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Starr K, Montesanto F, Perisho E, Aluthge N, Pegg M, Fernando SC. Gut Microbial Composition of Cyprinella lutrensis (Red Shiner) and Notropis stramineus (Sand Shiner): Insights from Wild Fish Populations. MICROBIAL ECOLOGY 2024; 87:75. [PMID: 38775958 PMCID: PMC11111511 DOI: 10.1007/s00248-024-02386-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 04/27/2024] [Indexed: 05/25/2024]
Abstract
The gut microbiome is a highly intricate ecosystem that exerts a pivotal influence on the host's physiology. Characterizing fish microbiomes is critical to understanding fish physiology and health, but little is known about the ecology and colonization dynamics of microorganisms inhabiting fish species. In this study, we investigated the bacterial communities of two small-bodied fish species, Cyprinella lutrensis (red shiner) and Notropis stramineus (sand shiner), two fish species where gut microbiomes have not been investigated previously and surrounding waters, collected from rivers in Nebraska, USA. Our study focused on evaluating microbial diversity in small-bodied fish and identifying autochthonous microbes present within these species irrespective of location to better understand bacterial community composition and possible roles of such bacterial species. Our results revealed that both red shiner and sand shiner exhibited gut bacterial communities dominated by typical bacterial phyla found in freshwater fish. The phylum Bacteroidota was minimally abundant in both species and significantly lower in relative abundance compared to the surrounding water microbial community. Furthermore, we found that the gut microbiomes of red shiner and sand shiner differed from the microbial community in the surrounding water, suggesting that these fish species contain host-associated bacterial species that may provide benefits to the host such as nutrient digestion and colonization resistance of environmental pathogens. The fish gut bacterial communities were sensitive to environmental conditions such as turbidity, dissolved oxygen, temperature, and total nitrogen. Our findings also show bacterial community differences between fish species; although they shared notable similarities in bacterial taxa at phyla level composition, ASV level analysis of bacterial taxa displayed compositional differences. These findings contribute to a better understanding of the gut bacterial composition of wild, freshwater, small-bodied fish and highlight the influence of intrinsic (host) and environmental factors on shaping the bacterial composition.
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Affiliation(s)
- Krista Starr
- University of NE-Lincoln, 3310 Holdrege Street, Lincoln, NE, 68583, USA
| | | | - Esther Perisho
- University of NE-Lincoln, 3310 Holdrege Street, Lincoln, NE, 68583, USA
| | - Nirosh Aluthge
- University of NE-Lincoln, 3310 Holdrege Street, Lincoln, NE, 68583, USA
| | - Mark Pegg
- University of NE-Lincoln, 3310 Holdrege Street, Lincoln, NE, 68583, USA.
| | - Samodha C Fernando
- University of NE-Lincoln, 3310 Holdrege Street, Lincoln, NE, 68583, USA.
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2
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Kumar V, Roy S, Parida SN, Bisai K, Dhar S, Jana AK, Das BK. Deciphering the impact of endoparasitic infection on immune response and gut microbial composition of Channa punctata. Front Cell Infect Microbiol 2024; 14:1296769. [PMID: 38476164 PMCID: PMC10927727 DOI: 10.3389/fcimb.2024.1296769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/19/2024] [Indexed: 03/14/2024] Open
Abstract
Intestinal parasitic infections caused by helminths are globally distributed and are a major cause of morbidity worldwide. Parasites may modulate the virulence, gut microbiota diversity and host responses during infection. Despite numerous works, little is known about the complex interaction between parasites and the gut microbiota. In the present study, the complex interplay between parasites and the gut microbiota was investigated. A total of 12 bacterial strains across four major families, including Enterobacteriaceae, Morganellaceae, Flavobacteriaceae, and Pseudomonadaceae, were isolated from Channa punctata, infected with the nematode species Aporcella sp., Axonchium sp., Tylencholaimus mirabilis, and Dioctophyme renale. The findings revealed that nematode infection shaped the fish gut bacterial microbiota and significantly affected their virulence levels. Nematode-infected fish bacterial isolates are more likely to be pathogenic, with elevated hemolytic activity and biofilm formation, causing high fish mortality. In contrast, isolates recovered further from non-parasitised C. punctata were observed to be non-pathogenic and had negligible hemolytic activity and biofilm formation. Antibiogram analysis of the bacterial isolates revealed a disproportionately high percentage of bacteria that were either marginally or multidrug resistant, suggesting that parasitic infection-induced stress modulates the gut microenvironment and enables colonization by antibiotic-resistant strains. This isolation-based study provides an avenue to unravel the influence of parasitic infection on gut bacterial characteristics, which is valuable for understanding the infection mechanism and designing further studies aimed at optimizing treatment strategies. In addition, the cultured isolates can supplement future gut microbiome studies by providing wet lab specimens to compare (meta)genomic information discovered within the gut microenvironment of fish.
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Affiliation(s)
| | | | | | | | | | | | - Basanta Kumar Das
- Aquatic Environmental Biotechnology and Nanotechnology (AEBN) Division, Indian Council of Agricultural Research (ICAR)-Central Inland Fisheries Research Institute (CIFRI), Barrackpore, India
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Soh M, Tay YC, Lee CS, Low A, Orban L, Jaafar Z, Seedorf H. The intestinal digesta microbiota of tropical marine fish is largely uncultured and distinct from surrounding water microbiota. NPJ Biofilms Microbiomes 2024; 10:11. [PMID: 38374184 PMCID: PMC10876542 DOI: 10.1038/s41522-024-00484-x] [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: 03/28/2023] [Accepted: 02/06/2024] [Indexed: 02/21/2024] Open
Abstract
Studying the gut microbes of marine fishes is an important part of conservation as many fish species are increasingly threatened by extinction. The gut microbiota of only a small fraction of the more than 32,000 known fish species has been investigated. In this study we analysed the intestinal digesta microbiota composition of more than 50 different wild fish species from tropical waters. Our results show that the fish harbour intestinal digesta microbiota that are distinct from that of the surrounding water and that location, domestication status, and host intrinsic factors are strongly associated with the microbiota composition. Furthermore, we show that the vast majority (~97%) of the fish-associated microorganisms do not have any cultured representative. Considering the impact of the microbiota on host health and physiology, these findings underpin the call to also preserve the microbiota of host species, especially those that may be exposed to habitat destruction.
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Affiliation(s)
- Melissa Soh
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore, 117604, Singapore
| | - Ywee Chieh Tay
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore, 117604, Singapore
| | - Co Sin Lee
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore, 117604, Singapore
| | - Adrian Low
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore, 117604, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, MD6-Centre for Translational Medicine, 14 Medical Drive, Singapore, 117599, Singapore
| | - Laszlo Orban
- Frontline Fish Genomics Research Group, Department of Applied Fish Biology, Institute of Aquaculture and Environmental Safety, Georgikon Campus, Hungarian University of Agriculture and Life Sciences, Keszthely, 8360, Hungary
| | - Zeehan Jaafar
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
| | - Henning Seedorf
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore, 117604, Singapore.
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore.
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4
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Berggren H, Nordahl O, Yıldırım Y, Larsson P, Tibblin P, Forsman A. Effects of environmental translocation and host characteristics on skin microbiomes of sun-basking fish. Proc Biol Sci 2023; 290:20231608. [PMID: 38113936 PMCID: PMC10730295 DOI: 10.1098/rspb.2023.1608] [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: 11/11/2022] [Accepted: 11/20/2023] [Indexed: 12/21/2023] Open
Abstract
Variation in the composition of skin-associated microbiomes has been attributed to host species, geographical location and habitat, but the role of intraspecific phenotypic variation among host individuals remains elusive. We explored if and how host environment and different phenotypic traits were associated with microbiome composition. We conducted repeated sampling of dorsal and ventral skin microbiomes of carp individuals (Cyprinus carpio) before and after translocation from laboratory conditions to a semi-natural environment. Both alpha and beta diversity of skin-associated microbiomes increased substantially within and among individuals following translocation, particularly on dorsal body sites. The variation in microbiome composition among hosts was significantly associated with body site, sun-basking, habitat switch and growth, but not temperature gain while basking, sex, personality nor colour morph. We suggest that the overall increase in the alpha and beta diversity estimates among hosts were induced by individuals expressing greater variation in behaviours and thus exposure to potential colonizers in the pond environment compared with the laboratory. Our results exemplify how biological diversity at one level of organization (phenotypic variation among and within fish host individuals) together with the external environment impacts biological diversity at a higher hierarchical level of organization (richness and composition of fish-associated microbial communities).
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Affiliation(s)
- Hanna Berggren
- Ecology and Evolution in Microbial model Systems, EEMiS Department of Biology and Environmental Science, Linnaeus University, 391 82 Kalmar, Sweden
| | - Oscar Nordahl
- Ecology and Evolution in Microbial model Systems, EEMiS Department of Biology and Environmental Science, Linnaeus University, 391 82 Kalmar, Sweden
| | - Yeşerin Yıldırım
- Ecology and Evolution in Microbial model Systems, EEMiS Department of Biology and Environmental Science, Linnaeus University, 391 82 Kalmar, Sweden
| | - Per Larsson
- Ecology and Evolution in Microbial model Systems, EEMiS Department of Biology and Environmental Science, Linnaeus University, 391 82 Kalmar, Sweden
| | - Petter Tibblin
- Ecology and Evolution in Microbial model Systems, EEMiS Department of Biology and Environmental Science, Linnaeus University, 391 82 Kalmar, Sweden
| | - Anders Forsman
- Ecology and Evolution in Microbial model Systems, EEMiS Department of Biology and Environmental Science, Linnaeus University, 391 82 Kalmar, Sweden
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Scheifler M, Magnanou E, Sanchez-Brosseau S, Desdevises Y. Host-microbiota-parasite interactions in two wild sparid fish species, Diplodus annularis and Oblada melanura (Teleostei, Sparidae) over a year: a pilot study. BMC Microbiol 2023; 23:340. [PMID: 37974095 PMCID: PMC10652623 DOI: 10.1186/s12866-023-03086-3] [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: 06/14/2023] [Accepted: 10/23/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND The microbiota in fish external mucus is mainly known for having a role in homeostasis and protection against pathogens, but recent evidence suggests it is also involved in the host-specificity of some ectoparasites. In this study, we investigated the influence of seasonality and environmental factors on both fish external microbiota and monogenean gill ectoparasites abundance and diversity and assessed the level of covariations between monogenean and bacterial communities across seasons. To do so, we assessed skin and gill microbiota of two sparid species, Oblada melanura and Diplodus annularis, over a year and collected their specific monogenean ectoparasites belonging to the Lamellodiscus genus. RESULTS Our results revealed that diversity and structure of skin and gill mucus microbiota were strongly affected by seasonality, mainly by the variations of temperature, with specific fish-associated bacterial taxa for each season. The diversity and abundance of parasites were also influenced by seasonality, with the abundance of some Lamellodiscus species significantly correlated to temperature. Numerous positive and negative correlations between the abundance of given bacterial genera and Lamellodiscus species were observed throughout the year, suggesting their differential interaction across seasons. CONCLUSIONS The present study is one of the first to demonstrate the influence of seasonality and related abiotic factors on fish external microbiota over a year. We further identified potential interactions between gill microbiota and parasite occurrence in wild fish populations, improving current knowledge and understanding of the establishment of host-specificity.
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Affiliation(s)
- Mathilde Scheifler
- Sorbonne Université, CNRS, Biologie Intégrative Des Organismes Marins, BIOM, Banyuls-sur-Mer, F-66650, France.
| | - Elodie Magnanou
- Sorbonne Université, CNRS, Biologie Intégrative Des Organismes Marins, BIOM, Banyuls-sur-Mer, F-66650, France
| | - Sophie Sanchez-Brosseau
- Sorbonne Université, CNRS, Biologie Intégrative Des Organismes Marins, BIOM, Banyuls-sur-Mer, F-66650, France
| | - Yves Desdevises
- Sorbonne Université, CNRS, Biologie Intégrative Des Organismes Marins, BIOM, Banyuls-sur-Mer, F-66650, France
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Mougin J, Lobanov V, Danion M, Roquigny R, Goardon L, Grard T, Morin T, Labbé L, Joyce A. Effects of dietary co-exposure to fungal and herbal functional feed additives on immune parameters and microbial intestinal diversity in rainbow trout (Oncorhynchus mykiss). FISH & SHELLFISH IMMUNOLOGY 2023; 137:108773. [PMID: 37105422 DOI: 10.1016/j.fsi.2023.108773] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 05/03/2023]
Abstract
Misuse and overuse of antibiotics in aquaculture has proven to be an unsustainable practice leading to increased bacterial resistance. An alternative strategy involves the inclusion of immunostimulants in fish diets, especially fungal and herbal compounds already authorized for human consumption, hence without environmental or public health concerns. In this study, we used a holistic and cross-disciplinary pipeline to assess the immunostimulatory properties of two fungi: Trametes versicolor and Ganoderma lucidum; one herbal supplement, capsaicin in the form of Espelette pepper (Capsicum annuum), and a combination of these fungal and herbal additives on rainbow trout (Oncorhynchus mykiss). We investigated the impact of diet supplementation for 7 weeks on survival, growth performance, cellular, humoral, and molecular immune parameters, as well as the intestinal microbial composition of the fish. Uptake of herbal and fungal compounds influenced the expression of immune related genes, without generating an inflammatory response. Significant differences were detected in the spleen-tlr2 gene expression. Supplementation with herbal additives correlated with structural changes in the fish intestinal microbiota and enhanced overall intestinal microbial diversity. Results demonstrated that the different treatments had no adverse effect on growth performance and survival, suggesting the safety of the different feed additives at the tested concentrations. While the mechanisms and multifactorial interactions remain unclear, this study provides insights not only in regard to nutrition and safety of these compounds, but also how a combined immune and gut microbiota approach can shed light on efficacy of immunostimulant compounds for potential commercial inclusion as feed supplements.
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Affiliation(s)
- Julia Mougin
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Victor Lobanov
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Morgane Danion
- French Agency for Food, Environmental and Occupational Health and Safety, Ploufragan-Plouzané-Niort Laboratory, Unit Virology, Immunology and Ecotoxicology of Fish, 29280, Plouzané, France
| | - Roxane Roquigny
- Univ. Littoral Côte d'Opale, UMRt 1158 BioEcoAgro, USC ANSES, INRAe, Univ. Artois, Univ. Lille, Univ. Picardie Jules Verne, Univ. Liège, Junia, F-62200, Boulogne-sur-Mer, France
| | - Lionel Goardon
- PEIMA-INRAe, UE0937, Fish Farming Systems Experimental Facility, Sizun, France
| | - Thierry Grard
- Univ. Littoral Côte d'Opale, UMRt 1158 BioEcoAgro, USC ANSES, INRAe, Univ. Artois, Univ. Lille, Univ. Picardie Jules Verne, Univ. Liège, Junia, F-62200, Boulogne-sur-Mer, France
| | - Thierry Morin
- French Agency for Food, Environmental and Occupational Health and Safety, Ploufragan-Plouzané-Niort Laboratory, Unit Virology, Immunology and Ecotoxicology of Fish, 29280, Plouzané, France
| | - Laurent Labbé
- PEIMA-INRAe, UE0937, Fish Farming Systems Experimental Facility, Sizun, France
| | - Alyssa Joyce
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden.
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7
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Abd-ELrahman SM, Gareh A, Mohamed HI, Alrashdi BM, Dyab AK, El-Khadragy MF, Khairy Elbarbary N, Fouad AM, El-Gohary FA, Elmahallawy EK, Mohamed SAA. Prevalence and Morphological Investigation of Parasitic Infection in Freshwater Fish (Nile Tilapia) from Upper Egypt. Animals (Basel) 2023; 13:ani13061088. [PMID: 36978630 PMCID: PMC10044437 DOI: 10.3390/ani13061088] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/28/2023] [Accepted: 03/13/2023] [Indexed: 03/22/2023] Open
Abstract
Fish are a source of high-quality protein with low cholesterol, but they are susceptible to parasitic infections, which have a significant impact on aquaculture, in addition to their zoonotic potential. The present study estimated parasitic infections and evaluated the diversity of zoonotic parasites in freshwater Nile tilapia (Oreochromis niloticus) in Assiut Governorate, Upper Egypt. A total of 300 samples were randomly collected from the Assiut Governorate. These fish were examined for both ectoparasites and endoparasites, followed by the experimental infection of mice with encysted metacercariae (EMC) for the retrieval of the adult worms. The overall prevalence of the variable parasites was 82% (246 of 300). Both ecto- and endoparasites were detected in 41% (123 of 300) of the examined fish. The identified ectoparasites were Gyrodactylus, Dactylogrus, Cichlidogyrus, Trichodina and Icthyophthirius multifiliis, in 5%, 4%, 22%, 6% and 4% of the fish, respectively. The endoparasites were trematodes (Orientocreadium batrachoides 3%), nematodes (Contracaecum. 2%), acanthocephala (Acanthosentis tilapiae 25%) and protozoa that included Isospora and Eimeria spp., in 1% and 8% of fish, respectively. Myxobolus was detected in 2% of the examined fish. The overall prevalence of encysted metacercariae (EMC) was 95% (285 of 300), while infection with macroscopic EMC had a prevalence of 37% and microscopic EMC had a prevalence of 58%. The adult worms recovered from the experimental infections were Prohemistomum vivax and Mesostephanus spp., which belong to the family Cyathocotylidae. Collectively, these findings reflect the relatively high occurrence of parasites among the studied fish, confirming the necessity of strict measures to control infection.
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Affiliation(s)
- Salwa Mahmoud Abd-ELrahman
- Department of Parasitology, Faculty of Veterinary Medicine Assiut University, Assiut 71515, Egypt; (S.M.A.-E.); (H.I.M.); (S.A.-A.M.)
| | - Ahmed Gareh
- Department of Parasitology, Faculty of Veterinary Medicine, Aswan University, Aswan 24101, Egypt;
| | - Hager Ibrahem Mohamed
- Department of Parasitology, Faculty of Veterinary Medicine Assiut University, Assiut 71515, Egypt; (S.M.A.-E.); (H.I.M.); (S.A.-A.M.)
| | - Barakat M. Alrashdi
- Biology Department, College of Science, Jouf University, Sakaka 72388, Saudi Arabia;
| | - Ahmed Kamal Dyab
- Department of Parasitology, Faculty of Medicine, Assiut University, Assiut 71515, Egypt;
| | - Manal F. El-Khadragy
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia;
| | - Nady Khairy Elbarbary
- Department of Food Hygiene, Faculty of Veterinary Medicine, Aswan University, Aswan 81528, Egypt;
| | - Alamira Marzouk Fouad
- Department of Aquatic Animal Medicine and Management, Faculty of Veterinary Medicine, Assuit University, Assiut 71526, Egypt;
| | - Fatma A. El-Gohary
- Department of Hygiene and Zoonoses, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Ehab Kotb Elmahallawy
- Department of Zoonoses, Faculty of Veterinary Medicine, Sohag University, Sohag 82524, Egypt
- Correspondence:
| | - Sara Abdel-Aal Mohamed
- Department of Parasitology, Faculty of Veterinary Medicine Assiut University, Assiut 71515, Egypt; (S.M.A.-E.); (H.I.M.); (S.A.-A.M.)
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Kodera SM, Sharma A, Martino C, Dsouza M, Grippo M, Lutz HL, Knight R, Gilbert JA, Negri C, Allard SM. Microbiome response in an urban river system is dominated by seasonality over wastewater treatment upgrades. ENVIRONMENTAL MICROBIOME 2023; 18:10. [PMID: 36805022 PMCID: PMC9938989 DOI: 10.1186/s40793-023-00470-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Microorganisms such as coliform-forming bacteria are commonly used to assess freshwater quality for drinking and recreational use. However, such organisms do not exist in isolation; they exist within the context of dynamic, interactive microbial communities which vary through space and time. Elucidating spatiotemporal microbial dynamics is imperative for discriminating robust community changes from ephemeral ecological trends, and for improving our overall understanding of the relationship between microbial communities and ecosystem health. We conducted a seven-year (2013-2019) microbial time-series investigation in the Chicago Area Waterways (CAWS): an urban river system which, in 2016, experienced substantial upgrades to disinfection processes at two wastewater reclamation plants (WRPs) that discharge into the CAWS and improved stormwater capture, to improve river water quality and reduce flooding. Using culture-independent and culture-dependent approaches, we compared CAWS microbial ecology before and after the intervention. RESULTS Examinations of time-resolved beta distances between WRP-adjacent sites showed that community similarity measures were often consistent with the spatial orientation of site locations to one another and to the WRP outfalls. Fecal coliform results suggested that upgrades reduced coliform-associated bacteria in the effluent and the downstream river community. However, examinations of whole community changes through time suggest that the upgrades did little to affect overall riverine community dynamics, which instead were overwhelmingly driven by yearly patterns consistent with seasonality. CONCLUSIONS This study presents a systematic effort to combine 16S rRNA gene amplicon sequencing with traditional culture-based methods to evaluate the influence of treatment innovations and systems upgrades on the microbiome of the Chicago Area Waterway System, representing the longest and most comprehensive characterization of the microbiome of an urban waterway yet attempted. We found that the systems upgrades were successful in improving specific water quality measures immediately downstream of wastewater outflows. Additionally, we found that the implementation of the water quality improvement measures to the river system did not disrupt the overall dynamics of the downstream microbial community, which remained heavily influenced by seasonal trends. Such results emphasize the dynamic nature of microbiomes in open environmental systems such as the CAWS, but also suggest that the seasonal oscillations remain consistent even when perturbed.
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Affiliation(s)
- Sho M Kodera
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Anukriti Sharma
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Cameron Martino
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | | | - Mark Grippo
- Environmental Science Division, Argonne National Laboratory, University of Chicago, Lemont, IL, USA
| | - Holly L Lutz
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Jack A Gilbert
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
| | - Cristina Negri
- Environmental Science Division, Argonne National Laboratory, University of Chicago, Lemont, IL, USA.
| | - Sarah M Allard
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
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9
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Couch CE, Neal WT, Herron CL, Kent ML, Schreck CB, Peterson JT. Gut microbiome composition associates with corticosteroid treatment, morbidity, and senescence in Chinook salmon (Oncorhynchus tshawytscha). Sci Rep 2023; 13:2567. [PMID: 36782001 PMCID: PMC9925776 DOI: 10.1038/s41598-023-29663-0] [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: 09/09/2022] [Accepted: 02/08/2023] [Indexed: 02/15/2023] Open
Abstract
Pacific salmon experience prolonged elevation in corticosteroid hormones during important life history events including migration, reproduction, and senescence. These periods of elevated corticosteroids correspond with changes to immunity and energy metabolism; therefore, fish may be particularly vulnerable to mortality at these times. Recent studies found that stress-induced cortisol release associated with microbial community shifts in salmonids, raising the question of how longer-term corticosteroid dynamics that accompany life history transitions affect salmonid microbiomes. In this work, we experimentally evaluated the relationships between gut microbiome composition, chronically elevated corticosteroids, and mortality in juvenile Chinook salmon (Oncorhynchus tshawytscha). We found that treatment with slow-release implants of the corticosteroids cortisol or dexamethasone resulted in changes to the gut microbiome. Morbidity was also associated with microbiome composition, suggesting that the gut microbiome reflects individual differences in susceptibility to opportunistic pathogens. Additionally, we analyzed a small number of samples from adult fish at various stages of senescence. Results from these samples suggest that microbiome composition associated with gut integrity, and that the microbial communities of corticosteroid treated juveniles shift in composition toward those of senescent adults. Overall, findings from this work indicate that the gut microbiome correlates with mortality risk during periods of chronic corticosteroid elevation.
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Affiliation(s)
- Claire E Couch
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, OR, USA.
| | - William T Neal
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, OR, USA
| | - Crystal L Herron
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, OR, USA
| | - Michael L Kent
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Carl B Schreck
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, OR, USA
| | - James T Peterson
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, OR, USA
- U.S. Geological Survey Oregon Cooperative Fish and Wildlife Research Unit, Corvallis, OR, USA
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10
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The Development of the Bacterial Community of Brown Trout ( Salmo trutta) during Ontogeny. Microorganisms 2023; 11:microorganisms11010211. [PMID: 36677503 PMCID: PMC9863972 DOI: 10.3390/microorganisms11010211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Brown trout (Salmo trutta) is an important aquaculture species in Germany, but its production faces challenges due to global warming and a high embryo mortality. Climate factors might influence the fish's bacterial community (BC) and thus increase embryo mortality. Yet, knowledge of the physiological BC during ontogeny in general is scarce. In this project, the BC of brown trout has been investigated in a period from unfertilized egg to 95 days post fertilization (dpf) using 16S rRNA gene amplicon sequencing. Developmental changes differed between early and late ontogeny and major differences in BC occurred especially during early developmental stages. Thus, analysis was conducted separately for 0 to 67 dpf and from 67 to 95 dpf. All analyzed stages were sampled in toto to avoid bias due to different sampling methods in different developmental stages. The most abundant phylum in the BC of all developmental stages was Pseudomonadota, while only two families (Comamonadaceae and Moraxellaceae) occurred in all developmental stages. The early developmental stages until 67 dpf displayed greater shifts in their BC regarding bacterial richness, microbial diversity, and taxonomic composition. Thereafter, in the fry stages, the BC seemed to stabilize and changes were moderate. In future studies, a reduction in the sampling time frames during early development, an increase in sampling numbers, and an attempt for biological reproduction in order to characterize the causes of these variations is recommended.
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Links between host genetics, metabolism, gut microbiome and amoebic gill disease (AGD) in Atlantic salmon. Anim Microbiome 2022; 4:53. [PMID: 36109797 PMCID: PMC9479442 DOI: 10.1186/s42523-022-00203-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/30/2022] [Indexed: 12/02/2022] Open
Abstract
Background Rapidly spreading parasitic infections like amoebic gill disease (AGD) are increasingly problematic for Atlantic salmon reared in aquaculture facilities and potentially pose a risk to wild fish species in surrounding waters. Currently, it is not known whether susceptibility to AGD differs between wild and farmed salmon. Wild Atlantic salmon populations are declining and this emerging disease could represent an additional threat to their long-term viability. A better understanding of how AGD affects fish health is therefore relevant for the accurate assessment of the associated risk, both to farming and to the well-being of wild populations. In this study, we assessed the impact of natural exposure to AGD on wild, hybrid and farmed post-smolt Atlantic salmon reared in a sea farm together under common garden conditions. Results Wild fish showed substantially higher mortality levels (64%) than farmed fish (25%), with intermediate levels for hybrid fish (39%) suggesting that AGD susceptibility has an additive genetic basis. Metabolic rate measures representing physiological performance were similar among the genetic groups but were significantly lower in AGD-symptomatic fish than healthy fish. Gut microbial diversity was significantly lower in infected fish. We observed major shifts in gut microbial community composition in response to AGD infections. In symptomatic fish the relative abundance of key taxa Aliivibrio, Marinomonas and Pseudoalteromonas declined, whereas the abundance of Polaribacter and Vibrio increased compared to healthy fish. Conclusions Our results highlight the stress AGD imposes on fish physiology and suggest that low metabolic-rate fish phenotypes may be associated with better infection outcomes. We consider the role increased AGD outbreak events and a warmer future may have in driving secondary bacterial infections and in reducing performance in farmed and wild fish. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-022-00203-x.
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Scheifler M, Sanchez-Brosseau S, Magnanou E, Desdevises Y. Diversity and structure of sparids external microbiota (Teleostei) and its link with monogenean ectoparasites. Anim Microbiome 2022; 4:27. [PMID: 35418308 PMCID: PMC9009028 DOI: 10.1186/s42523-022-00180-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 04/03/2022] [Indexed: 12/31/2022] Open
Abstract
Background Animal-associated microbial communities appear to be key factors in host physiology, ecology, evolution and its interactions with the surrounding environment. Teleost fish have received relatively little attention in the study of surface-associated microbiota. Besides the important role of microbiota in homeostasis and infection prevention, a few recent studies have shown that fish mucus microbiota may interact with and attract some specific parasitic species. However, our understanding of external microbial assemblages, in particular regarding the factors that determine their composition and potential interactions with parasites, is still limited. This is the objective of the present study that focuses on a well-known fish-parasite interaction, involving the Sparidae (Teleostei), and their specific monogenean ectoparasites of the Lamellodiscus genus. We characterized the skin and gill mucus bacterial communities using a 16S rRNA amplicon sequencing, tested how fish ecological traits and host evolutionary history are related to external microbiota, and assessed if some microbial taxa are related to some Lamellodiscus species. Results Our results revealed significant differences between skin and gill microbiota in terms of diversity and structure, and that sparids establish and maintain tissue and species-specific bacterial communities despite continuous exposure to water. No phylosymbiosis pattern was detected for either gill or skin microbiota, suggesting that other host-related and environmental factors are a better regulator of host-microbiota interactions. Diversity and structure of external microbiota were explained by host traits: host species, diet and body part. Numerous correlations between the abundance of given bacterial genera and the abundance of given Lamellodiscus species have been found in gill mucus, including species-specific associations. We also found that the external microbiota of the only unparasitized sparid species in this study, Boops boops, harbored significantly more Fusobacteria and three genera, Shewenella, Cetobacterium and Vibrio, compared to the other sparid species, suggesting their potential involvement in preventing monogenean infection. Conclusions This study is the first to explore the diversity and structure of skin and gill microbiota from a wild fish family and present novel evidence on the links between gill microbiota and monogenean species in diversity and abundance, paving the way for further studies on understanding host-microbiota-parasite interactions. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-022-00180-1.
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Affiliation(s)
- Mathilde Scheifler
- Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, Sorbonne Université - CNRS, 66650, Banyuls/Mer, France.
| | - Sophie Sanchez-Brosseau
- Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, Sorbonne Université - CNRS, 66650, Banyuls/Mer, France
| | - Elodie Magnanou
- Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, Sorbonne Université - CNRS, 66650, Banyuls/Mer, France
| | - Yves Desdevises
- Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, Sorbonne Université - CNRS, 66650, Banyuls/Mer, France
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Rosado D, Pérez-Losada M, Severino R, Xavier R. Monitoring Infection and Antibiotic Treatment in the Skin Microbiota of Farmed European Seabass (Dicentrarchus Labrax) Fingerlings. MICROBIAL ECOLOGY 2022; 83:789-797. [PMID: 34245329 DOI: 10.1007/s00248-021-01795-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
The microbiota of fish skin, the primary barrier against disease, is highly dynamic and modulated by several factors. In fish aquaculture, disease outbreaks occur mainly during early-life stages, with associated high economic losses. Antibiotic treatments sometimes remain the best option to control bacterial diseases, despite many reported negative impacts of its use on fish and associated microbiota. Notwithstanding, studies monitoring the effects of disease and antibiotic treatment on the microbiota of fingerlings are scarce. We sequenced the bacterial 16S rRNA V4 gene region using a metabarcoding approach to assess the impact of a mixed infection with Photobacterium damselae ssp. piscicida and Vibrio harveyi and subsequent antibiotic treatment with flumequine, on the skin microbiota of farmed seabass (Dicentrarchus labrax) fingerlings. Both infection and antibiotic treatment led to a significant increase in bacterial diversity and core microbial communities and impacted microbiome structure. Dysbiosis was confirmed by changes in the abundance of potential pathogenic and opportunistic bacterial taxa. Skin bacterial metabolic function was also significantly affected by flumequine administration, suggesting a detriment to fish skin health. Our results add to an increasing body of literature, showing how fish microbiome response to infection and antibiotics cannot be easily predicted.
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Affiliation(s)
- Daniela Rosado
- CIBIO-InBIO, Investigation Centre for Biodiversity, Genetics and Evolution, Porto University, Campus Agrário de Vairão, Vairão, 4485-661, Porto, Portugal.
| | - Marcos Pérez-Losada
- CIBIO-InBIO, Investigation Centre for Biodiversity, Genetics and Evolution, Porto University, Campus Agrário de Vairão, Vairão, 4485-661, Porto, Portugal
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052-0066, USA
| | - Ricardo Severino
- Piscicultura Vale da Lama, Sapal Do Vale da Lama, Odiáxere, 8600-258, Lagos, Portugal
| | - Raquel Xavier
- CIBIO-InBIO, Investigation Centre for Biodiversity, Genetics and Evolution, Porto University, Campus Agrário de Vairão, Vairão, 4485-661, Porto, Portugal.
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Yang H, Wu J, Du H, Zhang H, Li J, Wei Q. Quantifying the Colonization of Environmental Microbes in the Fish Gut: A Case Study of Wild Fish Populations in the Yangtze River. Front Microbiol 2022; 12:828409. [PMID: 35250916 PMCID: PMC8891936 DOI: 10.3389/fmicb.2021.828409] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/28/2021] [Indexed: 01/10/2023] Open
Abstract
In aquatic animals, gut microbial communities shift with host development and living environments. Understanding the mechanism by which the environment impacts the gut microbial communities of aquatic animals is crucial for assessing and managing aquatic ecosystem health. Here, we proposed a simplified framework for the colonization and dynamics of gut microbial communities. Then, to quantify the colonization of environmental microbes in the wild fish gut, the current study used 16S rRNA gene amplicon sequencing to obtain the structure of the water environmental microbial community and the gut microbial community in 10 wild fish populations (Leiocassis crassilabris, Leiocassis longirostris, Pelteobagrus vachelli, Silurus asotus, Siniperca chuatsi, Coilia brachygnathus, Aristichthys nobilis, Hypophthalmichthys molitrix, Coreius heterodon, and Xenocypris argentea) from the Wuhan section of the Yangtze River, and the relationship of these microbial communities was analyzed. The results identified that in most individuals, approximately 80% of gut microbes [at the operational taxonomic unit (OTU) level] were shared with the water environmental microbial community (except for individuals of Siniperca chuatsi and Coilia brachygnathus, approximately 74%). In approximately 80% of individuals, more than 95% of microbial species (OTUs) in the gut were transient. For fish species, more than 99% of microbial species (OTUs) that were introduced into the gut were transient. Nearly 79% of OTUs and 89% of species of water environmental microbes could be introduced into the fish gut. Driven by the introduction of transient microbes, fishes with similar feeding habits had similar gut microbial communities. The results indicated that for adult wild fishes, most gut microbiota were transient from the environmental microbiota that were related to fish feeding habits. We therefore encourage future research to focus on environmental microbiota monitoring and management to promote the better conservation of aquatic animals. It was important to note that, because of various influence factors, interspecific differences and individual variations on gut microbial community characteristics, the quantification of gut microbes in the current work was approximate rather than accurate. We hope that more comparable research could be conducted to outline the quantitative characteristics of the relationship between gut microbial community and aquatic environment microbial community as soon as possible.
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Affiliation(s)
- Haile Yang
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Jinming Wu
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Hao Du
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Hui Zhang
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Junyi Li
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Qiwei Wei
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
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15
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Franz M, Whyte L, Atwood TC, Laidre KL, Roy D, Watson SE, Góngora E, McKinney MA. Distinct gut microbiomes in two polar bear subpopulations inhabiting different sea ice ecoregions. Sci Rep 2022; 12:522. [PMID: 35017585 PMCID: PMC8752607 DOI: 10.1038/s41598-021-04340-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 12/13/2021] [Indexed: 11/09/2022] Open
Abstract
Gut microbiomes were analyzed by 16S rRNA gene metabarcoding for polar bears (Ursus maritimus) from the southern Beaufort Sea (SB), where sea ice loss has led to increased use of land-based food resources by bears, and from East Greenland (EG), where persistent sea ice has allowed hunting of ice-associated prey nearly year-round. SB polar bears showed a higher number of total (940 vs. 742) and unique (387 vs. 189) amplicon sequence variants and higher inter-individual variation compared to EG polar bears. Gut microbiome composition differed significantly between the two subpopulations and among sex/age classes, likely driven by diet variation and ontogenetic shifts in the gut microbiome. Dietary tracer analysis using fatty acid signatures for SB polar bears showed that diet explained more intrapopulation variation in gut microbiome composition and diversity than other tested variables, i.e., sex/age class, body condition, and capture year. Substantial differences in the SB gut microbiome relative to EG polar bears, and associations between SB gut microbiome and diet, suggest that the shifting foraging habits of SB polar bears tied to sea ice loss may be altering their gut microbiome, with potential consequences for nutrition and physiology.
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Affiliation(s)
- Megan Franz
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Lyle Whyte
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Todd C Atwood
- United States Geological Survey (USGS), Alaska Science Center, University Drive, Anchorage, AK, 99508, USA
| | - Kristin L Laidre
- Polar Science Center, Applied Physics Laboratory, University of Washington, Seattle, WA, USA
- Greenland Institute of Natural Resources, P.O. Box 570, Nuuk, Greenland
| | - Denis Roy
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Sophie E Watson
- School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff, UK
| | - Esteban Góngora
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Melissa A McKinney
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, H9X 3V9, Canada.
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Fernández I, de Los Ríos-Escalante P, Valenzuela A, Aguayo P, Smith CT, García-Cancino A, Sánchez-Alonso K, Oyarzún C, Campos VL. Gastrointestinal Microbiota and Parasite-Fauna of Wild Dissostichus eleginoides Smitt, 1898 Captured at the South-Central Coast of Chile. Microorganisms 2021; 9:microorganisms9122522. [PMID: 34946125 PMCID: PMC8706219 DOI: 10.3390/microorganisms9122522] [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: 09/15/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 12/02/2022] Open
Abstract
Dissotichus eleginoides has a discontinuous circumpolar geographic distribution restricted to mountains and platforms, mainly in Subantarctic and Antarctic waters of the southern hemisphere, including the Southeast Pacific, Atlantic and Indian oceans and in areas surrounding the peninsular platforms of subantarctic islands. The aim of this work was to determine and characterize the gastrointestinal parasitic and microbial fauna of specimens of D. eleginoides captured in waters of the south-central zone of Chile. The magnitude of parasitism in D. eleginoides captured in waters of the south-central zone of Chile is variable, and the parasite richness is different from that reported in specimens from subantarctic environments. Next-generation sequencing (NGS) of the microbial community associated to intestine showed a high diversity, where Proteobacteria, Firmicutes, and Bacteriodetes were the dominant phyla. However, both parasitic and microbial structures can vary between fish from different geographic regions
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Affiliation(s)
- Italo Fernández
- Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Casilla 160-C, Concepción 4070386, Chile; (I.F.); (C.T.S.); (A.G.-C.); (K.S.-A.)
| | - Patricio de Los Ríos-Escalante
- Departamento de Ciencias Biológicas y Químicas, Facultad de Recursos Naturales, Universidad Católica de Temuco, Temuco 4780000, Chile;
- Núcleo de Estudios Ambientales, Universidad Católica de Temuco, Temuco 4780000, Chile
| | - Ariel Valenzuela
- Laboratorio de Piscicultura y Patología Acuática, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción 4070386, Chile; (A.V.); (C.O.)
| | - Paulina Aguayo
- Institute of Natural Resources, Faculty of Veterinary Medicine and Agronomy, Universidad de Las Américas, Sede Concepción, Chacabuco 539, Concepción 3349001, Chile;
- EULA Environmental Sciences Center, Faculty of Environmental Sciences, Universidad de Concepción, Concepción 4070386, Chile
| | - Carlos T. Smith
- Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Casilla 160-C, Concepción 4070386, Chile; (I.F.); (C.T.S.); (A.G.-C.); (K.S.-A.)
| | - Apolinaria García-Cancino
- Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Casilla 160-C, Concepción 4070386, Chile; (I.F.); (C.T.S.); (A.G.-C.); (K.S.-A.)
| | - Kimberly Sánchez-Alonso
- Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Casilla 160-C, Concepción 4070386, Chile; (I.F.); (C.T.S.); (A.G.-C.); (K.S.-A.)
| | - Ciro Oyarzún
- Laboratorio de Piscicultura y Patología Acuática, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción 4070386, Chile; (A.V.); (C.O.)
| | - Víctor L. Campos
- Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Casilla 160-C, Concepción 4070386, Chile; (I.F.); (C.T.S.); (A.G.-C.); (K.S.-A.)
- Correspondence:
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Succession of Intestinal Microbial Structure of Giant Pandas ( Ailuropoda melanoleuca) during Different Developmental Stages and Its Correlation with Cellulase Activity. Animals (Basel) 2021; 11:ani11082358. [PMID: 34438815 PMCID: PMC8388744 DOI: 10.3390/ani11082358] [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: 05/17/2021] [Revised: 07/25/2021] [Accepted: 07/28/2021] [Indexed: 11/25/2022] Open
Abstract
Simple Summary Giant pandas (Ailuropoda melanoleuca) are endangered animals and are uniquely inhabitant in China. These rare animals have gradually developed bamboo-eating adaptability through persistent evolution. Intestinal microbes play an important role in the digestion, absorption, metabolism, and development of giant pandas especially by facilizing the degradation of bamboo polysaccharides such as cellulose. Currently, genes directly related to cellulose degradation have not been identified in the genome of giant panda, and cellulose digestion is therefore likely dependent on intestinal microbes. This study analyzed the changes in intestinal microbial structure of giant pandas (cubs, sub-adults, and adults) in different developmental stages. The impact was also assessed with the changes in food composition probed into the succession regularity of intestinal microbes and the activities of intestinal flora on the digestion and utilization of cellulose in bamboo. Abstract The interaction between intestinal microbial flora and giant pandas (Ailuropoda melanoleuca) is indispensable for the healthy development of giant pandas. In this study, we analysed the diversity of bacteria and fungi in the intestines of six giant pandas (two pandas in each development stage) with a high-throughput sequencing technique to expand the relative variation in abundance of dominant microbes and potential cellulose-degradation genera in the intestines of the giant pandas and to explore the correlation between dominant microbial genera in the intestines and cellulose digestion activities of giant pandas. The results showed that the intestinal bacterial diversity of young giant pandas was higher than that of sub-adult and adult giant pandas, and Shannon’s diversity index was about 2.0. The intestinal bacterial diversity of giant pandas from sub-adult to adult (mature stage) stage showed an increasing trend, but the intestinal fungal diversity showed no considerable regular relations with their ages. The microbial composition and abundance of giant pandas changed in different developmental stages. Pearson correlation analysis and path analysis showed that there was a close relationship between the dominant microbes in the intestines of giant pandas, and the interaction between microbial genera might affect the cellulose digestion ability of giant pandas. Generally, the digestibility of cellulose degraders in pandas was still insufficient, with low enzymic activity and immature microbial structure. Therefore, the utilization and digestion of bamboo cellulose still might not be a main source of energy for pandas.
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Čížková D, Ďureje Ľ, Piálek J, Kreisinger J. Experimental validation of small mammal gut microbiota sampling from faeces and from the caecum after death. Heredity (Edinb) 2021; 127:141-150. [PMID: 34045683 PMCID: PMC8322053 DOI: 10.1038/s41437-021-00445-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 02/04/2023] Open
Abstract
Data on the gut microbiota (GM) of wild animals are key to studies on evolutionary biology (host-GM interactions under natural selection), ecology and conservation biology (GM as a fitness component closely connected to the environment). Wildlife GM sampling often requires non-invasive techniques or sampling from dead animals. In a controlled experiment profiling microbial 16S rRNA in 52 house mice (Mus musculus) from eight families and four genetic backgrounds, we studied the effects of live- and snap-trapping on small mammal GM and evaluated the suitability of microbiota from non-fresh faeces as a proxy for caecal GM. We compared CM from individuals sampled 16-18 h after death with those in live traps and caged controls, and caecal and faecal GM collected from mice in live-traps. Sampling delay did not affect GM composition, validating data from fresh cadavers or snap-trapped animals. Animals trapped overnight displayed a slight but significant difference in GM composition to the caged controls, though the change only had negligible effect on GM diversity, composition and inter-individual divergence. Hence, the trapping process appears not to bias GM profiling. Despite their significant difference, caecal and faecal microbiota were correlated in composition and, to a lesser extent, diversity. Both showed congruent patterns of inter-individual divergence following the natural structure of the dataset. Thus, the faecal microbiome represents a good non-invasive proxy of the caecal microbiome, making it suitable for detecting biologically relevant patterns. However, care should be taken when analysing mixed datasets containing both faecal and caecal samples.
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Affiliation(s)
- Dagmar Čížková
- grid.418095.10000 0001 1015 3316Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Ľudovít Ďureje
- grid.418095.10000 0001 1015 3316Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jaroslav Piálek
- grid.418095.10000 0001 1015 3316Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jakub Kreisinger
- grid.4491.80000 0004 1937 116XFaculty of Science, Department of Zoology, Charles University, Prague, Czech Republic
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Salinas I, Fernández-Montero Á, Ding Y, Sunyer JO. Mucosal immunoglobulins of teleost fish: A decade of advances. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 121:104079. [PMID: 33785432 PMCID: PMC8177558 DOI: 10.1016/j.dci.2021.104079] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 05/03/2023]
Abstract
Immunoglobulins (Igs) are complex glycoproteins that play critical functions in innate and adaptive immunity of all jawed vertebrates. Given the unique characteristics of mucosal barriers, secretory Igs (sIgs) have specialized to maintain homeostasis and keep pathogens at bay at mucosal tissues from fish to mammals. In teleost fish, the three main IgH isotypes, IgM, IgD and IgT/Z can be found in different proportions at the mucosal secretions of the skin, gills, gut, nasal, buccal, and pharyngeal mucosae. Similar to the role of mammalian IgA, IgT plays a predominant role in fish mucosal immunity. Recent studies in IgT have illuminated the primordial role of sIgs in both microbiota homeostasis and pathogen control at mucosal sites. Ten years ago, IgT was discovered to be an immunoglobulin class specialized in mucosal immunity. Aiming at this 10-year anniversary, the goal of this review is to summarize the current status of the field of fish Igs since that discovery, while identifying knowledge gaps and future avenues that will move the field forward in both basic and applied science areas.
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Affiliation(s)
- Irene Salinas
- Center for Evolutionary and Theoretical Immunology (CETI), Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA.
| | - Álvaro Fernández-Montero
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yang Ding
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - J Oriol Sunyer
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Rosado D, Xavier R, Cable J, Severino R, Tarroso P, Pérez-Losada M. Longitudinal sampling of external mucosae in farmed European seabass reveals the impact of water temperature on bacterial dynamics. ISME COMMUNICATIONS 2021; 1:28. [PMID: 36739461 PMCID: PMC9723769 DOI: 10.1038/s43705-021-00019-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023]
Abstract
Fish microbiota are intrinsically linked to health and fitness, but they are highly variable and influenced by both biotic and abiotic factors. Water temperature particularly limits bacterial adhesion and growth, impacting microbial diversity and bacterial infections on the skin and gills. Aquaculture is heavily affected by infectious diseases, especially in warmer months, and industry practices often promote stress and microbial dysbiosis, leading to an increased abundance of potentially pathogenic bacteria. In this regard, fish mucosa health is extremely important because it provides a primary barrier against pathogens. We used 16 rRNA V4 metataxonomics to characterize the skin and gill microbiota of the European seabass, Dicentrarchus labrax, and the surrounding water over 12 months, assessing the impact of water temperature on microbial diversity and function. We show that the microbiota of external mucosae are highly dynamic with consistent longitudinal trends in taxon diversity. Several potentially pathogenic genera (Aliivibrio, Photobacterium, Pseudomonas, and Vibrio) were highly abundant, showing complex interactions with other bacterial genera, some of which with recognized probiotic activity, and were also significantly impacted by changes in temperature. The surrounding water temperature influenced fish microbial composition, structure and function over time (days and months). Additionally, dysbiosis was more frequent in warmer months and during transitions between cold/warm months. We also detected a strong seasonal effect in the fish microbiota, which is likely to result from the compound action of several unmeasured environmental factors (e.g., pH, nutrient availability) beyond temperature. Our results highlight the importance of performing longitudinal studies to assess the impact of environmental factors on fish microbiotas.
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Affiliation(s)
- Daniela Rosado
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal.
| | - Raquel Xavier
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal.
| | - Jo Cable
- School of Biosciences, Cardiff University, Cardiff, UK
| | - Ricardo Severino
- Piscicultura Vale da Lama, Sapal do Vale da Lama, Odiáxere, Lagos, Portugal
| | - Pedro Tarroso
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - Marcos Pérez-Losada
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
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21
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Orso G, Solovyev MM, Facchiano S, Tyrikova E, Sateriale D, Kashinskaya E, Pagliarulo C, Hoseinifar HS, Simonov E, Varricchio E, Paolucci M, Imperatore R. Chestnut Shell Tannins: Effects on Intestinal Inflammation and Dysbiosis in Zebrafish. Animals (Basel) 2021; 11:ani11061538. [PMID: 34070355 PMCID: PMC8228309 DOI: 10.3390/ani11061538] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 05/21/2021] [Indexed: 12/15/2022] Open
Abstract
Simple Summary With the increase in global population the production of animal proteins becomes increasingly crucial. Aquaculture is the first animal protein supply industry for human consumption. Intensive farming techniques are employed to increase productivity, but these may cause stressful conditions for fish, resulting in impaired growth and poor health conditions. Intestinal inflammation is one of the most common diseases of fish in intensive farming. Intestinal inflammation is usually accompanied by an alteration of the microbiota or dysbiosis. Inflammation and dysbiosis are so tightly intertwined that inflammation may contribute to or result from dysregulation of gut microbiota. Natural substances of plant origin rich in bioactive molecules or more simply phytochemicals, have been proved to be able to reduce inflammation and improve the general health status in various commercially relevant species. In this study, we evaluated the effect of tannins, a class of polyphenols, the most abundant phytochemicals, on intestinal inflammation and microbiota in zebrafish (Danio rerio), a small freshwater fish become an attractive biomedicine and aquaculture animal model during the last decades. The zebrafish has been employed in a vast array of studies aiming at investigating the essential processes underlying intestinal inflammation and injury due to its conservative gut morphology and functions. In this study, we administered a diet enriched with chestnut shell extract rich in tannins to a zebrafish model of intestinal inflammation. The treatment ameliorated the damaged intestinal morphophysiology and the microbiota asset. Our results sustain that products of natural origin with low environmental impact and low cost, such as tannins, may help to ease some of the critical issues affecting the aquaculture sector. Abstract The aim of the present study was to test the possible ameliorative efficacy of phytochemicals such as tannins on intestinal inflammation and dysbiosis. The effect of a chestnut shell (Castanea sativa) extract (CSE) rich in polyphenols, mainly represented by tannins, on k-carrageenan-induced intestinal inflammation in adult zebrafish (Danio rerio) was tested in a feeding trial. Intestinal inflammation was induced by 0.1% k-carrageenan added to the diet for 10 days. CSE was administered for 10 days after k-carrageenan induced inflammation. The intestinal morphology and histopathology, cytokine expression, and microbiota were analyzed. The k-carrageenan treatment led to gut lumen expansion, reduction of intestinal folds, and increase of the goblet cells number, accompanied by the upregulation of pro-inflammatory factors (TNFα, COX2) and alteration in the number and ratio of taxonomic groups of bacteria. CSE counteracted the inflammatory status enhancing the growth of health helpful bacteria (Enterobacteriaceae and Pseudomonas), decreasing the pro-inflammatory factors, and activating the anti-inflammatory cytokine IL-10. In conclusion, CSE acted as a prebiotic on zebrafish gut microbiota, sustaining the use of tannins as food additives to ameliorate the intestinal inflammation. Our results may be relevant for both aquaculture and medical clinic fields.
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Affiliation(s)
- Graziella Orso
- Department of Science and Technology (DST), University of Sannio, 82100 Benevento, Italy; (G.O.); (S.F.); (D.S.); (C.P.); (E.V.); (R.I.)
| | - Mikhail M. Solovyev
- Institute of Systematics and Ecology of Animals, Siberian Branch of RAS, 630091 Novosibirsk, Russia; (M.M.S.); (E.T.); (E.K.)
- Biological Institute, Tomsk State University, 634050 Tomsk, Russia
| | - Serena Facchiano
- Department of Science and Technology (DST), University of Sannio, 82100 Benevento, Italy; (G.O.); (S.F.); (D.S.); (C.P.); (E.V.); (R.I.)
| | - Evgeniia Tyrikova
- Institute of Systematics and Ecology of Animals, Siberian Branch of RAS, 630091 Novosibirsk, Russia; (M.M.S.); (E.T.); (E.K.)
- Department of Natural Sciences, Novosibirsk State University, 630091 Novosibirsk, Russia
| | - Daniela Sateriale
- Department of Science and Technology (DST), University of Sannio, 82100 Benevento, Italy; (G.O.); (S.F.); (D.S.); (C.P.); (E.V.); (R.I.)
| | - Elena Kashinskaya
- Institute of Systematics and Ecology of Animals, Siberian Branch of RAS, 630091 Novosibirsk, Russia; (M.M.S.); (E.T.); (E.K.)
| | - Caterina Pagliarulo
- Department of Science and Technology (DST), University of Sannio, 82100 Benevento, Italy; (G.O.); (S.F.); (D.S.); (C.P.); (E.V.); (R.I.)
| | - Hossein S. Hoseinifar
- Department of Fisheries, Gorgan University of Agricultural Sciences and Natural Resources, 49138-15739 Gorgan, Iran;
| | - Evgeniy Simonov
- Institute of Environmental and Agricultural Biology (X-BIO), University of Tyumen, 625003 Tyumen, Russia;
| | - Ettore Varricchio
- Department of Science and Technology (DST), University of Sannio, 82100 Benevento, Italy; (G.O.); (S.F.); (D.S.); (C.P.); (E.V.); (R.I.)
| | - Marina Paolucci
- Department of Science and Technology (DST), University of Sannio, 82100 Benevento, Italy; (G.O.); (S.F.); (D.S.); (C.P.); (E.V.); (R.I.)
- Correspondence:
| | - Roberta Imperatore
- Department of Science and Technology (DST), University of Sannio, 82100 Benevento, Italy; (G.O.); (S.F.); (D.S.); (C.P.); (E.V.); (R.I.)
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22
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Jing X, Su S, Zhang C, Zhu J, Hou Y, Li Z, Yang X, Zhou X, He X, Munganga BP, Tang Y, Xu P. Dynamic changes in microbial community structure in farming pond water and their effect on the intestinal microbial community profile in juvenile common carp (Cyprinus carpio L.). Genomics 2021; 113:2547-2560. [PMID: 34029696 DOI: 10.1016/j.ygeno.2021.05.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 05/03/2021] [Accepted: 05/19/2021] [Indexed: 11/29/2022]
Abstract
Water quality parameter dynamics, gut, sediment and water bacteria communities were studied to understand the environmental influence on the gut microbial community of a new strain of Huanghe common carp. A total of 3,384,078 raw tags and 5105 OTUs were obtained for the gut, water and sediment bacteria. The water quality had a stronger influence on the water bacteria community than gut and sediment bacteria communities. The ambient water quality parameters also significantly influenced the water and sediment bacteria communities. Comparing the gut, sediment, and water microbial communities, a relationship was found among them. However, gut bacteria were more closely related to sediment bacterial communities than to water bacteria communities. The results showed that the top three bacterial taxa were identical in gut and sediment samples in the early days of rearing. Interestingly, bacterial communities in the carp gut, water, and sediment had different adaptabilities to variations in environmental factors.
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Affiliation(s)
- Xiaojun Jing
- College of Fisheries, Huazhong Agricultural University, Wuhan, PR China; Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, PR China
| | - Shengyan Su
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, PR China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, PR China
| | - Chengfeng Zhang
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, PR China
| | - Jian Zhu
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, PR China
| | - Yiran Hou
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, PR China
| | - Zhixun Li
- Henan Academy of Fishery Sciences, Zhengzhou 2450044, PR China
| | - Xingli Yang
- Henan Academy of Fishery Sciences, Zhengzhou 2450044, PR China
| | - Xiaolin Zhou
- Henan Academy of Fishery Sciences, Zhengzhou 2450044, PR China
| | - Xugang He
- College of Fisheries, Huazhong Agricultural University, Wuhan, PR China.
| | | | - Yongkai Tang
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, PR China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, PR China
| | - Pao Xu
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, PR China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, PR China.
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23
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Probiotics in Fish Nutrition—Long-Standing Household Remedy or Native Nutraceuticals? WATER 2021. [DOI: 10.3390/w13101348] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Over the last decades, aquaculture production increased rapidly. The future development of the industry highly relies on the sustainable utilization of natural resources. The need for improving disease resistance, growth performance, food conversion, and product safety for human consumption has stimulated the application of probiotics in aquaculture. Probiotics increase growth and feed conversion, improve health status, raise disease resistance, decrease stress susceptibility, and improve general vigor. Currently, most probiotics still originate from terrestrial sources rather than fish. However, host-associated (autochthonous) probiotics are likely more persistent in the gastrointestinal tract of fish and may, therefore, exhibit longer-lasting effects on the host. Probiotic candidates are commonly screened in in vitro assays, but the transfer to in vivo assessment is often problematic. In conclusion, modulation of the host-associated microbiome by the use of complex probiotics is promising, but a solid understanding of the interactions involved is only in its infancy and requires further research. Probiotics could be used to explore novel ingredients such as chitin-rich insect meal, which cannot be digested by the fish host alone. Most importantly, probiotics offer the opportunity to improve stress and disease resistance, which is among the most pressing problems in aquaculture.
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24
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Karvonen A, Räihä V, Klemme I, Ashrafi R, Hyvärinen P, Sundberg LR. Quantity and Quality of Aquaculture Enrichments Influence Disease Epidemics and Provide Ecological Alternatives to Antibiotics. Antibiotics (Basel) 2021; 10:antibiotics10030335. [PMID: 33810018 PMCID: PMC8004632 DOI: 10.3390/antibiotics10030335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/10/2021] [Accepted: 03/16/2021] [Indexed: 11/16/2022] Open
Abstract
Environmental heterogeneity is a central component influencing the virulence and epidemiology of infectious diseases. The number and distribution of susceptible hosts determines disease transmission opportunities, shifting the epidemiological threshold between the spread and fadeout of a disease. Similarly, the presence and diversity of other hosts, pathogens and environmental microbes, may inhibit or accelerate an epidemic. This has important applied implications in farming environments, where high numbers of susceptible hosts are maintained in conditions of minimal environmental heterogeneity. We investigated how the quantity and quality of aquaculture enrichments (few vs. many stones; clean stones vs. stones conditioned in lake water) influenced the severity of infection of a pathogenic bacterium, Flavobacterium columnare, in salmonid fishes. We found that the conditioning of the stones significantly increased host survival in rearing tanks with few stones. A similar effect of increased host survival was also observed with a higher number of unconditioned stones. These results suggest that a simple increase in the heterogeneity of aquaculture environment can significantly reduce the impact of diseases, most likely operating through a reduction in pathogen transmission (stone quantity) and the formation of beneficial microbial communities (stone quality). This supports enriched rearing as an ecological and economic way to prevent bacterial infections with the minimal use of antimicrobials.
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Affiliation(s)
- Anssi Karvonen
- Department of Biological and Environmental Science, University of Jyvaskyla, P.O. Box 35, 40014 Jyvaskyla, Finland; (V.R.); (I.K.); (R.A.); (L.-R.S.)
- Correspondence: ; Tel.: +358-40-8053882; Fax: +358-14-2601021
| | - Ville Räihä
- Department of Biological and Environmental Science, University of Jyvaskyla, P.O. Box 35, 40014 Jyvaskyla, Finland; (V.R.); (I.K.); (R.A.); (L.-R.S.)
| | - Ines Klemme
- Department of Biological and Environmental Science, University of Jyvaskyla, P.O. Box 35, 40014 Jyvaskyla, Finland; (V.R.); (I.K.); (R.A.); (L.-R.S.)
| | - Roghaieh Ashrafi
- Department of Biological and Environmental Science, University of Jyvaskyla, P.O. Box 35, 40014 Jyvaskyla, Finland; (V.R.); (I.K.); (R.A.); (L.-R.S.)
| | - Pekka Hyvärinen
- Natural Resources and Bioproduction, Natural Resources Institute Finland (Luke), Manamansalontie 90, 88300 Paltamo, Finland;
| | - Lotta-Riina Sundberg
- Department of Biological and Environmental Science, University of Jyvaskyla, P.O. Box 35, 40014 Jyvaskyla, Finland; (V.R.); (I.K.); (R.A.); (L.-R.S.)
- Nanoscience Center, University of Jyvaskyla, P.O. Box 35, 40014 Jyvaskyla, Finland
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25
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Sehnal L, Brammer-Robbins E, Wormington AM, Blaha L, Bisesi J, Larkin I, Martyniuk CJ, Simonin M, Adamovsky O. Microbiome Composition and Function in Aquatic Vertebrates: Small Organisms Making Big Impacts on Aquatic Animal Health. Front Microbiol 2021; 12:567408. [PMID: 33776947 PMCID: PMC7995652 DOI: 10.3389/fmicb.2021.567408] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 02/05/2021] [Indexed: 01/03/2023] Open
Abstract
Aquatic ecosystems are under increasing stress from global anthropogenic and natural changes, including climate change, eutrophication, ocean acidification, and pollution. In this critical review, we synthesize research on the microbiota of aquatic vertebrates and discuss the impact of emerging stressors on aquatic microbial communities using two case studies, that of toxic cyanobacteria and microplastics. Most studies to date are focused on host-associated microbiomes of individual organisms, however, few studies take an integrative approach to examine aquatic vertebrate microbiomes by considering both host-associated and free-living microbiota within an ecosystem. We highlight what is known about microbiota in aquatic ecosystems, with a focus on the interface between water, fish, and marine mammals. Though microbiomes in water vary with geography, temperature, depth, and other factors, core microbial functions such as primary production, nitrogen cycling, and nutrient metabolism are often conserved across aquatic environments. We outline knowledge on the composition and function of tissue-specific microbiomes in fish and marine mammals and discuss the environmental factors influencing their structure. The microbiota of aquatic mammals and fish are highly unique to species and a delicate balance between respiratory, skin, and gastrointestinal microbiota exists within the host. In aquatic vertebrates, water conditions and ecological niche are driving factors behind microbial composition and function. We also generate a comprehensive catalog of marine mammal and fish microbial genera, revealing commonalities in composition and function among aquatic species, and discuss the potential use of microbiomes as indicators of health and ecological status of aquatic ecosystems. We also discuss the importance of a focus on the functional relevance of microbial communities in relation to organism physiology and their ability to overcome stressors related to global change. Understanding the dynamic relationship between aquatic microbiota and the animals they colonize is critical for monitoring water quality and population health.
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Affiliation(s)
- Ludek Sehnal
- RECETOX, Faculty of Science, Masaryk University, Brno, Czechia
| | - Elizabeth Brammer-Robbins
- Department of Large Animal Clinical Sciences, University of Florida, Gainesville, FL, United States
- Department of Physiological Sciences, University of Florida, Gainesville, FL, United States
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
| | - Alexis M. Wormington
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
- Department of Environmental and Global Health, University of Florida, Gainesville, FL, United States
| | - Ludek Blaha
- RECETOX, Faculty of Science, Masaryk University, Brno, Czechia
| | - Joe Bisesi
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
- Department of Environmental and Global Health, University of Florida, Gainesville, FL, United States
| | - Iske Larkin
- Department of Large Animal Clinical Sciences, University of Florida, Gainesville, FL, United States
| | - Christopher J. Martyniuk
- Department of Physiological Sciences, University of Florida, Gainesville, FL, United States
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
| | - Marie Simonin
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
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26
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Khurana H, Sharma M, Bharti M, Singh DN, Negi RK. Gut milieu shapes the bacterial communities of invasive silver carp. Genomics 2021; 113:815-826. [PMID: 33508444 DOI: 10.1016/j.ygeno.2021.01.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/12/2020] [Accepted: 01/22/2021] [Indexed: 11/29/2022]
Abstract
Silver carp is an invasive fish present in the Gobindsagar reservoir, India and has a profound impact on aquaculture. Understanding taxonomic diversity and functional attributes of gut microbiota will provide insights into the important role of bacteria in metabolism of silver carp that facilitated invasion of this exotic species. Microbial composition in foregut, midgut, hindgut and water samples was analysed using 16S rRNA gene amplicon sequencing. The bacterial communities of water samples were distinct from gut microbiota, and unique microbial assemblages were present in different regions of gut depicting profound impact of gut environment on microflora. Proteobacteria was the most abundant phyla across all samples. Ecological network analysis showed dominance of competitive interactions within posteriors region of the gut, promoting niche specialization. Predictive functional profiling revealed the microbiota specialized in digestive functions in different regions of the gut, which also reflects the dietary profile of silver carp.
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Affiliation(s)
- Himani Khurana
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India
| | - Monika Sharma
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India
| | - Meghali Bharti
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India
| | | | - Ram Krishan Negi
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India.
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27
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Abd-Elmonsef Mahmoud G, Osman YA, Abdel-Hakeem SS. Hydrolytic bacteria associated with natural helminth infection in the midgut of Red Sea marbled spinefoot rabbit fish Siganus rivulatus. Microb Pathog 2020; 147:104404. [PMID: 32781103 DOI: 10.1016/j.micpath.2020.104404] [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: 04/20/2020] [Revised: 07/15/2020] [Accepted: 07/17/2020] [Indexed: 10/23/2022]
Abstract
Fish infected with intestinal helminths or pathogenic bacteria can pose a serious risk of foodborne disease, threatening human and animal health, and require high attention. The current study investigates the diversity and composition of the microbiota in the midgut of rabbit fish Siganus rivulatus naturally infected with helminths. Six species of helminth parasites, including the digeneans Hexangium sigani and Gyliauchen volubilis, the acanthocephalans Sclerocollum rubrimaris and Neorhadinorhynchus macrospinosus, and the nematodes Procammalanus elatensis, and Ascaridoid larvae were recorded in the fish intestine. P. elatensis had the highest prevalence, occurring in 65% of infected fish; 72.2% of infected fish had concurrent infection with two or more helminth species. The total count of aerobic bacteria ranged from 1 to 305 colony-forming units (CFU)/g midgut contents. Four hydrolytic bacteria were recovered from the infected samples: Escherichia coli (ASU 31), Bacillus cereus (ASU 36) MN955553, Bacillus thuringiensis (ASU 34) MN955550, and Novosphingobium aromaticivorans (ASU 35) MN955552, which were identified using 16S rRNA genes. Bacterial richness was significantly correlated with concurrent parasitic infection and high content of extracellular hydrolytic amylases, proteases, cellulases, and lipases. The present results showed that the composition of the microbiota was affected by natural helminth infections in Siganus rivulatus, and the significant interaction between parasitic load and intestinal pathogenic bacteria, which may be primary in fish diseases etiology.
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Affiliation(s)
| | | | - Sara Salah Abdel-Hakeem
- Parasitology Laboratory, Zoology Department, Faculty of Science, Assiut University, Assiut, 71516, Egypt.
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28
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Bailey C, Holland JW, Secombes CJ, Tafalla C. A portrait of the immune response to proliferative kidney disease (PKD) in rainbow trout. Parasite Immunol 2020; 42:e12730. [PMID: 32403171 PMCID: PMC7507176 DOI: 10.1111/pim.12730] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 01/31/2020] [Accepted: 05/06/2020] [Indexed: 12/17/2022]
Abstract
Proliferative kidney disease (PKD), caused by the myxozoan Tetracapsuloides bryosalmonae, is one of the most serious parasitic diseases of salmonids in which outbreaks cause severe economic constraints for the aquaculture industry and declines of wild species throughout Europe and North America. Given that rainbow trout (Oncorhynchus mykiss) is one of the most widely farmed freshwater fish and an important model species for fish immunology, most of the knowledge on how the fish immune response is affected during PKD is from this organism. Once rainbow trout are infected, PKD pathogenesis results in a chronic kidney immunopathology mediated by decreasing myeloid cells and increasing lymphocytes. Transcriptional studies have revealed the regulation of essential genes related to T-helper (Th)-like functions and a dysregulated B-cell antibody type response. Recent reports have discovered unique details of teleost B-cell differentiation and functionality and characterized the differential immunoglobulin (Ig)-mediated response. These studies have solidified the rainbow trout T. bryosalmonae system as a sophisticated disease model capable of feeding key advances into mainstream immunology and have contributed essential information to design novel parasite disease prevention strategies. In our following perspective, we summarize these efforts to evaluate the immune mechanisms of rainbow trout during PKD pathogenesis.
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Affiliation(s)
- Christyn Bailey
- Centro de Investigación en Sanidad Animal (CISA‐INIA)MadridSpain
| | - Jason W. Holland
- Aberdeen Oomycete LaboratoryInstitute of Medical SciencesUniversity of AberdeenAberdeenUK
| | - Christopher J. Secombes
- Scottish Fish Immunology Research CentreInstitute of Biological and Environmental SciencesUniversity of AberdeenAberdeenUK
| | - Carolina Tafalla
- Centro de Investigación en Sanidad Animal (CISA‐INIA)MadridSpain
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29
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Luo ZW, Dong ZX, Chen YF, Li HY, Tang QH, Li JL, Guo J. Comparative analysis of the gut microbiota of Apis cerana in Yunnan using high-throughput sequencing. Arch Microbiol 2020; 202:2557-2567. [PMID: 32666301 DOI: 10.1007/s00203-020-01974-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 04/30/2020] [Accepted: 07/03/2020] [Indexed: 01/23/2023]
Abstract
Gut microbes play an important role in host disease and health. The Asian honey bee Apis cerana is an important pollinator of agricultural crops in China. However, there are still few studies on the structure and composition of the microbiota in the intestine of A. cerana, especially A. cerana in Yunnan. To understand the species and composition of the microbiota in the intestine of A. cerana in Yunnan, we used high-throughput sequencing technology to carry out 16S rRNA sequencing on 50 samples from Kunming, Xishuangbanna and Mengzi. The results show that both from the phylum level and the genus level, the structure and abundance of the microbiota in the gut of A. cerana from the three regions tended to be the same. At the phylum level, the abundance of Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Acidobacteria and other species was high in A. cerana from different areas. At the genus level, the abundance of Lactobacillus, Gilliamella, Snodgrassella, Apibacter, Candidatus Schmidhempelia and other species was high in A. cerana from different areas. Due to its unique geographical environment and climatic conditions, at the genus level, the diversity of bacterial communities in Xishuangbanna was significantly lower than that in the other two regions, which was about 100 genera less. In conclusion, our results reveal the composition and structure of the intestinal microbiota of bees in Yunnan and deepen our understanding of the intestinal microbiota of bees.
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Affiliation(s)
- Zhi-Wen Luo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Zhi-Xiang Dong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Yi-Fei Chen
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Huan-Yuan Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Qi-He Tang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Ji-Lian Li
- Institute of Apiculture, Chinese Academy of Agricultural Science/Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Beijing, 100093, China.
| | - Jun Guo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China.
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30
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Wu Y, Xiao F, Wang C, Shu L, Zheng X, Xu K, Yu X, Zhang K, Luo H, Yang Y, He Z, Yan Q. The Beta-Diversity of Siganus fuscescens-Associated Microbial Communities From Different Habitats Increases With Body Weight. Front Microbiol 2020; 11:1562. [PMID: 32733425 PMCID: PMC7358552 DOI: 10.3389/fmicb.2020.01562] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/16/2020] [Indexed: 01/05/2023] Open
Abstract
Fish-associated microbial communities play important roles in host growth, health and disease in the symbiont ecosystem; however, their diversity patterns and underlying mechanisms in different body habitats remain poorly understood. Siganus fuscescens is one of the most important consumers of macroalgae and an excellent natural marine source of nutritional lipids for humans, and widely distributes in shallow coastal areas. Here we systematically studied the microbial communities of 108 wild S. fuscescens in four body habitats (i.e., skin, gill, stomach, and hindgut) and surrounding water. We found that the β-diversity but not α-diversity of fish-associated microbial communities from each habitat significantly (p < 0.05) increased as body weight increased. Also, opportunistic pathogens and probiotics (e.g., Pseudomongs, Methylobacterium) appeared to be widely distributed in different body habitats, and many digestive bacteria (e.g., Clostridium) in the hindgut; the abundances of some core OTUs associated with digestive bacteria, “Anaerovorax” (OTU_6 and OTU_46724) and “Holdemania” (OTU_33295) in the hindgut increased as body weight increased. Additionally, the quantification of ecological processes indicated that heterogeneous selection was the major process (46–70%) governing the community assembly of fish microbiomes, whereas the undominated process (64%) was found to be more important for the water microbiome. The diversity pattern showed that β-diversity (75%) of the metacommunity overweight the α-diversity (25%), confirming that the niche separation of microbial communities in different habitats and host selection were important to shape the fish-associated microbial community structure. This study enhances our mechanistic understanding of fish-associated microbial communities in different habitats, and has important implications for analyzing host-associated metacommunities.
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Affiliation(s)
- Yongjie Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Fanshu Xiao
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Xiafei Zheng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Kui Xu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Xiaoli Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Keke Zhang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Hongtian Luo
- Department of Ecology, Institute of Hydrobiology, Jinan University, Guangzhou, China
| | - Yufeng Yang
- Department of Ecology, Institute of Hydrobiology, Jinan University, Guangzhou, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China.,College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
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31
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Variations and Potential Factors of Gut Prokaryotic Microbiome During Spawning Migration in Coilia nasus. Curr Microbiol 2020; 77:2802-2812. [PMID: 32583157 DOI: 10.1007/s00284-020-02088-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 06/12/2020] [Indexed: 02/01/2023]
Abstract
Coilia nasus is influenced by various external pressures during spawning migration and these anadromous transitions can lead to specific gut microbiome characteristics that affecting the host biological process. Therefore, the purpose of this study was to determine the variations of components and functions in the gut prokaryotic microbiome during spawning migration as well as the key factors that triggered the changes. The gut microbiome in C. nasus was mainly consisted of Proteobacteria, Bacteroidetes, Firmicutes, Deinococcus-Thermus and Fusobacteria via 16S rRNA Gene Amplicon Sequencing. The relative abundance of Acinetobacter and Clostridium increased, while Corynebacterium, Actinomyces, Bacillus, Klebsiella and Ochrobactrum decreased after entering freshwater, indicated the preference of C. nasus gut microbial members transferred from seawater to freshwater. Additionally, the proportion of Firmicutes significantly decreased and then increased, as well as the arise of some soil bacteria in gut, corresponding to the phenomenon that C. nasus are fasting during the upstream process and refeeding after entering the spawning grounds. The function prediction of gut microbiome was also consistent with the above results. The present study generally demonstrated the gut microbiome dynamics and the significant correlation between the gut microbiome and salinity and feeding behavior in the spawning migration of C. nasus.
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32
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Volkoff H, Rønnestad I. Effects of temperature on feeding and digestive processes in fish. Temperature (Austin) 2020; 7:307-320. [PMID: 33251280 PMCID: PMC7678922 DOI: 10.1080/23328940.2020.1765950] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/29/2020] [Accepted: 05/03/2020] [Indexed: 12/11/2022] Open
Abstract
As most fish are ectotherms, their physiology is strongly affected by temperature. Temperature affects their metabolic rate and thus their energy balance and behavior, including locomotor and feeding behavior. Temperature influences the ability/desire of the fish to obtain food, and how they process food through digestion, absorb nutrients within the gastrointestinal tract, and store excess energy. As fish display a large variability in habitats, feeding habits, and anatomical and physiological features, the effects of temperature are complex and species-specific. The effects of temperature depend on the timing, intensity, and duration of exposure as well as the speed at which temperature changes occur. Whereas acute short-term variations of temperature might have drastic, often detrimental, effects on fish physiology, long-term gradual variations might lead to acclimation, e.g. variations in metabolic and digestive enzyme profiles. The goal of this review is to summarize our current knowledge on the effects of temperature on energy homeostasis, with specific focus on metabolism, feeding, digestion, and how fish are often able to "adapt" to changing environments through phenotypic and physiological changes.
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Affiliation(s)
- Helene Volkoff
- Departments of Biology and Biochemistry, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Ivar Rønnestad
- Department of Biological Sciences, University of Bergen, Bergen, Norway
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33
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Solovyev MM, Kashinskaya EN, Bochkarev NA, Andree KB, Simonov E. The effect of diet on the structure of gut bacterial community of sympatric pair of whitefishes ( Coregonus lavaretus): one story more. PeerJ 2019; 7:e8005. [PMID: 31824755 PMCID: PMC6896945 DOI: 10.7717/peerj.8005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 10/07/2019] [Indexed: 12/16/2022] Open
Abstract
In the Coregonus lavaretus complex may be found lacustrine sympatric pairs, which serves as an intriguing model for studying different aspects of fish evolutionary biology. One such sympatric whitefish pair inhabits Teletskoye Lake (West Siberia, Russia) and includes a “large” form (Coregonus lavaretus pidschian (Gmelin, 1789)) and a “small” form (C. l. pravdinellus (Dulkeit, 1949)). C. l. pravdinellus has a narrow trophic specialization and feeds on zooplankton, whereas the diet of C. l. pidschian is based on benthic prey. In the present study we aimed to address the question of how the gut microbial community reflects the divergence in diet of a sympatric pair of whitefish. Studied samples included the mucosa and content were collected for cardiac and pyloric stomach, anterior, middle, and posterior intestine, but only mucosa was collected for the pyloric caeca. In addition, water, sediment, macrophyte (environmental microbiota) and invertebrate (microbiota of prey) samples were collected in the same location. The V3–V4 region of the 16S rRNA genes was chosen for microbiome analysis and the software PICRUSt used to estimate the difference functional roles of the microbiota. The number of OTUs and Chao1 index in mucosa and content of cardiac and pyloric stomach were significantly different between whitefish. Significant differences were observed between whitefish for content from different parts of the intestine in terms of OTU number and Chao1 indices, whereas for mucosa from the same parts of intestine these differences were absent. No significant differences were found for diversity estimates of mucosa and content of different parts of the gut (there were a few exceptions) between whitefish. The form of whitefish and the segment of the digestive system were factors with a significant determinative effect on the structure of the microbiota from gut mucosa and content. The most dominant phyla in mucosa and content of cardiac and pyloric stomach was Proteobacteria (57.0–84.0%) for both whitefish. Throughout the intestine of C. l. pidschian the dominant phyla in mucosa were Proteobacteria (38.8%) and Firmicutes (15.6%), whereas for C. l. pravdinellus–Tenericutes (49.6%) and Proteobacteria (28.1%). For both forms, the phylum Spirochaetes was found in a significant amount (20.0–25.0%) in the mucosa of the posterior intestine. While for the content obtained from anterior, middle and posterior intestines, the dominant bacterial phyla were the same as those described for mucosa from the same parts of the intestine for both whitefish. The bacterial community of the prey and environment was significantly different from bacterial communities found for all parts of the gut mucosa for both whitefish, with the exception of the mucosa of the cardiac stomach. According to PICRUSt the highest level of differences between whitefish at the L3 level were found for the intestinal mucosa (75.3%), whereas the lowest one was registered for stomach content (38.8%).
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Affiliation(s)
- Mikhail M Solovyev
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia.,Tomsk State University, Tomsk, Russia
| | - Elena N Kashinskaya
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Nickolai A Bochkarev
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Karl B Andree
- Instituto de Investigación y Tecnología Agroalimentarias, San Carlos de la Rapita, Tarragona, Spain
| | - Evgeniy Simonov
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia.,Institute of Environmental and Agricultural Biology, Tyumen State University, Tyumen, Russia
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34
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Fogarty C, Burgess CM, Cotter PD, Cabrera-Rubio R, Whyte P, Smyth C, Bolton DJ. Diversity and composition of the gut microbiota of Atlantic salmon (Salmo salar) farmed in Irish waters. J Appl Microbiol 2019; 127:648-657. [PMID: 31021487 DOI: 10.1111/jam.14291] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 04/01/2019] [Accepted: 04/04/2019] [Indexed: 12/25/2022]
Abstract
AIMS Information on the gut microbiota of salmon is essential for optimizing nutrition while maintaining host health and welfare. This study's objectives were to characterize the microbiota in the GI tract of Atlantic salmon (Salmo salar) farmed in waters off the west coast of Ireland and to investigate whether there is a difference in microbiota diversity between the proximal and distal regions of the intestine. METHODS AND RESULTS The microbiota from the proximal and distal intestine (PI and DI, respectively) of Atlantic salmon was examined using MiSeq Illumina high-throughput sequencing of the 16S ribosomal RNA gene. The PI region had greater bacterial diversity than the DI region. Six phyla were present in the DI samples, dominated by Tenericutes and Firmicutes. These six phyla were also amongst the 12 phyla detected in the PI samples. The PI microbiota was dominated by Tenericutes, Firmicutes, Bacteroidetes and Proteobacteria. A core microbiota of 20 operational taxonomic units (OTUs) common to both regions was observed. CONCLUSIONS It was concluded that Tenericutes were the dominant phylum in both PI and DI samples, and the PI region had greater Shannon and Simpson diversity of bacteria. However, further work is required to identify the functionality of the salmon microbiota. SIGNIFICANCE AND IMPACT OF THE STUDY Our study determined the composition and diversity of the intestinal microbiota in adult salmon from a commercial fishery and provides data to improve our understanding of their contributions to the nutrition, health and welfare of Atlantic salmon farmed in Irish waters.
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Affiliation(s)
- Colin Fogarty
- Teagasc Food Research Centre, Ashtown, Dublin 15, Ireland.,School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | | | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, and APC Microbiome Ireland, Cork, Ireland
| | - Raul Cabrera-Rubio
- Teagasc Food Research Centre, Moorepark, Fermoy, and APC Microbiome Ireland, Cork, Ireland
| | - Paul Whyte
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Conor Smyth
- Teagasc Food Research Centre, Ashtown, Dublin 15, Ireland.,School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
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35
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Fu PP, Xiong F, Feng WW, Zou H, Wu SG, Li M, Wang GT, Li WX. Effect of intestinal tapeworms on the gut microbiota of the common carp, Cyprinus carpio. Parasit Vectors 2019; 12:252. [PMID: 31113452 PMCID: PMC6530175 DOI: 10.1186/s13071-019-3510-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 05/16/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Parasitic protozoans, helminths, alter the gut microbiota in mammals, yet little is known about the influence of intestinal cestodes on gut microbiota in fish. In the present study, the composition and diversity of the hindgut microbiota were determined in the intestine of common carp (Cyprinus carpio) infected with two tapeworm species, Khawia japonensis and Atractolytocestus tenuicollis. RESULTS The intestine contained a core microbiota composed of Proteobacteria, Fusobacteria and Tenericutes. Infection with the two cestode species had no significant effect on the microbial diversity and richness, but it altered the microbial composition at the genus level. PCoA analysis indicated that microbial communities in the infected and uninfected common carp could not be distinguished from each other. However, a Mantel test indicated that the abundance of K. japonensis was significantly correlated with the microbial composition (P = 0.015), while the abundance of A. tenuicollis was not (P = 0.954). According to Pearson's correlation analysis, the abundance of K. japonensis exhibited an extremely significant (P < 0.001) positive correlation with the following gut microbiota taxa: Epulopiscium, U114, Bacteroides, Clostridium and Peptostreptococcaceae (0.8< r < 0.9); and a significant (P < 0.05) correlation with Enterobacteriaceae, Micrococcaceae, Rummeliibacillus, Lysinibacillus boronitolerans, Veillonellaceae, Oxalobacteraceae, Aeromonadaceae (negative), Marinibacillus and Chitinilyticum (0.4< r < 0.7). CONCLUSIONS These results suggest that the composition of gut microbiota was somewhat affected by the K. japonensis infection. Additionally, increased ratios of pathogenic bacteria (Lawsonia and Plesiomonas) were also associated with the K. japonensis infection, which may therefore increase the likelihood of disease.
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Affiliation(s)
- Pei P. Fu
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Fan Xiong
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Wen W. Feng
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
| | - Shan G. Wu
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
| | - Ming Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
| | - Gui T. Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
| | - Wen X. Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
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