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Ienes-Lima J, Prichula J, Abadie M, Borges-Martins M, Frazzon APG. Anthropic Impact on the Critically Endangered Melanophryniscus admirabilis (Admirable Redbelly Toad): Evidence from the Presence of Multiresistant Enterobacteriaceae. Curr Microbiol 2023; 80:339. [PMID: 37695536 DOI: 10.1007/s00284-023-03433-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/29/2023] [Indexed: 09/12/2023]
Abstract
Melanophryniscus admirabilis is a microendemic and critically endangered toad, known from a single population. This microendemic species inhabits a small fragment of the Atlantic Forest in South Brazil, an area significantly impacted by hydroelectric power plant projects, livestock farming, agricultural activities, biopiracy, and tourism. Given the exclusive and limited population of M. admirabilis, preserving and conserving this species is of utmost importance in Brazil. Research on this species primarily concentrates on its biology, ecology, and ecotoxicology. Currently, there is no knowledge about antimicrobial resistance (AMR) bacteria present in wild M. admirabilis, despite the potential for studying them to provide valuable insights into environmental pollution. To this end, Enterobacteriaceae species (n = 82) obtained from 15 wild M. admirabilis toads were subjected to the standard Kirby-Bauer disk diffusion method to test their AMR. The results showed that Enterobacteriaceae species had the highest antibiotic resistance to IPM (45.1%), CIP (39%), NIT (32.5%), AMP (31.3%), TET (18.3%), and FOX (17%). Of the tested species, 18 (21.9%) species tested were susceptible, 40 (48.8%) were resistant to 1 or 2 different antibiotic classes, and 24 (29.3%) were classified as multidrug-resistant. Overall, our findings suggest that the incidence of AMR in Enterobacteriaceae isolated from wild M. admirabilis is high, indicating environmental stress caused by anthropic pollution in their habit.
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Affiliation(s)
- Julia Ienes-Lima
- Post-Graduation Program in Agricultural and Environmental Microbiology, Department of Microbiology, Immunology and Parasitology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, USA
| | - Janira Prichula
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Michelle Abadie
- Post-Graduation Program in Animal Biology, Department of Zoology, Biosciences Institute, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
- National Center for Research and Conservation of Reptiles and Amphibians, Chico Mendes Institute for Biodiversity Conservation, Goiânia, Brazil
| | - Márcio Borges-Martins
- Post-Graduation Program in Animal Biology, Department of Zoology, Biosciences Institute, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Ana Paula Guedes Frazzon
- Post-Graduation Program in Agricultural and Environmental Microbiology, Department of Microbiology, Immunology and Parasitology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil.
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Martínez-Ugalde E, Ávila-Akerberg V, González Martínez TM, Vázquez Trejo M, Zavala Hernández D, Anaya-Morales SL, Rebollar EA. The skin microbiota of the axolotl Ambystoma altamirani is highly influenced by metamorphosis and seasonality but not by pathogen infection. Anim Microbiome 2022; 4:63. [PMID: 36503640 PMCID: PMC9743558 DOI: 10.1186/s42523-022-00215-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/16/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Microbiomes have been increasingly recognized as major contributors to host health and survival. In amphibians, bacterial members of the skin microbiota protect their hosts by inhibiting the growth of the fungal pathogen Batrachochytrium dendrobatidis (Bd). Even though several studies describe the influence of biotic and abiotic factors over the skin microbiota, it remains unclear how these symbiotic bacterial communities vary across time and development. This is particularly relevant for species that undergo metamorphosis as it has been shown that host physiology and ecology drastically influence diversity of the skin microbiome. RESULTS We found that the skin bacterial communities of the axolotl A. altamirani are largely influenced by the metamorphic status of the host and by seasonal variation of abiotic factors such as temperature, pH, dissolved oxygen and conductivity. Despite high Bd prevalence in these samples, the bacterial diversity of the skin microbiota did not differ between infected and non-infected axolotls, although relative abundance of particular bacteria were correlated with Bd infection intensity. CONCLUSIONS Our work shows that metamorphosis is a crucial process that shapes skin bacterial communities and that axolotls under different developmental stages respond differently to environmental seasonal variations. Moreover, this study greatly contributes to a better understanding of the factors that shape amphibian skin microbiota, especially in a largely underexplored group like axolotls (Mexican Ambystoma species).
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Affiliation(s)
- Emanuel Martínez-Ugalde
- grid.9486.30000 0001 2159 0001Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Víctor Ávila-Akerberg
- grid.412872.a0000 0001 2174 6731Instituto de Ciencias Agropecuarias y Rurales, Universidad Autónoma del Estado de México, Toluca, Mexico
| | - Tanya M. González Martínez
- grid.9486.30000 0001 2159 0001Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Montserrat Vázquez Trejo
- grid.9486.30000 0001 2159 0001Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Dalia Zavala Hernández
- grid.9486.30000 0001 2159 0001Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Sara Lucia Anaya-Morales
- grid.9486.30000 0001 2159 0001Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico ,grid.251313.70000 0001 2169 2489 Department of Biology, University of Mississippi, Oxford, MS USA
| | - Eria A. Rebollar
- grid.9486.30000 0001 2159 0001Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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Shaffer JP, Nothias LF, Thompson LR, Sanders JG, Salido RA, Couvillion SP, Brejnrod AD, Lejzerowicz F, Haiminen N, Huang S, Lutz HL, Zhu Q, Martino C, Morton JT, Karthikeyan S, Nothias-Esposito M, Dührkop K, Böcker S, Kim HW, Aksenov AA, Bittremieux W, Minich JJ, Marotz C, Bryant MM, Sanders K, Schwartz T, Humphrey G, Vásquez-Baeza Y, Tripathi A, Parida L, Carrieri AP, Beck KL, Das P, González A, McDonald D, Ladau J, Karst SM, Albertsen M, Ackermann G, DeReus J, Thomas T, Petras D, Shade A, Stegen J, Song SJ, Metz TO, Swafford AD, Dorrestein PC, Jansson JK, Gilbert JA, Knight R. Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity. Nat Microbiol 2022; 7:2128-2150. [PMID: 36443458 PMCID: PMC9712116 DOI: 10.1038/s41564-022-01266-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 10/10/2022] [Indexed: 11/30/2022]
Abstract
Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure and function of microbial communities across multiple habitats on a planetary scale. Here we present a multi-omics analysis of a diverse set of 880 microbial community samples collected for the Earth Microbiome Project. We include amplicon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry). We used standardized protocols and analytical methods to characterize microbial communities, focusing on relationships and co-occurrences of microbially related metabolites and microbial taxa across environments, thus allowing us to explore diversity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of an evolving community resource. We demonstrate the utility of this database by testing the hypothesis that every microbe and metabolite is everywhere but the environment selects. Our results show that metabolite diversity exhibits turnover and nestedness related to both microbial communities and the environment, whereas the relative abundances of microbially related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner. We additionally show the power of certain chemistry, in particular terpenoids, in distinguishing Earth's environments (for example, terrestrial plant surfaces and soils, freshwater and marine animal stool), as well as that of certain microbes including Conexibacter woesei (terrestrial soils), Haloquadratum walsbyi (marine deposits) and Pantoea dispersa (terrestrial plant detritus). This Resource provides insight into the taxa and metabolites within microbial communities from diverse habitats across Earth, informing both microbial and chemical ecology, and provides a foundation and methods for multi-omics microbiome studies of hosts and the environment.
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Affiliation(s)
- Justin P Shaffer
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Louis-Félix Nothias
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Luke R Thompson
- Northern Gulf Institute, Mississippi State University, Starkville, MS, USA
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL, USA
| | - Jon G Sanders
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Rodolfo A Salido
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Sneha P Couvillion
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Asker D Brejnrod
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Franck Lejzerowicz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Niina Haiminen
- IBM Research, T.J. Watson Research Center, Yorktown Heights, NY, USA
| | - Shi Huang
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Holly L Lutz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Qiyun Zhu
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
| | - Cameron Martino
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - James T Morton
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Smruthi Karthikeyan
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Mélissa Nothias-Esposito
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kai Dührkop
- Chair for Bioinformatics, Friedrich Schiller University, Jena, Germany
| | - Sebastian Böcker
- Chair for Bioinformatics, Friedrich Schiller University, Jena, Germany
| | - Hyun Woo Kim
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University, Gyeonggi-do, Korea
| | - Alexander A Aksenov
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Chemistry, University of Connecticut, Storrs, CT, USA
| | - Wout Bittremieux
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Jeremiah J Minich
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Clarisse Marotz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - MacKenzie M Bryant
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Karenina Sanders
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Tara Schwartz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Greg Humphrey
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Yoshiki Vásquez-Baeza
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Anupriya Tripathi
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Laxmi Parida
- IBM Research, T.J. Watson Research Center, Yorktown Heights, NY, USA
| | | | - Kristen L Beck
- IBM Research, Almaden Research Center, San Jose, CA, USA
| | - Promi Das
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Antonio González
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Joshua Ladau
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Søren M Karst
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institute, Copenhagen, Denmark
| | - Mads Albertsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Gail Ackermann
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jeff DeReus
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Science, The University of New South Wales, Sydney, New South Wales, Australia
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Baden-Württemberg, Germany
| | - Ashley Shade
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - James Stegen
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Se Jin Song
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Thomas O Metz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jack A Gilbert
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
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Effect of a Novel E3 Probiotics Formula on the Gut Microbiome in Atopic Dermatitis Patients: A Pilot Study. Biomedicines 2022; 10:biomedicines10112904. [PMID: 36428472 PMCID: PMC9687608 DOI: 10.3390/biomedicines10112904] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/03/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Atopic dermatitis (AD) has been shown to be closely related to gut dysbiosis mediated through the gut−skin axis, and thus the gut microbiome has recently been explored as a potential therapeutic target for the treatment of AD. Contrasting and varying efficacy have been reported since then. In order to investigate the determining factor of probiotics responsiveness in individuals with AD, we initiated the analysis of 41 AD patients with varying disease severity in Hong Kong, whereas the severity was assessed by Eczema Area and Severity Index (EASI) by board certified dermatologist. 16S rRNA sequencing on the fecal samples from AD patients were performed to obtain the metagenomics profile at baseline and after 8 weeks of oral administration of a novel E3 probiotics formula (including prebiotics, probiotics and postbiotics). While EASI of the participants were significantly lower after the probiotics treatment (p < 0.001, paired Wilcoxon signed rank), subjects with mild AD were found to be more likely to respond to the probiotics treatment. Species richness among responders regardless of disease severity were significantly increased (p < 0.001, paired Wilcoxon signed rank). Responders exhibited (1) elevated relative abundance of Clostridium, Fecalibacterium, Lactobacillus, Romboutsia, and Streptococcus, (2) reduced relative abundance of Collinsella, Bifidobacterium, Fusicatenibacter, and Escherichia-Shigella amid orally-intake probiotics identified using the machine learning algorithm and (3) gut microbiome composition and structure resembling healthy subjects after probiotics treatment. Here, we presented the gut microbiome dynamics in AD patients after the administration of the E3 probiotics formula and delineated the unique gut microbiome signatures in individuals with AD who were responding to the probiotics. These findings could guide the future development of probiotics use for AD management.
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Doolin ML, Weinstein SB, Dearing MD. PINWORMS ARE ASSOCIATED WITH TAXONOMIC BUT NOT FUNCTIONAL DIFFERENCES IN THE GUT MICROBIOME OF WHITE-THROATED WOODRATS (NEOTOMA ALBIGULA). J Parasitol 2022; 108:408-418. [PMID: 36066907 DOI: 10.1645/22-11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Vertebrates rely on their gut microbiome for digestion, and changes to gut microbial communities can impact host health. Past work, primarily in model organisms, has revealed that endoparasites disrupt the gut microbiome. Here, using wild-caught white-throated woodrats (Neotoma albigula), we tested whether naturally acquired parasite infections are associated with different microbiome structure and function. We surveyed wild N. albigula in eastern Utah for gastrointestinal parasites in the spring and fall of 2019, using traditional fecal float methods and testing a PCR-based approach to detect infection. We tested whether the host gut microbiome structure and function differed based on infection with the most prevalent parasite, the pinworm Lamotheoxyuris ackerti. In spring, infected and uninfected animals had significantly different microbiomes, but these differences were not detected in the fall. However, for both sampling periods, infection was associated with differences in particular microbial taxa determined by differential abundance analysis. As N. albigula rely on their microbiomes to digest both fiber and the plant defensive compound oxalate, we compared microbiome function by measuring dry matter digestibility and oxalate intake in infected and uninfected animals. Although we expected infected animals to have reduced fiber degradation and oxalate intake, we found no difference in microbiome function using these assays. This work suggests that parasite effects on the microbiome may be difficult to detect in complex natural systems, and more studies in wild organisms are warranted.
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Affiliation(s)
- Margaret L Doolin
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, Utah 84112
| | - Sara B Weinstein
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, Utah 84112
| | - M Denise Dearing
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, Utah 84112
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Gulliver EL, Young RB, Chonwerawong M, D'Adamo GL, Thomason T, Widdop JT, Rutten EL, Rossetto Marcelino V, Bryant RV, Costello SP, O'Brien CL, Hold GL, Giles EM, Forster SC. Review article: the future of microbiome-based therapeutics. Aliment Pharmacol Ther 2022; 56:192-208. [PMID: 35611465 PMCID: PMC9322325 DOI: 10.1111/apt.17049] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/29/2022] [Accepted: 05/12/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND From consumption of fermented foods and probiotics to emerging applications of faecal microbiota transplantation, the health benefit of manipulating the human microbiota has been exploited for millennia. Despite this history, recent technological advances are unlocking the capacity for targeted microbial manipulation as a novel therapeutic. AIM This review summarises the current developments in microbiome-based medicines and provides insight into the next steps required for therapeutic development. METHODS Here we review current and emerging approaches and assess the capabilities and weaknesses of these technologies to provide safe and effective clinical interventions. Key literature was identified through Pubmed searches with the following key words, 'microbiome', 'microbiome biomarkers', 'probiotics', 'prebiotics', 'synbiotics', 'faecal microbiota transplant', 'live biotherapeutics', 'microbiome mimetics' and 'postbiotics'. RESULTS Improved understanding of the human microbiome and recent technological advances provide an opportunity to develop a new generation of therapies. These therapies will range from dietary interventions, prebiotic supplementations, single probiotic bacterial strains, human donor-derived faecal microbiota transplants, rationally selected combinations of bacterial strains as live biotherapeutics, and the beneficial products or effects produced by bacterial strains, termed microbiome mimetics. CONCLUSIONS Although methods to identify and refine these therapeutics are continually advancing, the rapid emergence of these new approaches necessitates accepted technological and ethical frameworks for measurement, testing, laboratory practices and clinical translation.
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Affiliation(s)
- Emily L. Gulliver
- Centre for Innate Immunity and Infectious DiseasesHudson Institute of Medical ResearchClaytonVictoriaAustralia,Department of Molecular and Translational SciencesMonash UniversityClaytonVictoriaAustralia
| | - Remy B. Young
- Centre for Innate Immunity and Infectious DiseasesHudson Institute of Medical ResearchClaytonVictoriaAustralia,Department of Molecular and Translational SciencesMonash UniversityClaytonVictoriaAustralia
| | - Michelle Chonwerawong
- Centre for Innate Immunity and Infectious DiseasesHudson Institute of Medical ResearchClaytonVictoriaAustralia,Department of Molecular and Translational SciencesMonash UniversityClaytonVictoriaAustralia
| | - Gemma L. D'Adamo
- Centre for Innate Immunity and Infectious DiseasesHudson Institute of Medical ResearchClaytonVictoriaAustralia,Department of Molecular and Translational SciencesMonash UniversityClaytonVictoriaAustralia
| | - Tamblyn Thomason
- Centre for Innate Immunity and Infectious DiseasesHudson Institute of Medical ResearchClaytonVictoriaAustralia,Department of Molecular and Translational SciencesMonash UniversityClaytonVictoriaAustralia
| | - James T. Widdop
- Centre for Innate Immunity and Infectious DiseasesHudson Institute of Medical ResearchClaytonVictoriaAustralia,Department of Molecular and Translational SciencesMonash UniversityClaytonVictoriaAustralia
| | - Emily L. Rutten
- Centre for Innate Immunity and Infectious DiseasesHudson Institute of Medical ResearchClaytonVictoriaAustralia,Department of Molecular and Translational SciencesMonash UniversityClaytonVictoriaAustralia
| | - Vanessa Rossetto Marcelino
- Centre for Innate Immunity and Infectious DiseasesHudson Institute of Medical ResearchClaytonVictoriaAustralia,Department of Molecular and Translational SciencesMonash UniversityClaytonVictoriaAustralia
| | - Robert V. Bryant
- Department of GastroenterologyThe Queen Elizabeth HospitalWoodvilleSouth AustraliaAustralia,School of MedicineUniversity of AdelaideAdelaideSouth AustraliaAustralia
| | - Samuel P. Costello
- Department of GastroenterologyThe Queen Elizabeth HospitalWoodvilleSouth AustraliaAustralia,School of MedicineUniversity of AdelaideAdelaideSouth AustraliaAustralia
| | | | - Georgina L. Hold
- Microbiome Research Centre, St George & Sutherland Clinical SchoolUniversity of New South WalesSydneyNew South WalesAustralia
| | - Edward M. Giles
- Centre for Innate Immunity and Infectious DiseasesHudson Institute of Medical ResearchClaytonVictoriaAustralia,Department of Molecular and Translational SciencesMonash UniversityClaytonVictoriaAustralia,Department of PaediatricsMonash UniversityClaytonVictoriaAustralia
| | - Samuel C. Forster
- Centre for Innate Immunity and Infectious DiseasesHudson Institute of Medical ResearchClaytonVictoriaAustralia,Department of Molecular and Translational SciencesMonash UniversityClaytonVictoriaAustralia
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7
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Abstract
Gut microbiota can have diverse impacts on hosts, the nature of which often depend on the circumstances. For insect gut microbes, the quality and nature of host diets can be a significant force in swinging the pendulum from inconsequential to functionally important. In our study, we addressed whether beneficial microbes in one species impart similar functions to related species under identical conditions. Using fall armyworm (Spodoptera frugiperda), beet armyworm (Spodoptera exigua), and other noctuid hosts, we implemented an axenic rearing strategy and manipulated gut bacterial populations and dietary conditions. Our results revealed that some gut Enterococcus and Enterobacter isolates can facilitate utilization of a poor diet substrate by fall armyworm, but this was not the case for other more optimized diets. While Enterococcus provided benefits to fall armyworm, it was decidedly antagonistic to beet armyworm (Spodoptera exigua) under identical conditions. Unique isolates and bacterial introductions at early growth stages were critical to how both larval hosts performed. Our results provide robust evidence of the roles in which bacteria support lepidopteran larval growth, but also indicate that the directionality of these relationships can differ among congener hosts. IMPORTANCE Insects have intimate relationships with gut microbiota, where bacteria can contribute important functions to their invertebrate hosts. Lepidopterans are important insect pests, but how they engage with their gut bacteria and how that translates to impacts on the host are lacking. Here we demonstrate the facultative nature of gut microbiota in lepidopteran larvae and the importance of diet in driving mutualistic or antagonistic relationships. Using multiple lepidopteran species, we uncover that the same bacteria that can facilitate exploitation of a challenging diet in one host severely diminishes larval performance of another larval species. Additionally, we demonstrate the beneficial functions of gut microbiota on the hosts are not limited to one lineage, but rather multiple isolates can facilitate the exploitation of a suboptimal diet. Our results illuminate the context-dependent nature of the gut microbiomes in invertebrates, and how host-specific microbial engagement can produce dramatically different interactions.
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Cai H, Liao S, Li J, Liu Q, Luo S, Lv M, Lin X, Hu J, Zhang J, Qi N, Sun M. Single and Combined Effects of Clostridium butyricum and Coccidiosis Vaccine on Growth Performance and the Intestinal Microbiome of Broiler Chickens. Front Microbiol 2022; 13:811428. [PMID: 35547128 PMCID: PMC9083122 DOI: 10.3389/fmicb.2022.811428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 03/28/2022] [Indexed: 01/01/2023] Open
Abstract
Avian coccidiosis is an important intestinal protozoan disease that has caused major economic losses to the poultry industry. Clostridium butyricum can not only maintain the stability of the intestinal barrier, but can also improve the production performance of broiler chickens. We studied the effects of feeding C. butyricum alone, administration of coccidiosis vaccine alone, and the combined administration of C. butyricum and coccidiosis vaccine on body weight gain, feed consumption, and feed conversion ratio of broilers. Meanwhile, intestinal contents of 8- and 15-day-old broilers were collected, and their intestinal microbiome was characterized by high-throughput sequencing of the V3–V4 region of 16S rDNA. We analyzed the oocysts per gram values and lesion scores in the C. butyricum alone group, in a group challenged with the coccidiosis-causing parasite, Eimeria, and in groups simultaneously challenged Eimeria and pretreated with C. butyricum, the coccidiosis vaccine, or combined C. butyricum and coccidiosis vaccine. Intestinal tissue samples were collected from 32-day-old broilers for microbiome analysis. Our results showed that combination of C. butyricum with coccidiosis vaccine significantly improved the performance of broiler chickens and also significantly reduced the oocysts per gram value and intestinal lesions caused by Eimeria sp. infection. Furthermore, C. butyricum and coccidiosis vaccine administered alone or in combination significantly increased the relative abundance of the immune biomarker genus Barnesiella. The significant increase in the abundance of the Clostridia_UCG.014, Eubacterium coprostanoligenes group and Bacteroides was a key factor in controlling Eimeria sp. infection.
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Affiliation(s)
- Haiming Cai
- Zhaoqing/Maoming Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Shenquan Liao
- Zhaoqing/Maoming Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Juan Li
- Zhaoqing/Maoming Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Qihong Liu
- Jiangsu HFQ Biotechnology Co., Ltd., Haimen, China
| | - Shengjun Luo
- Zhaoqing/Maoming Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Qianyan Animal Health Care Co., Ltd, Guangzhou, China
| | - Minna Lv
- Zhaoqing/Maoming Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xuhui Lin
- Zhaoqing/Maoming Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Junjing Hu
- Zhaoqing/Maoming Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jianfei Zhang
- Zhaoqing/Maoming Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Nanshan Qi
- Zhaoqing/Maoming Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Mingfei Sun
- Zhaoqing/Maoming Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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9
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Couch CE, Epps CW. Host, microbiome, and complex space: applying population and landscape genetic approaches to gut microbiome research in wild populations. J Hered 2022; 113:221-234. [PMID: 34983061 DOI: 10.1093/jhered/esab078] [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: 09/28/2021] [Accepted: 01/03/2022] [Indexed: 11/14/2022] Open
Abstract
In recent years, emerging sequencing technologies and computational tools have driven a tidal wave of research on host-associated microbiomes, particularly the gut microbiome. These studies demonstrate numerous connections between the gut microbiome and vital host functions, primarily in humans, model organisms, and domestic animals. As the adaptive importance of the gut microbiome becomes clearer, interest in studying the gut microbiomes of wild populations has increased, in part due to the potential for discovering conservation applications. The study of wildlife gut microbiomes holds many new challenges and opportunities due to the complex genetic, spatial, and environmental structure of wild host populations, and the potential for these factors to interact with the microbiome. The emerging picture of adaptive coevolution in host-microbiome relationships highlights the importance of understanding microbiome variation in the context of host population genetics and landscape heterogeneity across a wide range of host populations. We propose a conceptual framework for understanding wildlife gut microbiomes in relation to landscape variables and host population genetics, including the potential of approaches derived from landscape genetics. We use this framework to review current research, synthesize important trends, highlight implications for conservation, and recommend future directions for research. Specifically, we focus on how spatial structure and environmental variation interact with host population genetics and microbiome variation in natural populations, and what we can learn from how these patterns of covariation differ depending on host ecological and evolutionary traits.
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Affiliation(s)
- Claire E Couch
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Clinton W Epps
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
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10
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De Santana CO, Spealman P, Melo V, Gresham D, de Jesus T, Oliveira E, Chinalia FA. Large-scale differences in diversity and functional adaptations of prokaryotic communities from conserved and anthropogenically impacted mangrove sediments in a tropical estuary. PeerJ 2021; 9:e12229. [PMID: 34631324 PMCID: PMC8465992 DOI: 10.7717/peerj.12229] [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: 04/13/2021] [Accepted: 09/08/2021] [Indexed: 12/24/2022] Open
Abstract
Mangroves are tropical ecosystems with strategic importance for climate change mitigation on local and global scales. They are also under considerable threat due to fragmentation degradation and urbanization. However, a complete understanding of how anthropogenic actions can affect microbial biodiversity and functional adaptations is still lacking. In this study, we carried out 16S rRNA gene sequencing analysis using sediment samples from two distinct mangrove areas located within the Serinhaém Estuary, Brazil. The first sampling area was located around the urban area of Ituberá, impacted by domestic sewage and urban runoff, while the second was an environmentally conserved site. Our results show significant changes in the structure of the communities between impacted and conserved sites. Biodiversity, along with functional potentials for the cycling of carbon, nitrogen, phosphorus and sulfur, were significantly increased in the urban area. We found that the environmental factors of organic matter, temperature and copper were significantly correlated with the observed shifts in the communities. Contributions of specific taxa to the functional potentials were negatively correlated with biodiversity, such that fewer numbers of taxa in the conserved area contributed to the majority of the metabolic potential. The results suggest that the contamination by urban runoff may have generated a different environment that led to the extinction of some taxa observed at the conserved site. In their place we found that the impacted site is enriched in prokaryotic families that are known human and animal pathogens, a clear negative effect of the urbanization process.
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Affiliation(s)
| | - Pieter Spealman
- Department of Biology, New York University, New York City, NY, United States of America
| | - Vania Melo
- Department of Biology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - David Gresham
- Department of Biology, New York University, New York City, NY, United States of America
| | - Taise de Jesus
- Department of Biology, State University of Feira de Santana, Feira de Santana, Bahia, Brazil
| | - Eddy Oliveira
- Department of Biology, State University of Feira de Santana, Feira de Santana, Bahia, Brazil
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11
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Gaio D, DeMaere MZ, Anantanawat K, Chapman TA, Djordjevic SP, Darling AE. Post-weaning shifts in microbiome composition and metabolism revealed by over 25 000 pig gut metagenome-assembled genomes. Microb Genom 2021; 7. [PMID: 34370660 PMCID: PMC8549361 DOI: 10.1099/mgen.0.000501] [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: 12/16/2022] Open
Abstract
Using a previously described metagenomics dataset of 27 billion reads, we reconstructed over 50 000 metagenome-assembled genomes (MAGs) of organisms resident in the porcine gut, 46.5 % of which were classified as >70 % complete with a <10 % contamination rate, and 24.4 % were nearly complete genomes. Here, we describe the generation and analysis of those MAGs using time-series samples. The gut microbial communities of piglets appear to follow a highly structured developmental programme in the weeks following weaning, and this development is robust to treatments including an intramuscular antibiotic treatment and two probiotic treatments. The high resolution we obtained allowed us to identify specific taxonomic ‘signatures’ that characterize the gut microbial development immediately after weaning. Additionally, we characterized the carbohydrate repertoire of the organisms resident in the porcine gut. We tracked the abundance shifts of 294 carbohydrate active enzymes, and identified the species and higher-level taxonomic groups carrying each of these enzymes in their MAGs. This knowledge can contribute to the design of probiotics and prebiotic interventions as a means to modify the piglet gut microbiome.
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Affiliation(s)
- Daniela Gaio
- iThree Institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Matthew Z DeMaere
- iThree Institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Kay Anantanawat
- iThree Institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Toni A Chapman
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales, Australia
| | - Steven P Djordjevic
- iThree Institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Aaron E Darling
- iThree Institute, University of Technology Sydney, Sydney, New South Wales, Australia
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12
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Barnes EM, Kutos S, Naghshineh N, Mesko M, You Q, Lewis JD. Assembly of the amphibian microbiome is influenced by the effects of land-use change on environmental reservoirs. Environ Microbiol 2021; 23:4595-4611. [PMID: 34190389 DOI: 10.1111/1462-2920.15653] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/15/2021] [Accepted: 06/28/2021] [Indexed: 01/04/2023]
Abstract
A growing focus in microbial ecology is understanding how beneficial microbiome function is created and maintained through various assembly mechanisms. This study explores the role of both the environment and disease in regulating the composition of microbial species in the soil and on amphibian hosts. We compared the microbial communities of Plethodon cinereus salamanders along a land-use gradient in the New York metropolitan area and paired these with associated soil cores. Additionally, we characterized the diversity of bacterial and fungal symbionts that putatively inhibit the pathogenic fungus Batrachochytrium dendrobatidis. We predicted that variation in skin microbial community composition would correlate with changes seen in the soil which functions as the regional species pool. We found that salamanders and soil share many microbial taxa but that these two communities exhibit differences in the relative abundances of the bacterial phyla Acidobacteria, Actinobacteria, and Proteobacteria and the fungal phyla Ascomycota and genus Basidiobolus. Microbial community composition varies with changes in land-use associated factors creating site-specific compositions. By employing a quantitative, null-based assembly model, we identified that dispersal limitation, variable selection, and drift guide assembly of microbes onto their skin, creating high dissimilarity between individuals with likely consequences in disease preventative function.
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Affiliation(s)
- Elle M Barnes
- Louis Calder Center - Biological Field Station, Fordham University, Armonk, NY, 10504, USA.,Department of Biological Sciences, Fordham University, Bronx, NY, 10458, USA
| | - Steve Kutos
- Louis Calder Center - Biological Field Station, Fordham University, Armonk, NY, 10504, USA.,Department of Biological Sciences, Fordham University, Bronx, NY, 10458, USA
| | - Nina Naghshineh
- Louis Calder Center - Biological Field Station, Fordham University, Armonk, NY, 10504, USA.,Department of Biological Sciences, Fordham University, Bronx, NY, 10458, USA
| | - Marissa Mesko
- Department of Biological Sciences, Fordham University, Bronx, NY, 10458, USA
| | - Qing You
- Department of Biological Sciences, Fordham University, Bronx, NY, 10458, USA
| | - J D Lewis
- Louis Calder Center - Biological Field Station, Fordham University, Armonk, NY, 10504, USA.,Department of Biological Sciences, Fordham University, Bronx, NY, 10458, USA
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13
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Toro F, Alarcón J, Márquez S, Capella J, Bahamonde P, Esperón F, Moreno-Switt A, Castro-Nallar E. Composition and structure of the skin microbiota of rorquals off the Eastern South Pacific. FEMS Microbiol Ecol 2021; 97:6179854. [PMID: 33749784 DOI: 10.1093/femsec/fiab050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 03/18/2021] [Indexed: 01/04/2023] Open
Abstract
Recent advances in high-throughput sequencing have enabled the large-scale interrogation of microbiota in the most diverse environments, including host-associated microbiota. This has led to the recognition that the skin microbiota of rorquals is specific and structurally different from that of the ocean. This study reveals the skin microbiome of 85 wild individuals along the Chilean coast belonging to Megaptera novaeangliae, Balaenoptera musculus and Balaenoptera physalus. Alpha diversity analysis revealed significant differences in richness and phylogenetic diversity, particularly among humpback whales from different locations and between blue and humpback whales. Beta diversity was partially explained by host and location but only accounting for up to 17% of microbiota variability (adjusted VPA). Overall, we found that microbiota composition was dominated by bacterial genera such as Cardiobacter, Moraxella, Tenacibaculum, Stenotrophomonas, Flavobacteria and Pseudomonas. We also found that no ASVs were associated with the three rorqual species. Up to four ASVs were specific of a location, indicating a great variability in the microbiota. To the best of our knowledge, this is the first report on the composition and structure of the skin microbiota of whales off the coast of Chile, providing a foundational dataset to understand the microbiota's role in rorquals.
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Affiliation(s)
- Frederick Toro
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Center for Bioinformatics and Integrative Biology, Avenida Republica 330, Santiago 8370186, Chile.,Doctorate in Conservation Medicine, Facultad de Ciencias de la Vida, Universidad Andres Bello, Departamento de Ecologia y Recursos Naturales, Avenida Republica 330, Santiago 8370186, Chile.,Panthalassa, Red de Estudios de Vertebrados Marinos de Chile Toesca 2002 P6, Santiago, Chile.,Facultad de Medicina Veterinaria y Recursos Naturales, Universidad Santo Tomás, Escuela de Medicina Veterinaria, Avenida Limonares 190, Viña del Mar, Chile
| | - Jaime Alarcón
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Center for Bioinformatics and Integrative Biology, Avenida Republica 330, Santiago 8370186, Chile
| | - Sebastián Márquez
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Center for Bioinformatics and Integrative Biology, Avenida Republica 330, Santiago 8370186, Chile
| | - Juan Capella
- Whalesound Ltda., Lautaro Navarro 1163, 2do piso. Punta Arenas, Chile.,Fundación Yubarta, Apartado Aéreo 33141, Cali, Colombia
| | - Paulina Bahamonde
- Melimoyu Ecosystem Research Institute, Avenida Kennedy 5682, Vitacura, Chile.,Universidad de Playa Ancha, HUB AMBIENTAL UPLA - Centro de Estudios Avanzados, Playa Ancha 850, Valparaíso, Chile
| | - Fernando Esperón
- Animal Health Research Center, INIA-CISA, Valdeolmos, Carretera Algete-El Casar de Talamanca, Km. 8,1, 28130 Valdeolmos, Madrid, Spain
| | - Andrea Moreno-Switt
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Avenida Las Condes 12.461, torre 3, oficina 205. Las Condes, Chile.,Facultad de Medicina Veterinaria, Pontificia Universidad Católica de Chile
| | - Eduardo Castro-Nallar
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Center for Bioinformatics and Integrative Biology, Avenida Republica 330, Santiago 8370186, Chile
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14
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Thompson AW, Ward AC, Sweeney CP, Sutherland KR. Host-specific symbioses and the microbial prey of a pelagic tunicate (Pyrosoma atlanticum). ISME COMMUNICATIONS 2021; 1:11. [PMID: 36721065 PMCID: PMC9723572 DOI: 10.1038/s43705-021-00007-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/12/2021] [Accepted: 02/24/2021] [Indexed: 02/03/2023]
Abstract
Pyrosomes are widely distributed pelagic tunicates that have the potential to reshape marine food webs when they bloom. However, their grazing preferences and interactions with the background microbial community are poorly understood. This is the first study of the marine microorganisms associated with pyrosomes undertaken to improve the understanding of pyrosome biology, the impact of pyrosome blooms on marine microbial systems, and microbial symbioses with marine animals. The diversity, relative abundance, and taxonomy of pyrosome-associated microorganisms were compared to seawater during a Pyrosoma atlanticum bloom in the Northern California Current System using high-throughput sequencing of the 16S rRNA gene, microscopy, and flow cytometry. We found that pyrosomes harbor a microbiome distinct from the surrounding seawater, which was dominated by a few novel taxa. In addition to the dominant taxa, numerous more rare pyrosome-specific microbial taxa were recovered. Multiple bioluminescent taxa were present in pyrosomes, which may be a source of the iconic pyrosome luminescence. We also discovered free-living marine microorganisms in association with pyrosomes, suggesting that pyrosome feeding impacts all microbial size classes but preferentially removes larger eukaryotic taxa. This study demonstrates that microbial symbionts and microbial prey are central to pyrosome biology. In addition to pyrosome impacts on higher trophic level marine food webs, the work suggests that pyrosomes also alter marine food webs at the microbial level through feeding and seeding of the marine microbial communities with their symbionts. Future efforts to predict pyrosome blooms, and account for their ecosystem impacts, should consider pyrosome interactions with marine microbial communities.
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Affiliation(s)
- Anne W Thompson
- Department of Biology, Portland State University, Portland, OR, USA.
| | - Anna C Ward
- Oregon Institute of Marine Biology, University of Oregon, Eugene, OR, USA
| | - Carey P Sweeney
- Department of Biology, Portland State University, Portland, OR, USA
| | - Kelly R Sutherland
- Oregon Institute of Marine Biology, University of Oregon, Eugene, OR, USA
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15
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Jack CN, Petipas RH, Cheeke TE, Rowland JL, Friesen ML. Microbial Inoculants: Silver Bullet or Microbial Jurassic Park? Trends Microbiol 2020; 29:299-308. [PMID: 33309525 DOI: 10.1016/j.tim.2020.11.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 01/04/2023]
Abstract
The appeal of using microbial inoculants to mediate plant traits and productivity in managed ecosystems has increased over the past decade, because microbes represent an alternative to fertilizers, pesticides, and direct genetic modification of plants. Using microbes bypasses many societal and environmental concerns because microbial products are considered a more sustainable and benign technology. In our desire to harness the power of plant-microbial symbioses, are we ignoring the possibility of precipitating microbial invasions, potentially setting ourselves up for a microbial Jurassic Park? Here, we outline potential negative consequences of microbial invasions and describe a set of practices (Testing, Regulation, Engineering, and Eradication, TREE) based on the four stages of invasion to prevent microbial inoculants from becoming invasive. We aim to stimulate discussion about best practices to proactively prevent microbial invasions.
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Affiliation(s)
- Chandra N Jack
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA.
| | - Renee H Petipas
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA
| | - Tanya E Cheeke
- Department of Biological Sciences, Washington State University, Richland, WA 99354, USA
| | - Jennifer L Rowland
- AAAS Science and Technology Policy Fellow hosted by United States Department of Agriculture- APHIS Plant Protection and Quarantine, Riverdale, MD 20737, USA
| | - Maren L Friesen
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA; Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA
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16
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Abstract
All multicellular organisms are associated with a diverse and specific community of microorganisms; consequently, the microbiome is of fundamental importance for health and fitness of the multicellular host. However, studies on microbiome contribution to host fitness are in their infancy, in particular, for less well-established hosts such as the moon jellyfish Aurelia aurita. Here, we studied the impact of the native microbiome on the asexual reproduction and on further fitness traits (health, growth, and feeding) of the basal metazoan due to induced changes in its microbiome. We observed significant impact on all fitness traits analyzed, in particular, in the absence of the protective microbial shield and when challenged with marine potentially pathogenic bacterial isolates. Notable is the identified crucial importance of the native microbiome for the generation of offspring, consequently affecting life cycle decisions. Thus, we conclude that the microbiome is essential for the maintenance of a healthy metaorganism. All multicellular organisms are associated with microbial communities, ultimately forming a metaorganism. Several studies conducted on well-established model organisms point to immunological, metabolic, and behavioral benefits of the associated microbiota for the host. Consequently, a microbiome can influence the physiology of a host; moreover, microbial community shifts can affect host health and fitness. The present study aimed to evaluate the significance and functional role of the native microbiota for life cycle transitions and fitness of the cnidarian moon jellyfish Aurelia aurita. A comprehensive host fitness experiment was conducted studying the polyp life stage and integrating 12 combinations of treatments with microbiota modification (sterile conditions, foreign food bacteria, and potential pathogens). Asexual reproduction, e.g., generation of daughter polyps, and the formation and release of ephyrae were highly affected in the absence of the native microbiota, ultimately resulting in a halt of strobilation and ephyra release. Assessment of further fitness traits showed that health, growth, and feeding rate were decreased in the absence and upon community changes of the native microbiota, e.g., when challenged with selected bacteria. Moreover, changes in microbial community patterns were detected by 16S rRNA amplicon sequencing during the course of the experiment. This demonstrated that six operational taxonomic units (OTUs) significantly correlated and explained up to 97% of fitness data variability, strongly supporting the association of impaired fitness with the absence/presence of specific bacteria. Conclusively, our study provides new insights into the importance and function of the microbiome for asexual reproduction, health, and fitness of the basal metazoan A. aurita.
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17
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Willis KA, Stewart JD, Ambalavanan N. Recent advances in understanding the ecology of the lung microbiota and deciphering the gut-lung axis. Am J Physiol Lung Cell Mol Physiol 2020. [PMID: 32877224 PMCID: PMC7642895 DOI: 10.1152/ajplung.00360.2020 10.1152/ajplung.00360.2020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
A rapidly expanding new field of lung research has been produced by the emergence of culture-independent next-generation sequencing technologies. While pulmonary microbiome research lags behind the exploration of the microbiome in other organ systems, the field is maturing and has recently produced multiple exciting discoveries. In this mini-review, we will explore recent advances in our understanding of the lung microbiome and the gut-lung axis from an ecological perspective.
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Affiliation(s)
- Kent A. Willis
- 1Division of Neonatology, Department of Pediatrics, College of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Justin D. Stewart
- 2Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Namasivayam Ambalavanan
- 1Division of Neonatology, Department of Pediatrics, College of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama,3Department of Pathology, College of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama,4Department of Cell, Developmental and Integrative Biology, College of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama
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18
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Jiménez RR, Alvarado G, Sandoval J, Sommer S. Habitat disturbance influences the skin microbiome of a rediscovered neotropical-montane frog. BMC Microbiol 2020; 20:292. [PMID: 32962670 PMCID: PMC7509932 DOI: 10.1186/s12866-020-01979-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 09/15/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The skin microbiome serves as a first line defense against pathogens in vertebrates. In amphibians, it has the potential to protect against the chytrid fungus Batrachochytrium dendrobatis (Bd), a likely agent of amphibian declines. Alteration of the microbiome associated with unfavorable environmental changes produced by anthropogenic activities may make the host more susceptible to pathogens. Some amphibian species that were thought to be "extinct" have been rediscovered years after population declines in the late 1980s probably due to evolved Bd-resistance and are now threatened by anthropogenic land-use changes. Understanding the effects of habitat disturbance on the host skin microbiome is relevant for understanding the health of these species, along with its susceptibility to pathogens such as Bd. Here, we investigate the influence of habitat alteration on the skin bacterial communities as well as specifically the putative Bd-inhibitory bacterial communities of the montane frog Lithobates vibicarius. This species, after years of not being observed, was rediscovered in small populations inhabiting undisturbed and disturbed landscapes, and with continuous presence of Bd. RESULTS We found that cutaneous bacterial communities of tadpoles and adults differed between undisturbed and disturbed habitats. The adults from disturbed habitats exhibited greater community dispersion than those from undisturbed habitats. We observed a higher richness of putative Bd-inhibitory bacterial strains in adults from disturbed habitats than in those from undisturbed habitats, as well as a greater number of these potential protective bacteria with a high relative abundance. CONCLUSIONS Our findings support the microbial "Anna Karenina principle", in which disturbance is hypothesized to cause greater microbial dispersion in communities, a so-called dysbiosis, which is a response of animal microbiomes to stress factors that decrease the ability of the host or its microbiome to regulate community composition. On the positive side, the high richness and relative abundance of putative Bd-inhibitory bacteria may indicate the development of a defense mechanism that enhances Bd-protection, attributed to a co-occurrence of more than 30-years of host and pathogen in these disturbed habitats. Our results provide important insight into the influence of human-modified landscapes on the skin microbiome and health implications of Bd-survivor species.
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Affiliation(s)
- Randall R Jiménez
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Albert-Einstein Allee 11, 89069, Ulm, Germany.
| | - Gilbert Alvarado
- Laboratory of Comparative Wildlife Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, Av. Orlando Marques de Paiva 87, São Paulo, Brazil
- Laboratory of Experimental and Comparative Pathology (LAPECOM), Biology School, University of Costa Rica, San José, Costa Rica
| | - José Sandoval
- Laboratory of Experimental and Comparative Pathology (LAPECOM), Biology School, University of Costa Rica, San José, Costa Rica
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Albert-Einstein Allee 11, 89069, Ulm, Germany
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Willis KA, Stewart JD, Ambalavanan N. Recent advances in understanding the ecology of the lung microbiota and deciphering the gut-lung axis. Am J Physiol Lung Cell Mol Physiol 2020; 319:L710-L716. [PMID: 32877224 DOI: 10.1152/ajplung.00360.2020] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A rapidly expanding new field of lung research has been produced by the emergence of culture-independent next-generation sequencing technologies. While pulmonary microbiome research lags behind the exploration of the microbiome in other organ systems, the field is maturing and has recently produced multiple exciting discoveries. In this mini-review, we will explore recent advances in our understanding of the lung microbiome and the gut-lung axis from an ecological perspective.
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Affiliation(s)
- Kent A Willis
- Division of Neonatology, Department of Pediatrics, College of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Justin D Stewart
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Namasivayam Ambalavanan
- Division of Neonatology, Department of Pediatrics, College of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama.,Department of Pathology, College of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama.,Department of Cell, Developmental and Integrative Biology, College of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama
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20
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Kruger A. Frog Skin Microbiota Vary With Host Species and Environment but Not Chytrid Infection. Front Microbiol 2020; 11:1330. [PMID: 32670233 PMCID: PMC7328345 DOI: 10.3389/fmicb.2020.01330] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 05/25/2020] [Indexed: 01/15/2023] Open
Abstract
Describing the structure and function of the amphibian cutaneous microbiome has gained importance with the spread of Batrachochytrium dendrobatidis (Bd), the fungal pathogen that can cause the skin disease chytridiomycosis. Sampling amphibian skin microbiota is needed to characterize current infection status and to help predict future susceptibility to Bd based on microbial composition since some skin microbes have antifungal capabilities that may confer disease resistance. Here, I use 16S rRNA sequencing to describe the composition and structure of the cutaneous microbiota of six species of amphibians. Frog skin samples were also tested for Bd, and I found 11.8% Bd prevalence among all individuals sampled (n = 76). Frog skin microbiota varied by host species and sampling site, but did not differ among Bd-positive and Bd-negative individuals. These results suggest that bacterial composition reflects host species and the environment, but does not reflect Bd infection among the species sampled here. Of the bacterial OTUs identified using an indicator species analysis as strongly associated with amphibians, significantly more indicator OTUs were putative anti-Bd taxa than would be expected based on the proportion of anti-Bd OTUs among all frog OTUs, suggesting strong associations between host species and anti-Bd OTUs. This relationship may partially explain why some of these frogs are asymptomatic carriers of Bd, but more work is needed to determine the other factors that contribute to interspecific variation in Bd susceptibility. This work provides important insights on inter- and intra-specific variation in microbial community composition, putative function, and disease dynamics in populations of amphibians that appear to be coexisting with Bd.
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Affiliation(s)
- Ariel Kruger
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ, United States
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