this review, we aim to summarize the studies that associate the tissue microbiome, rather than gut microbiome, with cancer and other diseases using whole-transcriptome analysis, along with 16S rRNA analysis. After providing several case studies for each relationship, we will discuss the potential role of transcriptome analysis on the broader portrayal of the pathophysiology of the breast, brain, and vaginal microbiome.
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Affiliation(s)
- Rana Salihoğlu
- Bioinformatics Department, Graduate School of Natural and Applied Sciences, Muğla Sıtkı Koçman University, Muğla, Turkey
| | - Tuğba Önal-Süzek
- Bioinformatics Department, Graduate School of Natural and Applied Sciences, Muğla Sıtkı Koçman University, Muğla, Turkey.,Computer Engineering Department, Faculty of Engineering, Muğla Sıtkı Koçman University, Muğla, Turkey
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14
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Stephens CRA, McAmmond BM, Van Hamme JD, Otter KA, Reudink MW, Bottos EM. Analysis of bacterial communities associated with Mountain Chickadees ( Poecile gambeli) across urban and rural habitats. Can J Microbiol 2021; 67:572-583. [PMID: 33656947 DOI: 10.1139/cjm-2020-0320] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Host-associated microbial communities play important roles in wildlife health, but these dynamics can be influenced by environmental factors. Urbanization has numerous effects on wildlife; however, the degree to which wildlife-associated bacterial communities and potential bacterial pathogens vary across urban-rural/native habitat gradients remains largely unknown. We used 16S rRNA gene amplicon sequencing to examine bacterial communities found on Mountain Chickadee (Poecile gambeli) feathers and nests in urban and rural habitats. The feathers and nests in urban and rural sites had similar abundances of major bacterial phyla and dominant genera with pathogenic members. However, richness of bacterial communities and potential pathogens on birds were higher in urban habitats, and potential pathogens accounted for some of the differences in bacterial occurrence between urban and rural environments. We predicted habitat using potential pathogen occurrence with a 90% success rate for feather bacteria, and a 72.2% success rate for nest bacteria, suggesting an influence of urban environments on the presence of potential pathogens. We additionally observed similarities in bacterial communities between nests and their occupants, suggesting bacterial transmission between them. These findings improve our understanding of the bacterial communities associated with urban wildlife and suggest that urbanization impacts the composition of wildlife-associated bacterial communities.
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Affiliation(s)
- Colton R A Stephens
- Department of Biological Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, BC V2C 0C8, Canada
| | - Breanne M McAmmond
- Department of Biological Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, BC V2C 0C8, Canada
| | - Jonathan D Van Hamme
- Department of Biological Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, BC V2C 0C8, Canada
| | - Ken A Otter
- Natural Resources and Environmental Studies, University of Northern British Columbia, 3333 University Way, Prince George, BC V2N 4Z9, Canada
| | - Matthew W Reudink
- Department of Biological Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, BC V2C 0C8, Canada
| | - Eric M Bottos
- Department of Biological Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, BC V2C 0C8, Canada
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15
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Song H, Kim J, Guk JH, Kim WH, Nam H, Suh JG, Seong JK, Cho S. Metagenomic Analysis of the Gut Microbiota of Wild Mice, a Newly Identified Reservoir of Campylobacter. Front Cell Infect Microbiol 2021; 10:596149. [PMID: 33604305 PMCID: PMC7884769 DOI: 10.3389/fcimb.2020.596149] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 12/17/2020] [Indexed: 12/12/2022] Open
Abstract
Campylobacter, the most common etiologic agent of zoonotic gastroenteritis in humans, is present in many reservoirs including livestock animals, wildlife, soil, and water. Previously, we reported a novel Campylobacter jejuni strain SCJK02 (MLST ST-8388) from the gut of wild mice (Micromys minutus) using culture-dependent methods. However, due to fastidious growth conditions and the presence of viable but non-culturable Campylobacter spp., it is unclear whether M. minutus is a Campylobacter reservoir. This study aimed to: 1) determine the distribution and proportion of Campylobacter spp. in the gut microbiota of wild mice using culture-independent methods and 2) investigate the gut microbiota of wild mice and the relationship of Campylobacter spp. with other gut microbes. The gut microbiota of 38 wild mice captured from perilla fields in Korea and without any clinical symptoms (18 M. minutus and 20 Mus musculus) were analyzed. Metagenomic analysis showed that 77.8% (14 of 18) of the captured M. minutus harbored Campylobacter spp. (0.24–32.92%) in the gut metagenome, whereas none of the captured M. musculus carried Campylobacter spp. in their guts. Notably, 75% (6 of 8) of M. minutus determined to be Campylobacter-negative using culture-dependent methods showed a high proportion of Campylobacter through metagenome analysis. The results of metagenome analysis and the absence of clinical symptoms suggest that Campylobacter may be a component of the normal gut flora of wild M. minutus. Furthermore, linear discriminant analysis (LDA) showed that Campylobacter was the most enriched genus in the gut microbiota of M. minutus (LDA score, 5.37), whereas Lactobacillus was the most enriched genus in M. musculus (LDA score, −5.96). The differences in the presence of Campylobacter between the two species of wild mice may be attributed to the differential abundance of Campylobacter and Lactobacillus in their respective gut microbiota. In conclusion, the results indicate that wild M. minutus may serve as a potential Campylobacter reservoir. This study presents the first metagenomics analysis of the M. minutus gut microbiota to explore its possible role as an environmental Campylobacter reservoir and provides a basis for future studies using culture-independent methods to determine the role of environmental reservoirs in Campylobacter transmission.
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Affiliation(s)
- Hyokeun Song
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Junhyung Kim
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Jae-Ho Guk
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Woo-Hyun Kim
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Hajin Nam
- Department of Medical Genetics, College of Medicine, Hallym University, Chuncheon, South Korea
| | - Jun Gyo Suh
- Department of Medical Genetics, College of Medicine, Hallym University, Chuncheon, South Korea
| | - Je Kyung Seong
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Seongbeom Cho
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
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16
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Maclot F, Candresse T, Filloux D, Malmstrom CM, Roumagnac P, van der Vlugt R, Massart S. Illuminating an Ecological Blackbox: Using High Throughput Sequencing to Characterize the Plant Virome Across Scales. Front Microbiol 2020; 11:578064. [PMID: 33178159 PMCID: PMC7596190 DOI: 10.3389/fmicb.2020.578064] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/24/2020] [Indexed: 01/08/2023] Open
Abstract
The ecology of plant viruses began to be explored at the end of the 19th century. Since then, major advances have revealed mechanisms of virus-host-vector interactions in various environments. These advances have been accelerated by new technlogies for virus detection and characterization, most recently including high throughput sequencing (HTS). HTS allows investigators, for the first time, to characterize all or nearly all viruses in a sample without a priori information about which viruses might be present. This powerful approach has spurred new investigation of the viral metagenome (virome). The rich virome datasets accumulated illuminate important ecological phenomena such as virus spread among host reservoirs (wild and domestic), effects of ecosystem simplification caused by human activities (and agriculture) on the biodiversity and the emergence of new viruses in crops. To be effective, however, HTS-based virome studies must successfully navigate challenges and pitfalls at each procedural step, from plant sampling to library preparation and bioinformatic analyses. This review summarizes major advances in plant virus ecology associated with technological developments, and then presents important considerations and best practices for HTS use in virome studies.
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Affiliation(s)
- François Maclot
- Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | | | - Denis Filloux
- CIRAD, BGPI, Montpellier, France
- BGPI, INRAE, CIRAD, Institut Agro, Montpellier University, Montpellier, France
| | - Carolyn M. Malmstrom
- Department of Plant Biology and Graduate Program in Ecology, Evolution and Behavior, Michigan State University, East Lansing, MI, United States
| | - Philippe Roumagnac
- CIRAD, BGPI, Montpellier, France
- BGPI, INRAE, CIRAD, Institut Agro, Montpellier University, Montpellier, France
| | - René van der Vlugt
- Laboratory of Virology, Wageningen University and Research Centre (WUR-PRI), Wageningen, Netherlands
| | - Sébastien Massart
- Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
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17
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Hoarau AOG, Mavingui P, Lebarbenchon C. Coinfections in wildlife: Focus on a neglected aspect of infectious disease epidemiology. PLoS Pathog 2020; 16:e1008790. [PMID: 32881983 PMCID: PMC7470396 DOI: 10.1371/journal.ppat.1008790] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Axel O. G. Hoarau
- Université de La Réunion, Processus Infectieux en Milieu Insulaire Tropical, INSERM 1187, CNRS 9192, IRD 249, Saint Denis, Réunion Island, France
- * E-mail:
| | - Patrick Mavingui
- Université de La Réunion, Processus Infectieux en Milieu Insulaire Tropical, INSERM 1187, CNRS 9192, IRD 249, Saint Denis, Réunion Island, France
| | - Camille Lebarbenchon
- Université de La Réunion, Processus Infectieux en Milieu Insulaire Tropical, INSERM 1187, CNRS 9192, IRD 249, Saint Denis, Réunion Island, France
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18
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Das P, Behera BK, Chatterjee S, Das BK, Mohapatra T. De novo transcriptome analysis of halotolerant bacterium Staphylococcus sp. strain P-TSB-70 isolated from East coast of India: In search of salt stress tolerant genes. PLoS One 2020; 15:e0228199. [PMID: 32040520 PMCID: PMC7010390 DOI: 10.1371/journal.pone.0228199] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 01/09/2020] [Indexed: 12/20/2022] Open
Abstract
In the present study, we identified salt stress tolerant genes from the marine bacterium Staphylococcus sp. strain P-TSB-70 through transcriptome sequencing. In favour of whole-genome transcriptome profiling of Staphylococcus sp. strain P-TSB-70 (GenBank Accn. No. KP117091) which tolerated upto 20% NaCl stress, the strain was cultured in the laboratory condition with 20% NaCl stress. Transcriptome analyses were performed by SOLiD4.0 sequencing technology from which 10280 and 9612 transcripts for control and treated, respectively, were obtained. The coverage per base (CPB) statistics were analyzed for both the samples. Gene ontology (GO) analysis has been categorized at varied graph levels based on three primary ontology studies viz. cellular components, biological processes, and molecular functions. The KEGG analysis of the assembled transcripts using KAAS showed presumed components of metabolic pathways which perhaps implicated in diverse metabolic pathways responsible for salt tolerance viz. glycolysis/gluconeogenesis, oxidative phosphorylation, glutathione metabolism, etc. further involving in salt tolerance. Overall, 90 salt stress tolerant genes were identified as of 186 salt-related transcripts. Several genes have been found executing normally in the TCA cycle pathway, integral membrane proteins, generation of the osmoprotectants, enzymatic pathway associated with salt tolerance. Recognized genes fit diverse groups of salt stress genes viz. abc transporter, betaine, sodium antiporter, sodium symporter, trehalose, ectoine, and choline, that belong to different families of genes involved in the pathway of salt stress. The control sample of the bacterium showed elevated high proportion of transcript contigs (29%) while upto 20% salt stress treated sample of the bacterium showed a higher percentage of transcript contigs (31.28%). A total of 1,288 and 1,133 transcript contigs were measured entirely as novel transcript contigs in both control and treated samples, respectively. The structure and function of 10 significant salt stress tolerant genes of Staphylococcus sp. have been analyzed in this study. The information acquired in the present study possibly used to recognize and clone the salt stress tolerant genes and support in developing the salt stress-tolerant plant varieties to expand the agricultural productivity in the saline system.
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Affiliation(s)
- Priyanka Das
- Fishery Resource and Environmental Management Division, Biotechnology Laboratory, ICAR- Central Inland Fisheries Research Institute, Barrackpore, West Bengal, India
| | - Bijay Kumar Behera
- Fishery Resource and Environmental Management Division, Biotechnology Laboratory, ICAR- Central Inland Fisheries Research Institute, Barrackpore, West Bengal, India
- * E-mail:
| | - Soumendranath Chatterjee
- Parasitology and Microbiology Research Laboratory, Department of Zoology, University of Burdwan, Burdwan, West Bengal, India
| | - Basanta Kumar Das
- Fishery Resource and Environmental Management Division, Biotechnology Laboratory, ICAR- Central Inland Fisheries Research Institute, Barrackpore, West Bengal, India
| | - Trilochan Mohapatra
- Secretary, DARE and Director General, Indian Council of Agricultural Research, New Delhi, India
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19
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Lin L, Zheng Q, Lin J, Yuk HG, Guo L. Immuno- and nucleic acid-based current technique for Salmonella detection in food. Eur Food Res Technol 2020. [DOI: 10.1007/s00217-019-03423-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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20
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Jacobs L, McMahon BH, Berendzen J, Longmire J, Gleasner C, Hengartner NW, Vuyisich M, Cohn JR, Jenkins M, Bartlow AW, Fair JM. California condor microbiomes: Bacterial variety and functional properties in captive-bred individuals. PLoS One 2019; 14:e0225858. [PMID: 31825977 PMCID: PMC6905524 DOI: 10.1371/journal.pone.0225858] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 11/13/2019] [Indexed: 12/02/2022] Open
Abstract
Around the world, scavenging birds such as vultures and condors have been experiencing drastic population declines. Scavenging birds have a distinct digestive process to deal with higher amounts of bacteria in their primary diet of carcasses in varying levels of decay. These observations motivate us to present an analysis of captive and healthy California condor (Gymnogyps californianus) microbiomes to characterize a population raised together under similar conditions. Shotgun metagenomic DNA sequences were analyzed from fecal and cloacal samples of captive birds. Classification of shotgun DNA sequence data with peptide signatures using the Sequedex package provided both phylogenetic and functional profiles, as well as individually annotated reads for targeted confirmatory analysis. We observed bacterial species previously associated with birds and gut microbiomes, including both virulent and opportunistic pathogens such as Clostridium perfringens, Propionibacterium acnes, Shigella flexneri, and Fusobacterium mortiferum, common flora such as Lactobacillus johnsonii, Lactobacillus ruminus, and Bacteroides vulgatus, and mucosal microbes such as Delftia acidovorans, Stenotrophomonas maltophilia, and Corynebacterium falsnii. Classification using shotgun metagenomic reads from phylogenetic marker genes was consistent with, and more specific than, analysis based on 16S rDNA data. Classification of samples based on either phylogenetic or functional profiles of genomic fragments differentiated three types of samples: fecal, mature cloacal and immature cloacal, with immature birds having approximately 40% higher diversity of microbes.
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Affiliation(s)
- Lindsey Jacobs
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Benjamin H. McMahon
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Joel Berendzen
- GenerisBio, Santa Fe, New Mexico, United States of America
| | - Jonathan Longmire
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Cheryl Gleasner
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | | | | | - Judith R. Cohn
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Marti Jenkins
- The Peregrine Fund, Boise, Idaho, United States of America
| | - Andrew W. Bartlow
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Jeanne M. Fair
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- * E-mail:
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21
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Lima-Barbero JF, Díaz-Sanchez S, Sparagano O, Finn RD, de la Fuente J, Villar M. Metaproteomics characterization of the alphaproteobacteria microbiome in different developmental and feeding stages of the poultry red mite Dermanyssus gallinae (De Geer, 1778). Avian Pathol 2019; 48:S52-S59. [PMID: 31267762 DOI: 10.1080/03079457.2019.1635679] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The poultry red mite (PRM), Dermanyssus gallinae (De Geer, 1778), is a worldwide distributed ectoparasite and considered a major pest affecting the laying hen industry in Europe. Based on available information in other ectoparasites, the mite microbiome might participate in several biological processes and the acquisition, maintenance and transmission of pathogens. However, little is known about the role of PRM as a mechanical carrier or a biological vector in the transmission of pathogenic bacteria. Herein, we used a metaproteomics approach to characterize the alphaproteobacteria in the microbiota of PRM, and variations in its profile with ectoparasite development (nymphs vs. adults) and feeding (unfed vs. fed). The results showed that the bacterial community associated with D. gallinae was mainly composed of environmental and commensal bacteria. Putative symbiotic bacteria of the genera Wolbachia, C. Tokpelaia and Sphingomonas were identified, together with potential pathogenic bacteria of the genera Inquilinus, Neorickettsia and Roseomonas. Significant differences in the composition of alphaproteobacterial microbiota were associated with mite development and feeding, suggesting that bacteria have functional implications in metabolic pathways associated with blood feeding. These results support the use of metaproteomics for the characterization of alphaproteobacteria associated with the D. gallinae microbiota that could provide relevant information for the understanding of mite-host interactions and the development of potential control interventions. Research highlights Metaproteomics is a valid approach for microbiome characterization in ectoparasites. Alphaproteobacteria putative bacterial symbionts were identified in D. gallinae. Mite development and feeding were related to variations in bacterial community. Potentially pathogenic bacteria were identified in mite microbiota.
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Affiliation(s)
- José Francisco Lima-Barbero
- SaBio. Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM , Ronda de Toledo 12, 13071 Ciudad Real , Spain.,Sabiotec, S.A. Ed. Polivalente UCLM Ciudad Real , Spain
| | - Sandra Díaz-Sanchez
- SaBio. Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM , Ronda de Toledo 12, 13071 Ciudad Real , Spain
| | - Olivier Sparagano
- Department of Infectious Diseases and Public Health, City University of Hong Kong , Kowloon , Hong Kong, SAR
| | - Robert D Finn
- Department of Applied Sciences, Faculty of Health & Life Sciences, Northumbria University , Newcastle Upon Tyne , UK
| | - José de la Fuente
- SaBio. Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM , Ronda de Toledo 12, 13071 Ciudad Real , Spain.,Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University , Stillwater , USA
| | - Margarita Villar
- SaBio. Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM , Ronda de Toledo 12, 13071 Ciudad Real , Spain
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22
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Culbreath K, Melanson S, Gale J, Baker J, Li F, Saebo O, Kommedal O, Contreras D, Garner OB, Yang S. Validation and Retrospective Clinical Evaluation of a Quantitative 16S rRNA Gene Metagenomic Sequencing Assay for Bacterial Pathogen Detection in Body Fluids. J Mol Diagn 2019; 21:913-923. [PMID: 31229651 DOI: 10.1016/j.jmoldx.2019.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/03/2019] [Accepted: 05/24/2019] [Indexed: 02/07/2023] Open
Abstract
Next-generation sequencing-based 16S rRNA gene metagenomic sequencing (16S MG) technology has tremendous potential for improving diagnosis of bacterial infections given its quantitative capability and culture-independent approach. We validated and used a quantitative 16S MG assay to identify and quantify bacterial species in clinical samples from a wide spectrum of infections, including meningitis, septic arthritis, brain abscess, intra-abdominal abscess, soft tissue abscess, and pneumonia. Twenty clinical samples were tested, and 16S MG identified a total of 34 species, compared with 22 species and three descriptive findings identified by culture. 16S MG results matched culture results in 75% (15/20) of the samples but detected at least one more species in five samples, including one culture-negative cerebrospinal fluid sample that was found to contain Streptococcus intermedius. Shotgun metagenomic sequencing verified the presence of all additional species. The 16S MG assay is highly sensitive, with a limit of detection of 10 to 100 colony-forming units/mL. Other performance characteristics, including linearity, precision, and specificity, all met the requirements for a clinical test. This assay showed the advantages of accurate identification and quantification of bacteria in culture-negative and polymicrobial infections for which conventional microbiology methods are limited. It also showed promises to serve unmet clinical needs for solving difficult infectious diseases cases.
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Affiliation(s)
- Karissa Culbreath
- Department of Pathlogy, University of New Mexico Health Sciences Center, Albuquerque, New Mexico; TriCore Reference Laboratories, Albuquerque, New Mexico
| | | | - James Gale
- TriCore Reference Laboratories, Albuquerque, New Mexico
| | - Justin Baker
- TriCore Reference Laboratories, Albuquerque, New Mexico
| | - Fan Li
- Department of Pediatrics, University of California Los Angeles, Los Angeles, California
| | | | - Oyvind Kommedal
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Deisy Contreras
- Clinical Microbiology Laboratory, Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California
| | - Omai B Garner
- Clinical Microbiology Laboratory, Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California
| | - Shangxin Yang
- Department of Pathlogy, University of New Mexico Health Sciences Center, Albuquerque, New Mexico; Clinical Microbiology Laboratory, Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California.
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23
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Sato Y, Mizuyama M, Sato M, Minamoto T, Kimura R, Toma C. Environmental DNA metabarcoding to detect pathogenic Leptospira and associated organisms in leptospirosis-endemic areas of Japan. Sci Rep 2019; 9:6575. [PMID: 31024059 PMCID: PMC6484013 DOI: 10.1038/s41598-019-42978-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/11/2019] [Indexed: 02/06/2023] Open
Abstract
Leptospires, which cause the zoonotic disease leptospirosis, persist in soil and aqueous environments. Several factors, including rainfall, the presence of reservoir animals, and various abiotic and biotic components interact to influence leptospiral survival, persistence, and pathogenicity in the environment. However, how these factors modulate the risk of infection is poorly understood. Here we developed an approach using environmental DNA (eDNA) metabarcoding for detecting the microbiome, vertebrates, and pathogenic Leptospira in aquatic samples. Specifically, we combined 4 sets of primers to generate PCR products for high-throughput sequencing of multiple amplicons through next-generation sequencing. Using our method to analyze the eDNA of leptospirosis-endemic areas in northern Okinawa, Japan, we found that the microbiota in each river shifted over time. Operating taxonomic units corresponding to pathogenic L. alstonii, L. kmetyi, and L. interrogans were detected in association with 12 nonpathogenic bacterial species. In addition, the frequencies of 11 of these species correlated with the amount of rainfall. Furthermore, 10 vertebrate species, including Sus scrofa, Pteropus dasymallus, and Cynops ensicauda, showed high correlation with leptospiral eDNA detection. Our eDNA metabarcoding method is a powerful tool for understanding the environmental phase of Leptospira and predicting human infection risk.
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Affiliation(s)
- Yukuto Sato
- Center for Strategic Research Project, Organization for Research Promotion, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan.
| | - Masaru Mizuyama
- Department of Bacteriology, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa, 903-0215, Japan.,Graduate School of Engineering and Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan
| | - Megumi Sato
- Graduate School of Health Sciences, Niigata University, 2-746 Asahimachi-dori, Chuo-ku, Niigata, 951-8122, Japan
| | - Toshifumi Minamoto
- Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe, 657-8501, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa, 903-0215, Japan
| | - Claudia Toma
- Department of Bacteriology, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa, 903-0215, Japan.
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Ellwanger JH, Kaminski VDL, Chies JAB. Emerging infectious disease prevention: Where should we invest our resources and efforts? J Infect Public Health 2019; 12:313-316. [PMID: 30928239 DOI: 10.1016/j.jiph.2019.03.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 02/25/2019] [Accepted: 03/11/2019] [Indexed: 02/07/2023] Open
Abstract
Strategies focused on the prevention of emerging infectious disease outbreaks are currently in the spotlight of discussions among researchers committed to infectious disease control. In this mini-review, we provided a brief update on this discussion and characterized the three main targets for investments in emerging infectious disease prevention: animals, human sentinels for spillover events, and the general human population. Furthermore, the pros and cons of each target are highlighted. Despite the particularities of the proposed targets, each of them can fill different gaps in the surveillance of infectious diseases. When all three targets are focused on together, they create a powerful strategy of emerging infectious disease prevention.
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Affiliation(s)
- Joel H Ellwanger
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - Valéria de Lima Kaminski
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - José A B Chies
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil.
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25
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Jiang H, Zhang X, Li L, Ma J, He N, Liu H, Han R, Li H, Wu Z, Chen J. Identification of Austwickia chelonae as cause of cutaneous granuloma in endangered crocodile lizards using metataxonomics. PeerJ 2019; 7:e6574. [PMID: 30886772 PMCID: PMC6420803 DOI: 10.7717/peerj.6574] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 02/05/2019] [Indexed: 12/11/2022] Open
Abstract
The crocodile lizard (Shinisaurus crocodilurus Ahl, 1930) is an endangered reptile species, and in recent years many have died from diseases, especially the rescued and breeding individuals. However, pathogens underlying these diseases are unclear. In this study, we report our effort in rapidly identifying and isolating the pathogen that causes high mortality in crocodile lizards from Guangdong Luokeng Shinisaurus crocodilurus National Nature Reserve. The typical symptom is cutaneous granuloma in the infected crocodile lizards. Metagenomic next-generation sequencing (mNGS) is a comprehensive approach for sequence-based identification of pathogenic microbes. In this study, 16S rDNA based mNGS was used for rapid identification of pathogens, and microscopy and microbe isolation were used to confirm the results. Austwickia chelonae was identified to be the dominant pathogen in the granuloma using 16S rDNA based mNGS. Chinese skinks were used as an animal model to verify the pathogenicity of A. chelonae to fulfill Koch's postulates. As expected, subcutaneous inoculation of A. chelonae induced granulomas in the healthy Chinese skinks and the A. chelonae was re-isolated from the induced granulomas. Therefore, A. chelonae was the primary pathogen that caused this high mortality disease, cutaneous granuloma, in crocodile lizards from Guangdong Luokeng Shinisaurus crocodilurus National Nature Reserve. Antibiotics analysis demonstrated that A. chelonae was sensitive to cephalothin, minocycline and ampicillin, but not to kanamycin, gentamicin, streptomycin and clarithromycin, suggesting a possible treatment for the infected crocodile lizards. However, surgical resection of the nodules as early as possible was recommended. This study is the first report of pathogenic analysis in crocodile lizards and provides a reference for disease control and conservations of the endangered crocodile lizards and other reptiles. In addition, this study indicated that mNGS of lesions could be used to detect the pathogens in animals with benefits in speed and convenient.
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Affiliation(s)
- Haiying Jiang
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China.,Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiujuan Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Linmiao Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Jinge Ma
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Nan He
- Guangdong Luokeng Shinisaurus crocodilurus National Nature Reserve, Shaoguan, Guangdong, China
| | - Haiyang Liu
- Guangdong Luokeng Shinisaurus crocodilurus National Nature Reserve, Shaoguan, Guangdong, China
| | - Richou Han
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Huiming Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Zhengjun Wu
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, Guangxi, China
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
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26
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Takhampunya R, Korkusol A, Pongpichit C, Yodin K, Rungrojn A, Chanarat N, Promsathaporn S, Monkanna T, Thaloengsok S, Tippayachai B, Kumfao N, Richards AL, Davidson SA. Metagenomic Approach to Characterizing Disease Epidemiology in a Disease-Endemic Environment in Northern Thailand. Front Microbiol 2019; 10:319. [PMID: 30863381 PMCID: PMC6399164 DOI: 10.3389/fmicb.2019.00319] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 02/06/2019] [Indexed: 02/01/2023] Open
Abstract
In this study, we used a metagenomic approach to analyze bacterial communities from diverse populations (humans, animals, and vectors) to investigate the role of these microorganisms as causative agents of disease in human and animal populations. Wild rodents and ectoparasites were collected from 2014 to 2018 in Nan province, Thailand where scrub typhus is highly endemic. Samples from undifferentiated febrile illness (UFI) patients were obtained from a local hospital. A total of 200 UFI patient samples were obtained and 309 rodents and 420 pools of ectoparasites were collected from rodents (n = 285) and domestic animals (n = 135). The bacterial 16S rRNA gene was amplified and sequenced with the Illumina. Real-time PCR and Sanger sequencing were used to confirm the next-generation sequencing (NGS) results and to characterize pathogen species. Several pathogens were detected by NGS in all populations studied and the most common pathogens identified included Bartonella spp., Rickettsia spp., Leptospira spp., and Orientia tsutsugamushi. Interestingly, Anaplasma spp. was detected in patient, rodent and tick populations, although they were not previously known to cause human disease from this region. Candidatus Neoehrlichia, Neorickettsia spp., Borrelia spp., and Ehrlichia spp. were detected in rodents and their associated ectoparasites. The same O. tsutsugamushi genotypes were shared among UFI patients, rodents, and chiggers in a single district indicating that the chiggers found on rodents were also likely responsible for transmitting to people. Serological testing using immunofluorescence assays in UFI samples showed high prevalence (IgM/IgG) of Rickettsia and Orientia pathogens, most notably among samples collected during September–November. Additionally, a higher number of seropositive samples belonged to patients in the working age population (20–60 years old). The results presented in this study demonstrate that the increased risk of human infection or exposure to chiggers and their associated pathogen (O. tsutsugamushi) resulted in part from two important factors; working age group and seasons for rice cultivation and harvesting. Evidence of pathogen exposure was shown to occur as there was seropositivity (IgG) in UFI patients for bartonellosis as well as for anaplasmosis. Using a metagenomic approach, this study demonstrated the circulation and transmission of several pathogens in the environment, some of which are known causative agents of illness in human populations.
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Affiliation(s)
- Ratree Takhampunya
- Department of Entomology, US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
| | - Achareeya Korkusol
- Department of Entomology, US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
| | | | | | - Artharee Rungrojn
- Department of Entomology, US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
| | - Nitima Chanarat
- Department of Entomology, US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
| | - Sommai Promsathaporn
- Department of Entomology, US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
| | - Taweesak Monkanna
- Department of Entomology, US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
| | - Sasikanya Thaloengsok
- Department of Entomology, US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
| | - Bousaraporn Tippayachai
- Department of Entomology, US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
| | | | - Allen L Richards
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, Silver Spring, MD, United States
| | - Silas A Davidson
- Department of Entomology, US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
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27
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Li Y, Jiang L, Lv W, Cui S, Zhang L, Wang Q, Meng F, Li B, Liu P, Suonan J, Renzeng W, Li X, Luo C, Zhang Z, Dorji T, Wang Y, Wang S. Fungal pathogens pose a potential threat to animal and plant health in desertified and pika-burrowed alpine meadows on the Tibetan Plateau. Can J Microbiol 2018; 65:365-376. [PMID: 30566369 DOI: 10.1139/cjm-2018-0338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Intact Tibetan meadows provide significant defense against soil-borne pathogen dispersal. However, dramatic meadow degradation has been observed due to climate change and pika damage, but their impacts on soil-borne pathogens are still unclear. With approximately 40% of the world's population living in Tibetan Plateau and its downstream watersheds, this lack of knowledge should be of great concern. Here, we used Illumina amplicon sequencing to characterize the changes in potential human, domestic animal, plant, and zoonotic bacterial and fungal pathogens in nondegraded, desertified, and pika-burrowed meadows. The relative abundance of bacterial domestic animal pathogens and zoonotic pathogens were significantly increased by desertification. Pika burrowing significantly increased the relative abundance of bacterial human pathogens and zoonotic pathogens. The species richness and relative abundance of fungal pathogens was significantly increased by desertification and pika burrowing. Accordingly, fungal plant and animal pathogens categorized by FUNGuid significantly increased in desertified and pika-burrowed meadows. Soil chemical and plant properties explained 38% and 64% of the bacterial and fungal pathogen community variance, respectively. Therefore, our study indicates for the first time that both alpine meadow desertification and pika burrowing could potentially increase infectious disease risks in the alpine ecosystem, especially for fungal diseases.
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Affiliation(s)
- Yaoming Li
- a Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Lili Jiang
- a Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Wangwang Lv
- a Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, P.R. China.,b University of the Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Shujuan Cui
- a Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, P.R. China.,b University of the Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Lirong Zhang
- a Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Qi Wang
- a Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, P.R. China.,b University of the Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Fandong Meng
- a Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Bowen Li
- a Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, P.R. China.,b University of the Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Peipei Liu
- a Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, P.R. China.,b University of the Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Ji Suonan
- a Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Wangmu Renzeng
- a Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, P.R. China.,b University of the Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Xine Li
- a Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Caiyun Luo
- c Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, P.R. China
| | - Zhenhua Zhang
- c Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, P.R. China
| | - Tsechoe Dorji
- a Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, P.R. China.,d CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing 100101, P.R. China.,e Naqu Integrated Observation and Research Station of Ecology and Environment, Tibet University and Institute of Tibetan Plateau Research of the Chinese Academy of Sciences, Lasa 850012, P.R. China
| | - Yanfen Wang
- b University of the Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Shiping Wang
- a Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, P.R. China.,d CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing 100101, P.R. China.,e Naqu Integrated Observation and Research Station of Ecology and Environment, Tibet University and Institute of Tibetan Plateau Research of the Chinese Academy of Sciences, Lasa 850012, P.R. China
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28
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Ishikawa D, Sasaki T, Takahashi M, Kuwahara-Arai K, Haga K, Ito S, Okahara K, Nakajima A, Shibuya T, Osada T, Hiramatsu K, Watanabe S, Nagahara A. The Microbial Composition of Bacteroidetes Species in Ulcerative Colitis Is Effectively Improved by Combination Therapy With Fecal Microbiota Transplantation and Antibiotics. Inflamm Bowel Dis 2018; 24:2590-2598. [PMID: 30124831 DOI: 10.1093/ibd/izy266] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Indexed: 12/18/2022]
Abstract
BACKGROUND We previously reported that fresh fecal microbiota transplantation (FMT) after triple-antibiotic therapy (amoxicillin, fosfomycin, and metronidazole [AFM]; A-FMT) synergistically contributed to the recovery of phylum Bacteroidetes composition associated with the endoscopic severity and treatment efficacy of ulcerative colitis (UC). Here, we performed further microbial analyses using a higher-resolution method to identify the key bacterial species in UC and determine whether viable Bacteroidetes species from donor feces were successfully colonized by A-FMT. METHODS The taxonomic composition of Bacteroidetes in 25 healthy donors and 27 UC patients at baseline was compared at the species level using a heat-shock protein (hsp) 60-based microbiome method. Microbiota alterations before and after treatment of UC patients were also analyzed in 24 cases (n = 17 A-FMT; n = 3 mono-AFM; n = 4 mono-FMT). RESULTS We found species-level dysbiosis within the phylum Bacteroidetes in UC samples, which was associated with reduced species diversity, resulting from hyperproliferation and hypoproliferation of particular species. Moreover, in responders treated with A-FMT, diversity was significantly recovered at 4 weeks after a fresh round of FMT, after which high degrees of similarity in Bacteroidetes species composition among recipients and donors were observed. CONCLUSIONS A-FMT alleviated intestinal dysbiosis, which is caused by the loss of Bacteroidetes species diversity in patients with UC. Eradication of dysbiotic indigenous Bacteroidetes species by AFM pretreatment might promote the colonization of viable Bacteroidetes cells, thereby improving the intestinal microbiota dysbiosis induced by UC. Our findings serve as a basis for further investigations into the mechanisms of FMT.
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Affiliation(s)
- Dai Ishikawa
- Department of Gastroenterology, Juntendo University School of Medicine, Tokyo Japan
| | - Takashi Sasaki
- Center of Excellence for Infection Control Science, Graduate School of Medicine, Juntendo University, Tokyo, Japan.,Animal Research Center, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Masahito Takahashi
- Department of Gastroenterology, Juntendo University School of Medicine, Tokyo Japan
| | - Kyoko Kuwahara-Arai
- Department of Microbiology, Juntendo University School of Medicine, Tokyo, Japan
| | - Keiichi Haga
- Department of Gastroenterology, Juntendo University School of Medicine, Tokyo Japan
| | - Shoko Ito
- Department of Gastroenterology, Juntendo University School of Medicine, Tokyo Japan
| | - Koki Okahara
- Department of Gastroenterology, Juntendo University School of Medicine, Tokyo Japan
| | - Akihito Nakajima
- Department of Gastroenterology, Juntendo University School of Medicine, Tokyo Japan
| | - Tomoyoshi Shibuya
- Department of Gastroenterology, Juntendo University School of Medicine, Tokyo Japan
| | - Taro Osada
- Department of Gastroenterology, Juntendo University Urayasu Hospital, Chiba, Japan
| | - Keiichi Hiramatsu
- Center of Excellence for Infection Control Science, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Sumio Watanabe
- Department of Gastroenterology, Juntendo University School of Medicine, Tokyo Japan
| | - Akihito Nagahara
- Department of Gastroenterology, Juntendo University School of Medicine, Tokyo Japan
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29
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Meng X, Lai XH, Lu S, Liu S, Chen C, Zhou D, Yang J, Jin D, Xu J. Actinomyces tangfeifanii sp. nov., isolated from the vulture Aegypius monachus. Int J Syst Evol Microbiol 2018; 68:3701-3706. [PMID: 30351263 DOI: 10.1099/ijsem.0.003013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A novel, Gram-stain-positive, catalase-positive, non-spore-forming, short rod-shaped strain (VUL4_3T) was isolated from rectal swabs of Old World vultures (Aegypius monachus) from the Tibet-Qinghai Plateau, China. Based on the results of biochemical tests and 16S rRNA gene sequence comparison, strain VUL4_3T was determined to be a member of the genus Actinomyces that is closely related to the type strains of Actinomyces liubingyangii (97.7 % 16S rRNA gene sequence similarity) and Actinomyces marimammalium (96.5 %). Optimal growth occurred at 37 °C, pH 6-7 and with 1 % (w/v) NaCl. The typical major cellular fatty acids of strain VUL4_3T were C18 : 1ω9c, C16 : 0 and C18 : 0. The VUL4_3T genome contained 2 207 832 bp with an average G+C content of 51.9 mol%. DNA-DNA hybridization values between strain VUL4_3T and the above two species of the genus Actinomyces showed less than 32 % DNA-DNA relatedness, supporting a novel species status of strain VUL4_3T. Based on the phenotypic data and phylogenetic inference, the novel species Actinomycestangfeifanii sp. nov. is proposed. The type strain is VUL4_3T (=CGMCC 4.7369T=DSM 103436T).
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Affiliation(s)
- Xiangli Meng
- 1State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
- 2Ningbo International Travel Healthcare Center, Ningbo Customs District People's Republic of China, Ningbo 315012, PR China
| | - Xin-He Lai
- 3School of Biology and Food Sciences, Shangqiu Normal University, Shangqiu, Henan 476000, PR China
| | - Shan Lu
- 1State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Sha Liu
- 1State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
- 4Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, PR China
| | - Cuixia Chen
- 1State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Donggen Zhou
- 2Ningbo International Travel Healthcare Center, Ningbo Customs District People's Republic of China, Ningbo 315012, PR China
| | - Jing Yang
- 1State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Dong Jin
- 1State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Jianguo Xu
- 1State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
- 5Shanghai Institute for Emerging and Re-emerging infectious diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China
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30
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Cortez V, Canal E, Dupont-Turkowsky JC, Quevedo T, Albujar C, Chang TC, Salmon-Mulanovich G, Guezala-Villavicencio MC, Simons MP, Margolis E, Schultz-Cherry S, Pacheco V, Bausch DG. Identification of Leptospira and Bartonella among rodents collected across a habitat disturbance gradient along the Inter-Oceanic Highway in the southern Amazon Basin of Peru. PLoS One 2018; 13:e0205068. [PMID: 30300359 PMCID: PMC6177132 DOI: 10.1371/journal.pone.0205068] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 09/18/2018] [Indexed: 11/19/2022] Open
Abstract
Background The southern Amazon Basin in the Madre de Dios region of Peru has undergone rapid deforestation and habitat disruption, leading to an unknown zoonotic risk to the growing communities in the area. Methodology/Principal findings We surveyed the prevalence of rodent-borne Leptospira and Bartonella, as well as potential environmental sources of human exposure to Leptospira, in 4 communities along the Inter-Oceanic Highway in Madre de Dios. During the rainy and dry seasons of 2014–2015, we captured a total of 97 rodents representing 8 genera in areas that had experienced different degrees of habitat disturbance. Primarily by using 16S metagenomic sequencing, we found that most of the rodents (78%) tested positive for Bartonella, whereas 24% were positive for Leptospira; however, the patterns differed across seasons and the extent of habitat disruption. A high prevalence of Bartonella was identified in animals captured across both trapping seasons (72%–83%) and the relative abundance was correlated with increasing level of land disturbance. Leptospira-positive animals were more than twice as prevalent during the rainy season (37%) as during the dry season (14%). A seasonal fluctuation across the rainy, dry, and mid seasons was also apparent in environmental samples tested for Leptospira (range, 55%–89% of samples testing positive), and there was a high prevalence of this bacteria across all sites that were sampled in the communities. Conclusions/Significance These data indicate the need for increased awareness of rodent-borne disease and the potential for environmental spread along the communities in areas undergoing significant land-use change.
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Affiliation(s)
- Valerie Cortez
- U.S. Naval Medical Research Unit No. 6, Callao, Peru
- St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
- * E-mail:
| | - Enrique Canal
- U.S. Naval Medical Research Unit No. 6, Callao, Peru
| | | | | | | | - Ti-Cheng Chang
- St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Gabriela Salmon-Mulanovich
- U.S. Naval Medical Research Unit No. 6, Callao, Peru
- Pontificia Universidad Católica del Peru, Lima, Peru
| | | | | | - Elisa Margolis
- St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | | | - Víctor Pacheco
- Universidad Nacional Mayor de San Marcos, Museo de Historia Natural, Lima, Peru
| | - Daniel G. Bausch
- U.S. Naval Medical Research Unit No. 6, Callao, Peru
- Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, United States of America
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Zoonotic pathogens in fluctuating common vole (Microtus arvalis) populations: occurrence and dynamics. Parasitology 2018; 146:389-398. [PMID: 30246665 DOI: 10.1017/s0031182018001543] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Diseases and host dynamics are linked, but their associations may vary in strength, be time-lagged, and depend on environmental influences. Where a vector is involved in disease transmission, its dynamics are an additional influence, and we often lack a general understanding on how diseases, hosts and vectors interact. We report on the occurrence of six zoonotic arthropod-borne pathogens (Anaplasma, Bartonella, Borrelia, Coxiella, Francisella and Rickettsia) in common voles (Microtus arvalis) throughout a population fluctuation and how their prevalence varies according to host density, seasonality and vector prevalence. We detected Francisella tularensis and four species of Bartonella, but not Anaplasma, Borrelia, Coxiella or Rickettsia. Bartonella taylorii and B. grahamii prevalence increased and decreased with current host (vole and mice) density, respectively, and increased with flea prevalence. Bartonella doshiae prevalence decreased with mice density. These three Bartonella species were also more prevalent during winter. Bartonella rochalimae prevalence varied with current and previous vole density (delayed-density dependence), but not with season. Coinfection with F. tularensis and Bartonella occurred as expected from the respective prevalence of each disease in voles. Our results highlight that simultaneously considering pathogen, vector and host dynamics provide a better understanding of the epidemiological dynamics of zoonoses in farmland rodents.
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Ge Y, Guo G, Ge B, Yin H, Yin H. The spleen microbiota of small wild mammals reveals distinct patterns with tick-borne bacteria. PLoS Negl Trop Dis 2018; 12:e0006499. [PMID: 29975692 PMCID: PMC6033388 DOI: 10.1371/journal.pntd.0006499] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 05/04/2018] [Indexed: 12/15/2022] Open
Abstract
Background Wild mammals serve as reservoirs for a variety of microbes and play an important role in the enzootic cycles of these microbes. Some of them are vector-borne bacteria in the genera Anaplasma, Ehrlichia and Rickettsia of the order Rickettsiales, which can cause febrile illnesses in human beings as well as animals. Anaplasma spp., Ehrlichia spp. and many spotted fever group (SFG) Rickettsia spp. are transmitted to mammalian hosts by tick vectors during blood meals. As a powerful sequencing method, the next generation sequencing can reveal the complexity of bacterial communities in humans and animals. Compared with limited studies on blood microbiota, however, much fewer studies have been carried out on spleen microbiota, which is very scarce in wild mammals. Chongming Island is the third biggest island in China. It was unclear whether there were any vector-borne bacteria in Chongming Island. In the present study, we explored the bacterial microbiota in the spleens of wild mice and shrews from the rural areas of Chongming Island and investigated the prevalence of vector-borne bacteria. Methodology/Principal findings Genomic DNAs were extracted from the spleen samples of 35 mice and shrews. The 16S rDNA V3-V4 regions of the DNA extracts were amplified by PCR and subjected to the 16S rDNA-targeted metagenomic sequencing on an Illumina MiSeq platform. All the 35 spleen samples obtained data with sufficient coverage (99.7–99.9%) for analysis. More than 1,300,000 sequences were obtained after quality control and classified into a total of 1,967 operational taxonomic units (OTUs) clustered at 97% similarity. The two most abundant bacterial phyla were Firmicutes and Proteobacteria according to the analysis of rarefied sequences. Among the bacterial communities detected in this study, Anaplasma, Rickettsia and Coxiella were adjacently clustered by hierarchical analysis. Significant differences in many bacterial features between Anaplasma-positive and Anaplasma-negative samples were identified by LEfSe analysis and Wilcoxon rank-sum test, suggesting that the Anaplasma-infection of small wild mammals was associated with a specific pattern of spleen microbiota. Conclusions/Significance Our study has comprehensively characterized the complex bacterial profiles in the spleens of wild mice and shrews from Chongming Island, Shanghai city. This work has revealed distinct spleen bacterial communities associated with tick-borne bacteria in wild animals. The detection of tick-borne bacteria highlights the risk of contracting pathogens with public health importance upon tick-exposure in the studied areas. In this study, the 16S rDNA-targeted metagenomic sequencing was used to determine the bacterial community and diversity in the spleens of small wild mammals from China. The 16S rDNAs were amplified from the spleen genomic DNAs of 35 small wild mice and shrews and sequenced by Illumina MiSeq technology. More than 1,300,000 sequences were obtained after quality control and classified into a total of 1,967 operational taxonomic units (OTUs) clustered at 97% similarity. The two most abundant bacterial phyla were Firmicutes and Proteobacteria according to the analysis of rarefied sequences. Within the bacterial communities detected in this study, vector-borne bacteria, Anaplasma, Rickettsia and Coxiella, were adjacently clustered by hierarchical analysis. Significant differences in many bacterial features between Anaplasma-positive and Anaplasma-negative samples were observed, suggesting that the infection of small wild mammals with Anaplasma is associated with a distinct pattern of spleen microbiota. This study has revealed the complex bacterial profiles in the spleens of wild mice and shrews. The detection of vector-borne bacteria highlights the role of wild mice and shrews as animal reservoirs with potential public health importance in the studied areas.
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Affiliation(s)
- Yan Ge
- Department of Immunology and Pathogen Biology, Tongji University School of Medicine, Shanghai, China
- * E-mail:
| | - Guangpu Guo
- Departement of Biotechnology, College of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Baoxue Ge
- Department of Immunology and Pathogen Biology, Tongji University School of Medicine, Shanghai, China
| | - Hongmei Yin
- Department of Immunology and Pathogen Biology, Tongji University School of Medicine, Shanghai, China
| | - Hong Yin
- The State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Gansu, China
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Integrated metatranscriptomics and metaproteomics for the characterization of bacterial microbiota in unfed Ixodes ricinus. Ticks Tick Borne Dis 2018; 9:1241-1251. [DOI: 10.1016/j.ttbdis.2018.04.020] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 04/28/2018] [Accepted: 04/29/2018] [Indexed: 12/12/2022]
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Development of a New Application for Comprehensive Viability Analysis Based on Microbiome Analysis by Next-Generation Sequencing: Insights into Staphylococcal Carriage in Human Nasal Cavities. Appl Environ Microbiol 2018; 84:AEM.00517-18. [PMID: 29625975 DOI: 10.1128/aem.00517-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 03/27/2018] [Indexed: 01/08/2023] Open
Abstract
The nasal carriage rate of Staphylococcus aureus in human is 25 to 30%, and S. aureus sporadically causes severe infections. However, the mechanisms underlying staphylococcal carriage remain largely unknown. In the present study, we constructed an rpoB-based microbiome method for staphylococcal species discrimination. Based on a microbiome scheme targeting viable cell DNA using propidium monoazide (PMA) dye (PMA microbiome method), we also developed a new method to allow the comprehensive viability analysis of any bacterial taxon. To clarify the ecological distribution of staphylococci in the nasal microbiota, we applied these methods in 46 nasal specimens from healthy adults. PMA microbiome results showed that Staphylococcaceae and Corynebacteriaceae were the most predominant viable taxa (average relative abundance: 0.435262 and 0.375195, respectively), and Staphylococcus epidermidis exhibited the highest viability in the nasal microbiota. Staphylococcus aureus detection rates from nasal specimens by rpoB-based conventional and PMA microbiome methods were 84.8% (39 of 46) and 69.5% (32 of 46), respectively, which substantially exceeded the values obtained by a culture method using identical specimens (36.9%). Our results suggest that Staphylococcaceae species, especially S. epidermidis, adapted most successfully to human nasal cavity. High detection of S. aureus DNA by microbiome methods suggests that almost all healthy adults are consistently exposed to S. aureus in everyday life. Furthermore, the large difference in S. aureus detection rates between culture and microbiome methods suggests that S. aureus cells frequently exist in a viable but nonculturable state in nasal cavities. Our method and findings will contribute to a better understanding of the mechanisms underlying carriage of indigenous bacteria.IMPORTANCE Metagenomic analyses, such as 16S rRNA microbiome methods, have provided new insights in various research fields. However, conventional 16S rRNA microbiome methods do not permit taxonomic analysis of only the viable bacteria in a sample and have poor resolving power below the genus level. Our new schemes allowed for viable cell-specific analysis and species discrimination, and nasal microbiome data using these methods provided some interesting findings regarding staphylococcal nasal carriage. According to our comprehensive viability analysis, the high viability of Staphylococcus species, especially Staphylococcus epidermidis, in human nasal carriage suggests that this taxon has adapted most successfully to human nasal tissue. Also, a higher detection rate of S. aureus DNA by microbiome methods (84.8%) than by a culture method (36.9%) suggests that almost all healthy adults are consistently exposed to Staphylococcus aureus in the medium and long term. Our findings will contribute to a better understanding of the mechanisms underlying the carriage of indigenous bacteria.
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Guernier V, Allan KJ, Goarant C. Advances and challenges in barcoding pathogenic and environmental Leptospira. Parasitology 2018; 145:595-607. [PMID: 28716157 PMCID: PMC6010154 DOI: 10.1017/s0031182017001147] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Leptospirosis is a zoonotic bacterial disease of global importance. A large spectrum of asymptomatic animal hosts can carry the infection and contribute to the burden of human disease. Environmental sources of human contamination also point to the importance of a hydrotelluric reservoir. Leptospirosis can be caused by as many as 15 different pathogenic or intermediate Leptospira species. However, classification of these bacteria remains complicated through the use of both serological and genetic classification systems that show poor correlation. With the advent of molecular techniques, DNA-based barcoding offers a conceptual framework that can be used for leptospirosis surveillance as well as source tracking. In this review, we summarize some of the current techniques, highlight significant successes and weaknesses and point to the future opportunities and challenges to successfully establish a widely applicable barcoding scheme for Leptospira.
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Affiliation(s)
- Vanina Guernier
- Australian Institute of Tropical Health and Medicine, James Cook University, 1 James Cook Drive, Townsville, QLD 4811, Australia
| | - Kathryn J. Allan
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Cyrille Goarant
- Institut Pasteur in New Caledonia, Institut Pasteur International Network, Leptospirosis Research and Expertise Unit, Noumea, New Caledonia. 11 rue Paul Doumer, BP 61; 98845 Noumea cedex, New Caledonia
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36
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Campanaro S, Treu L, Kougias PG, Zhu X, Angelidaki I. Taxonomy of anaerobic digestion microbiome reveals biases associated with the applied high throughput sequencing strategies. Sci Rep 2018; 8:1926. [PMID: 29386622 PMCID: PMC5792648 DOI: 10.1038/s41598-018-20414-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 01/17/2018] [Indexed: 11/20/2022] Open
Abstract
In the past few years, many studies investigated the anaerobic digestion microbiome by means of 16S rRNA amplicon sequencing. Results obtained from these studies were compared to each other without taking into consideration the followed procedure for amplicons preparation and data analysis. This negligence was mainly due to the lack of knowledge regarding the biases influencing specific steps of the microbiome investigation process. In the present study, the main technical aspects of the 16S rRNA analysis were checked giving special attention to the approach used for high throughput sequencing. More specifically, the microbial compositions of three laboratory scale biogas reactors were analyzed before and after addition of sodium oleate by sequencing the microbiome with three different approaches: 16S rRNA amplicon sequencing, shotgun DNA and shotgun RNA. This comparative analysis revealed that, in amplicon sequencing, abundance of some taxa (Euryarchaeota and Spirochaetes) was biased by the inefficiency of universal primers to hybridize all the templates. Reliability of the results obtained was also influenced by the number of hypervariable regions under investigation. Finally, amplicon sequencing and shotgun DNA underestimated the Methanoculleus genus, probably due to the low 16S rRNA gene copy number encoded in this taxon.
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Affiliation(s)
- Stefano Campanaro
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35121, Padova, Italy
| | - Laura Treu
- Department of Environmental Engineering, Technical University of Denmark, 2800, Kgs, Lyngby, Denmark.
| | - Panagiotis G Kougias
- Department of Environmental Engineering, Technical University of Denmark, 2800, Kgs, Lyngby, Denmark
| | - Xinyu Zhu
- Department of Environmental Engineering, Technical University of Denmark, 2800, Kgs, Lyngby, Denmark
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, 2800, Kgs, Lyngby, Denmark
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Vidal S, Kegler K, Posthaus H, Perreten V, Rodriguez-Campos S. Amplicon sequencing of bacterial microbiota in abortion material from cattle. Vet Res 2017; 48:64. [PMID: 29017611 PMCID: PMC5633877 DOI: 10.1186/s13567-017-0470-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/13/2017] [Indexed: 01/21/2023] Open
Abstract
Abortions in cattle have a significant economic impact on animal husbandry and require prompt diagnosis for surveillance of epizootic infectious agents. Since most abortions are not epizootic but sporadic with often undetected etiologies, this study examined the bacterial community present in the placenta (PL, n = 32) and fetal abomasal content (AC, n = 49) in 64 cases of bovine abortion by next generation sequencing (NGS) of the 16S rRNA gene. The PL and AC from three fetuses of dams that died from non-infectious reasons were included as controls. All samples were analyzed by bacterial culture, and 17 were examined by histopathology. We observed 922 OTUs overall and 267 taxa at the genus level. No detectable bacterial DNA was present in the control samples. The microbial profiles of the PL and AC differed significantly, both in their composition (PERMANOVA), species richness and Chao-1 (Mann-Whitney test). In both organs, Pseudomonas was the most abundant genus. The combination of NGS and culture identified opportunistic pathogens of interest in placentas with lesions, such as Vibrio metschnikovii, Streptococcus uberis, Lactococcus lactis and Escherichia coli. In placentas with lesions where culturing was unsuccessful, Pseudomonas and unidentified Aeromonadaceae were identified by NGS displaying high number of reads. Three cases with multiple possible etiologies and placentas presenting lesions were detected by NGS. Amplicon sequencing has the potential to uncover unknown etiological agents. These new insights on cattle abortion extend our focus to previously understudied opportunistic abortive bacteria.
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Affiliation(s)
- Sara Vidal
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Laenggassstrasse 122, 3012, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, Theodor Kocher Institute, University of Bern, Freiestrasse 1, 3001, Bern, Switzerland
| | - Kristel Kegler
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Laenggassstrasse 122, 3012, Bern, Switzerland
| | - Horst Posthaus
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Laenggassstrasse 122, 3012, Bern, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Laenggassstrasse 122, 3012, Bern, Switzerland
| | - Sabrina Rodriguez-Campos
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Laenggassstrasse 122, 3012, Bern, Switzerland.
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Infection of Rodents by Orientia tsutsugamushi, the Agent of Scrub Typhus in Relation to Land Use in Thailand. Trop Med Infect Dis 2017; 2:tropicalmed2040053. [PMID: 30270910 PMCID: PMC6082056 DOI: 10.3390/tropicalmed2040053] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/01/2017] [Accepted: 10/04/2017] [Indexed: 11/26/2022] Open
Abstract
The relationship between land use structures and occurrence of the scrub typhus agent, Orientia tsutsugamushi, in small wild mammals was investigated in three provinces of Thailand: Buriram, Loei, and Nan. O. tsutsugamushi detection was performed using 16S ribosomal DNA (rDNA) amplicon sequencing approach using Miseq Illumina platform. In total, 387 animals (rodents and shrews) were examined for the infection. The 16S rDNA sequences of the bacterium were found in nine animals, namely Bandicota savilei, Berylmys bowersi, Leopoldamys edwardsi, Rattus exulans, R. tanezumi, and Rattus sp. phylogenetic clade 3, yielding 2.3% infection rate, with two new rodent species found infected by the bacterium in Thailand: B. bowersi and L. edwardsi. Using a generalized linear mixed model (GLMM) and Random Forest analyses for investigating the association between human-land use and occurrence of the bacterium, forest habitat appeared as a strong explicative variable of rodent infection, meaning that O. tsutsugamushi-infected animals were more likely found in forest-covered habitats. In terms of public health implementation, our results suggest that heterogenous forested areas including forest-converted agricultural land, reforestation areas, or fallows, are potential habitats for O. tsutsugamushi transmission. Further understanding of population dynamics of the vectors and their hosts in these habitats could be beneficial for the prevention of this neglected zoonotic disease.
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Menke S, Meier M, Mfune JKE, Melzheimer J, Wachter B, Sommer S. Effects of host traits and land-use changes on the gut microbiota of the Namibian black-backed jackal (Canis mesomelas). FEMS Microbiol Ecol 2017; 93:4222788. [DOI: 10.1093/femsec/fix123] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 09/22/2017] [Indexed: 12/20/2022] Open
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Bank vole immunoheterogeneity may limit Nephropatia Epidemica emergence in a French non-endemic region. Parasitology 2017; 145:393-407. [PMID: 28931451 DOI: 10.1017/s0031182017001548] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ecoevolutionary processes affecting hosts, vectors and pathogens are important drivers of zoonotic disease emergence. In this study, we focused on nephropathia epidemica (NE), which is caused by Puumala hantavirus (PUUV) whose natural reservoir is the bank vole, Myodes glareolus. We questioned the possibility of NE emergence in a French region that is considered to be NE-free but that is adjacent to a NE-endemic region. We first confirmed the epidemiology of these two regions and we demonstrated the absence of spatial barriers that could have limited dispersal, and consequently, the spread of PUUV into the NE-free region. We next tested whether regional immunoheterogeneity could impact PUUV chances to circulate and persist in the NE-free region. We showed that bank voles from the NE-free region were sensitive to experimental PUUV infection. We observed high levels of immunoheterogeneity between individuals and also between regions. Antiviral gene expression (Tnf and Mx2) reached higher levels in bank voles from the NE-free region. During experimental infections, anti-PUUV antibody production was higher in bank voles from the NE-endemic region. These results indicated a lower susceptibility to PUUV for bank voles from this NE-free region, which might limit PUUV persistence and therefore, the risk of NE.
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Wasimuddin, Menke S, Melzheimer J, Thalwitzer S, Heinrich S, Wachter B, Sommer S. Gut microbiomes of free-ranging and captive Namibian cheetahs: Diversity, putative functions and occurrence of potential pathogens. Mol Ecol 2017; 26:5515-5527. [PMID: 28782134 DOI: 10.1111/mec.14278] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 07/18/2017] [Accepted: 07/19/2017] [Indexed: 12/27/2022]
Abstract
Although the significance of the gut microbiome for host health is well acknowledged, the impact of host traits and environmental factors on the interindividual variation of gut microbiomes of wildlife species is not well understood. Such information is essential; however, as changes in the composition of these microbial communities beyond the natural range might cause dysbiosis leading to increased susceptibility to infections. We examined the potential influence of sex, age, genetic relatedness, spatial tactics and the environment on the natural range of the gut microbiome diversity in free-ranging Namibian cheetahs (Acinonyx jubatus). We further explored the impact of an altered diet and frequent contact with roaming dogs and cats on the occurrence of potential bacterial pathogens by comparing free-ranging and captive individuals living under the same climatic conditions. Abundance patterns of particular bacterial genera differed between the sexes, and bacterial diversity and richness were higher in older (>3.5 years) than in younger individuals. In contrast, male spatial tactics, which probably influence host exposure to environmental bacteria, had no discernible effect on the gut microbiome. The profound resemblance of the gut microbiome of kin in contrast to nonkin suggests a predominant role of genetics in shaping bacterial community characteristics and functional similarities. We also detected various Operational Taxonomic Units (OTUs) assigned to potential pathogenic bacteria known to cause diseases in humans and wildlife species, such as Helicobacter spp., and Clostridium perfringens. Captive individuals did not differ in their microbial alpha diversity but exhibited higher abundances of OTUs related to potential pathogenic bacteria and shifts in disease-associated functional pathways. Our study emphasizes the need to integrate ecological, genetic and pathogenic aspects to improve our comprehension of the main drivers of natural variation and shifts in gut microbial communities possibly affecting host health. This knowledge is essential for in situ and ex situ conservation management.
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Affiliation(s)
- Wasimuddin
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Sebastian Menke
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Jörg Melzheimer
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | | | - Sonja Heinrich
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Bettina Wachter
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
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Consequences of organ choice in describing bacterial pathogen assemblages in a rodent population. Epidemiol Infect 2017; 145:3070-3075. [PMID: 28847331 DOI: 10.1017/s0950268817001893] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
High-throughput sequencing technologies now allow for rapid cost-effective surveys of multiple pathogens in many host species including rodents, but it is currently unclear if the organ chosen for screening influences the number and identity of bacteria detected. We used 16S rRNA amplicon sequencing to identify bacterial pathogens in the heart, liver, lungs, kidneys and spleen of 13 water voles (Arvicola terrestris) collected in Franche-Comté, France. We asked if bacterial pathogen assemblages within organs are similar and if all five organs are necessary to detect all of the bacteria present in an individual animal. We identified 24 bacteria representing 17 genera; average bacterial richness for each organ ranged from 1·5 ± 0·4 (mean ± standard error) to 2·5 ± 0·4 bacteria/organ and did not differ significantly between organs. The average bacterial richness when organ assemblages were pooled within animals was 4·7 ± 0·6 bacteria/animal; Operational Taxonomic Unit accumulation analysis indicates that all five organs are required to obtain this. Organ type influences bacterial assemblage composition in a systematic way (PERMANOVA, 999 permutations, pseudo-F 4,51 = 1·37, P = 0·001). Our results demonstrate that the number of organs sampled influences the ability to detect bacterial pathogens, which can inform sampling decisions in public health and wildlife ecology.
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43
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Genotyping ofBartonellabacteria and their animal hosts: current status and perspectives. Parasitology 2017; 145:543-562. [DOI: 10.1017/s0031182017001263] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
SUMMARYGrowing evidence demonstrates that bacterial species diversity is substantial, and many of these species are pathogenic in some contexts or hosts. At the same time, laboratories and museums have collected valuable animal tissue and ectoparasite samples that may contain substantial novel information on bacterial prevalence and diversity. However, the identification of bacterial species is challenging, partly due to the difficulty in culturing many microbes and the reliance on molecular data. Although the genomics revolution will surely add to our knowledge of bacterial systematics, these approaches are not accessible to all researchers and rely predominantly on cultured isolates. Thus, there is a need for comprehensive molecular analyses capable of accurately genotyping bacteria from animal tissues or ectoparasites using common methods that will facilitate large-scale comparisons of species diversity and prevalence. To illustrate the challenges of genotyping bacteria, we focus on the genusBartonella, vector-borne bacteria common in mammals. We highlight the value and limitations of commonly used techniques for genotyping bartonellae and make recommendations for researchers interested in studying the diversity of these bacteria in various samples. Our recommendations could be applicable to many bacterial taxa (with some modifications) and could lead to a more complete understanding of bacterial species diversity.
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Meng X, Lu S, Lai XH, Wang Y, Wen Y, Jin D, Yang J, Xu J. Actinomyces liubingyangii sp. nov. isolated from the vulture Gypaetus barbatus. Int J Syst Evol Microbiol 2017. [PMID: 28629506 DOI: 10.1099/ijsem.0.001884] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains (VUL4_1T and VUL4_2) of Gram-staining-positive, catalase-negative, non-spore-forming short rods were isolated from rectal swabs of Old World vultures (Gypaetus barbatus) in the Tibet-Qinghai Plateau, China. Analysis of morphological characteristics and biochemical tests indicated that the two strains closely resembled each other but were distinct from other species of the genus Actinomyces previously described. Based on the results of 16S rRNA gene sequence comparison and genome analysis, strains were determined to be members of the genus Actinomyces, closely related to the type strains of Actinomyces marimammalium (96.4 % 16S rRNA gene sequence similarity), Actinomyceshongkongensis (92.4 %), Actinomyceshordeovulneris (92.3 %) and Actinomycesnasicola (92.2 %), respectively. Optimal growth conditions were 37 °C, pH 6-7, with 1 % (w/v) NaCl. Strain VUL4_1T contained C18 : 1ω9c and C16 : 0 as the major cellular fatty acids and diphosphatidylglycerol as the major component of the polar lipids. The genomic DNA G+C content of VUL4_1T was 54.9 mol%. Strain VUL4_1T showed less than 70 % DNA-DNA relatedness with other species of the genus Actinomyces, further supporting strain VUL4_1T as a representative of a novel species. Based on the phenotypic data and phylogenetic inference, a novel species, Actinomyces liubingyangii sp. nov., is proposed with VUL4_1T (=CGMCC 4.7370T=DSM 104050T) as the type strain.
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Affiliation(s)
- Xiangli Meng
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Xin-He Lai
- Department of Pediatrics & Institute of Translational Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, PR China
| | - Yiting Wang
- Institute for Immunization and Prevention, Beijing Center for Diseases Prevention and Control, Beijing, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Yumeng Wen
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China.,Shanghai Institute for Emerging and Remerging Infectious Diseases, Shanghai Public Health Clinical Center, Jinshan, Shanghai, PR China
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Meng X, Lu S, Wang Y, Lai XH, Wen Y, Jin D, Yang J, Bai X, Zhang G, Pu J, Lan R, Xu J. Actinomyces vulturis sp. nov., isolated from Gyps himalayensis. Int J Syst Evol Microbiol 2017. [PMID: 28629509 DOI: 10.1099/ijsem.0.001851] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Two strains of Gram-stain-positive, facultatively anaerobic, non-spore-forming short rods (VUL7T and VUL8) were isolated from rectal swabs of Old World vultures, namely Gyps himalayensis, in Tibet-Qinghai Plateau, China. Optimal growth occurred at 37 °C, pH 6-7, with 1 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences classified the two strains to the genus Actinomyces, with highest 16S rRNA gene sequence similarity (95 %) to type strains of Actinomyces haliotis, Actinomyces radicidentis and Actinomyces urogenitalis. The major cellular fatty acids were C18 : 1ω9c and C16 : 0. MK-10(H4) was the major respiratory quinone. The genomic DNA G+C content of the isolate was 54.4 mol%. DNA-DNA hybridization values with the most closely related species ofthe genusActinomyces was 24.6 %. The two strains can be differentiated from the most closely related species such as A. haliotis, A. radicidentis, A. graevenitzii and A. urogenitalis by a list of carbohydrate fermentations and enzyme activities. On the basis of physiological, biochemical and phylogenetic analysis, strains VUL7T and VUL8 represent novel species of the genus Actinomyces, for which the name Actinomyces vulturis sp. nov. is proposed. The type strain is VUL7T (=CGMCC 4.7366T=DSM 103437T).
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Affiliation(s)
- Xiangli Meng
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Yiting Wang
- Institute for Immunization and Prevention, Beijing Center for Diseases Prevention and Control, Beijing 100013, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Xin-He Lai
- Institute of Translational Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, PR China
| | - Yumeng Wen
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Xiangning Bai
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Gui Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Riuting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Jianguo Xu
- Shanghai Institute for Emerging and Remerging Infectious Diseases, Shanghai Public Health Clinical Center, Jinshan, Shanghai, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
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46
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Bouquet J, Gardy JL, Brown S, Pfeil J, Miller RR, Morshed M, Avina-Zubieta A, Shojania K, McCabe M, Parker S, Uyaguari M, Federman S, Tang P, Steiner T, Otterstater M, Holt R, Moore R, Chiu CY, Patrick DM. RNA-Seq Analysis of Gene Expression, Viral Pathogen, and B-Cell/T-Cell Receptor Signatures in Complex Chronic Disease. Clin Infect Dis 2017; 64:476-481. [PMID: 28172519 PMCID: PMC5850034 DOI: 10.1093/cid/ciw767] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 12/27/2016] [Indexed: 01/09/2023] Open
Abstract
Background Chronic fatigue syndrome (CFS) remains poorly understood. Although infections are speculated to trigger the syndrome, a specific infectious agent and underlying pathophysiological mechanism remain elusive. In a previous study, we described similar clinical phenotypes in CFS patients and alternatively diagnosed chronic Lyme syndrome (ADCLS) patients—individuals diagnosed with Lyme disease by testing from private Lyme specialty laboratories but who test negative by reference 2-tiered serologic analysis. Methods Here, we performed blinded RNA-seq analysis of whole blood collected from 25 adults diagnosed with CFS and 13 ADCLS patients, comparing these cases to 25 matched controls and 11 patients with well-controlled systemic lupus erythematosus (SLE). Samples were collected at patient enrollment and not during acute symptom flares. RNA-seq data were used to study host gene expression, B-cell/T-cell receptor profiles (BCR/TCR), and potential viral infections. Results No differentially expressed genes (DEGs) were found to be significant when CFS or ADCLS cases were compared to controls. Forty-two DEGs were found when SLE cases were compared to controls, consistent with activation of interferon signaling pathways associated with SLE disease. BCR/TCR repertoire analysis did not show significant differences between CFS and controls or ADCLS and controls. Finally, viral sequences corresponding to anelloviruses, human pegivirus 1, herpesviruses, and papillomaviruses were detected in RNA-seq data, but proportions were similar (P = .73) across all genus-level taxonomic categories. Conclusions Our observations do not support a theory of transcriptionally mediated immune cell dysregulation in CFS and ADCLS, at least outside of periods of acute symptom flares.
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Affiliation(s)
- Jerome Bouquet
- Department of Laboratory Medicine, University of California, San Francisco, USA
| | - Jennifer L Gardy
- Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control, Vancouver, BC, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| | - Scott Brown
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
| | - Jacob Pfeil
- Department of Laboratory Medicine, University of California, San Francisco, USA
| | - Ruth R Miller
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| | - Muhammad Morshed
- British Columbia Centre for Disease Control Public Health Laboratory, 655 W 12th Ave., Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, 2211 Wesbrook Mall, Vancouver, British Columbia, Canada
| | - Antonio Avina-Zubieta
- Department of Medicine, Division of Rheumatology, University of British Columbia, Vancouver, BC, Canada
| | - Kam Shojania
- Department of Medicine, Division of Rheumatology, University of British Columbia, Vancouver, BC, Canada
| | - Mark McCabe
- Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control, Vancouver, BC, Canada
| | - Shoshana Parker
- Centre for Health Evaluation Outcome Sciences, Vancouver, Canada
| | - Miguel Uyaguari
- Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control, Vancouver, BC, Canada
| | - Scot Federman
- Department of Laboratory Medicine, University of California, San Francisco, USA
| | - Patrick Tang
- Department of Pathology, Sidra Medical and Research Centre, Doha, Qatar
| | - Ted Steiner
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, Canada
| | - Michael Otterstater
- Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control, Vancouver, BC, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| | - Rob Holt
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, Canada
| | - Richard Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, Canada
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, USA
| | - David M Patrick
- Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control, Vancouver, BC, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
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Koskela KA, Kalin-Mänttäri L, Hemmilä H, Smura T, Kinnunen PM, Niemimaa J, Henttonen H, Nikkari S. Metagenomic Evaluation of Bacteria from Voles. Vector Borne Zoonotic Dis 2017; 17:123-133. [DOI: 10.1089/vbz.2016.1969] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | | | | | - Teemu Smura
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Paula M. Kinnunen
- Centre for Military Medicine, Helsinki, Finland
- Defence Command Finland, Plans and Policy Division, Helsinki, Finland
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48
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Galan M, Razzauti M, Bard E, Bernard M, Brouat C, Charbonnel N, Dehne-Garcia A, Loiseau A, Tatard C, Tamisier L, Vayssier-Taussat M, Vignes H, Cosson JF. 16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife. mSystems 2016; 1:e00032-16. [PMID: 27822541 PMCID: PMC5069956 DOI: 10.1128/msystems.00032-16] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 06/17/2016] [Indexed: 11/20/2022] Open
Abstract
The human impact on natural habitats is increasing the complexity of human-wildlife interactions and leading to the emergence of infectious diseases worldwide. Highly successful synanthropic wildlife species, such as rodents, will undoubtedly play an increasingly important role in transmitting zoonotic diseases. We investigated the potential for recent developments in 16S rRNA amplicon sequencing to facilitate the multiplexing of the large numbers of samples needed to improve our understanding of the risk of zoonotic disease transmission posed by urban rodents in West Africa. In addition to listing pathogenic bacteria in wild populations, as in other high-throughput sequencing (HTS) studies, our approach can estimate essential parameters for studies of zoonotic risk, such as prevalence and patterns of coinfection within individual hosts. However, the estimation of these parameters requires cleaning of the raw data to mitigate the biases generated by HTS methods. We present here an extensive review of these biases and of their consequences, and we propose a comprehensive trimming strategy for managing these biases. We demonstrated the application of this strategy using 711 commensal rodents, including 208 Mus musculus domesticus, 189 Rattus rattus, 93 Mastomys natalensis, and 221 Mastomys erythroleucus, collected from 24 villages in Senegal. Seven major genera of pathogenic bacteria were detected in their spleens: Borrelia, Bartonella, Mycoplasma, Ehrlichia, Rickettsia, Streptobacillus, and Orientia. Mycoplasma, Ehrlichia, Rickettsia, Streptobacillus, and Orientia have never before been detected in West African rodents. Bacterial prevalence ranged from 0% to 90% of individuals per site, depending on the bacterial taxon, rodent species, and site considered, and 26% of rodents displayed coinfection. The 16S rRNA amplicon sequencing strategy presented here has the advantage over other molecular surveillance tools of dealing with a large spectrum of bacterial pathogens without requiring assumptions about their presence in the samples. This approach is therefore particularly suitable to continuous pathogen surveillance in the context of disease-monitoring programs. IMPORTANCE Several recent public health crises have shown that the surveillance of zoonotic agents in wildlife is important to prevent pandemic risks. High-throughput sequencing (HTS) technologies are potentially useful for this surveillance, but rigorous experimental processes are required for the use of these effective tools in such epidemiological contexts. In particular, HTS introduces biases into the raw data set that might lead to incorrect interpretations. We describe here a procedure for cleaning data before estimating reliable biological parameters, such as positivity, prevalence, and coinfection, using 16S rRNA amplicon sequencing on an Illumina MiSeq platform. This procedure, applied to 711 rodents collected in West Africa, detected several zoonotic bacterial species, including some at high prevalence, despite their never before having been reported for West Africa. In the future, this approach could be adapted for the monitoring of other microbes such as protists, fungi, and even viruses.
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Affiliation(s)
| | | | | | - Maria Bernard
- INRA, Sigenae, France
- INRA, GABI, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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49
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Cooper MK, Phalen DN, Donahoe SL, Rose K, Šlapeta J. The utility of diversity profiling using Illumina 18S rRNA gene amplicon deep sequencing to detect and discriminate Toxoplasma gondii among the cyst-forming coccidia. Vet Parasitol 2015; 216:38-45. [PMID: 26801593 DOI: 10.1016/j.vetpar.2015.12.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 12/10/2015] [Accepted: 12/14/2015] [Indexed: 12/21/2022]
Abstract
Next-generation sequencing (NGS) has the capacity to screen a single DNA sample and detect pathogen DNA from thousands of host DNA sequence reads, making it a versatile and informative tool for investigation of pathogens in diseased animals. The technique is effective and labor saving in the initial identification of pathogens, and will complement conventional diagnostic tests to associate the candidate pathogen with a disease process. In this report, we investigated the utility of the diversity profiling NGS approach using Illumina small subunit ribosomal RNA (18S rRNA) gene amplicon deep sequencing to detect Toxoplasma gondii in previously confirmed cases of toxoplasmosis. We then tested the diagnostic approach with species-specific PCR genotyping, histopathology and immunohistochemistry of toxoplasmosis in a Risso's dolphin (Grampus griseus) to systematically characterise the disease and associate causality. We show that the Euk7A/Euk570R primer set targeting the V1-V3 hypervariable region of the 18S rRNA gene can be used as a species-specific assay for cyst-forming coccidia and discriminate T. gondii. Overall, the approach is cost-effective and improves diagnostic decision support by narrowing the differential diagnosis list with more certainty than was previously possible. Furthermore, it supplements the limitations of cryptic protozoan morphology and surpasses the need for species-specific PCR primer combinations.
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Affiliation(s)
- Madalyn K Cooper
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - David N Phalen
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Shannon L Donahoe
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Karrie Rose
- Australian Registry of Wildlife Health, Taronga Conservation Society Australia, Mosman, NSW 2088, Australia
| | - Jan Šlapeta
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia.
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50
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A Comparison between Transcriptome Sequencing and 16S Metagenomics for Detection of Bacterial Pathogens in Wildlife. PLoS Negl Trop Dis 2015; 9:e0003929. [PMID: 26284930 PMCID: PMC4540314 DOI: 10.1371/journal.pntd.0003929] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Accepted: 06/22/2015] [Indexed: 12/30/2022] Open
Abstract
Background Rodents are major reservoirs of pathogens responsible for numerous zoonotic diseases in humans and livestock. Assessing their microbial diversity at both the individual and population level is crucial for monitoring endemic infections and revealing microbial association patterns within reservoirs. Recently, NGS approaches have been employed to characterize microbial communities of different ecosystems. Yet, their relative efficacy has not been assessed. Here, we compared two NGS approaches, RNA-Sequencing (RNA-Seq) and 16S-metagenomics, assessing their ability to survey neglected zoonotic bacteria in rodent populations. Methodology/Principal Findings We first extracted nucleic acids from the spleens of 190 voles collected in France. RNA extracts were pooled, randomly retro-transcribed, then RNA-Seq was performed using HiSeq. Assembled bacterial sequences were assigned to the closest taxon registered in GenBank. DNA extracts were analyzed via a 16S-metagenomics approach using two sequencers: the 454 GS-FLX and the MiSeq. The V4 region of the gene coding for 16S rRNA was amplified for each sample using barcoded universal primers. Amplicons were multiplexed and processed on the distinct sequencers. The resulting datasets were de-multiplexed, and each read was processed through a pipeline to be taxonomically classified using the Ribosomal Database Project. Altogether, 45 pathogenic bacterial genera were detected. The bacteria identified by RNA-Seq were comparable to those detected by 16S-metagenomics approach processed with MiSeq (16S-MiSeq). In contrast, 21 of these pathogens went unnoticed when the 16S-metagenomics approach was processed via 454-pyrosequencing (16S-454). In addition, the 16S-metagenomics approaches revealed a high level of coinfection in bank voles. Conclusions/Significance We concluded that RNA-Seq and 16S-MiSeq are equally sensitive in detecting bacteria. Although only the 16S-MiSeq method enabled identification of bacteria in each individual reservoir, with subsequent derivation of bacterial prevalence in host populations, and generation of intra-reservoir patterns of bacterial interactions. Lastly, the number of bacterial reads obtained with the 16S-MiSeq could be a good proxy for bacterial prevalence. The majority of human pathogens are of animal origin, i.e. zoonoses; both domestic and wild animals act as host reservoirs. Epidemiological surveys of wildlife may help to predict, prevent and control putative episodes of emerging zoonoses. Microbial diversity and their interactions at both the individual and population level may influence epidemiological infections. Developing generic approaches able to simultaneously detect multiple pathogens without any a priori information becomes essential. Here, we assess the relative efficacy of distinct next-generation sequencing (NGS) approaches to survey neglected zoonotic bacteria in rodent populations: RNA-sequencing (RNA-Seq) and 16S-metagenomics, with the latter resolved via two sequencing techniques, 454-pyrosequencing and MiSeq. The resulting data generated a thorough inventory of zoonotic bacteria in the rodent sample without any previous knowledge of their presence. We concluded that RNA-Seq and 16S-MiSeq are equally sensitive in bacterial genus detection. Nevertheless, only the 16S approach was able to determine bacterial diversity in each individual, which then permitted the derivation of bacterial prevalence and interaction patterns within host populations. We are persuaded that NGS techniques are very affordable candidates and could become routine approaches in future large-scale epidemiological studies.
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