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Milan M, Bernardini I, Bertolini C, Dalla Rovere G, Manuzzi A, Pastres R, Peruzza L, Smits M, Fabrello J, Breggion C, Sambo A, Boffo L, Gallocchio L, Carrer C, Sorrentino F, Bettiol C, Lodi GC, Semenzin E, Varagnolo M, Matozzo V, Bargelloni L, Patarnello T. Multidisciplinary long-term survey of Manila clam grown in farming sites subjected to different environmental conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 863:160796. [PMID: 36528093 DOI: 10.1016/j.scitotenv.2022.160796] [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: 08/09/2022] [Revised: 10/14/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
In recent years recurrent bivalve mass mortalities considerably increased around the world, causing the collapse of natural and farmed populations. Venice Lagoon has historically represented one of the major production areas of the Manila clam Ruditapes philippinarum in Europe. However, in the last 20 years a 75 % decrease in the annual production has been experienced. While climate change and anthropogenic interventions may have played a key role in natural and farmed stocks reductions, no studies investigated at multiple levels the environmental stressors affecting farmed Manila clam to date. In this work we carried out a long-term monitoring campaign on Manila clam reared in four farming sites located at different distances from the southern Venice Lagoon inlet, integrating (meta)genomic approaches (i.e. RNA-seq; microbiota characterization), biometric measurements and chemical-physical parameters. Our study allowed to characterize the molecular mechanisms adopted by this species to cope with the different environmental conditions characterizing farming sites and to propose hypotheses to explain mortality events observed in recent years. Among the most important findings, the disruption of clam's immune response, the spread of Vibrio spp., and the up-regulation of molecular pathways involved in xenobiotic metabolism suggested major environmental stressors affecting clams farmed in sites placed close to Chioggia's inlet, where highest mortality was also observed. Overall, our study provides knowledge-based tools for managing Manila clam farming on-growing areas. In addition, the collected data is a snapshot of the time immediately before the commissioning of MoSE, a system of mobile barriers aimed at protecting Venice from high tides, and will represent a baseline for future studies on the effects of MoSE on clams farming and more in general on the ecology of the Venice Lagoon.
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Affiliation(s)
- Massimo Milan
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, Agripolis, 35020 Legnaro, PD, Italy.
| | - Ilaria Bernardini
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, Agripolis, 35020 Legnaro, PD, Italy
| | - Camilla Bertolini
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Via torino 155, 30170 Venezia, Italy
| | - Giulia Dalla Rovere
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, Agripolis, 35020 Legnaro, PD, Italy
| | - Alice Manuzzi
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, Agripolis, 35020 Legnaro, PD, Italy
| | - Roberto Pastres
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Via torino 155, 30170 Venezia, Italy
| | - Luca Peruzza
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, Agripolis, 35020 Legnaro, PD, Italy
| | - Morgan Smits
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, Agripolis, 35020 Legnaro, PD, Italy
| | - Jacopo Fabrello
- Department of Biology, University of Padova, Via Bassi 58/B, 35131 Padova, Italy
| | - Cristina Breggion
- Department of Biology, University of Padova, Via Bassi 58/B, 35131 Padova, Italy
| | - Andrea Sambo
- Department of Biology, University of Padova, Via Bassi 58/B, 35131 Padova, Italy
| | | | - Loretta Gallocchio
- Thetis s.p.a., c /o Provveditorato Interregionale OO.PP. - Ufficio Tecnico Antinquinamento Laboratorio CSMO, Via Asconio Pediano, 9, 35127 Padova, PD, Italy
| | - Claudio Carrer
- Thetis s.p.a., c /o Provveditorato Interregionale OO.PP. - Ufficio Tecnico Antinquinamento Laboratorio CSMO, Via Asconio Pediano, 9, 35127 Padova, PD, Italy
| | - Francesco Sorrentino
- Provveditorato Interregionale OO.PP. - Ufficio Tecnico Antinquinamento, San Polo 19, 30124 Venezia, Italy)
| | - Cinzia Bettiol
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Via torino 155, 30170 Venezia, Italy
| | - Giulia Carolina Lodi
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Via torino 155, 30170 Venezia, Italy
| | - Elena Semenzin
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Via torino 155, 30170 Venezia, Italy
| | - Maurizio Varagnolo
- Societa' Agricola Kappa S. S. di Varagnolo Maurizio E. C., Chioggia, VE, Italy
| | - Valerio Matozzo
- Department of Biology, University of Padova, Via Bassi 58/B, 35131 Padova, Italy
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, Agripolis, 35020 Legnaro, PD, Italy
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, Agripolis, 35020 Legnaro, PD, Italy
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Doane MP, Johnson CJ, Johri S, Kerr EN, Morris MM, Desantiago R, Turnlund AC, Goodman A, Mora M, Lima LFO, Nosal AP, Dinsdale EA. The Epidermal Microbiome Within an Aggregation of Leopard Sharks (Triakis semifasciata) Has Taxonomic Flexibility with Gene Functional Stability Across Three Time-points. MICROBIAL ECOLOGY 2023; 85:747-764. [PMID: 35129649 PMCID: PMC9957878 DOI: 10.1007/s00248-022-01969-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/17/2022] [Indexed: 05/06/2023]
Abstract
The epidermis of Chondrichthyan fishes consists of dermal denticles with production of minimal but protein-rich mucus that collectively, influence the attachment and biofilm development of microbes, facilitating a unique epidermal microbiome. Here, we use metagenomics to provide the taxonomic and functional characterization of the epidermal microbiome of the Triakis semifasciata (leopard shark) at three time-points collected across 4 years to identify links between microbial groups and host metabolism. Our aims include (1) describing the variation of microbiome taxa over time and identifying recurrent microbiome members (present across all time-points); (2) investigating the relationship between the recurrent and flexible taxa (those which are not found consistently across time-points); (3) describing the functional compositions of the microbiome which may suggest links with the host metabolism; and (4) identifying whether metabolic processes are shared across microbial genera or are unique to specific taxa. Microbial members of the microbiome showed high similarity between all individuals (Bray-Curtis similarity index = 82.7, where 0 = no overlap, 100 = total overlap) with the relative abundance of those members varying across sampling time-points, suggesting flexibility of taxa in the microbiome. One hundred and eighty-eight genera were identified as recurrent, including Pseudomonas, Erythrobacter, Alcanivorax, Marinobacter, and Sphingopxis being consistently abundant across time-points, while Limnobacter and Xyella exhibited switching patterns with high relative abundance in 2013, Sphingobium and Sphingomona in 2015, and Altermonas, Leeuwenhoekiella, Gramella, and Maribacter in 2017. Of the 188 genera identified as recurrent, the top 19 relatively abundant genera formed three recurrent groups. The microbiome also displayed high functional similarity between individuals (Bray-Curtis similarity index = 97.6) with gene function composition remaining consistent across all time-points. These results show that while the presence of microbial genera exhibits consistency across time-points, their abundances do fluctuate. Microbial functions however remain stable across time-points; thus, we suggest the leopard shark microbiomes exhibit functional redundancy. We show coexistence of microbes hosted in elasmobranch microbiomes that encode genes involved in utilizing nitrogen, but not fixing nitrogen, degrading urea, and resistant to heavy metal.
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Affiliation(s)
- Michael P. Doane
- College of Science and Engineering, Flinders University, Bedford Park, South Australia Australia
| | - Colton J. Johnson
- Department of Biology, San Diego State University, San Diego, CA USA
| | - Shaili Johri
- Hopkins Marine Station, Stanford University, Pacific Grove, CA USA
| | - Emma N. Kerr
- College of Science and Engineering, Flinders University, Bedford Park, South Australia Australia
| | | | - Ric Desantiago
- Department of Biology, San Diego State University, San Diego, CA USA
| | - Abigail C. Turnlund
- Australian Centre for Ecogenomics, University of Queensland, St Lucia, QLD Australia
| | - Asha Goodman
- Department of Biology, San Diego State University, San Diego, CA USA
| | - Maria Mora
- Department of Biology, San Diego State University, San Diego, CA USA
| | | | - Andrew P. Nosal
- Department of Environmental and Ocean Sciences, University of San Diego, San Diego, CA USA
- Scripps Institution of Oceanography, University of California – San Diego, CA La Jolla, USA
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Bregman G, Lalzar M, Livne L, Bigal E, Zemah-Shamir Z, Morick D, Tchernov D, Scheinin A, Meron D. Preliminary study of shark microbiota at a unique mix-species shark aggregation site, in the Eastern Mediterranean Sea. Front Microbiol 2023; 14:1027804. [PMID: 36910211 PMCID: PMC9996248 DOI: 10.3389/fmicb.2023.1027804] [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: 08/25/2022] [Accepted: 01/16/2023] [Indexed: 02/25/2023] Open
Abstract
Sharks, as apex predators, play an essential ecological role in shaping the marine food web and maintaining healthy and balanced marine ecosystems. Sharks are sensitive to environmental changes and anthropogenic pressure and demonstrate a clear and rapid response. This designates them a "keystone" or "sentinel" group that may describe the structure and function of the ecosystem. As a meta-organism, sharks offer selective niches (organs) for microorganisms that can provide benefits for their hosts. However, changes in the microbiota (due to physiological or environmental changes) can turn the symbiosis into a dysbiosis and may affect the physiology, immunity and ecology of the host. Although the importance of sharks within the ecosystem is well known, relatively few studies have focused on the microbiome aspect, especially with long-term sampling. Our study was conducted at a site of coastal development in Israel where a mixed-species shark aggregation (November-May) is observed. The aggregation includes two shark species, the dusky (Carcharhinus obscurus) and sandbar (Carcharhinus plumbeus) which segregate by sex (females and males, respectively). In order to characterize the bacterial profile and examine the physiological and ecological aspects, microbiome samples were collected from different organs (gills, skin, and cloaca) from both shark species over 3 years (sampling seasons: 2019, 2020, and 2021). The bacterial composition was significantly different between the shark individuals and the surrounding seawater and between the shark species. Additionally, differences were apparent between all the organs and the seawater, and between the skin and gills. The most dominant groups for both shark species were Flavobacteriaceae, Moraxellaceae, and Rhodobacteraceae. However, specific microbial biomarkers were also identified for each shark. An unexpected difference in the microbiome profile and diversity between the 2019-2020 and 2021 sampling seasons, revealed an increase in the potential pathogen Streptococcus. The fluctuations in the relative abundance of Streptococcus between the months of the third sampling season were also reflected in the seawater. Our study provides initial information on shark microbiome in the Eastern Mediterranean Sea. In addition, we demonstrated that these methods were also able to describe environmental episodes and the microbiome is a robust measure for long-term ecological research.
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Affiliation(s)
- Goni Bregman
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Maya Lalzar
- Bioinformatics Services Unit, University of Haifa, Haifa, Israel
| | - Leigh Livne
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Eyal Bigal
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Ziv Zemah-Shamir
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Danny Morick
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Dan Tchernov
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Aviad Scheinin
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Dalit Meron
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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Zhang X, Ying C, Jiang M, Lin D, You L, Yin D, Zhang J, Liu K, Xu P. The bacteria of Yangtze finless porpoise ( Neophocaena asiaeorientalis asiaeorientalis) are site-specific and distinct from freshwater environment. Front Microbiol 2022; 13:1006251. [PMID: 36605503 PMCID: PMC9808046 DOI: 10.3389/fmicb.2022.1006251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/16/2022] [Indexed: 12/24/2022] Open
Abstract
Bacteria play an essential role in the health of marine mammals, and the bacteria of marine mammals are widely concerned, but less is known about freshwater mammals. In this study, we investigated the bacteria of various body sites of Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) and analyzed their association with freshwater environmental bacteria. The bacterial community and function of Yangtze finless porpoise showed apparent site-specificity. Various body sites have distinct differences in bacteria and have their dominant bacteria. Romboutsia, Plesiomonas, Actinobacillus, Candidatus Arthromitus dominated in the intestine (fecal and rectal samples). Fusobacterium, Streptococcus, and Acinetobacter dominated in the oral. The dominant genera in the blowhole include Suttonella, Psychrobacter, and two uncultured genera. Psychrobacter, Flavobacterium, and Acinetobacter were dominant in the skin. The alpha diversity of intestinal (fecal and rectal) bacteria was the lowest, while that of skin was the highest. The oral and skin bacteria of Yangtze finless porpoise significantly differed between the natural and semi-natural conditions, but no sex difference was observed. A clear boundary was found between the animal and the freshwater environmental bacteria. Even the skin bacteria, which are more affected by the environment, are significantly different from the environmental bacteria and harbor indigenous bacteria. Our results provide a comprehensive preliminary exploration of the bacteria of Yangtze finless porpoise and its association with bacteria in the freshwater environment.
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Affiliation(s)
- Xizhao Zhang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Congping Ying
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Min Jiang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Danqing Lin
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Lei You
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Denghua Yin
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Jialu Zhang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Kai Liu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China,*Correspondence: Kai Liu,
| | - Pao Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China,Pao Xu,
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A Review of Non-Invasive Sampling in Wildlife Disease and Health Research: What’s New? Animals (Basel) 2022; 12:ani12131719. [PMID: 35804619 PMCID: PMC9265025 DOI: 10.3390/ani12131719] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 12/14/2022] Open
Abstract
Simple Summary The interest in wildlife research has increased in the last decades as more scientists work within a One Health framework that regards human, livestock and wildlife health as connected entities. To minimise the impact of research on wildlife, collecting samples with as little disturbance of the animals as possible is important. In our review, we assess the use of so-called non-invasive sampling and summarise which samples can be used successfully when carrying out research on wildlife diseases and health status. Our results show that interest in minimally invasive sampling has steadily increased since the 2010s. Topics able to employ these methods include disease research, but also stress and other hormone assessments, pollution studies, and dietary studies. At the moment, such methods are mainly used to collect samples from land mammals, however, they can also be used in a wide range of other animals. Ever more capable analytical methods will allow for an even wider use of such “animal-friendly” sampling methods. Abstract In the last decades, wildlife diseases and the health status of animal populations have gained increasing attention from the scientific community as part of a One Health framework. Furthermore, the need for non-invasive sampling methods with a minimal impact on wildlife has become paramount in complying with modern ethical standards and regulations, and to collect high-quality and unbiased data. We analysed the publication trends on non-invasive sampling in wildlife health and disease research and offer a comprehensive review on the different samples that can be collected non-invasively. We retrieved 272 articles spanning from 1998 to 2021, with a rapid increase in number from 2010. Thirty-nine percent of the papers were focussed on diseases, 58% on other health-related topics, and 3% on both. Stress and other physiological parameters were the most addressed research topics, followed by viruses, helminths, and bacterial infections. Terrestrial mammals accounted for 75% of all publications, and faeces were the most widely used sample. Our review of the sampling materials and collection methods highlights that, although the use of some types of samples for specific applications is now consolidated, others are perhaps still underutilised and new technologies may offer future opportunities for an even wider use of non-invasively collected samples.
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Rhodes LD, Emmons CK, Wisswaesser G, Wells AH, Hanson MB. Bacterial microbiomes from mucus and breath of southern resident killer whales ( Orcinus orca). CONSERVATION PHYSIOLOGY 2022; 10:coac014. [PMID: 35492424 PMCID: PMC9041426 DOI: 10.1093/conphys/coac014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 02/07/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Opportunities to assess odontocete health are restricted due to their limited time at the surface, relatively quick movements and large geographic ranges. For endangered populations such as the southern resident killer whales (SKRWs) of the northeast Pacific Ocean, taking advantage of non-invasive samples such as expelled mucus and exhaled breath is appealing. Over the past 12 years, such samples were collected, providing a chance to analyse and assess their bacterial microbiomes using amplicon sequencing. Based on operational taxonomic units, microbiome communities from SRKW and transient killer whales showed little overlap between mucus, breath and seawater from SRKW habitats and six bacterial phyla were prominent in expelled mucus but not in seawater. Mollicutes and Fusobacteria were common and abundant in mucus, but not in breath or seawater, suggesting these bacterial classes may be normal constituents of the SRKW microbiome. Out of 134 bacterial families detected, 24 were unique to breath and mucus, including higher abundances of Burkholderiaceae, Moraxellaceae and Chitinophagaceae. Although there were multiple bacterial genera in breath or mucus that include pathogenic species (e.g. Campylobacter, Hemophilus, Treponema), the presence of these bacteria is not necessarily evidence of disease or infection. Future emphasis on genotyping mucus samples to the individual animal will allow further assessment in the context of that animal's history, including body condition index and prior contaminants burden. This study is the first to examine expelled mucus from cetaceans for microbiomes and demonstrates the value of analysing these types of non-invasive samples.
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Affiliation(s)
- Linda D Rhodes
- Corresponding author: Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Boulevard East, Seattle, WA 98112, USA.
| | - Candice K Emmons
- Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Boulevard East, Seattle, WA 98112, USA
| | - GabrielS Wisswaesser
- Lynker Technologies, under contract to Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Boulevard East, Seattle, WA 98112, USA
| | - Abigail H Wells
- Lynker Technologies, under contract to Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Boulevard East, Seattle, WA 98112, USA
| | - M Bradley Hanson
- Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Boulevard East, Seattle, WA 98112, USA
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McNally KL, Bowen JL, Brisson JO, Kennedy A, Innis CJ. Evaluation of the Respiratory Microbiome and the Use of Tracheal Lavage as a Diagnostic Tool in Kemp's Ridley Sea Turtles ( Lepidochelys kempii). Animals (Basel) 2021; 11:ani11102927. [PMID: 34679947 PMCID: PMC8532748 DOI: 10.3390/ani11102927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 11/22/2022] Open
Abstract
Simple Summary A tracheal lavage is commonly used to characterize the microbes that may be causing pneumonia in sea turtles, typically by culture-dependent methods. In this study, we characterized the tracheal lavage microbiome through culture-independent methods and compared the resulting sequence data to conventional cultures, the degree of radiographic lung abnormalities, and pathogens of sea turtles as previously reported in the literature. This study also evaluates the microbial communities at different sections of the respiratory tract from deceased sea turtles. We found that radiographic lung abnormalities do not correlate with the tracheal lavage microbiome, tracheal lavage cultures under-represent the microbial community as determined by culture-independent methods, many previously reported sea turtle pathogens are present in low abundance of the tracheal lavage microbiome, and tracheal lavages are not representative of other sections of the respiratory tract. Abstract Respiratory disease is a common cause of morbidity and mortality in sea turtles, including the Kemp’s ridley sea turtle (Lepidochelys kempii). Although culture-dependent methods are typically used to characterize microbes associated with pneumonia and to determine treatment, culture-independent methods can provide a deeper understanding of the respiratory microbial communities and lead to a more accurate diagnosis. In this study, we characterized the tracheal lavage microbiome from cold-stunned Kemp’s ridley sea turtles at three time points during rehabilitation (intake, rehabilitation, and convalescence) by analyzing the 16S rRNA gene collected from tracheal lavage samples. We retrospectively developed a radiographic scoring system to grade the severity of lung abnormalities in these turtles and found no differences in diversity or composition of microbial communities based on radiographic score. We also found that the culture isolates from tracheal lavage samples, as well as other previously reported sea turtle pathogens, were present in variable abundance across sequenced samples. In addition to the tracheal microbial community of live turtles, we characterized microbial communities from other segments of the respiratory tract (glottis, trachea, anterior lung, posterior lung) from deceased turtles. We found a high degree of variability within turtles and a high degree of dissimilarity between different segments of the respiratory tract and the tracheal lavage collected from the same turtle. In summary, we found that the pulmonary microbial community associated with pneumonia in sea turtles is complex and does not correlate well with the microbial community as identified by tracheal lavage. These results underscore the limitations of using tracheal lavage for identification of the causative agents of pneumonia in sea turtles.
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Affiliation(s)
- Kerry L. McNally
- Animal Health Department, New England Aquarium, Boston, MA 02110, USA;
- Correspondence:
| | - Jennifer L. Bowen
- Marine Science Center, Department of Marine and Environmental Sciences, Northeastern University, Nahant, MA 01908, USA;
| | - Jennifer O. Brisson
- Massachusetts Veterinary Referral Hospital, Ethos Veterinary Health, Woburn, MA 01801, USA;
| | - Adam Kennedy
- Rescue & Rehabilitation Department, New England Aquarium, Boston, MA 02110, USA;
| | - Charles J. Innis
- Animal Health Department, New England Aquarium, Boston, MA 02110, USA;
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McNally KL, Mott CR, Guertin JR, Bowen JL. Microbial communities of wild-captured Kemp’s ridley (Lepidochelys kempii) and green sea turtles (Chelonia mydas). ENDANGER SPECIES RES 2021. [DOI: 10.3354/esr01116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Conservation efforts for endangered sea turtle species, such as Kemp’s ridley turtles Lepidochelys kempii and green turtles Chelonia mydas, may benefit from information on the microbial communities that contribute to host health. Previous studies examining host-associated microbiomes of these species have been limited in geographic region, life stage, and/or health. Here, we characterized the microbiome of the oral cavity and cloaca from wild-captured Kemp’s ridley and green turtles off the west coast of Florida, USA, by using Illumina sequencing to analyze the 16S rRNA gene. Microbial communities were distinct between body sites as well as between turtle species, suggesting that the turtle species is more important than the local environment in determining the microbiome of sea turtles. We identified the core microbiome for each species at each body site and determined that there were very few bacteria shared among the oral samples of both species, and no taxa co-occurred in the cloaca samples among both species. The core microbiome of the green turtle cloaca was primarily from the order Clostridiales, which plays an important role in digestion for other herbivorous species. Due to high prevalence of fibropapillomatosis in the green turtles (90%), we also investigated the correlation between the microbiome and the severity of fibropapillomatosis, and we identified changes in beta diversity associated with the total number of tumors. This study provides the first glimpse of the microbiome in 2 sympatric species of sea turtle and sheds an important species-specific light on the microbiome of these endangered species.
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Affiliation(s)
- KL McNally
- Animal Health Department, New England Aquarium, Boston, Massachusetts 02110, USA
- University of Massachusetts, Boston, Massachusetts 20125, USA
| | - CR Mott
- Inwater Research Group, Inc., Jensen Beach, Florida 34957, USA
| | - JR Guertin
- Inwater Research Group, Inc., Jensen Beach, Florida 34957, USA
| | - JL Bowen
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, Nahant, Massachusetts 01908, USA
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Vendl C, Nelson T, Ferrari B, Thomas T, Rogers T. Highly abundant core taxa in the blow within and across captive bottlenose dolphins provide evidence for a temporally stable airway microbiota. BMC Microbiol 2021; 21:20. [PMID: 33421992 PMCID: PMC7796641 DOI: 10.1186/s12866-020-02076-z] [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: 03/09/2020] [Accepted: 12/20/2020] [Indexed: 12/15/2022] Open
Abstract
Background The analysis of blow microbiota has been proposed as a biomarker for respiratory health analysis in cetaceans. Yet, we lack crucial knowledge on the long-term stability of the blow microbiota and its potential changes during disease. Research in humans and mice have provided evidence that respiratory disease is accompanied by a shift in microbial communities of the airways. We investigate here the stability of the community composition of the blow microbiota for 13 captive bottlenose dolphins over eight months including both sick and healthy individuals. We used barcoded tag sequencing of the bacterial 16S rRNA gene. Four of the dolphins experienced distinct medical conditions and received systemic antimicrobial treatment during the study. Results We showed that each dolphin harboured a unique community of zero-radius operational taxonomic units (zOTUs) that was present throughout the entire sampling period (‘intra-core’). Although for most dolphins there was significant variation over time, overall the intra-core accounted for an average of 73% of relative abundance of the blow microbiota. In addition, the dolphins shared between 8 and 66 zOTUs on any of the sampling occasions (‘inter-core’), accounting for a relative abundance between 17 and 41% of any dolphin’s airway microbiota. The majority of the intra-core and all of the inter-core zOTUs in this study are commonly found in captive and free-ranging dolphins and have previously been reported from several different body sites. While we did not find a clear effect of microbial treatment on blow microbiota, age and sex of the dolphins did have such an effect. Conclusions The airways of dolphins were colonized by an individual intra-core ‘signature’ that varied in abundance relative to more temporary bacteria. We speculate that the intra-core bacteria interact with the immune response of the respiratory tract and support its function. This study provides the first evidence of individual-specific airway microbiota in cetaceans that is stable over eight months. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-020-02076-z.
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Affiliation(s)
- Catharina Vendl
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.
| | - Tiffanie Nelson
- Queensland Facility for Advanced Bioinformatics, Griffith University, Gold Coast, Southport, QLD, 4215, Australia
| | - Belinda Ferrari
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Tracey Rogers
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
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Groch KR, Blazquez DNH, Marcondes MCC, Santos J, Colosio A, Díaz Delgado J, Catão-Dias JL. Cetacean morbillivirus in Humpback whales' exhaled breath. Transbound Emerg Dis 2020; 68:1736-1743. [PMID: 33070446 DOI: 10.1111/tbed.13883] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 10/10/2020] [Accepted: 10/13/2020] [Indexed: 12/21/2022]
Abstract
The humpback whale (HW; Megaptera novaeangliae) population that seasonally resides along the Brazilian coast concentrates in the Abrolhos Bank (Bahia and Espírito Santo states) for breeding during austral winter and spring. Cetacean morbillivirus (CeMV, Paramyxoviridae family) is currently one of the most significant biological threats to cetaceans worldwide with high infection and mortality rates. CeMV is pleiotropic yet it has special tropism for the respiratory, lymphoid and nervous system and is primarily transmitted by the aerogenous route. A new lineage of CeMV, the Guiana dolphin morbillivirus (GDMV), is known to affect cetaceans off Brazil. GDMV was first detected in a Guiana dolphin (Sotalia guianensis) stranded in the Abrolhos Bank region, in 2010. In addition to pathologic examinations on stranded HW, pathogen survey of free-ranging HW may provide valuable insight into the epidemiology of diseases. We hypothesized that HW in the Brazilian breeding ground could be exposed to CeMV. Thus, in the present study, we investigated the presence of CeMV in exhaled breath condensates (EBC) of HW in the Abrolhos Bank. Overall, 73 samples of EBC from 48 groups of HW were collected during the breeding seasons of 2011 (n = 16) and 2012 (n = 57). One sample failed to have the reference gene amplified and was excluded from the study. CeMV was detected by a RT-qPCR method in 2 EBC samples, representing 2 whale groups. Phylogenetic analysis of partial morbillivirus phosphoprotein gene showed 100% homology to GDMV. Our results show that HW in Brazil are infected by CeMV with a relative prevalence of 4.3% (2/47) and demonstrate the suitability of using EBC and RT-qPCR as a non-invasive tool for CeMV survey in free-ranging whales. This pioneer study provides scientific basis for non-invasive CeMV monitoring of HW, suggests HW may play a role in the dynamics of CeMV and raises concern for potential conservation implications for this species.
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Respiratory microbiota of humpback whales may be reduced in diversity and richness the longer they fast. Sci Rep 2020; 10:12645. [PMID: 32724137 PMCID: PMC7387350 DOI: 10.1038/s41598-020-69602-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 07/08/2020] [Indexed: 12/31/2022] Open
Abstract
Humpback whales endure several months of fasting while undertaking one of the longest annual migrations of any mammal, which depletes the whales’ energy stores and likely compromises their physiological state. Airway microbiota are linked to respiratory health in mammals. To illuminate the dynamics of airway microbiota in a physiologically challenged mammal, we investigated the bacterial communities in the blow of East Australian humpback whales at two stages of their migration: at the beginning (n = 20) and several months into their migration (n = 20), using barcoded tag sequencing of the bacterial 16S rRNA gene. We show that early in the fasting the whale blow samples had a higher diversity and richness combined with a larger number of core taxa and a different bacterial composition than later in the fasting. This study provides some evidence that the rich blow microbiota at the beginning of their fasting might reflect the whales’ uncompromised physiology and that changes in the microbiota occur during the whales’ migration.
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12
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Vendl C, Ferrari BC, Thomas T, Slavich E, Zhang E, Nelson T, Rogers T. Interannual comparison of core taxa and community composition of the blow microbiota from East Australian humpback whales. FEMS Microbiol Ecol 2020; 95:5526219. [PMID: 31260051 DOI: 10.1093/femsec/fiz102] [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: 01/31/2019] [Accepted: 06/28/2019] [Indexed: 02/07/2023] Open
Abstract
Cetacean represent vulnerable species impacted by multiple stressors, including reduction in prey species, habitat destruction, whaling and infectious disease. The composition of blow microbiota has been claimed to provide a promising tool for non-invasive health monitoring aiming to inform conservation management. Still, little is known about the temporal stability and composition of blow microbiota in whales. We used East Australian humpback whales (Megaptera novaeangliae) as a model species and collected blow and control samples in August 2016 and 2017 for an interannual comparison. We analysed the blow by barcode tag sequencing of the bacterial 16S rRNA gene. We found that the microbial communities in 2016 and 2017 were statistically similar regarding alpha and beta diversity but distinct to seawater. Zero-radius operational taxonomic units (zOTUs) shared by both groups accounted for about 50% of all zOTUs present. Still, the large individual variability in the blow microbiota resulted in a small number of core taxa (defined as present in at least 60% of whales). We conclude that the blow microbiota of humpback whales is either generally limited and of transient nature or the reduced airway microbiota is the symptom of a compromised physiological state potentially due to the challenges of the whales' annual migration.
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Affiliation(s)
- C Vendl
- Evolution & Ecology Research Centre, School of Biological, Environmental and Earth Science, UNSW Sydney, NSW 2052, Australia
| | - B C Ferrari
- The School of Biotechnology and Biomolecular Sciences, UNSW Sydney, NSW 2052, Australia
| | - T Thomas
- Centre of Marine Bio-Innovation (CMB), School of Biological, Environmental and Earth Science, UNSW Sydney, NSW 2052, Australia
| | - E Slavich
- Stats Central, Mark Wainwright Analytical Centre, UNSW, Sydney, NSW 2052, Australia
| | - E Zhang
- The School of Biotechnology and Biomolecular Sciences, UNSW Sydney, NSW 2052, Australia
| | - T Nelson
- Queensland Facility for Advanced Bioinformatics, Griffith University, Gold Coast, Southport, QLD 4215, Australia
| | - T Rogers
- Evolution & Ecology Research Centre, School of Biological, Environmental and Earth Science, UNSW Sydney, NSW 2052, Australia
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Vendl C, Slavich E, Nelson T, Acevedo-Whitehouse K, Montgomery K, Ferrari B, Thomas T, Rogers T. Does sociality drive diversity and composition of airway microbiota in cetaceans? ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:324-333. [PMID: 32162479 DOI: 10.1111/1758-2229.12835] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 02/25/2020] [Accepted: 03/09/2020] [Indexed: 05/23/2023]
Abstract
The number of social contacts of mammals is positively correlated with the diversity of their gut microbes. There is some evidence that sociality also affects microbes in the respiratory tract. We tested whether the airway microbiota of cetacean species differ depending on the whales' level of sociality. We sampled the blow of blue (Balaenoptera musculus), grey (Eschrichtius robustus), humpback (Megaptera novaeangliae) and long-finned pilot whales (PWs) (Globicephala melas) and analysed the blow microbiota by barcode tag sequencing targeting the V4 region of the bacterial 16S rRNA gene. Humpback whales (HWs) show higher levels of sociality than blue (BW) and grey (GW), while PWs are the most gregarious among the four species. The blow samples of the HWs showed the highest richness and diversity. HWs were also the only species with a species-specific clustering of their microbial community composition and a relatively large number of core taxa. Therefore, we conclude that it cannot be sociality alone shaping the diversity and composition of airway microbiota. We suggest the whale species' lung volume and size of the plume of exhaled air as an additional factor impacting the transmission potential of blow microbiota from one individual whale to another.
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Affiliation(s)
- Catharina Vendl
- Evolution & Ecology Research Centre, School of Biological, Environmental and Earth Science, UNSW Sydney, NSW, 2052, Australia
| | - Eve Slavich
- Evolution & Ecology Research Centre, School of Biological, Environmental and Earth Science, UNSW Sydney, NSW, 2052, Australia
- Stats Central, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, UNSW, 2052, Australia
| | - Tiffanie Nelson
- Queensland Facility for Advanced Bioinformatics, School of Medicine, Menzies Health Institute Queensland, Building G40, Level 9, Gold Coast Campus, Griffith University, Southport, QLD, 4215, Australia
| | - Karina Acevedo-Whitehouse
- Unit for Basic and Applied Microbiology, School of Natural Sciences, Autonomous University of Queretaro, Queretaro, 76230, Mexico
| | - Kate Montgomery
- The School of Biotechnology and Biomolecular Sciences, UNSW Sydney, NSW, 2052, Australia
| | - Belinda Ferrari
- The School of Biotechnology and Biomolecular Sciences, UNSW Sydney, NSW, 2052, Australia
| | - Torsten Thomas
- Centre of Marine Bio-Innovation (CMB), School of Biological, Environmental and Earth Science, UNSW Sydney, NSW, 2052, Australia
| | - Tracey Rogers
- Evolution & Ecology Research Centre, School of Biological, Environmental and Earth Science, UNSW Sydney, NSW, 2052, Australia
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14
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Robles-Malagamba MJ, Walsh MT, Ahasan MS, Thompson P, Wells RS, Jobin C, Fodor AA, Winglee K, Waltzek TB. Characterization of the bacterial microbiome among free-ranging bottlenose dolphins ( Tursiops truncatus). Heliyon 2020; 6:e03944. [PMID: 32577542 PMCID: PMC7305398 DOI: 10.1016/j.heliyon.2020.e03944] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/07/2020] [Accepted: 05/05/2020] [Indexed: 12/11/2022] Open
Abstract
Marine animals represent a dynamic and complex habitat for diverse microbial communities. The microbiota associated with bottlenose dolphins (Tursiops truncatus) are believed to influence their health status, but it remains poorly understood. We therefore characterized and compared the bacterial microbiome of bottlenose dolphins from six different anatomical sites that represent four different body systems (respiratory, digestive, reproductive, and integumentary). In this study, a total of 14 free-ranging bottlenose dolphins were sampled during the 2015 Sarasota Bay Dolphin Health Assessment. Bacterial diversity and abundance were assessed by PCR amplification of the hypervariable V3-V4 regions of the bacterial 16S rRNA gene for each sample, followed by sequencing on an Illumina MiSeq platform. Analysis showed that bottlenose dolphins harbor diverse bacterial communities with a unique microbial community at each body system. Additionally, the bottlenose dolphin bacterial microbiome was clearly distinct to the aquatic microbiome from their surrounding habitat. These results are in close agreement with other cetacean microbiome studies, while our study is the first to explore what was found to be a diverse bottlenose dolphin genital microbiome. The core bacterial communities identified in this study in apparently healthy animals might be informative for future health monitoring of bottlenose dolphins.
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Affiliation(s)
- María José Robles-Malagamba
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - Michael T. Walsh
- Department of Comparative, Diagnostic and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - Mohammad Shamim Ahasan
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
- Department of Medicine, Surgery and Obstetrics, Faculty of Veterinary and Animal Sciences, Hajee Mohammad Danesh Science and Technology University, Dinajpur, Bangladesh
| | - Patrick Thompson
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - Randall S. Wells
- Chicago Zoological Society's Sarasota Dolphin Research Program, Mote Marine Laboratory, Sarasota, Florida, USA
| | - Christian Jobin
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
- Division of Gastroenterology, Hepatology, and Nutrition, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Anthony A. Fodor
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, North Carolina, USA
| | - Kathryn Winglee
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, North Carolina, USA
| | - Thomas B. Waltzek
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
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15
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Microbiota and Metabolite Profiling of Spoiled Spanish-Style Green Table Olives. Metabolites 2018; 8:metabo8040073. [PMID: 30384453 PMCID: PMC6316098 DOI: 10.3390/metabo8040073] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 10/23/2018] [Accepted: 10/29/2018] [Indexed: 12/25/2022] Open
Abstract
The aim of the present study was to assess the malodorous spoilages of Spanish-style green table olives through microbial and metabolite composition using current measuring techniques (e.g., high-throughput DNA sequencing, headspace solid-phase microextraction combined with gas chromatography-mass spectrometry). Under different alkaline and washing conditions, the spoilage fermentations were reproduced with Gordal and Manzanilla olive cultivars using a low salt concentration (71 g L−1 NaCl) in the initial brine. The degradation of lactic acid and significant increases in volatile fatty acids and phenols were found in all the spoiled samples in comparison with the unspoiled control samples. According to high-throughput DNA sequencing, Cardiobacteriaceae and Ruminococcus were the dominant bacteria in the spoiled samples. PLS regression and Pearson’s correlation coefficient analyses revealed positive and negative correlations among microbial communities, metabolites, and sensory spoilage descriptors. Notably, the “zapatera” descriptor was significantly associated with Propionibacterium, which was positively correlated with acetic acid, propionic acid, succinic acid, and methyl propanoate; while the “butyric” descriptor exhibited a significant positive relationship with the genus Ruminococcus, which gave an almost significant correlation with propionic and butyric acids.
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16
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Milan M, Carraro L, Fariselli P, Martino ME, Cavalieri D, Vitali F, Boffo L, Patarnello T, Bargelloni L, Cardazzo B. Microbiota and environmental stress: how pollution affects microbial communities in Manila clams. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2018; 194:195-207. [PMID: 29202271 DOI: 10.1016/j.aquatox.2017.11.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/13/2017] [Accepted: 11/26/2017] [Indexed: 06/07/2023]
Abstract
Given the crucial role of microbiota in host development, health, and environmental interactions, genomic analyses focusing on host-microbiota interactions should certainly be considered in the investigation of the adaptive mechanisms to environmental stress. Recently, several studies suggested that microbiota associated to digestive tract is a key, although still not fully understood, player that must be considered to assess the toxicity of environmental contaminants. Bacteria-dependent metabolism of xenobiotics may indeed modulate the host toxicity. Conversely, environmental variables (including pollution) may alter the microbial community and/or its metabolic activity leading to host physiological alterations that may contribute to their toxicity. Here, 16s rRNA gene amplicon sequencing has been applied to characterize the hepatopancreas microbiota composition of the Manila clam, Ruditapes philippinarum. The animals were collected in the Venice lagoon area, which is subject to different anthropogenic pressures, mainly represented by the industrial activities of Porto Marghera (PM). Seasonal and geographic differences in clam microbiotas were explored and linked to host response to chemical stress identified in a previous study at the transcriptome level, establishing potential interactions among hosts, microbes, and environmental parameters. The obtained results showed the recurrent presence of putatively detoxifying bacterial taxa in PM clams during winter and over-representation of several metabolic pathways involved in xenobiotic degradation, which suggested the potential for host-microbial synergistic detoxifying actions. Strong interaction between seasonal and chemically-induced responses was also observed, which partially obscured such potentially synergistic actions. Seasonal variables and exposure to toxicants were therefore shown to interact and substantially affect clam microbiota, which appeared to mirror host response to environmental variation. It is clear that understanding how animals respond to chemical stress cannot ignore a key component of such response, the microbiota.
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Affiliation(s)
- M Milan
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020, Legnaro, Italy; CONISMA - Consorzio Nazionale Interuniversitario per le Scienze del Mare, Roma, Italy
| | - L Carraro
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020, Legnaro, Italy
| | - P Fariselli
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020, Legnaro, Italy
| | - M E Martino
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon, Lyon, France
| | - D Cavalieri
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Firenze, Italy
| | - F Vitali
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Firenze, Italy
| | - L Boffo
- Associazione "Vongola Verace di Chioggia", Italy
| | - T Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020, Legnaro, Italy
| | - L Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020, Legnaro, Italy; CONISMA - Consorzio Nazionale Interuniversitario per le Scienze del Mare, Roma, Italy
| | - B Cardazzo
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020, Legnaro, Italy
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17
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Captive bottlenose dolphins and killer whales harbor a species-specific skin microbiota that varies among individuals. Sci Rep 2017; 7:15269. [PMID: 29127421 PMCID: PMC5681658 DOI: 10.1038/s41598-017-15220-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/23/2017] [Indexed: 02/06/2023] Open
Abstract
Marine animals surfaces host diverse microbial communities, which play major roles for host’s health. Most inventories of marine animal surface microbiota have focused on corals and fishes, while cetaceans remain overlooked. The few studies focused on wild cetaceans, making difficult to distinguish intrinsic inter- and/or intraspecific variability in skin microbiota from environmental effects. We used high-throughput sequencing to assess the skin microbiota from 4 body zones of 8 bottlenose dolphins (Tursiops truncatus) and killer whales (Orcinus orca), housed in captivity (Marineland park, France). Overall, cetacean skin microbiota is more diverse than planktonic communities and is dominated by different phylogenetic lineages and functions. In addition, the two cetacean species host different skin microbiotas. Within each species, variability was higher between individuals than between body parts, suggesting a high individuality of cetacean skin microbiota. Overall, the skin microbiota of the assessed cetaceans related more to the humpback whale and fishes’ than to microbiotas of terrestrial mammals.
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18
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Borras E, Aksenov AA, Baird M, Novick B, Schivo M, Zamuruyev KO, Pasamontes A, Parry C, Foutouhi S, Venn-Watson S, Weimer BC, Davis CE. Exhaled breath condensate methods adapted from human studies using longitudinal metabolomics for predicting early health alterations in dolphins. Anal Bioanal Chem 2017; 409:6523-6536. [PMID: 29063162 DOI: 10.1007/s00216-017-0581-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 07/30/2017] [Accepted: 08/10/2017] [Indexed: 10/18/2022]
Abstract
Monitoring health conditions is essential to detect early asymptomatic stages of a disease. To achieve this, blood, urine and breath samples are commonly used as a routine clinical diagnostic. These samples offer the opportunity to detect specific metabolites related to diseases and provide a better understanding of their development. Although blood samples are commonly used routinely to monitor health, the implementation of a relatively noninvasive technique, such as exhaled breath condensate (EBC) analysis, may further benefit the well-being of both humans and other animals. EBC analysis can be used to track possible physical or biochemical alterations caused by common diseases of the bottlenose dolphin (Tursiops truncatus), such as infections or inflammatory-mediated processes. We have used an untargeted metabolomic method with liquid chromatography-mass spectrometry analysis of EBC samples to determine biomarkers related to disease development. In this study, five dolphins under human care were followed up for 1 year. We collected paired blood, physical examination information, and EBC samples. We then statistically correlated this information to predict specific health alterations. Three dolphins provided promising case study information about biomarkers related to cutaneous infections, respiratory infections, dental disease, or hormonal changes (pregnancy). The use of complementary liquid chromatography platforms, with hydrophilic interaction chromatography and reverse-phased columns, allowed us to detect a wide spectrum of EBC biomarker compounds that could be related to these health alterations. Moreover, these two analytical techniques not only provided complementary metabolite information but in both cases they also provided promising diagnostic information for these health conditions. Graphical abstract Collection of the exhaled condensed breath from a bottlenose dolphin from U.S. Navy Marine Mammal Program (MMP).
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Affiliation(s)
- Eva Borras
- Department of Mechanical and Aerospace Engineering, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Alexander A Aksenov
- Department of Mechanical and Aerospace Engineering, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Mark Baird
- Translational Medicine and Research Program, National Marine Mammal Foundation, 2240 Shelter Island Drive, Suite 200, San Diego, CA, 92106, USA
| | - Brittany Novick
- Translational Medicine and Research Program, National Marine Mammal Foundation, 2240 Shelter Island Drive, Suite 200, San Diego, CA, 92106, USA
| | - Michael Schivo
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, University of California, Davis, Sacramento, CA, 95617, USA
- Center for Comparative Respiratory Biology and Medicine, University of California, Davis, Davis, CA, 95616, USA
| | - Konstantin O Zamuruyev
- Department of Mechanical and Aerospace Engineering, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Alberto Pasamontes
- Department of Mechanical and Aerospace Engineering, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Celeste Parry
- Translational Medicine and Research Program, National Marine Mammal Foundation, 2240 Shelter Island Drive, Suite 200, San Diego, CA, 92106, USA
| | - Soraya Foutouhi
- School of Veterinary Medicine, University of California, Davis, 1089 Veterinary Medicine Drive, Davis, CA, 95616, USA
| | - Stephanie Venn-Watson
- Translational Medicine and Research Program, National Marine Mammal Foundation, 2240 Shelter Island Drive, Suite 200, San Diego, CA, 92106, USA
| | - Bart C Weimer
- School of Veterinary Medicine, University of California, Davis, 1089 Veterinary Medicine Drive, Davis, CA, 95616, USA
| | - Cristina E Davis
- Department of Mechanical and Aerospace Engineering, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA.
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Extensive Core Microbiome in Drone-Captured Whale Blow Supports a Framework for Health Monitoring. mSystems 2017; 2:mSystems00119-17. [PMID: 29034331 PMCID: PMC5634792 DOI: 10.1128/msystems.00119-17] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 09/13/2017] [Indexed: 01/21/2023] Open
Abstract
The pulmonary system is a common site for bacterial infections in cetaceans, but very little is known about their respiratory microbiome. We used a small, unmanned hexacopter to collect exhaled breath condensate (blow) from two geographically distinct populations of apparently healthy humpback whales (Megaptera novaeangliae), sampled in the Massachusetts coastal waters off Cape Cod (n = 17) and coastal waters around Vancouver Island (n = 9). Bacterial and archaeal small-subunit rRNA genes were amplified and sequenced from blow samples, including many of sparse volume, as well as seawater and other controls, to characterize the associated microbial community. The blow microbiomes were distinct from the seawater microbiomes and included 25 phylogenetically diverse bacteria common to all sampled whales. This core assemblage comprised on average 36% of the microbiome, making it one of the more consistent animal microbiomes studied to date. The closest phylogenetic relatives of 20 of these core microbes were previously detected in marine mammals, suggesting that this core microbiome assemblage is specialized for marine mammals and may indicate a healthy, noninfected pulmonary system. Pathogen screening was conducted on the microbiomes at the genus level, which showed that all blow and few seawater microbiomes contained relatives of bacterial pathogens; no known cetacean respiratory pathogens were detected in the blow. Overall, the discovery of a shared large core microbiome in humpback whales is an important advancement for health and disease monitoring of this species and of other large whales. IMPORTANCE The conservation and management of large whales rely in part upon health monitoring of individuals and populations, and methods generally necessitate invasive sampling. Here, we used a small, unmanned hexacopter drone to noninvasively fly above humpback whales from two populations, capture their exhaled breath (blow), and examine the associated microbiome. In the first extensive examination of the large-whale blow microbiome, we present surprising results about the discovery of a large core microbiome that was shared across individual whales from geographically separated populations in two ocean basins. We suggest that this core microbiome, in addition to other microbiome characteristics, could be a useful feature for health monitoring of large whales worldwide.
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Wan X, McLaughlin RW, Zhou J, Hao Y, Zheng J, Wang D. Isolation of culturable aerobic bacteria and evidence of Kerstersia gyiorum from the blowhole of captive Yangtze finless porpoises. Antonie van Leeuwenhoek 2016; 109:1167-75. [DOI: 10.1007/s10482-016-0713-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 05/09/2016] [Indexed: 10/21/2022]
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Bik EM, Costello EK, Switzer AD, Callahan BJ, Holmes SP, Wells RS, Carlin KP, Jensen ED, Venn-Watson S, Relman DA. Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea. Nat Commun 2016; 7:10516. [PMID: 26839246 PMCID: PMC4742810 DOI: 10.1038/ncomms10516] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 12/18/2015] [Indexed: 12/15/2022] Open
Abstract
Marine mammals play crucial ecological roles in the oceans, but little is known about their microbiotas. Here we study the bacterial communities in 337 samples from 5 body sites in 48 healthy dolphins and 18 healthy sea lions, as well as those of adjacent seawater and other hosts. The bacterial taxonomic compositions are distinct from those of other mammals, dietary fish and seawater, are highly diverse and vary according to body site and host species. Dolphins harbour 30 bacterial phyla, with 25 of them in the mouth, several abundant but poorly characterized Tenericutes species in gastric fluid and a surprisingly paucity of Bacteroidetes in distal gut. About 70% of near-full length bacterial 16S ribosomal RNA sequences from dolphins are unique. Host habitat, diet and phylogeny all contribute to variation in marine mammal distal gut microbiota composition. Our findings help elucidate the factors structuring marine mammal microbiotas and may enhance monitoring of marine mammal health.
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Affiliation(s)
- Elisabeth M. Bik
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
- Veterans Affairs Palo Alto Health Care System, Palo Alto, California 94304, USA
| | - Elizabeth K. Costello
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Alexandra D. Switzer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | | | - Susan P. Holmes
- Department of Statistics, Stanford University, Stanford, California 94305, USA
| | - Randall S. Wells
- Sarasota Dolphin Research Program, Chicago Zoological Society, c/o Mote Marine Laboratory, Sarasota, Florida 34236, USA
| | - Kevin P. Carlin
- Translational Medicine and Research Program, National Marine Mammal Foundation, San Diego, California 92106, USA
| | - Eric D. Jensen
- Space and Naval Warfare Systems Center Pacific, San Diego, California 92152, USA
| | - Stephanie Venn-Watson
- Translational Medicine and Research Program, National Marine Mammal Foundation, San Diego, California 92106, USA
| | - David A. Relman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
- Veterans Affairs Palo Alto Health Care System, Palo Alto, California 94304, USA
- Department of Medicine (Infectious Diseases and Geographic Medicine), Stanford University School of Medicine, Stanford, California 94305, USA
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Jaing C, Thissen JB, Gardner S, McLoughlin K, Slezak T, Bossart GD, Fair PA. Pathogen surveillance in wild bottlenose dolphins Tursiops truncatus. DISEASES OF AQUATIC ORGANISMS 2015; 116:83-91. [PMID: 26480911 DOI: 10.3354/dao02917] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The number and prevalence of diseases is rapidly increasing in the marine ecosystem. Although there is an increase in the number of marine diseases observed world-wide, current understanding of the pathogens associated with marine mammals is limited. An important need exists to develop and apply platforms for rapid detection and characterization of pathogenic agents to assess, prevent and respond to disease outbreaks. In this study, a broad-spectrum molecular detection technology capable of detecting all sequenced microbial organisms, the Lawrence Livermore Microbial Detection Array, was used to assess the microbial agents that could be associated with wild Atlantic dolphins. Blowhole, gastric, and fecal samples from 8 bottlenose dolphins were collected in Charleston, SC, as part of the dolphin assessment effort. The array detected various microbial agents from the dolphin samples. Clostridium perfringens was most prevalent in the samples surveyed using the microarray. This pathogen was also detected using microbiological culture techniques. Additionally, Campylobacter sp., Staphylococcus sp., Erwinia amylovora, Helicobacter pylori, and Frankia sp. were also detected in more than one dolphin using the microarray, but not in culture. This study provides the first survey of pathogens associated with 3 tissue types in dolphins using a broad-spectrum microbial detection microarray and expands insight on the microbial community profile in dolphins.
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Affiliation(s)
- Crystal Jaing
- Physical & Life Sciences Directorate, Computations Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
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Lokmer A, Mathias Wegner K. Hemolymph microbiome of Pacific oysters in response to temperature, temperature stress and infection. THE ISME JOURNAL 2015; 9:670-82. [PMID: 25180968 PMCID: PMC4331581 DOI: 10.1038/ismej.2014.160] [Citation(s) in RCA: 185] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 05/13/2014] [Accepted: 07/19/2014] [Indexed: 12/24/2022]
Abstract
Microbiota provide their hosts with a range of beneficial services, including defense from external pathogens. However, host-associated microbial communities themselves can act as a source of opportunistic pathogens depending on the environment. Marine poikilotherms and their microbiota are strongly influenced by temperature, but experimental studies exploring how temperature affects the interactions between both parties are rare. To assess the effects of temperature, temperature stress and infection on diversity, composition and dynamics of the hemolymph microbiota of Pacific oysters (Crassostrea gigas), we conducted an experiment in a fully-crossed, three-factorial design, in which the temperature acclimated oysters (8 or 22 °C) were exposed to temperature stress and to experimental challenge with a virulent Vibrio sp. strain. We monitored oyster survival and repeatedly collected hemolymph of dead and alive animals to determine the microbiome composition by 16s rRNA gene amplicon pyrosequencing. We found that the microbial dynamics and composition of communities in healthy animals (including infection survivors) were significantly affected by temperature and temperature stress, but not by infection. The response was mediated by changes in the incidence and abundance of operational taxonomic units (OTUs) and accompanied by little change at higher taxonomic levels, indicating dynamic stability of the hemolymph microbiome. Dead and moribund oysters, on the contrary, displayed signs of community structure disruption, characterized by very low diversity and proliferation of few OTUs. We can therefore link short-term responses of host-associated microbial communities to abiotic and biotic factors and assess the potential feedback between microbiota dynamics and host survival during disease.
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Affiliation(s)
- Ana Lokmer
- Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Coastal Ecology, Wadden Sea Station Sylt, List, Sylt, Germany
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Evolutionary Ecology of Marine Fishes, Kiel, Germany
| | - Karl Mathias Wegner
- Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Coastal Ecology, Wadden Sea Station Sylt, List, Sylt, Germany
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Nelson TM, Apprill A, Mann J, Rogers TL, Brown MV. The marine mammal microbiome: current knowledge and future directions. MICROBIOLOGY AUSTRALIA 2015. [DOI: 10.1071/ma15004] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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