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Viquez C, Rojas-Gätjens D, Mesén-Porras E, Avendaño R, Sasa M, Lomonte B, Chavarría M. Venom-microbiomics of eight species of Neotropical spiders from the Theraphosidae family. J Appl Microbiol 2024; 135:lxae113. [PMID: 38692848 DOI: 10.1093/jambio/lxae113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 04/22/2024] [Accepted: 04/30/2024] [Indexed: 05/03/2024]
Abstract
AIM Tarantulas are one of the largest predatory arthropods in tropical regions. Tarantulas though not lethal to humans, their venomous bite kills small animals and insect upon which they prey. To understand the abiotic and biotic components involved in Neotropical tarantula bites, we conducted a venom-microbiomics study in eight species from Costa Rica. METHODS AND RESULTS We determined that the toxin profiles of tarantula venom are highly diverse using shotgun proteomics; the most frequently encountered toxins were ω-Ap2 toxin, neprilysin-1, and several teraphotoxins. Through culture-independent and culture-dependent methods, we determined the microbiota present in the venom and excreta to evaluate the presence of pathogens that could contribute to primary infections in animals, including humans. The presence of opportunistic pathogens with hemolytic activity was observed, with a prominence of Stenotrophomonas in the venoms. Other bacteria found in venoms and excreta with hemolytic activity included members of the genera Serratia, Bacillus, Acinetobacter, Microbacterium, and Morganella. CONCLUSIONS Our data shed light on the venom- and gut-microbiome associated with Neotropical tarantulas. This information may be useful for treating bites from these arthropods in both humans and farm animals, while also providing insight into the toxins and biodiversity of this little-explored microenvironment.
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Affiliation(s)
- Carlos Viquez
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José 1174-1200, Costa Rica
- Oficina subregional de Alajuela, Sistema Nacional de Áreas de Conservación (SINAC), Ministerio Ambiente y Energía (MINAE), Alajuela 20101, Costa Rica
| | - Diego Rojas-Gätjens
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José 1174-1200, Costa Rica
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José 11501-2060, Costa Rica
| | - Esteve Mesén-Porras
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José 1174-1200, Costa Rica
| | - Roberto Avendaño
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José 1174-1200, Costa Rica
| | - Mahmood Sasa
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José 11501-2060, Costa Rica
- Museo de Zoología, Centro de Investigación de Biodiversidad y Ecología Tropical, Universidad de Costa Rica, San José 11501-2060, Costa Rica
| | - Bruno Lomonte
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José 11501-2060, Costa Rica
| | - Max Chavarría
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José 1174-1200, Costa Rica
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José 11501-2060, Costa Rica
- Escuela de Química, Universidad de Costa Rica, San José 11501-2060, Costa Rica
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Li P, Hong J, Yuan Z, Huang Y, Wu M, Ding T, Wu Z, Sun X, Lin D. Gut microbiota in parasite-transmitting gastropods. Infect Dis Poverty 2023; 12:105. [PMID: 38001502 PMCID: PMC10668521 DOI: 10.1186/s40249-023-01159-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND Gastropoda, the largest class within the phylum Mollusca, houses diverse gut microbiota, and some gastropods serve as intermediate hosts for parasites. Studies have revealed that gut bacteria in gastropods are associated with various biological aspects, such as growth, immunity and host-parasite interactions. Here, we summarize our current knowledge of gastropod gut microbiomes and highlight future research priorities and perspectives. METHODS A literature search was undertaken using PubMed, Web of Science and CNKI for the articles on the gut microbiota of gastropods until December 31, 2022. We retrieved a total of 166 articles and identified 73 eligible articles for inclusion in this review based on the inclusion and exclusion criteria. RESULTS Our analysis encompassed freshwater, seawater and land snails, with a specific focus on parasite-transmitting gastropods. We found that most studies on gastropod gut microbiota have primarily utilized 16S rRNA gene sequencing to analyze microbial composition, rather than employing metagenomic, metatranscriptomic, or metabolomic approaches. This comprehensive review provided an overview of the parasites carried by snail species in the context of gut microbiota studies. We presented the gut microbial trends, a comprehensive summary of the diversity and composition, influencing factors, and potential functions of gastropod gut microbiota. Additionally, we discussed the potential applications, research gaps and future perspectives of gut microbiomes in parasite-transmitting gastropods. Furthermore, several strategies for enhancing our comprehension of gut microbiomes in snails were also discussed. CONCLUSIONS This review comprehensively summarizes the current knowledge on the composition, potential function, influencing factors, potential applications, limitations, and challenges of gut microbiomes in gastropods, with a specific emphasis on parasite-transmitting gastropods. These findings provide important insights for future studies aiming to understand the potential role of gastropod gut microbiota in controlling snail populations and snail-borne diseases.
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Affiliation(s)
- Peipei Li
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China
- Chinese Atomic Energy Agency Center of Excellence on Nuclear Technology Applications for Insect Control, Provincial Engineering Technology Research Center for Diseases-Vectors Control, Sun Yat-Sen University, Guangzhou, China
| | - Jinni Hong
- Department of Traditional Chinese Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Zhanhong Yuan
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China
| | - Yun Huang
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China
| | - Mingrou Wu
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China
| | - Tao Ding
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China
| | - Zhongdao Wu
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China.
- Chinese Atomic Energy Agency Center of Excellence on Nuclear Technology Applications for Insect Control, Provincial Engineering Technology Research Center for Diseases-Vectors Control, Sun Yat-Sen University, Guangzhou, China.
| | - Xi Sun
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China.
| | - Datao Lin
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China.
- Chinese Atomic Energy Agency Center of Excellence on Nuclear Technology Applications for Insect Control, Provincial Engineering Technology Research Center for Diseases-Vectors Control, Sun Yat-Sen University, Guangzhou, China.
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3
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Du L, Haldar S, King JB, Mattes AO, Srivastava S, Wendt KL, You J, Cunningham C, Cichewicz RH. Persephacin Is a Broad-Spectrum Antifungal Aureobasidin Metabolite That Overcomes Intrinsic Resistance in Aspergillus fumigatus. JOURNAL OF NATURAL PRODUCTS 2023; 86:1980-1993. [PMID: 37523665 DOI: 10.1021/acs.jnatprod.3c00382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Fungi pose a persistent threat to humankind with worrying indications that emerging and re-emerging pathogens (e.g., Candida auris, Coccidioides spp., drug-resistant Aspergilli, and more) exhibit resistance to the limited number of approved antifungals. To address this problem, our team is exploring endophytic fungi as a resource for the discovery of new antifungal natural products. The rationale behind this decision is based on evidence that endophytes engage with plants in mutualistic relationships wherein some fungi actively participate by producing chemical defense measures that suppress pathogenic microorganisms. To improve the odds of bioactive metabolite discovery, we developed a new hands-free laser-cutting system capable of generating >50 plant samples per minute that, in turn, enabled our team to prepare and screen large numbers of endophytic fungi. One of the fungal isolates obtained in this way was identified as an Elsinoë sp. that produced a unique aureobasidin analogue, persephacin (1). Some distinctive features of 1 are the absence of both phenylalanine residues combined with the incorporation of a novel amino acid residue, persephanine (9). Compound 1 exhibits potent antifungal effects against a large number of pathogenic yeast (including several clinical C. auris strains), as well as phylogenetically diverse filamentous fungi (e.g., Aspergillus fumigatus). In an ex vivo eye infection model, compound 1 outperformed standard-of-care treatments demonstrating the ability to suppress fluconazole-resistant Candida albicans and A. fumigatus at a concentration (0.1% solution) well below the clinically recommended levels used for fluconazole and natamycin (2% and 5% solutions, respectively). In 3D tissue models for acute dermal and ocular safety, 1 was found to be nontoxic and nonirritating at concentrations required to elicit antifungal activity. Natural product 1 appears to be a promising candidate for further investigation as a broad-spectrum antifungal capable of controlling a range of pathogens that negatively impact human, animal, and plant health.
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Affiliation(s)
- Lin Du
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Saikat Haldar
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Jarrod B King
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Allison O Mattes
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Shikha Srivastava
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Karen L Wendt
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Jianlan You
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Chad Cunningham
- Electronics & Instrument Shop, Department of Physics and Astronomy, Nielsen Hall, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Robert H Cichewicz
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
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Gritti MA, González KY, Tavares FL, Teibler GP, Peichoto ME. Exploring the antibacterial potential of venoms from Argentinian animals. Arch Microbiol 2023; 205:121. [PMID: 36934358 DOI: 10.1007/s00203-023-03465-4] [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: 12/07/2022] [Revised: 02/27/2023] [Accepted: 03/03/2023] [Indexed: 03/20/2023]
Abstract
The resistance to antimicrobials developed by several bacterial species has become one of the main health problems in recent decades. It has been widely reported that natural products are important sources of antimicrobial compounds. Considering that animal venoms are under-explored in this line of research, in this study, we screened the antibacterial activity of venoms of eight snake and five lepidopteran species from northeastern Argentina. Twofold serial dilutions of venoms were tested by the agar well-diffusion method and the minimum inhibitory concentration (MIC) determination against seven bacterial strains. We studied the comparative protein profile of the venoms showing antibacterial activity. Only the viperid and elapid venoms showed remarkable dose-dependent antibacterial activity towards most of the strains tested. Bothrops diporus venom showed the lowest MIC values against all the strains, and S. aureus ATCC 25923 was the most sensitive strain for all the active venoms. Micrurus baliocoryphus venom was unable to inhibit the growth of Enterococcus faecalis. Neither colubrid snake nor lepidopteran venoms exhibited activity on any bacterial strain tested. The snake venoms exhibiting antibacterial activity showed distinctive protein profiles by SDS-PAGE, highlighting that we could reveal for the first time the main protein families which may be thought to contribute to the antibacterial activity of M. baliocoryphus venom. This study paves the way to search for new antibacterial agents from Argentinian snake venoms, which may be a further opportunity to give an added value to the local biodiversity.
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Affiliation(s)
- Micaela A Gritti
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Instituto Nacional de Medicina Tropical (INMeT)-ANLIS "Dr. Carlos G Malbrán", Almafuerte y Ambar s/n, 3370, Puerto Iguazú, Argentina
| | - Karen Y González
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Facultad de Ciencias Veterinarias (FCV), Universidad Nacional del Nordeste (UNNE), Sargento Cabral 2139, 3400, Corrientes, Argentina
| | - Flavio L Tavares
- Universidade Federal da Integração Latino-Americana (UNILA), Av. Tarquínio Joslin dos Santos, nº. 1.000, Jd. Universitário, Foz do Iguaçu, PR, CEP 85870-901, Brazil
| | - Gladys P Teibler
- Facultad de Ciencias Veterinarias (FCV), Universidad Nacional del Nordeste (UNNE), Sargento Cabral 2139, 3400, Corrientes, Argentina
| | - María E Peichoto
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
- Instituto Nacional de Medicina Tropical (INMeT)-ANLIS "Dr. Carlos G Malbrán", Almafuerte y Ambar s/n, 3370, Puerto Iguazú, Argentina.
- Universidade Federal da Integração Latino-Americana (UNILA), Av. Tarquínio Joslin dos Santos, nº. 1.000, Jd. Universitário, Foz do Iguaçu, PR, CEP 85870-901, Brazil.
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5
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Esmaeilishirazifard E, Usher L, Trim C, Denise H, Sangal V, Tyson GH, Barlow A, Redway KF, Taylor JD, Kremyda-Vlachou M, Davies S, Loftus TD, Lock MMG, Wright K, Dalby A, Snyder LAS, Wuster W, Trim S, Moschos SA. Bacterial Adaptation to Venom in Snakes and Arachnida. Microbiol Spectr 2022; 10:e0240821. [PMID: 35604233 PMCID: PMC9248900 DOI: 10.1128/spectrum.02408-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/14/2022] [Indexed: 11/20/2022] Open
Abstract
Animal venoms are considered sterile sources of antimicrobial compounds with strong membrane-disrupting activity against multidrug-resistant bacteria. However, venomous bite wound infections are common in developing nations. Investigating the envenomation organ and venom microbiota of five snake and two spider species, we observed venom community structures that depend on the host venomous animal species and evidenced recovery of viable microorganisms from black-necked spitting cobra (Naja nigricollis) and Indian ornamental tarantula (Poecilotheria regalis) venoms. Among the bacterial isolates recovered from N. nigricollis, we identified two venom-resistant, novel sequence types of Enterococcus faecalis whose genomes feature 16 virulence genes, indicating infectious potential, and 45 additional genes, nearly half of which improve bacterial membrane integrity. Our findings challenge the dogma of venom sterility and indicate an increased primary infection risk in the clinical management of venomous animal bite wounds. IMPORTANCE Notwithstanding their 3 to 5% mortality, the 2.7 million envenomation-related injuries occurring annually-predominantly across Africa, Asia, and Latin America-are also major causes of morbidity. Venom toxin-damaged tissue will develop infections in some 75% of envenomation victims, with E. faecalis being a common culprit of disease; however, such infections are generally considered to be independent of envenomation. Here, we provide evidence on venom microbiota across snakes and arachnida and report on the convergent evolution mechanisms that can facilitate adaptation to black-necked cobra venom in two independent E. faecalis strains, easily misidentified by biochemical diagnostics. Therefore, since inoculation with viable and virulence gene-harboring bacteria can occur during envenomation, acute infection risk management following envenomation is warranted, particularly for immunocompromised and malnourished victims in resource-limited settings. These results shed light on how bacteria evolve for survival in one of the most extreme environments on Earth and how venomous bites must be also treated for infections.
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Affiliation(s)
- Elham Esmaeilishirazifard
- Department of Biomedical Sciences, Faculty of Science and Technology, University of Westminster, London, United Kingdom
- Westminster Genomic Services, Faculty of Science and Technology, University of Westminster, London, United Kingdom
| | - Louise Usher
- Department of Biomedical Sciences, Faculty of Science and Technology, University of Westminster, London, United Kingdom
- Westminster Genomic Services, Faculty of Science and Technology, University of Westminster, London, United Kingdom
| | - Carol Trim
- School of Psychology and Life Sciences, Faculty of Science, Engineering and Social Sciences, Canterbury Christ Church University, Canterbury, Kent, United Kingdom
| | - Hubert Denise
- EMBL-EBI European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Vartul Sangal
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle, Tyne and Wear, United Kingdom
| | - Gregory H. Tyson
- Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Laurel, Maryland, USA
| | - Axel Barlow
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Keith F. Redway
- Department of Biomedical Sciences, Faculty of Science and Technology, University of Westminster, London, United Kingdom
| | - John D. Taylor
- Department of Biomedical Sciences, Faculty of Science and Technology, University of Westminster, London, United Kingdom
- Westminster Genomic Services, Faculty of Science and Technology, University of Westminster, London, United Kingdom
- School of Environment and Life Sciences, University of Salford, Salford, Greater Manchester, United Kingdom
| | - Myrto Kremyda-Vlachou
- Department of Biomedical Sciences, Faculty of Science and Technology, University of Westminster, London, United Kingdom
| | - Sam Davies
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle, Tyne and Wear, United Kingdom
| | | | | | - Kstir Wright
- Department of Biomedical Sciences, Faculty of Science and Technology, University of Westminster, London, United Kingdom
| | - Andrew Dalby
- Department of Biomedical Sciences, Faculty of Science and Technology, University of Westminster, London, United Kingdom
| | - Lori A. S. Snyder
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, London, United Kingdom
| | - Wolfgang Wuster
- Molecular Ecology and Evolution at Bangor, School of Biological Sciences, College of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom
| | - Steve Trim
- Venomtech, Ltd., Sandwich, Kent, United Kingdom
| | - Sterghios A. Moschos
- Department of Biomedical Sciences, Faculty of Science and Technology, University of Westminster, London, United Kingdom
- Westminster Genomic Services, Faculty of Science and Technology, University of Westminster, London, United Kingdom
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle, Tyne and Wear, United Kingdom
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6
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Chalifour B, Li J. A Review of the Molluscan Microbiome: Ecology, Methodology and Future. MALACOLOGIA 2021. [DOI: 10.4002/040.063.0208] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Bridget Chalifour
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 334 UCB, Boulder, Colorado, 80309, U.S.A
| | - Jingchun Li
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 334 UCB, Boulder, Colorado, 80309, U.S.A
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Ul-Hasan S, Rodríguez-Román E, Reitzel AM, Adams RM, Herzig V, Nobile CJ, Saviola AJ, Trim SA, Stiers EE, Moschos SA, Keiser CN, Petras D, Moran Y, Colston TJ. The emerging field of venom-microbiomics for exploring venom as a microenvironment, and the corresponding Initiative for Venom Associated Microbes and Parasites (iVAMP). Toxicon X 2019; 4:100016. [PMID: 32550573 PMCID: PMC7286055 DOI: 10.1016/j.toxcx.2019.100016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Venom is a known source of novel antimicrobial natural products. The substantial, increasing number of these discoveries have unintentionally culminated in the misconception that venom and venom-producing glands are largely sterile environments. Culture-dependent and -independent studies on the microbial communities in venom microenvironments reveal the presence of archaea, algae, bacteria, fungi, protozoa, and viruses. Venom-centric microbiome studies are relatively sparse to date with the adaptive advantages that venom-associated microbes might offer to their hosts, or that hosts might provide to venom-associated microbes, remaining largely unknown. We highlight the potential for the discovery of venom microbiomes within the adaptive landscape of venom systems. The considerable number of convergently evolved venomous animals, juxtaposed with the comparatively few known studies to identify microbial communities in venom, provides new possibilities for both biodiversity and therapeutic discoveries. We present an evidence-based argument for integrating microbiology as part of venomics (i.e., venom-microbiomics) and introduce iVAMP, the Initiative for Venom Associated Microbes and Parasites (https://ivamp-consortium.github.io/), as a growing collaborative consortium. We express commitment to the diversity, inclusion and scientific collaboration among researchers interested in this emerging subdiscipline through expansion of the iVAMP consortium.
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Affiliation(s)
- Sabah Ul-Hasan
- Quantitative and Systems Biology Graduate Program, University of California Merced, Merced, CA, 95343, USA
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, CA, 95343, USA
| | - Eduardo Rodríguez-Román
- Center for Microbiology and Cell Biology, Venezuelan Institute for Scientific Research. Caracas, 1020A, Venezuela
| | - Adam M. Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Rachelle M.M. Adams
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, 43212, USA
| | - Volker Herzig
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Clarissa J. Nobile
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, CA, 95343, USA
| | - Anthony J. Saviola
- Department of Molecular Medicine and Neurobiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Steven A. Trim
- Venomtech Ltd, Discovery Park, Sandwich, Kent, CT13 9ND, UK
| | - Erin E. Stiers
- Department of Biological Science, Clemson University, Clemson, SC, 29634, USA
| | - Sterghios A. Moschos
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle, Tyne and Wear, NE1 8ST, UK
| | - Carl N. Keiser
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, USA
- Scripps Institution of Oceanography, University of California, San Diego, USA
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Timothy J. Colston
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
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8
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Small CM, Currey M, Beck EA, Bassham S, Cresko WA. Highly Reproducible 16S Sequencing Facilitates Measurement of Host Genetic Influences on the Stickleback Gut Microbiome. mSystems 2019; 4:e00331-19. [PMID: 31409661 PMCID: PMC6697441 DOI: 10.1128/msystems.00331-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 07/19/2019] [Indexed: 12/18/2022] Open
Abstract
Multicellular organisms interact with resident microbes in important ways, and a better understanding of host-microbe interactions is aided by tools such as high-throughput 16S sequencing. However, rigorous evaluation of the veracity of these tools in a different context from which they were developed has often lagged behind. Our goal was to perform one such critical test by examining how variation in tissue preparation and DNA isolation could affect inferences about gut microbiome variation between two genetically divergent lines of threespine stickleback fish maintained in the same laboratory environment. Using careful experimental design and intensive sampling of individuals, we addressed technical and biological sources of variation in 16S-based estimates of microbial diversity. After employing a two-tiered bead beating approach that comprised tissue homogenization followed by microbial lysis in subsamples, we found an extremely minor effect of DNA isolation protocol relative to among-host microbial diversity differences. Abundance estimates for rare operational taxonomic units (OTUs), however, showed much lower reproducibility. Gut microbiome composition was highly variable across fish-even among cohoused siblings-relative to technical replicates, but a subtle effect of host genotype (stickleback line) was nevertheless detected for some microbial taxa.IMPORTANCE Our findings demonstrate the importance of appropriately quantifying biological and technical variance components when attempting to understand major influences on high-throughput microbiome data. Our focus was on understanding among-host (biological) variance in community metrics and its magnitude in relation to within-host (technical) variance, because meaningful comparisons among individuals are necessary in addressing major questions in host-microbe ecology and evolution, such as heritability of the microbiome. Our study design and insights should provide a useful example for others desiring to quantify microbiome variation at biological levels in the face of various technical factors in a variety of systems.
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Affiliation(s)
- Clayton M Small
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Mark Currey
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Emily A Beck
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Susan Bassham
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - William A Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
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9
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Tayyrov A, Stanley CE, Azevedo S, Künzler M. Combining microfluidics and RNA-sequencing to assess the inducible defensome of a mushroom against nematodes. BMC Genomics 2019; 20:243. [PMID: 30909884 PMCID: PMC6434838 DOI: 10.1186/s12864-019-5607-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 03/14/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Fungi are an attractive source of nutrients for predators. As part of their defense, some fungi are able to induce the production of anti-predator protein toxins in response to predation. A previous study on the interaction of the model mushroom Coprinopsis cinerea by the fungivorous nematode Aphelenchus avenae on agar plates has shown that the this fungal defense response is most pronounced in the part of the mycelium that is in direct contact with the nematode. Hence, we hypothesized that, for a comprehensive characterization of this defense response, an experimental setup that maximizes the zone of direct interaction between the fungal mycelium and the nematode, was needed. RESULTS In this study, we conducted a transcriptome analysis of C. cinerea vegetative mycelium upon challenge with A. avenae using a tailor-made microfluidic device. The device was designed such that the interaction between the fungus and the nematode was confined to a specific area and that the mycelium could be retrieved from this area for analysis. We took samples from the confrontation area after different time periods and extracted and sequenced the poly(A)+ RNA thereof. The identification of 1229 differentially expressed genes (DEGs) shows that this setup profoundly improved sensitivity over co-cultivation on agar plates where only 37 DEGs had been identified. The product of one of the most highly upregulated genes shows structural homology to bacterial pore-forming toxins, and revealed strong toxicity to various bacterivorous nematodes. In addition, bacteria associated with the fungivorous nematode A. avenae were profiled with 16S rRNA deep sequencing. Similar to the bacterivorous and plant-feeding nematodes, Proteobacteria and Bacteroidetes were the most dominant phyla in A. avenae. CONCLUSIONS The use of a novel experimental setup for the investigation of the defense response of a fungal mycelium to predation by fungivorous nematodes resulted in the identification of a comprehensive set of DEGs and the discovery of a novel type of fungal defense protein against nematodes. The bacteria found to be associated with the fungivorous nematode are a possible explanation for the induction of some antibacterial defense proteins upon nematode challenge.
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Affiliation(s)
- Annageldi Tayyrov
- Institute of Microbiology, Department of Biology, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093 Zürich, Switzerland
| | - Claire E. Stanley
- Agroecology and Environment Research Division, Agroscope, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland
| | - Sophie Azevedo
- Institute of Microbiology, Department of Biology, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093 Zürich, Switzerland
| | - Markus Künzler
- Institute of Microbiology, Department of Biology, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093 Zürich, Switzerland
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