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Ochoa-Sánchez M, Acuña Gomez EP, Ramírez-Fenández L, Eguiarte LE, Souza V. Current knowledge of the Southern Hemisphere marine microbiome in eukaryotic hosts and the Strait of Magellan surface microbiome project. PeerJ 2023; 11:e15978. [PMID: 37810788 PMCID: PMC10557944 DOI: 10.7717/peerj.15978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/07/2023] [Indexed: 10/10/2023] Open
Abstract
Host-microbe interactions are ubiquitous and play important roles in host biology, ecology, and evolution. Yet, host-microbe research has focused on inland species, whereas marine hosts and their associated microbes remain largely unexplored, especially in developing countries in the Southern Hemisphere. Here, we review the current knowledge of marine host microbiomes in the Southern Hemisphere. Our results revealed important biases in marine host species sampling for studies conducted in the Southern Hemisphere, where sponges and marine mammals have received the greatest attention. Sponge-associated microbes vary greatly across geographic regions and species. Nevertheless, besides taxonomic heterogeneity, sponge microbiomes have functional consistency, whereas geography and aging are important drivers of marine mammal microbiomes. Seabird and macroalgal microbiomes in the Southern Hemisphere were also common. Most seabird microbiome has focused on feces, whereas macroalgal microbiome has focused on the epibiotic community. Important drivers of seabird fecal microbiome are aging, sex, and species-specific factors. In contrast, host-derived deterministic factors drive the macroalgal epibiotic microbiome, in a process known as "microbial gardening". In turn, marine invertebrates (especially crustaceans) and fish microbiomes have received less attention in the Southern Hemisphere. In general, the predominant approach to study host marine microbiomes has been the sequencing of the 16S rRNA gene. Interestingly, there are some marine holobiont studies (i.e., studies that simultaneously analyze host (e.g., genomics, transcriptomics) and microbiome (e.g., 16S rRNA gene, metagenome) traits), but only in some marine invertebrates and macroalgae from Africa and Australia. Finally, we introduce an ongoing project on the surface microbiome of key species in the Strait of Magellan. This is an international project that will provide novel microbiome information of several species in the Strait of Magellan. In the short-term, the project will improve our knowledge about microbial diversity in the region, while long-term potential benefits include the use of these data to assess host-microbial responses to the Anthropocene derived climate change.
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Affiliation(s)
- Manuel Ochoa-Sánchez
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | - Lia Ramírez-Fenández
- Facultad de Recursos Naturales Renovables, Universidad Arturo Prat, Iquique, Chile
- Centro de Desarrollo de Biotecnología Industrial y Bioproductos, Antofagasta, Chile
| | - Luis E. Eguiarte
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Valeria Souza
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
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Pereida-Aguilar JC, Barragán-Vargas C, Domínguez-Sánchez C, Álvarez-Martínez RC, Acevedo-Whitehouse K. Bacterial dysbiosis and epithelial status of the California sea lion (Zalophus californianus) in the Gulf of California. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 113:105474. [PMID: 37356747 DOI: 10.1016/j.meegid.2023.105474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 06/11/2023] [Accepted: 06/22/2023] [Indexed: 06/27/2023]
Abstract
Despite the high incidence of urogenital carcinoma (UGC) in California sea lions stranded along California, no UGC has been reported in other areas of their distribution; however, cell morphologies typical of premalignant states have been found. Risk factors for UGC include high of organochlorines and infection with a gammaherpesvirus, OtHV-1, but the importance of the bacteriome for epithelial status remains unknown. We characterized the genital bacteriome of adult female California sea lions along their distribution in the Gulf of California and examined whether the diversity and abundance of the bacteriome varied spatially, whether there were detectable differences in the bacteriome between healthy and altered epithelia, and whether the bacteriome was different in California sea lions infected with OtHV-1 or papillomavirus. We detected 2270 ASVs in the genital samples, of which 35 met the criteria for inclusion in the core bacteriome. Fusobacteriia and Clostridia were present in all samples, at high abundances, and Actinobacteria, Alphaproteobacteria, and Campylobacteria were also well-represented. Alpha diversity and abundance of the California sea lion genital bacteriome varied geographically. The abundance of bacterial ASVs varied depending on the genital epithelial status and inflammation, with differences driven by classes Fusobacteriia, Clostridia, Campylobacteria and Alphaproteobacteria. Alpha diversity and abundance were lowest in samples in which OtHV-1 was detected, and highest those with papillomavirus. Our study is the first investigation of how the bacteriome is related to epithelial status in a wild marine species prone to developing cancer.
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Affiliation(s)
- Juan Carlos Pereida-Aguilar
- Unit for Basic and Applied Microbiology, School of Natural Sciences, Autonomous University of Queretaro, Santiago de Queretaro 76146, Mexico
| | - Cecilia Barragán-Vargas
- Unit for Basic and Applied Microbiology, School of Natural Sciences, Autonomous University of Queretaro, Santiago de Queretaro 76146, Mexico
| | - Carlos Domínguez-Sánchez
- Unit for Basic and Applied Microbiology, School of Natural Sciences, Autonomous University of Queretaro, Santiago de Queretaro 76146, Mexico
| | - Roberto Carlos Álvarez-Martínez
- Unit for Basic and Applied Microbiology, School of Natural Sciences, Autonomous University of Queretaro, Santiago de Queretaro 76146, Mexico
| | - Karina Acevedo-Whitehouse
- Unit for Basic and Applied Microbiology, School of Natural Sciences, Autonomous University of Queretaro, Santiago de Queretaro 76146, Mexico.
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Foo A, Cerdeira L, Hughes GL, Heinz E. Recovery of metagenomic data from the Aedes aegypti microbiome using a reproducible snakemake pipeline: MINUUR. Wellcome Open Res 2023; 8:131. [PMID: 37577055 PMCID: PMC10412942 DOI: 10.12688/wellcomeopenres.19155.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2023] [Indexed: 08/15/2023] Open
Abstract
Background: Ongoing research of the mosquito microbiome aims to uncover novel strategies to reduce pathogen transmission. Sequencing costs, especially for metagenomics, are however still significant. A resource that is increasingly used to gain insights into host-associated microbiomes is the large amount of publicly available genomic data based on whole organisms like mosquitoes, which includes sequencing reads of the host-associated microbes and provides the opportunity to gain additional value from these initially host-focused sequencing projects. Methods: To analyse non-host reads from existing genomic data, we developed a snakemake workflow called MINUUR (Microbial INsights Using Unmapped Reads). Within MINUUR, reads derived from the host-associated microbiome were extracted and characterised using taxonomic classifications and metagenome assembly followed by binning and quality assessment. We applied this pipeline to five publicly available Aedes aegypti genomic datasets, consisting of 62 samples with a broad range of sequencing depths. Results: We demonstrate that MINUUR recovers previously identified phyla and genera and is able to extract bacterial metagenome assembled genomes (MAGs) associated to the microbiome. Of these MAGS, 42 are high-quality representatives with >90% completeness and <5% contamination. These MAGs improve the genomic representation of the mosquito microbiome and can be used to facilitate genomic investigation of key genes of interest. Furthermore, we show that samples with a high number of KRAKEN2 assigned reads produce more MAGs. Conclusions: Our metagenomics workflow, MINUUR, was applied to a range of Aedes aegypti genomic samples to characterise microbiome-associated reads. We confirm the presence of key mosquito-associated symbionts that have previously been identified in other studies and recovered high-quality bacterial MAGs. In addition, MINUUR and its associated documentation are freely available on GitHub and provide researchers with a convenient workflow to investigate microbiome data included in the sequencing data for any applicable host genome of interest.
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Affiliation(s)
- Aidan Foo
- Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Louise Cerdeira
- Vector Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Grant L. Hughes
- Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Eva Heinz
- Vector Biology and Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
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Filek K, Lebbe L, Willems A, Chaerle P, Vyverman W, Žižek M, Bosak S. More than just hitchhikers: a survey of bacterial communities associated with diatoms originating from sea turtles. FEMS Microbiol Ecol 2022; 98:6693935. [PMID: 36073481 DOI: 10.1093/femsec/fiac104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/15/2022] [Accepted: 09/02/2022] [Indexed: 12/14/2022] Open
Abstract
Diatoms and bacteria are known for being the first colonizers of submerged surfaces including the skin of marine reptiles. Sea turtle carapace and skin harbor diverse prokaryotic and eukaryotic microbes, including several epizoic diatoms. However, the importance of diatom-bacteria associations is hardly investigated in biofilms associated with animal hosts. This study provides an inventory of diatoms, bacteria and diatom-associated bacteria originating from loggerhead sea turtles using both metabarcoding and culturing approaches. Amplicon sequencing of the carapace and skin samples chloroplast gene rbcL and 16S rRNA gene detected, in total, 634 diatom amplicon sequence variants (ASVs) and 3661 bacterial ASVs, indicating high diversity. Cultures of putative epizoic and non-epizoic diatoms contained 458 bacterial ASVs and their bacterial assemblages reflected those of their host. Diatom strains allowed for enrichment and isolation of bacterial families rarely observed on turtles, such as Marinobacteraceae, Alteromonadaceae and Alcanivoracaceae. When accounting for phylogenetic relationships between bacterial ASVs, we observed that related diatom genera might retain similar microbial taxa in culture, regardless of the turtle's skin or carapace source. These data provide deeper insights into the sea turtle-associated microbial communities, and reveal the potential of epizoic biofilms as a source of novel microbes and possibly important diatom-bacteria associations.
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Affiliation(s)
- Klara Filek
- University of Zagreb, Faculty of Science, Department of Biology, Rooseveltov trg 6, 10000 Zagreb, Croatia
| | - Liesbeth Lebbe
- Ghent University, Faculty of Sciences, Department of Biochemistry and Microbiology, Laboratory of Microbiology, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Anne Willems
- Ghent University, Faculty of Sciences, Department of Biochemistry and Microbiology, Laboratory of Microbiology, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Peter Chaerle
- Ghent University, Faculty of Sciences, Department of Biology, Protistology and Aquatic Ecology, Krijgslaan 281-S8, B-9000 Ghent, Belgium
| | - Wim Vyverman
- Ghent University, Faculty of Sciences, Department of Biology, Protistology and Aquatic Ecology, Krijgslaan 281-S8, B-9000 Ghent, Belgium
| | - Marta Žižek
- University of Zagreb, Faculty of Science, Department of Biology, Rooseveltov trg 6, 10000 Zagreb, Croatia
| | - Sunčica Bosak
- University of Zagreb, Faculty of Science, Department of Biology, Rooseveltov trg 6, 10000 Zagreb, Croatia
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Gadoin E, Desnues C, d'Orbcastel ER, Bouvier T, Auguet JC, Dagorn L, Moroh JL, Adingra A, Bettarel Y. Fishing for the Microbiome of Tropical Tuna. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02096-4. [PMID: 35962839 DOI: 10.1007/s00248-022-02096-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Although tunas represent a significant part of the global fish economy and a major nutritional resource worldwide, their microbiome still remains poorly documented. Here, we conducted an analysis of the taxonomic composition of the bacterial communities inhabiting the gut, skin, and liver of two most consumed tropical tuna species (skipjack and yellowfin), from individuals caught in the Atlantic and Indian oceans. We hypothesized that each organ harbors a specific microbial assemblage whose composition might vary according to different biotic (sex, species) and/or abiotic (environmental) factors. Our results revealed that the composition of the tuna microbiome was totally independent of fish sex, regardless of the species and ocean considered. Instead, the main determinants of observed diversity were (i) tuna species for the gut and (ii) sampling site for the skin mucus layer and (iii) a combination of both parameters for the liver. Interestingly, 4.5% of all amplicon sequence variants (ASV) were shared by the three organs, highlighting the presence of a core-microbiota whose most abundant representatives belonged to the genera Mycoplasma, Cutibacterium, and Photobacterium. Our study also revealed the presence of a unique and diversified bacterial assemblage within the tuna liver, comprising a substantial proportion of potential histamine-producing bacteria, well known for their pathogenicity and their contribution to fish poisoning cases. These results indicate that this organ is an unexplored microbial niche whose role in the health of both the host and consumers remains to be elucidated.
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Affiliation(s)
- Elsa Gadoin
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Place Eugène Bataillon - Bat 24, 34095, Montpellier, France
| | - Christelle Desnues
- Institut Méditerranéen d'Océanologie (MIO), Aix-Marseille Université, Université de Toulon, CNRS, Campus Technologique Et Scientifique de Luminy, 163 avenue de Luminy - Bat. Méditerranée, 13288, Marseille, IRD, France
| | - Emmanuelle Roque d'Orbcastel
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Place Eugène Bataillon - Bat 24, 34095, Montpellier, France
| | - Thierry Bouvier
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Place Eugène Bataillon - Bat 24, 34095, Montpellier, France
| | - Jean-Christophe Auguet
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Place Eugène Bataillon - Bat 24, 34095, Montpellier, France
| | - Laurent Dagorn
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Place Eugène Bataillon - Bat 24, 34095, Montpellier, France
| | - Jean-Luc Moroh
- Université Peleforo Gbon Coulibaly, Korhogo, Ivory Coast
| | - Antoinette Adingra
- Centre de Recherches Océanologiques (CRO) - 29 rue des pêcheurs, Zone 3, Treichville, BP V 18 00225, Abidjan, Ivory Coast
| | - Yvan Bettarel
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Place Eugène Bataillon - Bat 24, 34095, Montpellier, France.
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Kanjer L, Filek K, Mucko M, Majewska R, Gračan R, Trotta A, Panagopoulou A, Corrente M, Di Bello A, Bosak S. Surface microbiota of Mediterranean loggerhead sea turtles unraveled by 16S and 18S amplicon sequencing. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.907368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The loggerhead sea turtle is considered a keystone species with a major ecological role in Mediterranean marine environment. As is the case with other wild reptiles, their outer microbiome is rarely studied. Although there are several studies on sea turtle’s macro-epibionts and endo-microbiota, there has been little research on epibiotic microbiota associated with turtle skin and carapace. Therefore we aimed to provide the identification of combined epibiotic eukaryotic, bacterial and archaeal microbiota on Mediterranean loggerhead sea turtles. In this study, we sampled skins and carapaces of 26 loggerheads from the Mediterranean Sea during 2018 and 2019. To investigate the overall microbial diversity and composition, amplicon sequencing of 16S and 18S rRNA genes was performed. We found that the Mediterranean loggerhead sea turtle epibiotic microbiota is a reservoir of a vast variety of microbial species. Microbial communities mostly varied by different locations and seas, while within bacterial communities’ significant difference was observed between sampled body sites (carapace vs. skin). In terms of relative abundance, Proteobacteria and Bacteroidota were the most represented phyla within prokaryotes, while Alveolata and Stramenopiles thrived among eukaryotes. This study, besides providing a first survey of microbial eukaryotes on loggerheads via metabarcoding, identifies fine differences within both bacterial and eukaryotic microbial communities that seem to reflect the host anatomy and habitat. Multi-domain epi-microbiome surveys provide additional layers of information that are complementary with previous morphological studies and enable better understanding of the biology and ecology of these vulnerable marine reptiles.
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Pratte ZA, Perry C, Dove ADM, Hoopes LA, Ritchie KB, Hueter RE, Fischer C, Newton AL, Stewart FJ. Microbiome structure in large pelagic sharks with distinct feeding ecologies. Anim Microbiome 2022; 4:17. [PMID: 35246276 PMCID: PMC8895868 DOI: 10.1186/s42523-022-00168-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 02/16/2022] [Indexed: 02/07/2023] Open
Abstract
Background Sharks play essential roles in ocean food webs and human culture, but also face population declines worldwide due to human activity. The relationship between sharks and the microbes on and in the shark body is unclear, despite research on other animals showing the microbiome as intertwined with host physiology, immunity, and ecology. Research on shark-microbe interactions faces the significant challenge of sampling the largest and most elusive shark species. We leveraged a unique sampling infrastructure to compare the microbiomes of two apex predators, the white (Carcharodon carcharias) and tiger shark (Galeocerdo cuvier), to those of the filter-feeding whale shark (Rhincodon typus), allowing us to explore the effects of feeding mode on intestinal microbiome diversity and metabolic function, and environmental exposure on the diversity of microbes external to the body (on the skin, gill). Results The fecal microbiomes of white and whale sharks were highly similar in taxonomic and gene category composition despite differences in host feeding mode and diet. Fecal microbiomes from these species were also taxon-poor compared to those of many other vertebrates and were more similar to those of predatory teleost fishes and toothed whales than to those of filter-feeding baleen whales. In contrast, microbiomes of external body niches were taxon-rich and significantly influenced by diversity in the water column microbiome. Conclusions These results suggest complex roles for host identity, diet, and environmental exposure in structuring the shark microbiome and identify a small, but conserved, number of intestinal microbial taxa as potential contributors to shark physiology. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-022-00168-x.
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Affiliation(s)
- Zoe A Pratte
- Department of Microbiology & Cell Biology, Montanta State University, 621 Leon Johnson Hall, Bozeman, MT, 59717, USA.
| | - Cameron Perry
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | | | | | - Kim B Ritchie
- University of South Carolina Beaufort, Beaufort, SC, USA
| | - Robert E Hueter
- OCEARCH, 1790 Bonanza Drive, Park City, UT, USA.,Center for Shark Research, Mote Marine Laboratory, 1600 Ken Thompson Parkway, Sarasota, FL, USA
| | | | - Alisa L Newton
- Disney's Animals, Science and Environment, 1200 N. Savannah Circle East, Bay Lake, FL, USA
| | - Frank J Stewart
- Department of Microbiology & Cell Biology, Montanta State University, 621 Leon Johnson Hall, Bozeman, MT, 59717, USA.,Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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Saldarriaga-Córdoba M, Irgang R, Avendaño-Herrera R. Comparison between genome sequences of Chilean Tenacibaculum dicentrarchi isolated from red conger eel (Genypterus chilensis) and Atlantic salmon (Salmo salar) focusing on bacterial virulence determinants. JOURNAL OF FISH DISEASES 2021; 44:1843-1860. [PMID: 34369594 DOI: 10.1111/jfd.13503] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/20/2021] [Accepted: 07/23/2021] [Indexed: 06/13/2023]
Abstract
Tenacibaculum dicentrarchi is an emerging pathogen for salmonid cultures and red conger eel (Genypterus chilensis) in Chile, causing high economic losses not only in Chile but also to the global salmon industry. Infected fish show severe gross skin lesions that are sometimes accompanied by bone exposure. Despite pathogenicity demonstrated by Koch's postulates, no knowledge is currently available regarding the virulence machinery of T. dicentrarchi strains. Comparisons between the genome sequences of the eight T. dicentrarchi strains obtained from G. chilensis and Atlantic salmon (Salmo salar) provide insights on the existence of genomic diversity within this bacterium. The T. dicentrarchi type strain 3509T was used as a reference genome. Depending on the T. dicentrarchi strain, the discovered diversity included genes associated with iron acquisition mechanisms, copper homeostasis encoding, resistance to tetracycline and fluoroquinolones, pathogenic genomic islands and phages. Interestingly, genes encoding the T9SS membrane protein PorP/SprF were retrieved in all of the analysed T. dicentrarchi strains, regardless of the host fish (i.e. red conger eel or Atlantic salmon). However, the T6SS core component protein VgrG was identified in only one Atlantic salmon strain. Three types of peptidase genes and proteins associated with quorum sensing were detected in all of the T. dicentrarchi strains. In turn, all eight strains presented a total of 17 proteins associated with biofilm formation, which was previously confirmed through physiological studies. This comparative analysis will help elucidate and describe the genes and pathways that are likely involved in the virulence process of T. dicentrarchi. All or part of these predicted genes could aid the pathogen during the infective process in fish, making further physiological research necessary for clarification.
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Affiliation(s)
- Mónica Saldarriaga-Córdoba
- Centro de Investigación en Recursos Naturales y Sustentabilidad, Universidad Bernardo O'Higgins, Santiago, Chile
| | - Rute Irgang
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Viña del Mar, Chile
- Centro FONDAP, Interdisciplinary Center for Aquaculture Research (INCAR), Universidad Andrés Bello, Viña del Mar, Chile
| | - Ruben Avendaño-Herrera
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Viña del Mar, Chile
- Centro FONDAP, Interdisciplinary Center for Aquaculture Research (INCAR), Universidad Andrés Bello, Viña del Mar, Chile
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay, Chile
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Filek K, Trotta A, Gračan R, Di Bello A, Corrente M, Bosak S. Characterization of oral and cloacal microbial communities of wild and rehabilitated loggerhead sea turtles (Caretta caretta). Anim Microbiome 2021; 3:59. [PMID: 34479653 PMCID: PMC8417999 DOI: 10.1186/s42523-021-00120-5] [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] [Received: 04/27/2021] [Accepted: 08/24/2021] [Indexed: 02/07/2023] Open
Abstract
Background Microbial communities of wild animals are being increasingly investigated to provide information about the hosts’ biology and promote conservation. Loggerhead sea turtles (Caretta caretta) are a keystone species in marine ecosystems and are considered vulnerable in the IUCN Red List, which led to growing efforts in sea turtle conservation by rescue centers around the world. Understanding the microbial communities of sea turtles in the wild and how affected they are by captivity, is one of the stepping stones in improving the conservation efforts. Describing oral and cloacal microbiota of wild animals could shed light on the previously unknown aspects of sea turtle holobiont biology, ecology, and contribute to best practices for husbandry conditions. Results We describe the oral and cloacal microbiota of Mediterranean loggerhead sea turtles by 16S rRNA gene sequencing to compare the microbial communities of wild versus turtles in, or after, rehabilitation at the Adriatic Sea rescue centers and clinics. Our results show that the oral microbiota is more sensitive to environmental shifts than the cloacal microbiota, and that it does retain a portion of microbial taxa regardless of the shift from the wild and into rehabilitation. Additionally, Proteobacteria and Bacteroidetes dominated oral and cloacal microbiota, while Kiritimatiellaeota were abundant in cloacal samples. Unclassified reads were abundant in the aforementioned groups, which indicates high incidence of yet undiscovered bacteria of the marine reptile microbial communities. Conclusions We provide the first insights into the oral microbial communities of wild and rehabilitated loggerhead sea turtles, and establish a framework for quick and non-invasive sampling of oral and cloacal microbial communities, useful for the expansion of the sample collection in wild loggerhead sea turtles. Finally, our investigation of effects of captivity on the gut-associated microbial community provides a baseline for studying the impact of husbandry conditions on turtles’ health and survival upon their return to the wild. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00120-5.
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Affiliation(s)
- Klara Filek
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10 000, Zagreb, Croatia
| | - Adriana Trotta
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Str. Prov. Per Casamassima Km 3, 70010, Valenzano, BA, Italy
| | - Romana Gračan
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10 000, Zagreb, Croatia
| | - Antonio Di Bello
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Str. Prov. Per Casamassima Km 3, 70010, Valenzano, BA, Italy
| | - Marialaura Corrente
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Str. Prov. Per Casamassima Km 3, 70010, Valenzano, BA, Italy
| | - Sunčica Bosak
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10 000, Zagreb, Croatia.
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DeCandia AL, Cassidy KA, Stahler DR, Stahler EA, vonHoldt BM. Social environment and genetics underlie body site-specific microbiomes of Yellowstone National Park gray wolves ( Canis lupus). Ecol Evol 2021; 11:9472-9488. [PMID: 34306636 PMCID: PMC8293786 DOI: 10.1002/ece3.7767] [Citation(s) in RCA: 3] [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: 02/16/2021] [Revised: 04/20/2021] [Accepted: 05/24/2021] [Indexed: 12/17/2022] Open
Abstract
The host-associated microbiome is an important player in the ecology and evolution of species. Despite growing interest in the medical, veterinary, and conservation communities, there remain numerous questions about the primary factors underlying microbiota, particularly in wildlife. We bridged this knowledge gap by leveraging microbial, genetic, and observational data collected in a wild, pedigreed population of gray wolves (Canis lupus) inhabiting Yellowstone National Park. We characterized body site-specific microbes across six haired and mucosal body sites (and two fecal samples) using 16S rRNA amplicon sequencing. At the phylum level, we found that the microbiome of gray wolves primarily consists of Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria, consistent with previous studies within Mammalia and Canidae. At the genus level, we documented body site-specific microbiota with functions relevant to microenvironment and local physiological processes. We additionally employed observational and RAD sequencing data to examine genetic, demographic, and environmental correlates of skin and gut microbiota. We surveyed individuals across several levels of pedigree relationships, generations, and social groups, and found that social environment (i.e., pack) and genetic relatedness were two primary factors associated with microbial community composition to differing degrees between body sites. We additionally reported body condition and coat color as secondary factors underlying gut and skin microbiomes, respectively. We concluded that gray wolf microbiota resemble similar host species, differ between body sites, and are shaped by numerous endogenous and exogenous factors. These results provide baseline information for this long-term study population and yield important insights into the evolutionary history, ecology, and conservation of wild wolves and their associated microbes.
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Affiliation(s)
- Alexandra L. DeCandia
- Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNJUSA
- Smithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | - Kira A. Cassidy
- Yellowstone Center for ResourcesNational Park ServiceYellowstone National ParkWYUSA
| | - Daniel R. Stahler
- Yellowstone Center for ResourcesNational Park ServiceYellowstone National ParkWYUSA
| | - Erin A. Stahler
- Yellowstone Center for ResourcesNational Park ServiceYellowstone National ParkWYUSA
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11
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Doña J, Virrueta Herrera S, Nyman T, Kunnasranta M, Johnson KP. Patterns of Microbiome Variation Among Infrapopulations of Permanent Bloodsucking Parasites. Front Microbiol 2021; 12:642543. [PMID: 33935998 PMCID: PMC8085356 DOI: 10.3389/fmicb.2021.642543] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/26/2021] [Indexed: 12/22/2022] Open
Abstract
While interspecific variation in microbiome composition can often be readily explained by factors such as host species identity, there is still limited knowledge of how microbiomes vary at scales lower than the species level (e.g., between individuals or populations). Here, we evaluated variation in microbiome composition of individual parasites among infrapopulations (i.e., populations of parasites of the same species living on a single host individual). To address this question, we used genome-resolved and shotgun metagenomic data of 17 infrapopulations (balanced design) of the permanent, bloodsucking seal louse Echinophthirius horridus sampled from individual Saimaa ringed seals Pusa hispida saimensis. Both genome-resolved and read-based metagenomic classification approaches consistently show that parasite infrapopulation identity is a significant factor that explains both qualitative and quantitative patterns of microbiome variation at the intraspecific level. This study contributes to the general understanding of the factors driving patterns of intraspecific variation in microbiome composition, especially of bloodsucking parasites, and has implications for understanding how well-known processes occurring at higher taxonomic levels, such as phylosymbiosis, might arise in these systems.
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Affiliation(s)
- Jorge Doña
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States.,Departamento de Biología Animal, Universidad de Granada, Granada, Spain
| | - Stephany Virrueta Herrera
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Tommi Nyman
- Department of Ecosystems in the Barents Region, Norwegian Institute of Bioeconomy Research, Svanvik, Norway
| | - Mervi Kunnasranta
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland.,Natural Resources Institute Finland, Joensuu, Finland
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States
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12
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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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13
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Keller AG, Apprill A, Lebaron P, Robbins J, Romano TA, Overton E, Rong Y, Yuan R, Pollara S, Whalen KE. Characterizing the culturable surface microbiomes of diverse marine animals. FEMS Microbiol Ecol 2021; 97:6157762. [PMID: 33681975 PMCID: PMC8012112 DOI: 10.1093/femsec/fiab040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 03/01/2021] [Indexed: 11/14/2022] Open
Abstract
Biofilm-forming bacteria have the potential to contribute to the health, physiology, behavior and ecology of the host and serve as its first line of defense against adverse conditions in the environment. While metabarcoding and metagenomic information furthers our understanding of microbiome composition, fewer studies use cultured samples to study the diverse interactions among the host and its microbiome, as cultured representatives are often lacking. This study examines the surface microbiomes cultured from three shallow-water coral species and two whale species. These unique marine animals place strong selective pressures on their microbial symbionts and contain members under similar environmental and anthropogenic stress. We developed an intense cultivation procedure, utilizing a suite of culture conditions targeting a rich assortment of biofilm-forming microorganisms. We identified 592 microbial isolates contained within 15 bacterial orders representing 50 bacterial genera, and two fungal species. Culturable bacteria from coral and whale samples paralleled taxonomic groups identified in culture-independent surveys, including 29% of all bacterial genera identified in the Megaptera novaeangliae skin microbiome through culture-independent methods. This microbial repository provides raw material and biological input for more nuanced studies which can explore how members of the microbiome both shape their micro-niche and impact host fitness.
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Affiliation(s)
- Abigail G Keller
- Department of Biology, Haverford College, 370 Lancaster Ave., Haverford, PA, 19041-1392, USA
| | - Amy Apprill
- Marine Chemistry & Geochemistry Department, Woods Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, MA, 02543, USA
| | - Philippe Lebaron
- Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Université (UPMC) Paris 6 et CNRS Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Jooke Robbins
- Center for Coastal Studies, 5 Holway Ave., Provincetown, MA, 02657, USA
| | - Tracy A Romano
- Mystic Aquarium, a division of Sea Research Foundation Inc., 55 Coogan Blvd., Mystic, CT, 06355, USA
| | - Ellysia Overton
- Department of Biology, Haverford College, 370 Lancaster Ave., Haverford, PA, 19041-1392, USA
| | - Yuying Rong
- Department of Biology, Haverford College, 370 Lancaster Ave., Haverford, PA, 19041-1392, USA
| | - Ruiyi Yuan
- Department of Biology, Haverford College, 370 Lancaster Ave., Haverford, PA, 19041-1392, USA
| | - Scott Pollara
- Department of Biology, Haverford College, 370 Lancaster Ave., Haverford, PA, 19041-1392, USA
| | - Kristen E Whalen
- Department of Biology, Haverford College, 370 Lancaster Ave., Haverford, PA, 19041-1392, USA
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14
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Nowlan JP, Britney SR, Lumsden JS, Russell S. Application of Quantitative-PCR to Monitor Netpen Sites in British Columbia (Canada) for Tenacibaculum Species. Pathogens 2021; 10:pathogens10040414. [PMID: 33915806 PMCID: PMC8066307 DOI: 10.3390/pathogens10040414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 03/23/2021] [Accepted: 03/30/2021] [Indexed: 12/31/2022] Open
Abstract
Tenacibaculum are frequently detected from fish with tenacibaculosis at aquaculture sites; however, information on the ecology of these bacteria is sparse. Quantitative-PCR assays were used to detect T. maritimum and T. dicentrarchi at commercial Atlantic salmon (Salmo salar) netpen sites throughout several tenacibaculosis outbreaks. T. dicentrarchi and T. maritimum were identified in live fish, dead fish, other organisms associated with netpens, water samples and on inanimate substrates, which indicates a ubiquitous distribution around stocked netpen sites. Before an outbreak, T. dicentrarchi was found throughout the environment and from fish, and T. maritimum was infrequently identified. During an outbreak, increases in the bacterial load in were recorded and no differences were recorded after an outbreak supporting the observed recrudescence of mouthrot. More bacteria were recorded in the summer months, with more mortality events and antibiotic treatments, indicating that seasonality may influence tenacibaculosis; however, outbreaks occurred in both seasons. Relationships were identified between fish mortalities and antimicrobial use to water quality parameters (temperature, salinity, dissolved oxygen) (p < 0.05), but with low R2 values (<0.25), other variables are also involved. Furthermore, Tenacibaculum species appear to have a ubiquitous spatial and temporal distribution around stocked netpen sites, and with the potential to induce disease in Atlantic salmon, continued research is needed.
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Affiliation(s)
- Joseph P. Nowlan
- Center of Innovation for Fish Health, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada; (S.R.B.); (S.R.)
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada;
- Correspondence:
| | - Scott R. Britney
- Center of Innovation for Fish Health, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada; (S.R.B.); (S.R.)
| | - John S. Lumsden
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Spencer Russell
- Center of Innovation for Fish Health, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada; (S.R.B.); (S.R.)
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15
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Sehnal L, Brammer-Robbins E, Wormington AM, Blaha L, Bisesi J, Larkin I, Martyniuk CJ, Simonin M, Adamovsky O. Microbiome Composition and Function in Aquatic Vertebrates: Small Organisms Making Big Impacts on Aquatic Animal Health. Front Microbiol 2021; 12:567408. [PMID: 33776947 PMCID: PMC7995652 DOI: 10.3389/fmicb.2021.567408] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 02/05/2021] [Indexed: 01/03/2023] Open
Abstract
Aquatic ecosystems are under increasing stress from global anthropogenic and natural changes, including climate change, eutrophication, ocean acidification, and pollution. In this critical review, we synthesize research on the microbiota of aquatic vertebrates and discuss the impact of emerging stressors on aquatic microbial communities using two case studies, that of toxic cyanobacteria and microplastics. Most studies to date are focused on host-associated microbiomes of individual organisms, however, few studies take an integrative approach to examine aquatic vertebrate microbiomes by considering both host-associated and free-living microbiota within an ecosystem. We highlight what is known about microbiota in aquatic ecosystems, with a focus on the interface between water, fish, and marine mammals. Though microbiomes in water vary with geography, temperature, depth, and other factors, core microbial functions such as primary production, nitrogen cycling, and nutrient metabolism are often conserved across aquatic environments. We outline knowledge on the composition and function of tissue-specific microbiomes in fish and marine mammals and discuss the environmental factors influencing their structure. The microbiota of aquatic mammals and fish are highly unique to species and a delicate balance between respiratory, skin, and gastrointestinal microbiota exists within the host. In aquatic vertebrates, water conditions and ecological niche are driving factors behind microbial composition and function. We also generate a comprehensive catalog of marine mammal and fish microbial genera, revealing commonalities in composition and function among aquatic species, and discuss the potential use of microbiomes as indicators of health and ecological status of aquatic ecosystems. We also discuss the importance of a focus on the functional relevance of microbial communities in relation to organism physiology and their ability to overcome stressors related to global change. Understanding the dynamic relationship between aquatic microbiota and the animals they colonize is critical for monitoring water quality and population health.
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Affiliation(s)
- Ludek Sehnal
- RECETOX, Faculty of Science, Masaryk University, Brno, Czechia
| | - Elizabeth Brammer-Robbins
- Department of Large Animal Clinical Sciences, University of Florida, Gainesville, FL, United States.,Department of Physiological Sciences, University of Florida, Gainesville, FL, United States.,Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
| | - Alexis M Wormington
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States.,Department of Environmental and Global Health, University of Florida, Gainesville, FL, United States
| | - Ludek Blaha
- RECETOX, Faculty of Science, Masaryk University, Brno, Czechia
| | - Joe Bisesi
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States.,Department of Environmental and Global Health, University of Florida, Gainesville, FL, United States
| | - Iske Larkin
- Department of Large Animal Clinical Sciences, University of Florida, Gainesville, FL, United States
| | - Christopher J Martyniuk
- Department of Physiological Sciences, University of Florida, Gainesville, FL, United States.,Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
| | - Marie Simonin
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
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16
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Nowlan JP, Lumsden JS, Russell S. Advancements in Characterizing Tenacibaculum Infections in Canada. Pathogens 2020; 9:pathogens9121029. [PMID: 33302445 PMCID: PMC7763822 DOI: 10.3390/pathogens9121029] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022] Open
Abstract
Tenacibaculum is a genus of gram negative, marine, filamentous bacteria, associated with the presence of disease (tenacibaculosis) at aquaculture sites worldwide; however, infections induced by this genus are poorly characterized. Documents regarding the genus Tenacibaculum and close relatives were compiled for a literature review, concentrating on ecology, identification, and impacts of potentially pathogenic species, with a focus on Atlantic salmon in Canada. Tenacibaculum species likely have a cosmopolitan distribution, but local distributions around aquaculture sites are unknown. Eight species of Tenacibaculum are currently believed to be related to numerous mortality events of fishes and few mortality events in bivalves. The clinical signs in fishes often include epidermal ulcers, atypical behaviors, and mortality. Clinical signs in bivalves often include gross ulcers and discoloration of tissues. The observed disease may differ based on the host, isolate, transmission route, and local environmental conditions. Species-specific identification techniques are limited; high sequence similarities using conventional genes (16S rDNA) indicate that new genes should be investigated. Annotating full genomes, next-generation sequencing, multilocus sequence analysis/typing (MLSA/MLST), matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF), and fatty acid methylesters (FAME) profiles could be further explored for identification purposes. However, each aforementioned technique has disadvantages. Since tenacibaculosis has been observed world-wide in fishes and other eukaryotes, and the disease has substantial economic impacts, continued research is needed.
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Affiliation(s)
- Joseph P. Nowlan
- Department of Pathobiology, University of Guelph, Guelph, OT N1G 2W1, Canada;
- Center for Innovation in Fish Health, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada;
- Correspondence:
| | - John S. Lumsden
- Department of Pathobiology, University of Guelph, Guelph, OT N1G 2W1, Canada;
| | - Spencer Russell
- Center for Innovation in Fish Health, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada;
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17
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Brealey JC, Leitão HG, van der Valk T, Xu W, Bougiouri K, Dalén L, Guschanski K. Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome. Mol Biol Evol 2020; 37:3003-3022. [PMID: 32467975 PMCID: PMC7530607 DOI: 10.1093/molbev/msaa135] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Dental calculus, the calcified form of the mammalian oral microbial plaque biofilm, is a rich source of oral microbiome, host, and dietary biomolecules and is well preserved in museum and archaeological specimens. Despite its wide presence in mammals, to date, dental calculus has primarily been used to study primate microbiome evolution. We establish dental calculus as a valuable tool for the study of nonhuman host microbiome evolution, by using shotgun metagenomics to characterize the taxonomic and functional composition of the oral microbiome in species as diverse as gorillas, bears, and reindeer. We detect oral pathogens in individuals with evidence of oral disease, assemble near-complete bacterial genomes from historical specimens, characterize antibiotic resistance genes, reconstruct components of the host diet, and recover host genetic profiles. Our work demonstrates that metagenomic analyses of dental calculus can be performed on a diverse range of mammalian species, which will allow the study of oral microbiome and pathogen evolution from a comparative perspective. As dental calculus is readily preserved through time, it can also facilitate the quantification of the impact of anthropogenic changes on wildlife and the environment.
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Affiliation(s)
- Jaelle C Brealey
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Henrique G Leitão
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Tom van der Valk
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Wenbo Xu
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Katia Bougiouri
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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18
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Abstract
Advances in sequencing, bioinformatics and analytics now allow the structure, function and interrelations of whole microbial communities to be studied in greater detail. Collaborative efforts and multidisciplinary studies, crossing the boundary between environmental and medical microbiology, have allowed specific environmental, animal and human microbiomes to be characterized. One of the main challenges for microbial ecology is to link the phylogenetic diversity of host-associated microbes to their functional roles within the community. Much remains to be learned on the way microbes colonize the skin of different living organisms and the way the skin microbiome reacts to the surrounding environment (air, water, etc.). In this review, we discuss examples of recent studies that have used modern technology to provide insights into microbial communities in water and on skin, such as those in natural resources (thermal spring water), large mammals (humpback whales) and humans (the skin microbiome). The results of these studies demonstrate how a greater understanding of the structure and functioning of microbiota, together with their interactions with the environment, may facilitate the discovery of new probiotics or postbiotics, provide indicators for the quality of the environment, and show how changes in lifestyle and living environment, such as urbanization, can impact on the skin microbiome and skin health and disease in humans.
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Affiliation(s)
- Chris Callewaert
- Center for Microbial Ecology and Technology, Ghent University, Coupure Links 653, Ghent, Belgium
- Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Katia Ravard Helffer
- Pierre Fabre Dermo-Cosmétique R&D Center, 3 Avenue Hubert Curien, 31035, Toulouse Cedex 01, France
| | - Philippe Lebaron
- Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Sorbonne Université, CNRS, Observatoire Océanologique de Banyuls-sur-Mer, Avenue Pierre Fabre, 66650, Banyuls-sur-Mer, France.
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19
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Levican A, Fisher JC, McLellan SL, Avendaño-Herrera R. Microbial Communities Associated with Farmed Genypterus chilensis: Detection in Water Prior to Bacterial Outbreaks Using Culturing and High-Throughput Sequencing. Animals (Basel) 2020; 10:ani10061055. [PMID: 32570967 PMCID: PMC7341507 DOI: 10.3390/ani10061055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/15/2020] [Accepted: 06/15/2020] [Indexed: 12/19/2022] Open
Abstract
The red conger eel (Genypterus chilensis, Guichenot) is a native species included in the Chilean Aquaculture Diversification Program due to high commercial demand. In the context of intensified farming, prior reports link two disease outbreaks with emerging pathogens in the Vibrio and Tenacibaculum genera. However, the roles remain unclear for the bacterial community and each specific bacterium is associated with the rearing environment for healthy specimens. The success of red conger eel farming therefore warrants research into the bacterial composition of aquaculture conditions and the antimicrobial susceptibilities thereof. This study used culturing methods and high-throughput sequencing to describe the bacterial community associated with water in which G. chilensis was farmed. With culturing methods, the predominant genera were Vibrio (21.6%), Pseudolteromonas (15.7%), Aliivibrio (13.7%), and Shewanella (7.8%). Only a few bacterial isolates showed amylase, gelatinase, or lipase activity, and almost all showed inhibition zones to commonly-used antibiotics in aquaculture. By contrast, high-throughput sequencing established Paraperlucidibaca, Colwellia, Polaribacter, Saprospiraceae, and Tenacibaculum as the predominant genera, with Vibrio ranking twenty-seventh in abundance. High-throughput sequencing also established a link between previous outbreaks with increased relative abundances of Vibrio and Tenacibaculum. Therefore, monitoring the presence and abundance of these potential pathogens could be useful in providing prophylactic measures to prevent future outbreaks.
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Affiliation(s)
- Arturo Levican
- Tecnología Médica, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Avenida Universidad 330, Valparaíso 2373223, Chile
- Correspondence: or (A.L.); or (R.A.-H.)
| | - Jenny C. Fisher
- Biology Department, Indiana University Northwest, Gary, IN 46408, USA;
| | - Sandra L. McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53204, USA;
| | - Ruben Avendaño-Herrera
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Viña del Mar 2571015, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción 4030000, Chile
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Casablanca 2480000, Chile
- Correspondence: or (A.L.); or (R.A.-H.)
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20
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Apprill A, Miller CA, Van Cise AM, U'Ren JM, Leslie MS, Weber L, Baird RW, Robbins J, Landry S, Bogomolni A, Waring G. Marine mammal skin microbiotas are influenced by host phylogeny. ROYAL SOCIETY OPEN SCIENCE 2020; 7:192046. [PMID: 32537203 PMCID: PMC7277249 DOI: 10.1098/rsos.192046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/28/2020] [Indexed: 06/11/2023]
Abstract
Skin-associated microorganisms have been shown to play a role in immune function and disease of humans, but are understudied in marine mammals, a diverse animal group that serve as sentinels of ocean health. We examined the microbiota associated with 75 epidermal samples opportunistically collected from nine species within four marine mammal families, including: Balaenopteridae (sei and fin whales), Phocidae (harbour seal), Physeteridae (sperm whales) and Delphinidae (bottlenose dolphins, pantropical spotted dolphins, rough-toothed dolphins, short-finned pilot whales and melon-headed whales). The skin was sampled from free-ranging animals in Hawai'i (Pacific Ocean) and off the east coast of the United States (Atlantic Ocean), and the composition of the bacterial community was examined using the sequencing of partial small subunit (SSU) ribosomal RNA genes. Skin microbiotas were significantly different among host species and taxonomic families, and microbial community distance was positively correlated with mitochondrial-based host genetic divergence. The oceanic location could play a role in skin microbiota variation, but skin from species sampled in both locations is necessary to determine this influence. These data suggest that a phylosymbiotic relationship may exist between microbiota and their marine mammal hosts, potentially providing specific health and immune-related functions that contribute to the success of these animals in diverse ocean ecosystems.
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Affiliation(s)
- Amy Apprill
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Carolyn A. Miller
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Amy M. Van Cise
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Jana M. U'Ren
- BIO5 Institute and Department of Biosystems Engineering, University of Arizona, Tucson, AZ, USA
| | | | - Laura Weber
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | | | | | - Scott Landry
- Center for Coastal Studies, Provincetown, MA, USA
| | - Andrea Bogomolni
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Gordon Waring
- NOAA Northeast Fisheries Science Center, Protected Species Branch, Woods Hole, MA, USA
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21
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DeCandia AL, Brenner LJ, King JL, vonHoldt BM. Ear mite infection is associated with altered microbial communities in genetically depauperate Santa Catalina Island foxes (Urocyon littoralis catalinae). Mol Ecol 2020; 29:1463-1475. [PMID: 31821650 DOI: 10.1111/mec.15325] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 11/11/2019] [Accepted: 11/26/2019] [Indexed: 12/12/2022]
Abstract
The host-associated microbiome is increasingly recognized as a critical player in health and immunity. Recent studies have shown that disruption of commensal microbial communities can contribute to disease pathogenesis and severity. Santa Catalina Island foxes (Urocyon littoralis catalinae) present a compelling system in which to examine microbial dynamics in wildlife due to their depauperate genomic structure and extremely high prevalence of ceruminous gland tumors. Although the precise cause is yet unknown, infection with ear mites (Otodectes cynotis) has been linked to chronic inflammation, which is associated with abnormal cell growth and tumor development. Given the paucity of genomic variation in these foxes, other dimensions of molecular diversity, such as commensal microbes, may be critical to host response and disease pathology. We characterized the host-associated microbiome across six body sites of Santa Catalina Island foxes, and performed differential abundance testing between healthy and mite-infected ear canals. We found that mite infection was significantly associated with reduced microbial diversity and evenness, with the opportunistic pathogen Staphylococcus pseudintermedius dominating the ear canal community. These results suggest that secondary bacterial infection may contribute to the sustained inflammation associated with tumor development. As the emergence of antibiotic resistant strains remains a concern of the medical, veterinary, and conservation communities, uncovering high relative abundance of S. pseudintermedius provides critical insight into the pathogenesis of this complex system. Through use of culture-independent sequencing techniques, this study contributes to the broader effort of applying a more inclusive understanding of molecular diversity to questions within wildlife disease ecology.
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Affiliation(s)
- Alexandra L DeCandia
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | | | | | - Bridgett M vonHoldt
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, USA
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22
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Roslin T, Traugott M, Jonsson M, Stone GN, Creer S, Symondson WOC. Introduction: Special issue on species interactions, ecological networks and community dynamics - Untangling the entangled bank using molecular techniques. Mol Ecol 2019; 28:157-164. [PMID: 30548494 DOI: 10.1111/mec.14974] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 11/23/2018] [Accepted: 12/05/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Tomas Roslin
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Michael Traugott
- Mountain Agriculture Research Unit, Institute of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Mattias Jonsson
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Graham N Stone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Natural Sciences, Bangor University, Gwynedd, UK
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23
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Microbiota fingerprints within the oral cavity of cetaceans as indicators for population biomonitoring. Sci Rep 2019; 9:13679. [PMID: 31548611 PMCID: PMC6757053 DOI: 10.1038/s41598-019-50139-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 09/05/2019] [Indexed: 12/13/2022] Open
Abstract
The composition of mammalian microbiota has been related with the host health status. In this study, we assessed the oral microbiome of 3 cetacean species most commonly found stranded in Iberian Atlantic waters (Delphinus delphis, Stenella coeruleoalba and Phocoena phocoena), using 16S rDNA-amplicon metabarcoding. All oral microbiomes were dominated by Proteobacteria, Firmicutes, Bacteroidetes and Fusobacteria bacteria, which were also predominant in the oral cavity of Tursiops truncatus. A Constrained Canonical Analysis (CCA) showed that the major factors shaping the composition of 38 oral microbiomes (p-value < 0.05) were: (i) animal species and (ii) age class, segregating adults and juveniles. The correlation analysis also grouped the microbiomes by animal stranding location and health status. Similar discriminatory patterns were detected using the data from a previous study on Tursiops truncatus, indicating that this correlation approach may facilitate data comparisons between different studies on several cetacean species. This study identified a total of 15 bacterial genera and 27 OTUs discriminating between the observed CCA groups, which can be further explored as microbiota fingerprints to develop (i) specific diagnostic assays for cetacean population conservation and (ii) bio-monitoring approaches to assess the health of marine ecosystems from the Iberian Atlantic basin, using cetaceans as bioindicators.
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24
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Li C, Tan X, Bai J, Xu Q, Liu S, Guo W, Yu C, Fan G, Lu Y, Zhang H, Yang H, Chen J, Liu X. A survey of the sperm whale ( Physeter catodon) commensal microbiome. PeerJ 2019; 7:e7257. [PMID: 31309006 PMCID: PMC6612419 DOI: 10.7717/peerj.7257] [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] [Received: 12/18/2018] [Accepted: 06/05/2019] [Indexed: 01/18/2023] Open
Abstract
Background Mammalian commensal microbiota play important roles in the health of its host. In comparison to terrestrial mammals, commensal microbiota of marine mammals is mainly focused on the composition and function of skin and gut microbiota, with less attention paid to the health impact of bacteria and viruses. Previous studies on sperm whales (Physeter catodon) have affirmed their important phylogenetic position; however, studies on their commensal microbiota have not been published, due to difficulty in sample collection. Methods Here, we sequenced the metagenomes of blood, muscle and fecal samples from a stranded sperm whale using the BGISEQ-500 platform. We compared the diversity and abundance of microbiomes from three different tissues and tried to search pathogenic bacterial and virulence genes probably related to the health of the sperm whale. We also performed 16S rDNA sequencing of the fecal sample to compare to published gut metagenome data from other marine mammals. Results Our results demonstrated notable differences in species richness and abundance in the three samples. Extensive bacteria, including Enterococcus faecium, Fusobacterium nucleatum, Pseudomonas aeruginosa, Streptococcus anginosus, Streptococcus pneumoniae, and Streptococcus suis, and five toxigenic Clostridium species usually associated with infection, were found in the three samples. We also found the taxa composition of sperm whale gut microbiota was similar to that of other whales, suggesting co-evolution with its host. This study is the first report of the sperm whale gut microbiome, and provides a foundation for the pathogen detection and health assessment of the sperm whale.
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Affiliation(s)
- Chang Li
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | | | - Jie Bai
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Qiwu Xu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Shanshan Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,Shandong Technology Innovation Center of Synthetic Biology, Qingdao, China
| | - Wenjie Guo
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Cong Yu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,State Key Laboratory of Quality Research of Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau, China.,BGI-Shenzhen, Shenzhen, China
| | - Yishan Lu
- Guangdong Ocean University, Shenzhen, China
| | - He Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Huanming Yang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | | | - Xin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,State Key Laboratory of Agricultural Genomics, Shenzhen, China
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25
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Hammer TJ, Sanders JG, Fierer N. Not all animals need a microbiome. FEMS Microbiol Lett 2019; 366:5499024. [DOI: 10.1093/femsle/fnz117] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 05/25/2019] [Indexed: 02/07/2023] Open
Abstract
ABSTRACTIt is often taken for granted that all animals host and depend upon a microbiome, yet this has only been shown for a small proportion of species. We propose that animals span a continuum of reliance on microbial symbionts. At one end are the famously symbiont-dependent species such as aphids, humans, corals and cows, in which microbes are abundant and important to host fitness. In the middle are species that may tolerate some microbial colonization but are only minimally or facultatively dependent. At the other end are species that lack beneficial symbionts altogether. While their existence may seem improbable, animals are capable of limiting microbial growth in and on their bodies, and a microbially independent lifestyle may be favored by selection under some circumstances. There is already evidence for several ‘microbiome-free’ lineages that represent distantly related branches in the animal phylogeny. We discuss why these animals have received such little attention, highlighting the potential for contaminants, transients, and parasites to masquerade as beneficial symbionts. We also suggest ways to explore microbiomes that address the limitations of DNA sequencing. We call for further research on microbiome-free taxa to provide a more complete understanding of the ecology and evolution of macrobe-microbe interactions.
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Affiliation(s)
- Tobin J Hammer
- Department of Integrative Biology, University of Texas at Austin, 2506 Speedway, NMS 4.216, Austin, TX 78712, USA
| | - Jon G Sanders
- Cornell Institute of Host–Microbe Interactions and Disease, Cornell University, E145 Corson Hall, Ithaca, NY 14853, USA
| | - Noah Fierer
- Department of Ecology & Evolutionary Biology, University of Colorado at Boulder, 216 UCB, Boulder, CO 80309, USA
- Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, CIRES Bldg. Rm. 318, Boulder, CO 80309, USA
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26
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Grosser S, Sauer J, Paijmans AJ, Caspers BA, Forcada J, Wolf JBW, Hoffman JI. Fur seal microbiota are shaped by the social and physical environment, show mother–offspring similarities and are associated with host genetic quality. Mol Ecol 2019; 28:2406-2422. [DOI: 10.1111/mec.15070] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 02/26/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Stefanie Grosser
- Department of Animal Behaviour Bielefeld University Bielefeld Germany
- Division of Evolutionary Biology, Faculty of Biology LMU Munich Planegg‐Martinsried Germany
| | - Jan Sauer
- Department of Animal Behaviour Bielefeld University Bielefeld Germany
| | | | | | - Jaume Forcada
- British Antarctic Survey Natural Environment Research Council Cambridge UK
| | - Jochen B. W. Wolf
- Division of Evolutionary Biology, Faculty of Biology LMU Munich Planegg‐Martinsried Germany
- Department of Evolutionary Biology Uppsala University Uppsala Sweden
| | - Joseph I. Hoffman
- Department of Animal Behaviour Bielefeld University Bielefeld Germany
- British Antarctic Survey Natural Environment Research Council Cambridge UK
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27
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Hooper R, Brealey JC, van der Valk T, Alberdi A, Durban JW, Fearnbach H, Robertson KM, Baird RW, Bradley Hanson M, Wade P, Gilbert MTP, Morin PA, Wolf JBW, Foote AD, Guschanski K. Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin. Mol Ecol 2019; 28:484-502. [PMID: 30187987 PMCID: PMC6487819 DOI: 10.1111/mec.14860] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 08/15/2018] [Accepted: 08/27/2018] [Indexed: 12/20/2022]
Abstract
Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the host's biology, health and associated micro-organisms. Whereas amplicon sequencing has traditionally been used to characterize the microbiome, the increasing number of published population genomics data sets offers an underexploited opportunity to study microbial profiles from the host shotgun sequencing data. Here, we use sequence data originally generated from killer whale Orcinus orca skin biopsies for population genomics, to characterize the skin microbiome and investigate how host social and geographical factors influence the microbial community composition. Having identified 845 microbial taxa from 2.4 million reads that did not map to the killer whale reference genome, we found that both ecotypic and geographical factors influence community composition of killer whale skin microbiomes. Furthermore, we uncovered key taxa that drive the microbiome community composition and showed that they are embedded in unique networks, one of which is tentatively linked to diatom presence and poor skin condition. Community composition differed between Antarctic killer whales with and without diatom coverage, suggesting that the previously reported episodic migrations of Antarctic killer whales to warmer waters associated with skin turnover may control the effects of potentially pathogenic bacteria such as Tenacibaculum dicentrarchi. Our work demonstrates the feasibility of microbiome studies from host shotgun sequencing data and highlights the importance of metagenomics in understanding the relationship between host and microbial ecology.
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Affiliation(s)
- Rebecca Hooper
- Animal EcologyDepartment of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Jaelle C. Brealey
- Animal EcologyDepartment of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Tom van der Valk
- Animal EcologyDepartment of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Antton Alberdi
- Centre for GeoGeneticsNatural History Museum of DenmarkUniversity of CopenhagenCopenhagen KDenmark
| | - John W. Durban
- Marine Mammal and Turtle DivisionSouthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationLa JollaCalifornia
| | - Holly Fearnbach
- SR3, SeaLife Response, Rehabilitation, and ResearchSeattleWashington
| | - Kelly M. Robertson
- Marine Mammal and Turtle DivisionSouthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationLa JollaCalifornia
| | | | - M. Bradley Hanson
- Northwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWashington
| | - Paul Wade
- National Marine Mammal LaboratoryAlaska Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWashington
| | - M. Thomas P. Gilbert
- Centre for GeoGeneticsNatural History Museum of DenmarkUniversity of CopenhagenCopenhagen KDenmark
- NTNU University MuseumTrondheimNorway
| | - Phillip A. Morin
- Marine Mammal and Turtle DivisionSouthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationLa JollaCalifornia
| | - Jochen B. W. Wolf
- Science of Life Laboratories and Department of Evolutionary BiologyEvolutionary Biology CentreUppsala UniversityUppsalaSweden
- Section of Evolutionary BiologyFaculty of BiologyLMU MunichMunichGermany
| | - Andrew D. Foote
- Molecular Ecology and Fisheries Genetics LaboratorySchool of Biological SciencesBangor UniversityBangorGwyneddUK
| | - Katerina Guschanski
- Animal EcologyDepartment of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
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