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Gignoux-Wolfsohn S, Garcia Ruiz M, Portugal Barron D, Ruiz G, Lohan K. Bivalve microbiomes are shaped by host species, size, parasite infection, and environment. PeerJ 2024; 12:e18082. [PMID: 39399422 PMCID: PMC11468899 DOI: 10.7717/peerj.18082] [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: 12/06/2023] [Accepted: 08/20/2024] [Indexed: 10/15/2024] Open
Abstract
Many factors affect an organism's microbiome including its environment, proximity to other organisms, and physiological condition. As filter feeders, bivalves have highly plastic microbiomes that are especially influenced by the surrounding seawater, yet they also maintain a unique core set of microbes. Using 16S ribosomal RNA sequencing, we characterized the bacterial microbiomes of four species of bivalves native to the Mid-Atlantic East Coast of North America: Crassostrea virginica, Macoma balthica, Ameritella mitchelli, and Ischadium recurvum and assessed the impact of their external environment, internal parasites, and size on their microbial communities. We found significant differences in bacterial amplicon sequence variants (ASVs) across species, with each species harboring a core ASV present across all individuals. We further found that some C. virginica co-cultured with I. recurvum had high abundances of the I. recurvum core ASV. We identified ASVs associated with infection by the parasites Perkinsus marinus and Zaops ostreum as well others associated with bivalve size. Several of these ASV are candidates for further investigation as potential probiotics, as they were found positively correlated with bivalve size and health. This research represents the first description of the microbiomes of A. mitchelli, I. recurvum, and M. balthica. We document that all four species have highly plastic microbiomes, while maintaining certain core bacteria, with important implications for growth, health, and adaptation to new environments.
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Affiliation(s)
- Sarah Gignoux-Wolfsohn
- Biological Sciences, University of Massachusetts at Lowell, Lowell, MA, United States
- Coastal Disease Ecology Laboratory, Smithsonian Environmental Research Center, Edgewater, MD, United States
| | - Monserrat Garcia Ruiz
- Coastal Disease Ecology Laboratory, Smithsonian Environmental Research Center, Edgewater, MD, United States
| | - Diana Portugal Barron
- Coastal Disease Ecology Laboratory, Smithsonian Environmental Research Center, Edgewater, MD, United States
- Department of Neurology, Brain Research Institute, Mary S. Easton Center for Alzheimer’s Research and Care, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Gregory Ruiz
- Marine Invasions Laboratory, Smithsonian Environmental Research Center, Edgewater, MD, United States
| | - Katrina Lohan
- Coastal Disease Ecology Laboratory, Smithsonian Environmental Research Center, Edgewater, MD, United States
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Tsoukalas D, Hamed I, Hoel S, Lerfall J, Jakobsen AN. Effect of harvesting season and location on the microbial quality and community composition of the edible sea urchin (Echinus esculentus) gonads. Food Microbiol 2024; 123:104594. [PMID: 39038897 DOI: 10.1016/j.fm.2024.104594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 06/07/2024] [Accepted: 07/01/2024] [Indexed: 07/24/2024]
Abstract
Despite the crucial role of microbial community composition in the quality and stability of seafood, little emphasis has been given to the microbiota profile of sea urchin gonads. This study investigates the microbial quality and community composition of sea urchin gonads (Echinus esculentus) as a function of harvesting season (autumn, winter, spring, and summer) and location (one site proximal to urban activity areas while the other is located in open water close to the coastline). Significant season-dependent variations were found in psychrotrophic and aerobic plate counts, with higher counts in summer, followed by autumn, spring, and winter. H2S-producing bacteria and Pseudomonas spp. counts were unaffected by harvesting season or location. Sea urchin gonad microbial composition proved resilient and dynamic, primarily shaped by seasonal variations, and minimally influenced by location. Winter and spring samples exhibited higher diversity than autumn and summer. Key genera like Pseudomonas, Psychromonas, Vibrio, Chryseobacterium, Shewanella, and Photobacterium varied seasonally. Pseudomonas, Vibrio, and Photobacterium are crucial in assessing microbial quality and safety due to their roles as specific spoilage organisms (SSOs) and, in some cases, human pathogens. Though relative abundances differed slightly between locations, harvesting location did not notably impact microbial community shaping in gonads. However, the results suggest that harvesting locations near areas with urban activity may lead to contamination with specific bacterial species, possibly due to water quality variations. These findings emphasize the importance of considering seasonality when evaluating sea urchin gonad microbial quality. Identifying key genera enhances insights into potential SSOs and human pathogens, enhancing food safety considerations in the consumption of raw or lightly processed sea urchin gonads and guiding the development of preservation methods to extend shelf life.
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Affiliation(s)
- Dionysios Tsoukalas
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), NO-7491, Trondheim, Norway.
| | - Imen Hamed
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), NO-7491, Trondheim, Norway
| | - Sunniva Hoel
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), NO-7491, Trondheim, Norway
| | - Jørgen Lerfall
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), NO-7491, Trondheim, Norway
| | - Anita Nordeng Jakobsen
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), NO-7491, Trondheim, Norway
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Pathak A, Marquez M, Stothard P, Chukwujindu C, Su JQ, Zhou Y, Zhou XY, Jagoe CH, Chauhan A. A seasonal study on the microbiomes of Diploid vs. Triploid eastern oysters and their denitrification potential. iScience 2024; 27:110193. [PMID: 38984199 PMCID: PMC11231605 DOI: 10.1016/j.isci.2024.110193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 04/09/2024] [Accepted: 06/03/2024] [Indexed: 07/11/2024] Open
Abstract
Oyster reefs are hotspots of denitrification mediated removal of dissolved nitrogen (N), however, information on their denitrifier microbiota is scarce. Furthermore, in oyster aquaculture, triploids are often preferred over diploids, yet again, microbiome differences between oyster ploidies are unknown. To address these knowledge gaps, farmed diploid and triploid oysters were collected over an annual growth cycle and analyzed using shotgun metagenomics and quantitative microbial elemental cycling (QMEC) techniques. Regardless of ploidy, Psychrobacter genus was abundant, with positive correlations found for genes of central metabolism, DNA metabolism, and carbohydrate metabolism. MAGs (metagenome-assembled genomes) yielded multiple Psychrobacter genomes harboring norB, narH, narI, and nirK denitrification genes, indicating their functional relevance within the eastern oysters. QMEC analysis indicated the predominance of carbon (C) and nitrogen (N) cycling genes, with no discernable patterns between ploidies. Among the N-cycling genes, the nosZII clade was overrepresented, suggesting its role in the eastern oyster's N removal processes.
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Affiliation(s)
- Ashish Pathak
- School of the Environment, Florida A&M University, 1515 S. Martin Luther King Boulevard, Tallahassee, FL 32307, USA
| | - Mario Marquez
- Texas Sea Grant College Program, 4115 TAMU Eller O&M 306, Texas A&M University, College Station, TX 77843, USA
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, General Services Bldg, Edmonton, AB 2-31 T6G 2H1, Canada
| | - Christian Chukwujindu
- Material & Energy Technology Department, Projects Development Institute, Emene Industrial Layout, Enugu-Nigeria 400104
| | - Jian-Qiang Su
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yanyan Zhou
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xin-Yuan Zhou
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Charles H. Jagoe
- School of the Environment, Florida A&M University, 1515 S. Martin Luther King Boulevard, Tallahassee, FL 32307, USA
| | - Ashvini Chauhan
- School of the Environment, Florida A&M University, 1515 S. Martin Luther King Boulevard, Tallahassee, FL 32307, USA
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Wang B, Junaid M, Chen G, Wang J. Interfacial effects of perfluorooctanoic acid and its alternative hexafluoropropylene oxide dimer acid with polystyrene nanoplastics on oxidative stress, histopathology and gut microbiota in Crassostrea hongkongensis oysters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 932:172864. [PMID: 38697532 DOI: 10.1016/j.scitotenv.2024.172864] [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: 02/28/2024] [Revised: 04/02/2024] [Accepted: 04/27/2024] [Indexed: 05/05/2024]
Abstract
The increasing interfacial impacts of polystyrene nanoplastics (PS) and per- and polyfluoroalkyl substances (PFAS) complex aquatic environments are becoming more evident, drawing attention to the potential risks to aquatic animal health and human seafood safety. This study aims to investigate the relative impacts following exposure (7 days) of Crassostrea hongkongensis oysters to the traditional PFAS congener, perfluorooctanoic acid (PFOA) at 50 μg/L, and its novel alternative, hexafluoropropylene oxide dimer acid (HFPO-DA), also known as GenX at 50 μg/L, in conjunction with fluorescent polystyrene nanoplastics (PS, 80 nm) at 1 mg/L. The research focuses on assessing the effects of combined exposure on oxidative stress responses and gut microbiota in the C. hongkongensis. Comparing the final results of PS + GenX (PG) and PS + PFOA (PF) groups, we observed bioaccumulation of PS in both groups, with the former causing more pronounced histopathological damage to the gills and intestines. Furthermore, the content of antioxidant enzymes induced by PG was higher than that of PF, including Superoxide Dismutase (SOD), Catalase (CAT), Glutathione Reductase (GR) and Glutathione Peroxidase (GSH). Additionally, in both PG and PF groups, the expression levels of several immune-related genes were significantly upregulated, including tnfα, cat, stat, tlr-4, sod, and β-gbp, with no significant difference between these two groups (p > 0.05). Combined exposure induced significant changes in the gut microbiota of C. hongkongensis at its genus level, with a significant increase in Legionella and a notable decrease in Endozoicomonas and Lactococcus caused by PG. These shifts led to beneficial bacteria declining and pathogenic microbes increasing. Consequently, the microbial community structure might be disrupted. In summary, our findings contribute to a deeper understanding of the comparative toxicities of marine bivalves under combined exposure of traditional and alternative PFAS.
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Affiliation(s)
- Bin Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510641, China
| | - Muhammad Junaid
- College of Marine Sciences, South China Agricultural University, Guangzhou 510641, China; Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan 512005, China
| | - Guanglong Chen
- Institute of Eco-Environmental Research, Guangxi Academy of Sciences, Nanning 530007, China
| | - Jun Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510641, China; Institute of Eco-Environmental Research, Guangxi Academy of Sciences, Nanning 530007, China.
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Alcaraz CM, Séneca J, Kunert M, Pree C, Sudo M, Petersen JM. Sulfur-oxidizing symbionts colonize the digestive tract of their lucinid hosts. THE ISME JOURNAL 2024; 18:wrae200. [PMID: 39388223 PMCID: PMC11549920 DOI: 10.1093/ismejo/wrae200] [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: 03/12/2024] [Revised: 09/01/2024] [Accepted: 10/09/2024] [Indexed: 10/15/2024]
Abstract
Like many marine invertebrates, marine lucinid clams have an intimate relationship with beneficial sulfur-oxidizing bacteria located within specialized gill cells known as bacteriocytes. Most previous research has focused on the symbionts in the gills of these (and other) symbiotic bivalves, often assuming that the symbionts only persistently colonize the gills, at least in the adult stage. We used 16S rRNA gene sequencing and digital polymerase chain reaction with symbiont-specific primers targeting the soxB gene on the foot, mantle, visceral mass, and gills of the lucinid clam Loripes orbiculatus. We also used fluorescence in situ hybridization with symbiont-specific probes to examine symbiont distribution at the level of the whole holobiont. Despite 40 years of research on these symbioses, we detected previously unknown populations of symbiont cells in several organs, including the digestive tract. As in the well-studied gills, symbionts in the digestive tract may be housed within host cells. A 14-month starvation experiment without hydrogen sulfide to power symbiont metabolism caused a larger reduction in symbiont numbers in the gills compared to the visceral mass, raising the possibility that symbionts in the digestive tract are persistent and may have a distinct physiology and role in the symbiosis compared with the gill symbionts. Our results highlight the unexpectedly complex relationships between marine lucinid clams and their symbionts and challenge the view that chemosynthetic symbionts are restricted to the gills of these hosts.
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Affiliation(s)
- Cristina M Alcaraz
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Djerassiplatz 1, 1030 Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Joana Séneca
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Djerassiplatz 1, 1030 Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Martin Kunert
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Djerassiplatz 1, 1030 Vienna, Austria
| | - Christopher Pree
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Djerassiplatz 1, 1030 Vienna, Austria
| | - Marta Sudo
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Djerassiplatz 1, 1030 Vienna, Austria
- Center for Electromicrobiology, Section for Microbiology, Department of Biology, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
| | - Jillian M Petersen
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Djerassiplatz 1, 1030 Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
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Trapella G, Cinti N, Parma L, De Marco A, Dell'Acqua AN, Turroni S, Rampelli S, Scicchitano D, Iuffrida L, Bonaldo A, Franzellitti S, Candela M, Palladino G. Microbiome variation at the clam-sediment interface may explain changes in local productivity of Chamelea gallina in the North Adriatic sea. BMC Microbiol 2023; 23:402. [PMID: 38114947 PMCID: PMC10729368 DOI: 10.1186/s12866-023-03146-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/07/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND The clam Chamelea gallina is an ecologically and economically important marine species in the Northwestern Adriatic Sea, which currently suffers from occasional, and still unexplained, widespread mortality events. In order to provide some glimpses in this direction, this study explores the connections between microbiome variations at the clam-sediment interface and the nutritional status of clams collected at four Italian production sites along the Emilia Romagna coast, with different mortality incidence, higher in the Northern sites and lower in the Southern sites. RESULTS According to our findings, each production site showed a peculiar microbiome arrangement at the clam-sediment interface, with features that clearly differentiate the Northern and Southern sites, with the latter also being associated with a better nutritional status of the animal. Interestingly, the C. gallina digestive gland microbiome from the Southern sites was enriched in some health-promoting microbiome components, capable of supplying the host with essential nutrients and defensive molecules. Furthermore, in experiments conducted under controlled conditions in aquaria, we provided preliminary evidence of the prebiotic action of sediments from the Southern sites, allowing to boost the acquisition of previously identified health-promoting components of the digestive gland microbiome by clams from the Northern sites. CONCLUSIONS Taken together, our findings may help define innovative microbiome-based management strategies for the preservation of the productivity of C. gallina clams in the Adriatic Sea, through the identification and maintenance of a probiotic niche at the animal-sediment interface.
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Affiliation(s)
- Giulia Trapella
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Bologna, 40126, Italy
- Fano Marine Center, The Inter-Institute Center for Research on Marine Bioaffiliationersity, Resources and Biotechnologies, Fano, 61032, Italy
| | - Nicolò Cinti
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Bologna, 40126, Italy
- Fano Marine Center, The Inter-Institute Center for Research on Marine Bioaffiliationersity, Resources and Biotechnologies, Fano, 61032, Italy
| | - Luca Parma
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano Emilia (Bologna), 40064, Italy
| | - Antonina De Marco
- Fano Marine Center, The Inter-Institute Center for Research on Marine Bioaffiliationersity, Resources and Biotechnologies, Fano, 61032, Italy
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano Emilia (Bologna), 40064, Italy
| | - Andrea Nicolò Dell'Acqua
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Bologna, 40126, Italy
- Fano Marine Center, The Inter-Institute Center for Research on Marine Bioaffiliationersity, Resources and Biotechnologies, Fano, 61032, Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Bologna, 40126, Italy
| | - Simone Rampelli
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Bologna, 40126, Italy
- Fano Marine Center, The Inter-Institute Center for Research on Marine Bioaffiliationersity, Resources and Biotechnologies, Fano, 61032, Italy
| | - Daniel Scicchitano
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Bologna, 40126, Italy
- Fano Marine Center, The Inter-Institute Center for Research on Marine Bioaffiliationersity, Resources and Biotechnologies, Fano, 61032, Italy
| | - Letizia Iuffrida
- Fano Marine Center, The Inter-Institute Center for Research on Marine Bioaffiliationersity, Resources and Biotechnologies, Fano, 61032, Italy
- Animal and Environmental Physiology Laboratory, Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Ravenna, 48123, Italy
| | - Alessio Bonaldo
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano Emilia (Bologna), 40064, Italy
| | - Silvia Franzellitti
- Fano Marine Center, The Inter-Institute Center for Research on Marine Bioaffiliationersity, Resources and Biotechnologies, Fano, 61032, Italy
- Animal and Environmental Physiology Laboratory, Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Ravenna, 48123, Italy
| | - Marco Candela
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Bologna, 40126, Italy
- Fano Marine Center, The Inter-Institute Center for Research on Marine Bioaffiliationersity, Resources and Biotechnologies, Fano, 61032, Italy
| | - Giorgia Palladino
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Bologna, 40126, Italy.
- Fano Marine Center, The Inter-Institute Center for Research on Marine Bioaffiliationersity, Resources and Biotechnologies, Fano, 61032, Italy.
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Griffin TW, Darsan MA, Collins HI, Holohan BA, Pierce ML, Ward JE. A multi-study analysis of gut microbiome data from the blue mussel (Mytilus edulis) emphasises the impact of depuration on biological interpretation. Environ Microbiol 2023; 25:3435-3449. [PMID: 37941484 DOI: 10.1111/1462-2920.16537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/27/2023] [Indexed: 11/10/2023]
Abstract
The blue mussel (Mytilus edulis) is a suspension feeder which has been used in gut-microbiome surveys. Although raw 16S sequence data are often publicly available, unifying secondary analyses are lacking. The present work analysed raw data from seven projects conducted by one group over 7 years. Although each project had different motivations, experimental designs and conclusions, all selected samples were from the guts of M. edulis collected from a single location in Long Island Sound. The goal of this analysis was to determine which independent factors (e.g., collection date, depuration status) were responsible for governing composition and diversity in the gut microbiomes. Results indicated that whether mussels had undergone depuration, defined here as voidance of faeces in a controlled, no-food period, was the primary factor that governed gut microbiome composition. Gut microbiomes from non-depurated mussels were mixtures of resident and transient communities and were influenced by temporal factors. Resident communities from depurated mussels were influenced by the final food source and length of time host mussels were held under laboratory conditions. These findings reinforce the paradigm that gut microbiota are divided into resident and transient components and suggest that depuration status should be taken into consideration when designing and interpreting future experiments.
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Affiliation(s)
- Tyler W Griffin
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, USA
| | - Mya A Darsan
- Department of Biological Sciences, University at Albany, Albany, New York, USA
- Department of Marine and Environmental Science, Northeastern University, Nahant, Massachusetts, USA
| | - Hannah I Collins
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, USA
| | - Bridget A Holohan
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, USA
| | - Melissa L Pierce
- Discovery Partners Institute, Applied R&D, University of Illinois System, Chicago, Illinois, USA
| | - J Evan Ward
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, USA
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