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Zhang B, Yang H, Cai G, Nie Q, Sun Y. The interactions between the host immunity and intestinal microorganisms in fish. Appl Microbiol Biotechnol 2024; 108:30. [PMID: 38170313 DOI: 10.1007/s00253-023-12934-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/31/2023] [Accepted: 11/07/2023] [Indexed: 01/05/2024]
Abstract
There is a huge quantity of microorganisms in the gut of fish, which exert pivotal roles in maintaining host intestinal and general health. The fish immunity can sense and shape the intestinal microbiota and maintain the intestinal homeostasis. In the meantime, the intestinal commensal microbes regulate the fish immunity, control the extravagant proliferation of pathogenic microorganisms, and ensure the intestinal health of the host. This review summarizes developments and progress on the known interactions between host immunity and intestinal microorganisms in fish, focusing on the recent advances in zebrafish (Danio rerio) showing the host immunity senses and shapes intestinal microbiota, and intestinal microorganisms tune host immunity. This review will offer theoretical references for the development, application, and commercialization of intestinal functional microorganisms in fish. KEY POINTS: • The interactions between the intestinal microorganisms and host immunity in zebrafish • Fish immunity senses and shapes the microbiota • Intestinal microbes tune host immunity in fish.
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Affiliation(s)
- Biyun Zhang
- Xiamen Key Laboratory for Feed Quality Testing and Safety Evaluation, Fisheries College, Jimei University, Xiamen, 361021, Fujian, China
| | - Hongling Yang
- Xiamen Key Laboratory for Feed Quality Testing and Safety Evaluation, Fisheries College, Jimei University, Xiamen, 361021, Fujian, China
| | - Guohe Cai
- Xiamen Key Laboratory for Feed Quality Testing and Safety Evaluation, Fisheries College, Jimei University, Xiamen, 361021, Fujian, China
| | - Qingjie Nie
- Xiamen Key Laboratory for Feed Quality Testing and Safety Evaluation, Fisheries College, Jimei University, Xiamen, 361021, Fujian, China
| | - Yunzhang Sun
- Xiamen Key Laboratory for Feed Quality Testing and Safety Evaluation, Fisheries College, Jimei University, Xiamen, 361021, Fujian, China.
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2
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Rojoni SA, Ahmed MT, Rahman M, Hossain MMM, Ali MS, Haq M. Advances of microplastics ingestion on the morphological and behavioral conditions of model zebrafish: A review. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2024; 272:106977. [PMID: 38820743 DOI: 10.1016/j.aquatox.2024.106977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/20/2024] [Accepted: 05/26/2024] [Indexed: 06/02/2024]
Abstract
Concerns have been conveyed regarding the availability and hazards of microplastics (MPs) in aquatic biota due to their widespread presence in aquatic habitats. Zebrafish (Danio rerio) are widely used as a model organism to study the adverse impacts of MPs due to their several compelling advantages, such as their small size, ease of breeding, inexpensive maintenance, short life cycle, year-round spawning, high fecundity, fewer legal restrictions, and genetic resemblances to humans. Exposure of organisms to MPs produces physical and chemical toxic effects, including abnormal behavior, oxidative stress, neurotoxicity, genotoxicity, immune toxicity, reproductive imbalance, and histopathological effects. But the severity of the effects is size and concentration-dependent. It has been demonstrated that smaller particles could reach the gut and liver, while larger particles are only confined to the gill, the digestive tract of adult zebrafish. This thorough review encapsulates the current body of literature concerning research on MPs in zebrafish and demonstrates an overview of MPs size and concentration effects on the physiological, morphological, and behavioral characteristics of zebrafish. Finding gaps in the literature paves the way for further investigation.
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Affiliation(s)
- Suraiya Alam Rojoni
- Department of Fisheries and Marine Bioscience, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Md Tanvir Ahmed
- Department of Fisheries and Marine Bioscience, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Mostafizur Rahman
- Department of Fisheries and Marine Bioscience, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Md Mer Mosharraf Hossain
- Department of Fisheries and Marine Bioscience, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Md Sadek Ali
- Department of Fisheries and Marine Bioscience, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Monjurul Haq
- Department of Fisheries and Marine Bioscience, Jashore University of Science and Technology, Jashore 7408, Bangladesh.
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Abbasi E, Akçay E. Host control and species interactions jointly determine microbiome community structure. Theor Popul Biol 2024:S0040-5809(24)00066-2. [PMID: 38925487 DOI: 10.1016/j.tpb.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/21/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024]
Abstract
The host microbiome can be considered an ecological community of microbes present inside a complex and dynamic host environment. The host is under selective pressure to ensure that its microbiome remains beneficial. The host can impose a range of ecological filters including the immune response that can influence the assembly and composition of the microbial community. How the host immune response interacts with the within-microbiome community dynamics to affect the assembly of the microbiome has been largely unexplored. We present here a mathematical framework to elucidate the role of host immune response and its interaction with the balance of ecological interactions types within the microbiome community. We find that highly mutualistic microbial communities characteristic of high community density are most susceptible to changes in immune control and become invasion prone as host immune control strength is increased. Whereas highly competitive communities remain relatively stable in resisting invasion to changing host immune control. Our model reveals that the host immune control can interact in unexpected ways with a microbial community depending on the prevalent ecological interactions types for that community. We stress the need to incorporate the role of host-control mechanisms to better understand microbiome community assembly and stability.
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Affiliation(s)
- Eeman Abbasi
- Department of Biology, University of Pennsylvania, 433 S University Ave, Philadelphia, PA 19104, USA.
| | - Erol Akçay
- Department of Biology, University of Pennsylvania, 433 S University Ave, Philadelphia, PA 19104, USA
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Bornbusch SL, Power ML, Schulkin J, Drea CM, Maslanka MT, Muletz-Wolz CR. Integrating microbiome science and evolutionary medicine into animal health and conservation. Biol Rev Camb Philos Soc 2024; 99:458-477. [PMID: 37956701 DOI: 10.1111/brv.13030] [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: 04/03/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023]
Abstract
Microbiome science has provided groundbreaking insights into human and animal health. Similarly, evolutionary medicine - the incorporation of eco-evolutionary concepts into primarily human medical theory and practice - is increasingly recognised for its novel perspectives on modern diseases. Studies of host-microbe relationships have been expanded beyond humans to include a wide range of animal taxa, adding new facets to our understanding of animal ecology, evolution, behaviour, and health. In this review, we propose that a broader application of evolutionary medicine, combined with microbiome science, can provide valuable and innovative perspectives on animal care and conservation. First, we draw on classic ecological principles, such as alternative stable states, to propose an eco-evolutionary framework for understanding variation in animal microbiomes and their role in animal health and wellbeing. With a focus on mammalian gut microbiomes, we apply this framework to populations of animals under human care, with particular relevance to the many animal species that suffer diseases linked to gut microbial dysfunction (e.g. gut distress and infection, autoimmune disorders, obesity). We discuss diet and microbial landscapes (i.e. the microbes in the animal's external environment), as two factors that are (i) proposed to represent evolutionary mismatches for captive animals, (ii) linked to gut microbiome structure and function, and (iii) potentially best understood from an evolutionary medicine perspective. Keeping within our evolutionary framework, we highlight the potential benefits - and pitfalls - of modern microbial therapies, such as pre- and probiotics, faecal microbiota transplants, and microbial rewilding. We discuss the limited, yet growing, empirical evidence for the use of microbial therapies to modulate animal gut microbiomes beneficially. Interspersed throughout, we propose 12 actionable steps, grounded in evolutionary medicine, that can be applied to practical animal care and management. We encourage that these actionable steps be paired with integration of eco-evolutionary perspectives into our definitions of appropriate animal care standards. The evolutionary perspectives proposed herein may be best appreciated when applied to the broad diversity of species under human care, rather than when solely focused on humans. We urge animal care professionals, veterinarians, nutritionists, scientists, and others to collaborate on these efforts, allowing for simultaneous care of animal patients and the generation of valuable empirical data.
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Affiliation(s)
- Sally L Bornbusch
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Ave. NW, Washington, DC, 20008, USA
- Department of Nutrition Science, Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Ave. NW, Washington, DC, 20008, USA
| | - Michael L Power
- Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Washington, 3001 Connecticut Ave. NW, Washington, DC, 20008, USA
| | - Jay Schulkin
- Department of Obstetrics & Gynecology, University of Washington School of Medicine, 1959 NE Pacific St., Box 356460, Seattle, WA, 98195, USA
| | - Christine M Drea
- Department of Evolutionary Anthropology, Duke University, 104 Biological Sciences, Campus Box 90383, Durham, NC, 27708, USA
| | - Michael T Maslanka
- Department of Nutrition Science, Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Ave. NW, Washington, DC, 20008, USA
| | - Carly R Muletz-Wolz
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Ave. NW, Washington, DC, 20008, USA
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Auclert LZ, Chhanda MS, Derome N. Interwoven processes in fish development: microbial community succession and immune maturation. PeerJ 2024; 12:e17051. [PMID: 38560465 PMCID: PMC10981415 DOI: 10.7717/peerj.17051] [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: 07/06/2023] [Accepted: 02/13/2024] [Indexed: 04/04/2024] Open
Abstract
Fishes are hosts for many microorganisms that provide them with beneficial effects on growth, immune system development, nutrition and protection against pathogens. In order to avoid spreading of infectious diseases in aquaculture, prevention includes vaccinations and routine disinfection of eggs and equipment, while curative treatments consist in the administration of antibiotics. Vaccination processes can stress the fish and require substantial farmer's investment. Additionally, disinfection and antibiotics are not specific, and while they may be effective in the short term, they have major drawbacks in the long term. Indeed, they eliminate beneficial bacteria which are useful for the host and promote the raising of antibiotic resistance in beneficial, commensal but also in pathogenic bacterial strains. Numerous publications highlight the importance that plays the diversified microbial community colonizing fish (i.e., microbiota) in the development, health and ultimately survival of their host. This review targets the current knowledge on the bidirectional communication between the microbiota and the fish immune system during fish development. It explores the extent of this mutualistic relationship: on one hand, the effect that microbes exert on the immune system ontogeny of fishes, and on the other hand, the impact of critical steps in immune system development on the microbial recruitment and succession throughout their life. We will first describe the immune system and its ontogeny and gene expression steps in the immune system development of fishes. Secondly, the plurality of the microbiotas (depending on host organism, organ, and development stage) will be reviewed. Then, a description of the constant interactions between microbiota and immune system throughout the fish's life stages will be discussed. Healthy microbiotas allow immune system maturation and modulation of inflammation, both of which contribute to immune homeostasis. Thus, immune equilibrium is closely linked to microbiota stability and to the stages of microbial community succession during the host development. We will provide examples from several fish species and describe more extensively the mechanisms occurring in zebrafish model because immune system ontogeny is much more finely described for this species, thanks to the many existing zebrafish mutants which allow more precise investigations. We will conclude on how the conceptual framework associated to the research on the immune system will benefit from considering the relations between microbiota and immune system maturation. More precisely, the development of active tolerance of the microbiota from the earliest stages of life enables the sustainable establishment of a complex healthy microbial community in the adult host. Establishing a balanced host-microbiota interaction avoids triggering deleterious inflammation, and maintains immunological and microbiological homeostasis.
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Affiliation(s)
- Lisa Zoé Auclert
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
| | - Mousumi Sarker Chhanda
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
- Department of Aquaculture, Faculty of Fisheries, Hajee Mohammad Danesh Science and Technology University, Basherhat, Bangladesh
| | - Nicolas Derome
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
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Zhang B, Xiao J, Liu H, Zhai D, Wang Y, Liu S, Xiong F, Xia M. Vertical habitat preferences shape the fish gut microbiota in a shallow lake. Front Microbiol 2024; 15:1341303. [PMID: 38572242 PMCID: PMC10987288 DOI: 10.3389/fmicb.2024.1341303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/06/2024] [Indexed: 04/05/2024] Open
Abstract
Understanding the interactions between fish gut microbiota and the aquatic environment is a key issue for understanding aquatic microorganisms. Environmental microorganisms enter fish intestines through feeding, and the amount of invasion varies due to different feeding habits. Traditional fish feeding habitat preferences are determined by fish morphology or behavior. However, little is known about how the feeding behavior of fish relative to the vertical structure in a shallow lake influences gut microbiota. In our study, we used nitrogen isotopes to measure the trophic levels of fish. Then high-throughput sequencing was used to describe the composition of environmental microbiota and fish gut microbiota, and FEAST (fast expectation-maximization for microbial source tracking) method was used to trace the source of fish gut microbiota. We investigated the microbial diversity of fish guts and their habitats in Lake Sanjiao and verified that the sediments indeed played an important role in the assembly of fish gut microbiota. Then, the FEAST analysis indicated that microbiota in water and sediments acted as the primary sources in half of the fish gut microbiota respectively. Furthermore, we classified the vertical habitat preferences using microbial data and significant differences in both composition and function of fish gut microbiota were observed between groups with distinct habitat preferences. The performance of supervised and unsupervised machine learning in classifying fish gut microbiota by habitat preferences actually exceeded classification by fish species taxonomy and fish trophic level. Finally, we described the stability of fish co-occurrence networks with different habitat preferences. Interestingly, the co-occurrence network seemed more stable in pelagic fish than in benthic fish. Our results show that the preferences of fish in the vertical structure of habitat was the main factor affecting their gut microbiota. We advocated the use of microbial interactions between fish gut and their surrounding environment to reflect fish preferences in vertical habitat structure. This approach not only offers a novel perspective for understanding the interactions between fish gut microbiota and environmental factors, but also provides new methods and ideas for studying fish habitat selection in aquatic ecosystems.
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Affiliation(s)
- Bowei Zhang
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Sciences, Jianghan University, Wuhan, China
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, China
| | - Jiaman Xiao
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Sciences, Jianghan University, Wuhan, China
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, China
| | - Hongyan Liu
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Sciences, Jianghan University, Wuhan, China
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, China
| | - Dongdong Zhai
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Sciences, Jianghan University, Wuhan, China
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, China
| | - Ying Wang
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Sciences, Jianghan University, Wuhan, China
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, China
| | - Shujun Liu
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Sciences, Jianghan University, Wuhan, China
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, China
| | - Fei Xiong
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Sciences, Jianghan University, Wuhan, China
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, China
| | - Ming Xia
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Sciences, Jianghan University, Wuhan, China
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, China
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Lokesh J, Siriyappagouder P, Fernandes JMO. Unravelling the temporal and spatial variation of fungal phylotypes from embryo to adult stages in Atlantic salmon. Sci Rep 2024; 14:981. [PMID: 38200059 PMCID: PMC10781754 DOI: 10.1038/s41598-023-50883-x] [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: 07/14/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
Early microbial colonization has a profound impact on host physiology during different stages of ontogeny. Although several studies have focused on early bacterial colonization and succession, the composition and role of fungal communities are poorly known in fish. Here, we sequenced the internal transcribed spacer 2 (ITS2) region of fungi to profile the mycobiome associated with the eggs, hatchlings and intestine of Atlantic salmon at various freshwater and marine stages. In most of the stages studied, fungal diversity was lower than bacterial diversity. There were several stage-specific fungal phylotypes belonging to different stages of ontogeny but some groups, such as Candida tropicalis, Saccharomyces cerevisiae, Alternaria metachromatica, Davidiella tassiana and Humicola nigrescens, persisted during successive stages of ontogeny. We observed significant changes in the intestinal fungal communities during the first feeding. Prior to first feeding, Humicola nigrescens dominated, but Saccharomyces cerevisiae (10 weeks post hatch) and Candida tropicalis (12 weeks post hatch) became dominant subsequently. Seawater transfer resulted in a decrease in alpha diversity and an increase in Candida tropicalis abundance. We also observed notable variations in beta diversity and composition between the different farms. Overall, the present study sheds light on the fungal communities of Atlantic salmon from early ontogeny to adulthood. These novel findings will also be useful in future studies investigating host-microbiota interactions in the context of developing better nutritional and health management strategies for Atlantic salmon farming.
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Affiliation(s)
- Jep Lokesh
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway.
- Université de Pau et des Pays de l'Adour, E2S UPPA. INRAE, NUMEA, Saint-Pée-Sur-Nivelle, France.
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Roland MM, Peacock TE, Hall N, Mohammed AD, Ball R, Jolly A, Alexeev S, Dopkins N, Nagarkatti M, Nagarkatti P, Kubinak JL. B-cell-specific MhcII regulates microbiota composition in a primarily IgA-independent manner. Front Immunol 2023; 14:1253674. [PMID: 38187389 PMCID: PMC10766766 DOI: 10.3389/fimmu.2023.1253674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 11/30/2023] [Indexed: 01/09/2024] Open
Abstract
Background The expression of major histocompatibility complex class II (MhcII) molecules on B cells is required for the development of germinal centers (GCs) in lymphoid follicles; the primary sites for the generation of T-cell-dependent (TD) antibody responses. Peyer's patches (PPs) are secondary lymphoid tissues (SLOs) in the small intestine (SI) that give rise to high-affinity, TD antibodies (mainly immunoglobulin A (IgA)) generated against the microbiota. While several studies have demonstrated that MhcII antigen presentation by other immune cells coordinate TD IgA responses and regulate microbiota composition, whether or not B-cell-specific MhcII influences gut microbial ecology is unknown. Methods Here, we developed a novel Rag1 -/- adoptive co-transfer model to answer this question. In this model, Rag1 -/- mice were reconstituted with naïve CD4+ T cells and either MhcII-sufficient or MhcII-deficient naïve B cells. Subsequent to this, resulting shifts in microbiota composition was characterized via 16S rRNA gene sequencing of SI-resident and fecal bacterial communities. Results Results from our experiments indicate that SLO development and reconstitution of an anti-commensal TD IgA response can be induced in Rag1 -/- mice receiving T cells and MhcII-sufficient B cells, but not in mice receiving T cells and MhcII-deficient B cells. Results from our 16S experiments confirmed that adaptive immunity is a relevant host factor shaping microbial ecology in the gut, and that its impact was most pronounced on SI-resident bacterial communities. Conclusion Our data also clearly establishes that MhcII-mediated cognate interactions between B cells and T cells regulates this effect by maintaining species richness in the gut, which is a phenotype commonly associated with good health. Finally, contrary to expectations, our experimental results indicate that IgA was not responsible for driving any of the effects on the microbiota ascribed to the loss of B cell-specific MhcII. Collectively, results from our experiments support that MhcII-mediated antigen presentation by B cells regulates microbiota composition and promotes species richness through an IgA-independent mechanism.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Jason L. Kubinak
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, Columbia, SC, United States
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Wang LC, Chen LH, Chiu YC, Liou CY, Chen HC, Lu CY, Chen JL. Teleost skin microbiome: An intimate interplay between the environment and the host immunity. FISH & SHELLFISH IMMUNOLOGY 2023; 139:108869. [PMID: 37285875 DOI: 10.1016/j.fsi.2023.108869] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/22/2023] [Accepted: 05/31/2023] [Indexed: 06/09/2023]
Abstract
The mucosal microbiome plays a role in regulating host health. The research conducted in humans and mice has governed and detailed the information on microbiome-host immunity interactions. Teleost fish, different from humans and mice, lives in and relies on the aquatic environment and is subjected to environmental variation. The growth of teleost mucosal microbiome studies, the majority in the gastrointestinal tract, has emphasized the essential role of the teleost microbiome in growth and health. However, research in the teleost external surface microbiome, as the skin microbiome, has just started. In this review, we examine the general findings in the colonization of the skin microbiome, how the skin microbiome is subjected to environmental change and the reciprocal regulation with the host immune system, and the current challenges that potential study models can address. The information collected from teleost skin microbiome-host immunity research would help future teleost culturing from the potential parasitic infestation and bacterial infection as foreseeing growing threats.
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Affiliation(s)
- Liang-Chun Wang
- Marine and Pathogenic Microbiology Laboratory, Department of Marine Biotechnology and Resources, College of Marine Science, National Sun Yat-sen University, Kaohsiung City, Taiwan; Committee of Fisheries Extension Service, College of Marine Science, National Sun Yat-sen University, Kaohsiung City, Taiwan.
| | - Li-Hsuan Chen
- Marine and Pathogenic Microbiology Laboratory, Department of Marine Biotechnology and Resources, College of Marine Science, National Sun Yat-sen University, Kaohsiung City, Taiwan; Department of Veterinary and Animal Sciences, Aarhus University, Tjele, Denmark
| | - Yu-Che Chiu
- Marine and Pathogenic Microbiology Laboratory, Department of Marine Biotechnology and Resources, College of Marine Science, National Sun Yat-sen University, Kaohsiung City, Taiwan
| | - Chung-Yi Liou
- Marine and Pathogenic Microbiology Laboratory, Department of Marine Biotechnology and Resources, College of Marine Science, National Sun Yat-sen University, Kaohsiung City, Taiwan
| | - Han-Chung Chen
- Marine and Pathogenic Microbiology Laboratory, Department of Marine Biotechnology and Resources, College of Marine Science, National Sun Yat-sen University, Kaohsiung City, Taiwan
| | - Chia-Yun Lu
- Marine and Pathogenic Microbiology Laboratory, Department of Marine Biotechnology and Resources, College of Marine Science, National Sun Yat-sen University, Kaohsiung City, Taiwan
| | - Jian-Lin Chen
- Marine and Pathogenic Microbiology Laboratory, Department of Marine Biotechnology and Resources, College of Marine Science, National Sun Yat-sen University, Kaohsiung City, Taiwan
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10
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Morshed SM, Lee TH. The role of the microbiome on fish mucosal immunity under changing environments. FISH & SHELLFISH IMMUNOLOGY 2023:108877. [PMID: 37302678 DOI: 10.1016/j.fsi.2023.108877] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/13/2023]
Abstract
The environment is crucial for fish as their mucosal surfaces face continuous challenges in the water. Fish mucosal surfaces harbor the microbiome and mucosal immunity. Changes in the environment could affect the microbiome, thus altering mucosal immunity. Homeostasis between the microbiome and mucosal immunity is crucial for the overall health of fish. To date, very few studies have investigated mucosal immunity and its interaction with the microbiome in response to environmental changes. Based on the existing studies, we can infer that environmental factors can modulate the microbiome and mucosal immunity. However, we need to retrospectively examine the existing literature to investigate the possible interaction between the microbiome and mucosal immunity under specific environmental conditions. In this review, we summarize the existing literature on the effects of environmental changes on the fish microbiome and mucosal immunity. This review mainly focuses on temperature, salinity, dissolved oxygen, pH, and photoperiod. We also point out a gap in the literature and provide directions to go further in this research field. In-depth knowledge about mucosal immunity-microbiome interaction will also improve aquaculture practices by reducing loss during environmental stressful conditions.
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Affiliation(s)
- Syed Monzur Morshed
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan; The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Tsung-Han Lee
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan; The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.
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11
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Henry LP, Bergelson J. Evolutionary implications of host genetic control for engineering beneficial microbiomes. CURRENT OPINION IN SYSTEMS BIOLOGY 2023; 34:None. [PMID: 37287906 PMCID: PMC10242548 DOI: 10.1016/j.coisb.2023.100455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Engineering new functions in the microbiome requires understanding how host genetic control and microbe-microbe interactions shape the microbiome. One key genetic mechanism underlying host control is the immune system. The immune system can promote stability in the composition of the microbiome by reshaping the ecological dynamics of its members, but the degree of stability will depend on the interplay between ecological context, immune system development, and higher-order microbe-microbe interactions. The eco-evolutionary interplay affecting composition and stability should inform the strategies used to engineer new functions in the microbiome. We conclude with recent methodological developments that provide an important path forward for both engineering new functionality in the microbiome and broadly understanding how ecological interactions shape evolutionary processes in complex biological systems.
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12
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Prüter H, Gillingham MAF, Krietsch J, Kuhn S, Kempenaers B. Sexual transmission may drive pair similarity of the cloacal microbiome in a polyandrous species. J Anim Ecol 2023. [PMID: 37230950 DOI: 10.1111/1365-2656.13961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 05/05/2023] [Indexed: 05/27/2023]
Abstract
All animals host a microbial community within and on their reproductive organs, known as the reproductive microbiome. In free-living birds, studies on the sexual transmission of bacteria have typically focused on a few pathogens instead of the bacterial community as a whole, despite a potential link to reproductive function. Theory predicts higher sexual transmission of the reproductive microbiome in females via the males' ejaculates and higher rates of transmission in promiscuous systems. We studied the cloacal microbiome of breeding individuals of a socially polyandrous, sex-role-reversed shorebird, the red phalarope (Phalaropus fulicarius). We expected (i) higher microbial diversity in females compared to males; (ii) low compositional differentiation between sexes; (iii) lower variation in composition between individuals (i.e. microbiome dispersion) in females than in males; (iv) convergence in composition as the breeding season progresses as a consequence of sexual transmission and/or shared habitat use; and (v) higher similarity in microbial composition between social pair members than between two random opposite-sex individuals. We found no or small between-sex differences in cloacal microbiome diversity/richness and composition. Dispersion of predicted functional pathways was lower in females than in males. As predicted, microbiome dispersion decreased with sampling date relative to clutch initiation of the social pair. Microbiome composition was significantly more similar among social pair members than among two random opposite-sex individuals. Pair membership explained 21.5% of the variation in taxonomic composition and 10.1% of functional profiles, whereas temporal and sex effects explained only 0.6%-1.6%. Consistent with evidence of functional convergence of reproductive microbiomes within pairs, some select taxa and predicted functional pathways were less variable between social pair members than between random opposite-sex individuals. As predicted if sexual transmission of the reproductive microbiome is high, sex differences in microbiome composition were weak in a socially polyandrous system with frequent copulations. Moreover, high within-pair similarity in microbiome composition, particularly for a few taxa spanning the spectrum of the beneficial-pathogenic axis, demonstrates the link between mating behaviour and the reproductive microbiome. Our study is consistent with the hypothesis that sexual transmission plays an important role in driving reproductive microbiome ecology and evolution.
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Affiliation(s)
- Hanna Prüter
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Biological Intelligence, Seewiesen, Germany
| | - Mark A F Gillingham
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Biological Intelligence, Seewiesen, Germany
- Biodiversity Research Institute (CSIC, Oviedo University, Principality of Asturias), University of Oviedo, Mieres, Spain
| | - Johannes Krietsch
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Biological Intelligence, Seewiesen, Germany
| | - Sylvia Kuhn
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Biological Intelligence, Seewiesen, Germany
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Biological Intelligence, Seewiesen, Germany
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13
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Xia H, Chen H, Cheng X, Yin M, Yao X, Ma J, Huang M, Chen G, Liu H. Zebrafish: an efficient vertebrate model for understanding role of gut microbiota. Mol Med 2022; 28:161. [PMID: 36564702 PMCID: PMC9789649 DOI: 10.1186/s10020-022-00579-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022] Open
Abstract
Gut microbiota plays a critical role in the maintenance of host health. As a low-cost and genetically tractable vertebrate model, zebrafish have been widely used for biological research. Zebrafish and humans share some similarities in intestinal physiology and function, and this allows zebrafish to be a surrogate model for investigating the crosstalk between the gut microbiota and host. Especially, zebrafish have features such as high fecundity, external fertilization, and early optical transparency. These enable the researchers to employ the fish to address questions not easily addressed in other animal models. In this review, we described the intestine structure of zebrafish. Also, we summarized the methods of generating a gnotobiotic zebrafish model, the factors affecting its intestinal flora, and the study progress of gut microbiota functions in zebrafish. Finally, we discussed the limitations and challenges of the zebrafish model for gut microbiota studies. In summary, this review established that zebrafish is an attractive research tool to understand mechanistic insights into host-microbe interaction.
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Affiliation(s)
- Hui Xia
- grid.257143.60000 0004 1772 1285College of Basic Medicine, Hubei University of Chinese Medicine, Huangjiahu West Road 16, Hongshan Disctrict, Wuhan, 430065 China
| | - Huimin Chen
- grid.257143.60000 0004 1772 1285College of Basic Medicine, Hubei University of Chinese Medicine, Huangjiahu West Road 16, Hongshan Disctrict, Wuhan, 430065 China
| | - Xue Cheng
- grid.257143.60000 0004 1772 1285College of Basic Medicine, Hubei University of Chinese Medicine, Huangjiahu West Road 16, Hongshan Disctrict, Wuhan, 430065 China
| | - Mingzhu Yin
- grid.257143.60000 0004 1772 1285College of Basic Medicine, Hubei University of Chinese Medicine, Huangjiahu West Road 16, Hongshan Disctrict, Wuhan, 430065 China
| | - Xiaowei Yao
- grid.257143.60000 0004 1772 1285College of Basic Medicine, Hubei University of Chinese Medicine, Huangjiahu West Road 16, Hongshan Disctrict, Wuhan, 430065 China
| | - Jun Ma
- grid.257143.60000 0004 1772 1285College of Basic Medicine, Hubei University of Chinese Medicine, Huangjiahu West Road 16, Hongshan Disctrict, Wuhan, 430065 China
| | - Mengzhen Huang
- grid.257143.60000 0004 1772 1285College of Basic Medicine, Hubei University of Chinese Medicine, Huangjiahu West Road 16, Hongshan Disctrict, Wuhan, 430065 China
| | - Gang Chen
- grid.477392.cHubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, 430061 China
| | - Hongtao Liu
- grid.257143.60000 0004 1772 1285College of Basic Medicine, Hubei University of Chinese Medicine, Huangjiahu West Road 16, Hongshan Disctrict, Wuhan, 430065 China
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14
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Juottonen H, Moghadam NN, Murphy L, Mappes J, Galarza JA. Host's genetic background determines the outcome of reciprocal faecal transplantation on life-history traits and microbiome composition. Anim Microbiome 2022; 4:67. [PMID: 36564793 PMCID: PMC9789590 DOI: 10.1186/s42523-022-00210-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/09/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Microbes play a role in their host's fundamental ecological, chemical, and physiological processes. Host life-history traits from defence to growth are therefore determined not only by the abiotic environment and genotype but also by microbiota composition. However, the relative importance and interactive effects of these factors may vary between organisms. Such connections remain particularly elusive in Lepidoptera, which have been argued to lack a permanent microbiome and have microbiota primarily determined by their diet and environment. We tested the microbiome specificity and its influence on life-history traits of two colour genotypes of the wood tiger moth (Arctia plantaginis) that differ in several traits, including growth. All individuals were grown in the laboratory for several generations with standardized conditions. We analyzed the bacterial community of the genotypes before and after a reciprocal frass (i.e., larval faeces) transplantation and followed growth rate, pupal mass, and the production of defensive secretion. RESULTS After transplantation, the fast-growing genotype grew significantly slower compared to the controls, but the slow-growing genotype did not change its growth rate. The frass transplant also increased the volume of defensive secretions in the fast-growing genotype but did not affect pupal mass. Overall, the fast-growing genotype appeared more susceptible to the transplantation than the slow-growing genotype. Microbiome differences between the genotypes strongly suggest genotype-based selective filtering of bacteria from the diet and environment. A novel cluster of insect-associated Erysipelotrichaceae was exclusive to the fast-growing genotype, and specific Enterococcaceae were characteristic to the slow-growing genotype. These Enterococcaceae became more prevalent in the fast-growing genotype after the transplant, which suggests that a slower growth rate is potentially related to their presence. CONCLUSIONS We show that reciprocal frass transplantation can reverse some genotype-specific life-history traits in a lepidopteran host. The results indicate that genotype-specific selective filtering can fine-tune the bacterial community at specific life stages and tissues like the larval frass, even against a background of a highly variable community with stochastic assembly. Altogether, our findings suggest that the host's genotype can influence its susceptibility to being colonized by microbiota, impacting key life-history traits.
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Affiliation(s)
- Heli Juottonen
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Sciences, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Neda N. Moghadam
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Sciences, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Liam Murphy
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Sciences, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Johanna Mappes
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Sciences, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland ,grid.7737.40000 0004 0410 2071Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikki Biocenter 3, 00014 Helsinki, Finland
| | - Juan A. Galarza
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Sciences, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland ,grid.7737.40000 0004 0410 2071Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikki Biocenter 3, 00014 Helsinki, Finland
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15
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The Role of Histo-Blood Group Antigens and Microbiota in Human Norovirus Replication in Zebrafish Larvae. Microbiol Spectr 2022; 10:e0315722. [PMID: 36314930 PMCID: PMC9769672 DOI: 10.1128/spectrum.03157-22] [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] [Indexed: 12/24/2022] Open
Abstract
Human norovirus (HuNoV) is the major agent for viral gastroenteritis, causing >700 million infections yearly. Fucose-containing carbohydrates named histo-blood group antigens (HBGAs) are known (co)receptors for HuNoV. Moreover, bacteria of the gut microbiota expressing HBGA-like structures have shown an enhancing effect on HuNoV replication in an in vitro model. Here, we studied the role of HBGAs and the host microbiota during HuNoV infection in zebrafish larvae. Using whole-mount immunohistochemistry, we visualized the fucose expression in the zebrafish gut for the HBGA Lewis X [LeX, α(1,3)-fucose] and core fucose [α(1,6)-fucose]. Costaining of HuNoV-infected larvae proved colocalization of LeX and to a lower extent core fucose with the viral capsid protein VP1, indicating the presence of fucose residues on infected cells. Upon blocking of fucose expression by a fluorinated fucose analogue, HuNoV replication was strongly reduced. Furthermore, by comparing HuNoV replication in conventional and germfree zebrafish larvae, we found that the natural zebrafish microbiome does not have an effect on HuNoV replication, contrary to earlier reports about the human gut microbiome. Interestingly, monoassociation with the HBGA-expressing Enterobacter cloacae resulted in a minor decrease in HuNoV replication, which was not triggered by a stronger innate immune response. Overall, we show here that fucose has an essential role for HuNoV infection in zebrafish larvae, as in the human host, but their natural gut microbiome does not affect viral replication. IMPORTANCE Despite causing over 700 million infections yearly, many gaps remain in the knowledge of human norovirus (HuNoV) biology due to an historical lack of efficient cultivation systems. Fucose-containing carbohydrate structures, named histo-blood group antigens, are known to be important (co)receptors for viral entry in humans, while the natural gut microbiota is suggested to enhance viral replication. This study shows a conserved mechanism of entry for HuNoV in the novel zebrafish infection model, highlighting the pivotal opportunity this model represents to study entry mechanisms and identify the cellular receptor of HuNoV. Our results shed light on the interaction of HuNoV with the zebrafish microbiota, contributing to the understanding of the interplay between gut microbiota and enteric viruses. The ease of generating germfree animals that can be colonized with human gut bacteria is an additional advantage of using zebrafish larvae in virology. This small animal model constitutes an innovative alternative to high-severity animal models.
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16
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Levraud JP, Rawls JF, Clatworthy AE. Using zebrafish to understand reciprocal interactions between the nervous and immune systems and the microbial world. J Neuroinflammation 2022; 19:170. [PMID: 35765004 PMCID: PMC9238045 DOI: 10.1186/s12974-022-02506-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 06/01/2022] [Indexed: 11/10/2022] Open
Abstract
Animals rely heavily on their nervous and immune systems to perceive and survive within their environment. Despite the traditional view of the brain as an immunologically privileged organ, these two systems interact with major consequences. Furthermore, microorganisms within their environment are major sources of stimuli and can establish relationships with animal hosts that range from pathogenic to mutualistic. Research from a variety of human and experimental animal systems are revealing that reciprocal interactions between microbiota and the nervous and immune systems contribute significantly to normal development, homeostasis, and disease. The zebrafish has emerged as an outstanding model within which to interrogate these interactions due to facile genetic and microbial manipulation and optical transparency facilitating in vivo imaging. This review summarizes recent studies that have used the zebrafish for analysis of bidirectional control between the immune and nervous systems, the nervous system and the microbiota, and the microbiota and immune system in zebrafish during development that promotes homeostasis between these systems. We also describe how the zebrafish have contributed to our understanding of the interconnections between these systems during infection in fish and how perturbations may result in pathology.
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Affiliation(s)
- Jean-Pierre Levraud
- Université Paris-Saclay, CNRS, Institut Pasteur, Université Paris-Cité, Institut des Neurosciences Paris-Saclay, 91400, Saclay, France.
| | - John F. Rawls
- grid.26009.3d0000 0004 1936 7961Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, 213 Research Drive, Durham, NC 27710 USA
| | - Anne E. Clatworthy
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA ,grid.32224.350000 0004 0386 9924Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114 USA
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17
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Li P, Zhang J, Liu X, Gan L, Xie Y, Zhang H, Si J. The Function and the Affecting Factors of the Zebrafish Gut Microbiota. Front Microbiol 2022; 13:903471. [PMID: 35722341 PMCID: PMC9201518 DOI: 10.3389/fmicb.2022.903471] [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: 03/24/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Gut microbiota has become a topical issue in unraveling the research mechanisms underlying disease onset and progression. As an important and potential “organ,” gut microbiota plays an important role in regulating intestinal epithelial cell differentiation, proliferation, metabolic function and immune response, angiogenesis and host growth. More recently, zebrafish models have been used to study the interactions between gut microbiota and hosts. It has several advantages, such as short reproductive cycle, low rearing cost, transparent larvae, high genomic similarity to humans, and easy construction of germ-free (GF) and transgenic zebrafish. In our review, we reviewed a large amount of data focusing on the close relationship between gut microbiota and host health. Moreover, we outlined the functions of gut microbiota in regulating intestinal epithelial cell differentiation, intestinal epithelial cell proliferation, metabolic function, and immune response. More, we summarized major factors that can influence the composition, abundance, and diversity of gut microbiota, which will help us to understand the significance of gut microbiota in regulating host biological functions and provide options for maintaining the balance of host health.
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Affiliation(s)
- Pingping Li
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jinhua Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoyi Liu
- College of Life Science, Lanzhou University, Lanzhou, China
| | - Lu Gan
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, China
| | - Yi Xie
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, China
| | - Hong Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, China
| | - Jing Si
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, China
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18
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Xiao F, Zhu W, Yu Y, Huang J, Li J, He Z, Wang J, Yin H, Yu H, Liu S, Chen P, Huang Z, He J, Wang C, Shu L, Yan Q. Interactions and Stability of Gut Microbiota in Zebrafish Increase with Host Development. Microbiol Spectr 2022; 10:e0169621. [PMID: 35311546 PMCID: PMC9045336 DOI: 10.1128/spectrum.01696-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 02/28/2022] [Indexed: 12/04/2022] Open
Abstract
Understanding interactions within the gut microbiome and its stability are of critical importance for deciphering ecological issues within the gut ecosystem. Recent studies indicate that long-term instability of gut microbiota is associated with human diseases, and recovery of stability is helpful in the return to health. However, much less is known about such topics in fish, which encompass nearly half of all vertebrate diversity. Here, we examined the assembly and succession of gut microbiota in more than 550 zebrafish, and evaluated the variations of microbial interactions and stability across fish development from larva to adult using molecular ecological network analysis. We found that microbial interactions and stability in the fish gut ecosystem generally increased with host development. This could be attributed to the development of the zebrafish immune system, the increasing amount of space available for microbial colonization within the gut, and the greater stability of nutrients available for the colonized microbiota in adult zebrafish. Moreover, the potential keystone taxa, even those with relatively low abundances, played important roles in affecting the microbial interactions and stability. These findings indicate that regulating rare keystone taxa in adult fish may have great potential in gut microbial management to maintain gut ecosystem stability, which could also provide references for managing gut microbiota in humans and other animals. IMPORTANCE Understanding gut microbial stability and the underlying mechanisms is an important but largely ignored ecological issue in vertebrate fish. Here, using a zebrafish model and network analysis of the gut microbiota we found that microbial interactions and stability in the gut ecosystem increase with fish development. This finding has important implications for microbial management to maintain gut homeostasis and provide better gut ecosystem services for the host. First, future studies should always consider using fish of different age groups to gain a full understanding of gut microbial networks. Second, management of the keystone taxa, even those that are only present at a low abundance, during the adult stage may be a viable pathway to maintain gut ecosystem stability. This study greatly expands our current knowledge regarding gut ecosystem stability in terms of ecological networks affected by fish development, and also highlights potential directions for gut microbial management in humans and other animals.
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Affiliation(s)
- Fanshu Xiao
- Center for Precision Medicine, Medical Research Center, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, China
| | - Wengen Zhu
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Yuhe Yu
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jie Huang
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Juan Li
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, China
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, China
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Jianjun Wang
- Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Huang Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, China
| | - Shengwei Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, China
| | - Pubo Chen
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, China
| | - Zhijian Huang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, China
| | - Jianguo He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, 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), State Key Laboratory for Biocontrol, 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), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, China
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19
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Chen P, Huang J, Rao L, Zhu W, Yu Y, Xiao F, Yu H, Wu Y, Hu R, Liu X, He Z, Yan Q. Environmental effects of nanoparticles on the ecological succession of gut microbiota across zebrafish development. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150963. [PMID: 34656599 DOI: 10.1016/j.scitotenv.2021.150963] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/03/2021] [Accepted: 10/09/2021] [Indexed: 06/13/2023]
Abstract
The environmental stresses could significantly affect the structure and functions of microbial communities colonized in the gut ecosystem. However, little is known about how engineered nanoparticles (ENPs), which have recently become a common pollutant in the environment, affect the gut microbiota across fish development. Based on the high-throughput sequencing of the 16S rRNA gene amplicon, we explored the ecological succession of gut microbiota in zebrafish exposed to nanoparticles for three months. The nanoparticles used herein including titanium dioxide nanoparticles (nTiO2, 100 μg/L), zinc oxide nanoparticles (nZnO, 100 μg/L), and selenium nanoparticles (nSe, 100 μg/L). Our results showed that nanoparticles exposure reduced the alpha diversity of gut microbiota at 73-90 days post-hatching (dph), but showed no significant effects at 14-36 dph. Moreover, nTiO2 significantly (p < 0.05) altered the composition of the gut microbial communities at 73-90 dph (e.g., decreasing abundance of Cetobacterium and Vibrio). Moreover, we found that homogeneous selection was the major process (16.6-57.8%) governing the community succession of gut microbiota. Also, nanoparticles exposure caused topological alterations to microbial networks and led to increased positive interactions to destabilize the gut microbial community. This study reveals the environmental effects of nanoparticles on the ecological succession of gut microbiota across zebrafish development, which provides novel insights to understand the gut microbial responses to ENPs over the development of aquatic animals.
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Affiliation(s)
- Pubo Chen
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Jie Huang
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Liuyu Rao
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Wengen Zhu
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yuhe Yu
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, 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 510006, China.
| | - Huang Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - 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 510006, China
| | - Ruiwen Hu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Xingyu Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, 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 510006, China; College of Agronomy, Hunan Agricultural University, Changsha 410128, 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 510006, China.
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20
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Zhu J, Li H, Jing ZZ, Zheng W, Luo YR, Chen SX, Guo F. Robust host source tracking building on the divergent and non-stochastic assembly of gut microbiomes in wild and farmed large yellow croaker. MICROBIOME 2022; 10:18. [PMID: 35081990 PMCID: PMC8790850 DOI: 10.1186/s40168-021-01214-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 12/12/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND Given the lack of genetic background, the source tracking unknown individuals of fish species with both farmed and wild populations often cannot be robustly achieved. The gut microbiome, which is shaped by both deterministic and stochastic processes, can serve as a molecular marker of fish host source tracking, particularly as an alternative to the yet-to-be-established host genetic marker. A candidate for testing the feasibility is the large yellow croaker, Larimichthys crocea, which is carnivorous and ranks the top mariculture fish in China. Wild resource of this fish was depleted decades ago and might have potential problematic estimation because of escaping of farmed individuals. RESULTS The rectums of wild (n = 212) and farmed (n = 79) croakers from multiple batches were collected for the profiling of their gut bacterial communities. The farmed individuals had a higher alpha diversity and lower bacterial load than the wild individuals. The gut microbiota of the two sources exhibited divergence and high inter-batch variation, as featured by the dominance of Psychrobacter spp. in the wild group. Predicted functional capacity of the gut microbiome and representative isolates showed differences in terms of host source. This difference can be linked to the potential diet divergence between farmed and wild fishes. The non-stochastic distribution pattern of the core gut microbiota of the wild and farmed individuals supports the feasibility of microbiota-based host source tracking via the machine learning algorithm. A random forest classifier based on the divergence and non-stochastic assembly of the gut microbiome was robust in terms of host source tracking the individuals from all batches of croaker, including a newly introduced batch. CONCLUSIONS Our study revealed the divergence of gut microbiota and related functional profiles between wild and farmed croakers. For the first time, with representative datasets and non-stochastic patterns, we have verified that gut microbiota can be robustly applied to the tracking of host source even in carnivorous fish. Video abstract.
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Affiliation(s)
- Jun Zhu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Hao Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Ze Zhou Jing
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Wei Zheng
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yuan Rong Luo
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen, China
| | - Shi Xi Chen
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.
| | - Feng Guo
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
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21
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Shi X, Zhang Y, Zhu T, Li N, Sun S, Zhu M, Pan J, Shen Z, Hu X, Zhang X, Gong C. Response to Bombyx mori nucleopolyhedrovirus infection in silkworm: Gut metabolites and microbiota. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 125:104227. [PMID: 34363835 DOI: 10.1016/j.dci.2021.104227] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/31/2021] [Accepted: 07/31/2021] [Indexed: 06/13/2023]
Abstract
The diversity of microbiota and metabolites in the digestive tract gut is important in physiology and homeostasis, nutrient uptake and virus infection. In lepidopteran insect model silkworms, little is known about how microbiota and metabolites are altered after oral infection with BmNPV. Herein, we used 16S rDNA sequencing and metabolomics to show that the gut microbiota and metabolites of silkworm midgut are significantly altered after BmNPV infection. Kyoto Encyclopedia of Genes and Genomes analysis revealed enrichment of flavone and flavonol biosynthesis, glycosyltransferases, and electron transfer carriers signaling pathways, suggesting potential roles in viral infection. Infection also changed the abundance of metabolites in the digestive tract gut, where most pathways were related to metabolism of amino acids, fatty acids and other pathways (e.g., citrate cycle). In addition, a correlation was observed between digestive tract gut microbiota and metabolites. These results shed light on the interaction between digestive tract gut microbiota, metabolites and host-virus interaction, and enhance our understanding of viral infection links to midgut microbiota and metabolic activity in the silkworm.
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Affiliation(s)
- Xiu Shi
- School of Biology & Basic Medical Science, Soochow University, Suzhou, 215123, China
| | - Yaxin Zhang
- School of Biology & Basic Medical Science, Soochow University, Suzhou, 215123, China
| | - Tianchen Zhu
- School of Biology & Basic Medical Science, Soochow University, Suzhou, 215123, China
| | - Nan Li
- School of Biology & Basic Medical Science, Soochow University, Suzhou, 215123, China
| | - Sufei Sun
- School of Biology & Basic Medical Science, Soochow University, Suzhou, 215123, China
| | - Min Zhu
- School of Biology & Basic Medical Science, Soochow University, Suzhou, 215123, China
| | - Jun Pan
- School of Biology & Basic Medical Science, Soochow University, Suzhou, 215123, China
| | - Zeen Shen
- School of Biology & Basic Medical Science, Soochow University, Suzhou, 215123, China
| | - Xiaolong Hu
- School of Biology & Basic Medical Science, Soochow University, Suzhou, 215123, China; Institute of Agricultural Biotechnology and Ecological Research, Soochow University, Suzhou, 215123, China.
| | - Xing Zhang
- School of Biology & Basic Medical Science, Soochow University, Suzhou, 215123, China
| | - Chengliang Gong
- School of Biology & Basic Medical Science, Soochow University, Suzhou, 215123, China; Institute of Agricultural Biotechnology and Ecological Research, Soochow University, Suzhou, 215123, China.
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22
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Liu C, Zhao LP, Shen YQ. A systematic review of advances in intestinal microflora of fish. FISH PHYSIOLOGY AND BIOCHEMISTRY 2021; 47:2041-2053. [PMID: 34750711 DOI: 10.1007/s10695-021-01027-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 10/13/2021] [Indexed: 05/26/2023]
Abstract
Intestinal flora is closely related to the health of organisms and the occurrence and development of diseases. The study of intestinal flora will provide a reference for the research and treatment of disease pathogenesis. Upon hatching, fish begin to acquire a microbial community in the intestine. In response to the environment and the host itself, the fish gut eventually develops a unique set of microflora, with some microorganisms being common to different fish. The existence of intestinal microorganisms creates an excellent microecological environment for the host, while the fish symbiotically provides conditions for the growth and reproduction of intestinal microflora. The intestinal flora and the host are interdependent and mutually restrictive. This review mainly describes the formation of fish intestinal flora, the function of normal intestinal flora, factors affecting intestinal flora, and a series of fish models.
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Affiliation(s)
- Chang Liu
- Wuxi Medical School of Jiangnan University, Wuxi, China
| | - Li-Ping Zhao
- Wuxi Medical School of Jiangnan University, Wuxi, China
| | - Yan-Qin Shen
- Wuxi Medical School of Jiangnan University, Wuxi, China.
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23
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Vega NM, Ludington WB. From a parts list to assembly instructions and an operating manual: how small host models can re-write microbiome theory. Curr Opin Microbiol 2021; 64:146-151. [PMID: 34739919 DOI: 10.1016/j.mib.2021.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 08/10/2021] [Accepted: 10/08/2021] [Indexed: 10/20/2022]
Affiliation(s)
- Nic M Vega
- Biology Department, Emory University, Atlanta, GA, United States.
| | - William B Ludington
- Department of Embryology, Carnegie Institution of Washington, Baltimore, MD, United States
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Zhang FL, Yang YL, Zhang Z, Yao YY, Xia R, Gao CC, Du DD, Hu J, Ran C, Liu Z, Zhou ZG. Surface-Displayed Amuc_1100 From Akkermansia muciniphila on Lactococcus lactis ZHY1 Improves Hepatic Steatosis and Intestinal Health in High-Fat-Fed Zebrafish. Front Nutr 2021; 8:726108. [PMID: 34722607 PMCID: PMC8548614 DOI: 10.3389/fnut.2021.726108] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/07/2021] [Indexed: 01/14/2023] Open
Abstract
Fatty liver and intestinal barrier damage were widespread in most farmed fish, which severely restrict the development of aquaculture. Therefore, there was an urgent need to develop green feed additives to maintain host liver and intestinal health. In this study, a probiotic pili-like protein, Amuc_1100 (AM protein), was anchored to the surface of Lactococcus lactis ZHY1, and the effects of the recombinant bacteria AM-ZHY1 on liver fat accumulation and intestinal health were evaluated. Zebrafish were fed a basal diet, high-fat diet, and high-fat diet with AM-ZHY1 (108 cfu/g) or control bacteria ZHY1 for 4 weeks. Treatment with AM-ZHY1 significantly reduced hepatic steatosis in zebrafish. Quantitative PCR (qPCR) detection showed that the expression of the lipogenesis [peroxisome-proliferator-activated receptors (PPARγ), sterol regulatory element-binding proteins-1c (SREBP-1c), fatty acid synthase (FAS), and acetyl-CoA carboxylase 1 (ACC1)] and lipid transport genes (CD36 and FABP6) in the liver were significantly downregulated (p < 0.05), indicating that AM-ZHY1 could reduce liver fat accumulation by inhibiting lipid synthesis and absorption. Moreover, supplementing AM-ZHY1 to a high-fat diet could significantly reduce serum aspartate aminotransferase (AST) and alanine aminotransferase (ALT) levels, indicating that liver injury caused by high-fat diets was improved. The expression of tumor necrosis factor (TNF)-a and interleukin (IL)-6 in the liver decreased significantly (p < 0.05), while IL-1β and IL-10 did not change significantly in the AM-ZHY1 group. Compared to the high-fat diet-fed group, the AM-ZHY1 group, but not the ZHY1 group, significantly increased the expression of intestinal tight junction (TJ) proteins (TJP1a, claudina, claudin7, claudin7b, claudin11a, claudin12, and claudin15a; p < 0.05). Compared to the high-fat diet group, the Proteobacteria and Fusobacteria were significantly reduced and increased in the AM-ZHY1 group, respectively. In conclusion, the recombinant bacteria AM-ZHY1 has the capacity to maintain intestinal health by protecting intestinal integrity and improving intestinal flora structure and improving fatty liver disease by inhibiting lipid synthesis and absorption. This study will lay a foundation for the application of AM protein in improving abnormal fat deposition and restoring the intestinal barrier in fish.
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Affiliation(s)
- Feng-Li Zhang
- Sino-Norway Fish Gastrointestinal Microbiota Joint Lab, Institute of Feed Research of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ya-Lin Yang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Institute of Feed Research of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhen Zhang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Institute of Feed Research of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuan-Yuan Yao
- Sino-Norway Fish Gastrointestinal Microbiota Joint Lab, Institute of Feed Research of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rui Xia
- Sino-Norway Fish Gastrointestinal Microbiota Joint Lab, Institute of Feed Research of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chen-Chen Gao
- Sino-Norway Fish Gastrointestinal Microbiota Joint Lab, Institute of Feed Research of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dong-Dong Du
- Sino-Norway Fish Gastrointestinal Microbiota Joint Lab, Institute of Feed Research of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Juan Hu
- Sino-Norway Fish Gastrointestinal Microbiota Joint Lab, Institute of Feed Research of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chao Ran
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Institute of Feed Research of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhen Liu
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Zhi-Gang Zhou
- Sino-Norway Fish Gastrointestinal Microbiota Joint Lab, Institute of Feed Research of Chinese Academy of Agricultural Sciences, Beijing, China
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25
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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: 45] [Impact Index Per Article: 15.0] [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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Kaup M, Trull S, Hom EFY. On the move: sloths and their epibionts as model mobile ecosystems. Biol Rev Camb Philos Soc 2021; 96:2638-2660. [PMID: 34309191 PMCID: PMC9290738 DOI: 10.1111/brv.12773] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 12/20/2022]
Abstract
Sloths are unusual mobile ecosystems, containing a high diversity of epibionts living and growing in their fur as they climb slowly through the canopies of tropical forests. These epibionts include poorly studied algae, arthropods, fungi, and bacteria, making sloths likely reservoirs of unexplored biodiversity. This review aims to identify gaps and eliminate misconceptions in our knowledge of sloths and their epibionts, and to identify key questions to stimulate future research into the functions and roles of sloths within a broader ecological and evolutionary context. This review also seeks to position the sloth fur ecosystem as a model for addressing fundamental questions in metacommunity and movement ecology. The conceptual and evidence-based foundation of this review aims to serve as a guide for future hypothesis-driven research into sloths, their microbiota, sloth health and conservation, and the coevolution of symbioses in general.
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Affiliation(s)
- Maya Kaup
- Department of Biology and Center for Biodiversity and Conservation Research, University of Mississippi, University, MS, 38677-1848, U.S.A
| | - Sam Trull
- The Sloth Institute, Tulemar Gardens, Provincia de Puntarenas, Manuel Antonio, 60601, Costa Rica
| | - Erik F Y Hom
- Department of Biology and Center for Biodiversity and Conservation Research, University of Mississippi, University, MS, 38677-1848, U.S.A
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Bonanomi G, Idbella M, Abd-ElGawad AM. Microbiota Management for Effective Disease Suppression: A Systematic Comparison between Soil and Mammals Gut. SUSTAINABILITY 2021; 13:7608. [DOI: 10.3390/su13147608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Both soil and the human gut support vast microbial biodiversity, in which the microbiota plays critical roles in regulating harmful organisms. However, the functional link between microbiota taxonomic compositions and disease suppression has not been explained yet. Here, we provide an overview of pathogen regulation in soil and mammals gut, highlighting the differences and the similarities between the two systems. First, we provide a review of the ecological mechanisms underlying the regulation of soil and pathogens, as well as the link between disease suppression and soil health. Particular emphasis is thus given to clarifying how soil and the gut microbiota are associated with organic amendment and the human diet, respectively. Moreover, we provide several insights into the importance of organic amendment and diet composition in shaping beneficial microbiota as an efficient way to support crop productivity and human health. This review also discusses novel ways to functionally characterize organic amendments and the proper operational combining of such materials with beneficial microbes for stirring suppressive microbiota against pathogens. Furthermore, specific examples are given to describe how agricultural management practices, including the use of antibiotics and fumigants, hinder disease suppression by disrupting microbiota structure, and the potentiality of entire microbiome transplant. We conclude by discussing general strategies to promote soil microbiota biodiversity, the connection with plant yield and health, and their possible integration through a “One Health” framework.
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Non-Specific Immunity Associated Gut Microbiome in Aristichthys nobilis under Different Rearing Strategies. Genes (Basel) 2021; 12:genes12060916. [PMID: 34198687 PMCID: PMC8232146 DOI: 10.3390/genes12060916] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 05/31/2021] [Accepted: 06/07/2021] [Indexed: 01/20/2023] Open
Abstract
To understand the intestinal microbial diversity and community structure of bighead carp (Aristichthys nobilis) under different feeding strategies, 39 fish from three groups (A: 9 fish, natural live food only; B: 15 fish, natural live food + fish formulated feeds; C: 15 fish, natural live food + fish formulated feed + lactic acid bacteria) were obtained for the high throughput 16S rRNA gene sequencing. We first examined five non-specific immunity indications of the carp—lysozyme (LZM), catalase (CAT), glutathione reductase (GR), glutathione peroxidase (GSH-PX), and superoxide dismutase (SOD). Interestingly, the composition of gut microbiota and related non-specific immune indices were affected by the feeding treatment of the bighead carp. Notably, all enzyme activity indexes were significantly different (p < 0.01) in the spleen and three enzyme activity indexes (LZM, GSH-PX, and SOD) had significant differences in the hepatopancreas (p < 0.001) of the carp from the three groups. The 16S rRNA gene sequencing showed higher diversity in groups B and C. Compared to group A, the relative abundance of Actinobacteria increased significantly and the relative abundance of Proteobacteria and Firmicutes decreased significantly in groups B and C at the phylum level. Functional analysis revealed the association between non-specific immune indicators and import genera in the hepatopancreas and spleen of bighead carp. This study provides new insights into the gut microbiomes and non-specific immune of bighead carp.
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29
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Zebrafish model for human gut microbiome-related studies: advantages and limitations. MEDICINE IN MICROECOLOGY 2021. [DOI: 10.1016/j.medmic.2021.100042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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Mallott EK, Amato KR. Host specificity of the gut microbiome. Nat Rev Microbiol 2021; 19:639-653. [PMID: 34045709 DOI: 10.1038/s41579-021-00562-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2021] [Indexed: 02/07/2023]
Abstract
Developing general principles of host-microorganism interactions necessitates a robust understanding of the eco-evolutionary processes that structure microbiota. Phylosymbiosis, or patterns of microbiome composition that can be predicted by host phylogeny, is a unique framework for interrogating these processes. Identifying the contexts in which phylosymbiosis does and does not occur facilitates an evaluation of the relative importance of different ecological processes in shaping the microbial community. In this Review, we summarize the prevalence of phylosymbiosis across the animal kingdom on the basis of the current literature and explore the microbial community assembly processes and related host traits that contribute to phylosymbiosis. We find that phylosymbiosis is less prevalent in taxonomically richer microbiomes and hypothesize that this pattern is a result of increased stochasticity in the assembly of complex microbial communities. We also note that despite hosting rich microbiomes, mammals commonly exhibit phylosymbiosis. We hypothesize that this pattern is a result of a unique combination of mammalian traits, including viviparous birth, lactation and the co-evolution of haemochorial placentas and the eutherian immune system, which compound to ensure deterministic microbial community assembly. Examining both the individual and the combined importance of these traits in driving phylosymbiosis provides a new framework for research in this area moving forward.
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Affiliation(s)
- Elizabeth K Mallott
- Department of Anthropology, Northwestern University, Evanston, IL, USA.,Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, IL, USA.
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Wu B, Huang L, Chen J, Zhang Y, Wang J, He J. Gut microbiota of homologous Chinese soft-shell turtles (Pelodiscus sinensis) in different habitats. BMC Microbiol 2021; 21:142. [PMID: 33975559 PMCID: PMC8112038 DOI: 10.1186/s12866-021-02209-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 04/29/2021] [Indexed: 12/22/2022] Open
Abstract
Background Chinese soft-shell turtle (Pelodiscus sinensis) is an important commercial species for their high nutritional value and unique taste, but it has been a vulnerable species due to habitat loss. In this study, homologous juvenile turtles were allocated to lake, pond and paddy field to investigate the habitat effects on turtles. Results The growth, morphology and gut microbial communities were monitored during the 4 months cultural period. It showed higher growth rate of turtles in paddy field and pond. The appearance, visceral coefficients, gut morphology and microbial communities in turtles were distinct among different habitats. The microbial community richness on Chao1 was obviously lower in initial turtle guts from greenhouses, whereas it was relative higher in turtle guts sampled from paddy fields than ponds and lake. Significant differences on dominant microbes were found among initial and subsequent samples from different habitats. Firmicutes was the most abundant phylum in the guts of turtles sampled from the greenhouse initially, while Proteobacteria was the most abundant phylum after cultivation in different habitats, followed by Bacteroidetes. The microbial composition were distinct in different habitats at 60d, and the appearance of dominant phyla and genera was more driven by sampling time than habitats at 120d. Both the sampling time and habitats affected the appearance of dominant phyla and genera during the cultivation. The functional predictions indicated that both habitat type and sampling time had significant effects on metabolic pathways, especially amino acid and carbohydrate metabolism. Conclusions The turtles could adapt to natural lakes, artificial ponds and paddy fields. The gut microbial abundance was different among the habitats and sampling time. The species of microbes were significantly more diverse in paddy field specimens than in those from ponds and lakes. Rice-turtle coculture is a potential ecological and economic farming mode that plays important roles in wild turtle protection and food security. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02209-y.
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Affiliation(s)
- Benli Wu
- Key Laboratory of Aquaculture & Stock Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, No.40 Nongkenan Road, Luyang District, Hefei, 230031, Anhui Province, China
| | - Long Huang
- Key Laboratory of Aquaculture & Stock Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, No.40 Nongkenan Road, Luyang District, Hefei, 230031, Anhui Province, China
| | - Jing Chen
- Key Laboratory of Aquaculture & Stock Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, No.40 Nongkenan Road, Luyang District, Hefei, 230031, Anhui Province, China
| | - Ye Zhang
- Key Laboratory of Aquaculture & Stock Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, No.40 Nongkenan Road, Luyang District, Hefei, 230031, Anhui Province, China
| | - Jun Wang
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, 710048, Xi'an, China
| | - Jixiang He
- Key Laboratory of Aquaculture & Stock Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, No.40 Nongkenan Road, Luyang District, Hefei, 230031, Anhui Province, China.
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Feng Z, Shen H, Nie Y, Wu XL. The Impacts of the Occupants on the Bacterial Communities of Classrooms. Curr Microbiol 2021; 78:2112-2121. [PMID: 33768385 DOI: 10.1007/s00284-021-02451-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/10/2021] [Indexed: 11/29/2022]
Abstract
In modern societies, people spend most of their time in the built environment which harbors unique microbial assemblages with the potential to influence human health. However, how the occupants of buildings influence indoor microbial communities remains under-researched. Here, we investigated the diversities of the bacterial communities of a typical Chinese middle school to demonstrate the effects of occupant activities on bacterial communities inside classrooms. The results showed that samples taken from classrooms exhibited higher microbial diversity compared to samples collected from public areas such as gym and restaurant, suggesting the occupant activities could increase the diversities of the indoor microbial communities. Moreover, we also found that the duration of occupation strongly influence the presence/absence of phylogenetic lineages of the bacterial communities, the type of occupants, on the other hand, affect the relative abundances of bacterial taxa. In addition, samples taken from classrooms with longer occupation time exhibited a better fit to the Sloan Neutral Community Model for Prokaryotes, suggesting that room occupation influences the assembly process of microbial communities. In conclusion, our study demonstrates that the duration of occupation and the type of occupants influence the microbiome of the built environment.
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Affiliation(s)
- Zhou Feng
- College of Engineering, Peking University, Beijing, 100871, China
| | - He Shen
- The Experimental High School Attached to Beijing Normal University, Beijing, 100032, China
| | - Yong Nie
- College of Engineering, Peking University, Beijing, 100871, China.
| | - Xiao-Lei Wu
- College of Engineering, Peking University, Beijing, 100871, China. .,Institute of Ocean Research, Peking University, Beijing, 100871, China. .,Institute of Ecology, Peking University, Beijing, 100871, China.
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Maraci Ö, Antonatou-Papaioannou A, Jünemann S, Castillo-Gutiérrez O, Busche T, Kalinowski J, Caspers BA. The Gut Microbial Composition Is Species-Specific and Individual-Specific in Two Species of Estrildid Finches, the Bengalese Finch and the Zebra Finch. Front Microbiol 2021; 12:619141. [PMID: 33679641 PMCID: PMC7933042 DOI: 10.3389/fmicb.2021.619141] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/25/2021] [Indexed: 12/29/2022] Open
Abstract
Microbial communities residing in the gastrointestinal tracts of animals have profound impacts on the physiological processes of their hosts. In humans, host-specific and environmental factors likely interact together to shape gut microbial communities, resulting in remarkable inter-individual differences. However, we still lack a full understanding of to what extent microbes are individual-specific and controlled by host-specific factors across different animal taxa. Here, we document the gut microbial characteristics in two estrildid finch species, the Bengalese finch (Lonchura striata domestica) and the zebra finch (Taeniopygia guttata) to investigate between-species and within-species differences. We collected fecal samples from breeding pairs that were housed under strictly controlled environmental and dietary conditions. All individuals were sampled at five different time points over a range of 120 days covering different stages of the reproductive cycle. We found significant species-specific differences in gut microbial assemblages. Over a period of 3 months, individuals exhibited unique, individual-specific microbial profiles. Although we found a strong individual signature in both sexes, within-individual variation in microbial communities was larger in males of both species. Furthermore, breeding pairs had more similar microbial profiles, compared to randomly chosen males and females. Our study conclusively shows that host-specific factors contribute structuring of gut microbiota.
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Affiliation(s)
- Öncü Maraci
- Department of Behavioural Ecology, Bielefeld University, Bielefeld, Germany
| | - Anna Antonatou-Papaioannou
- Evolutionary Biology, Bielefeld University, Bielefeld, Germany
- Institute of Biology-Zoology, Freie Universität Berlin, Berlin, Germany
| | - Sebastian Jünemann
- Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Omar Castillo-Gutiérrez
- Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Barbara A. Caspers
- Department of Behavioural Ecology, Bielefeld University, Bielefeld, Germany
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Host development overwhelms environmental dispersal in governing the ecological succession of zebrafish gut microbiota. NPJ Biofilms Microbiomes 2021; 7:5. [PMID: 33469034 PMCID: PMC7815754 DOI: 10.1038/s41522-020-00176-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 12/03/2020] [Indexed: 02/06/2023] Open
Abstract
Clarifying mechanisms underlying the ecological succession of gut microbiota is a central theme of gut ecology. Under experimental manipulations of zebrafish hatching and rearing environments, we test our core hypothesis that the host development will overwhelm environmental dispersal in governing fish gut microbial community succession due to host genetics, immunology, and gut nutrient niches. We find that zebrafish developmental stage substantially explains the gut microbial community succession, whereas the environmental effects do not significantly affect the gut microbiota succession from larvae to adult fish. The gut microbiotas of zebrafish are clearly separated according to fish developmental stages, and the degree of homogeneous selection governing gut microbiota succession is increasing with host development. This study advances our mechanistic understanding of the gut microbiota assembly and succession by integrating the host and environmental effects, which also provides new insights into the gut ecology of other aquatic animals.
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Phylogenetic Integration Reveals the Zebrafish Core Microbiome and Its Sensitivity to Environmental Exposures. TOXICS 2021; 9:toxics9010010. [PMID: 33467528 PMCID: PMC7829988 DOI: 10.3390/toxics9010010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 12/19/2022]
Abstract
Zebrafish are increasingly used to study how environmental exposures impact vertebrate gut microbes. However, we understand little about which microbial taxa are common to the zebrafish gut across studies and facilities. Here, we define the zebrafish core gut microbiome to resolve microbiota that are both relatively robust to study or facility effects and likely to drive proper microbiome assembly and functioning due to their conservation. To do so, we integrated publicly available gut microbiome 16S gene sequence data from eight studies into a phylogeny and identified monophyletic clades of gut bacteria that are unexpectedly prevalent across individuals. Doing so revealed 585 core clades of bacteria in the zebrafish gut, including clades within Aeromonas, Pseudomonas, Cetobacterium, Shewanella, Chitinibacter, Fluviicola, Flectobacillus, and Paucibacter. We then applied linear regression to discern which of these core clades are sensitive to an array of different environmental exposures. We found that 200 core clades were insensitive to any exposure we assessed, while 134 core clades were sensitive to more than two exposures. Overall, our analysis defines the zebrafish core gut microbiome and its sensitivity to exposure, which helps future studies to assess the robustness of their results and prioritize taxa for empirical assessments of how gut microbiota mediate the effects of exposure on the zebrafish host.
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Xiao F, Liao L, Xu Q, He Z, Xiao T, Wang J, Huang J, Yu Y, Wu B, Yan Q. Host-microbiota interactions and responses to grass carp reovirus infection in Ctenopharyngodon idellus. Environ Microbiol 2020; 23:431-447. [PMID: 33201573 DOI: 10.1111/1462-2920.15330] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 11/09/2020] [Accepted: 11/15/2020] [Indexed: 01/16/2023]
Abstract
Gut microbiota could facilitate host to defense diseases, but fish-microbiota interactions during viral infection and the underlying mechanism are poorly understood. We examined interactions and responses of gut microbiota to grass carp reovirus (GCRV) infection in Ctenopharyngodon idellus, which is the most important aquaculture fish worldwide. We found that GCRV infection group with serious haemorrhagic symptoms (G7s) showed considerably different gut microbiota, especially with an abnormally high abundance of gram-negative anaerobic Cetobacterium somerae. It also showed the lowest (p < 0.05) alpha-diversity but with much higher ecological process of homogenizing dispersal (28.8%), confirming a dysbiosis of the gut microbiota after viral infection. Interestingly, signaling pathways of NOD-like receptors (NLRs), toll-like receptors (TLRs), and lipopolysaccharide (LPS) stimulation genes were significantly (q-value < 0.01) enriched in G7s, which also significantly (p < 0.01) correlated with the core gut microbial genera of Cetobacterium and Acinetobacter. The results suggested that an expansion of C. somerae initiated by GCRV could aggravate host inflammatory reactions through the LPS-related NLRs and TLRs pathways. This study advances our understanding of the interplay between fish immunity and gut microbiota challenged by viruses; it also sheds new insights for ecological defense of fish diseases with the help of gut microbiota.
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Affiliation(s)
- 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, 510006, China
| | - Lanjie Liao
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Qiaoqing Xu
- School of Animal Science, Yangtze University, Jingzhou, 434020, 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, 510006, China.,College of Agronomy, College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, China
| | - Tiaoyi Xiao
- College of Agronomy, College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Jie Huang
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yuhe Yu
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, 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, 510006, China
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Kamareddine L, Najjar H, Sohail MU, Abdulkader H, Al-Asmakh M. The Microbiota and Gut-Related Disorders: Insights from Animal Models. Cells 2020; 9:cells9112401. [PMID: 33147801 PMCID: PMC7693214 DOI: 10.3390/cells9112401] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 10/23/2020] [Accepted: 10/29/2020] [Indexed: 02/06/2023] Open
Abstract
Over the past decade, the scientific committee has called for broadening our horizons in understanding host–microbe interactions and infectious disease progression. Owing to the fact that the human gut harbors trillions of microbes that exhibit various roles including the production of vitamins, absorption of nutrients, pathogen displacement, and development of the host immune system, particular attention has been given to the use of germ-free (GF) animal models in unraveling the effect of the gut microbiota on the physiology and pathophysiology of the host. In this review, we discuss common methods used to generate GF fruit fly, zebrafish, and mice model systems and highlight the use of these GF model organisms in addressing the role of gut-microbiota in gut-related disorders (metabolic diseases, inflammatory bowel disease, and cancer), and in activating host defense mechanisms and amending pathogenic virulence.
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Affiliation(s)
- Layla Kamareddine
- Department of Biomedical Science, College of Health Sciences, QU Health, Qatar University, P.O. Box 2713 Doha, Qatar; (L.K.); (H.N.); (M.U.S.); (H.A.)
| | - Hoda Najjar
- Department of Biomedical Science, College of Health Sciences, QU Health, Qatar University, P.O. Box 2713 Doha, Qatar; (L.K.); (H.N.); (M.U.S.); (H.A.)
| | - Muhammad Umar Sohail
- Department of Biomedical Science, College of Health Sciences, QU Health, Qatar University, P.O. Box 2713 Doha, Qatar; (L.K.); (H.N.); (M.U.S.); (H.A.)
- Biomedical Research Center, QU Health, Qatar University, P.O. Box 2713 Doha, Qatar
| | - Hadil Abdulkader
- Department of Biomedical Science, College of Health Sciences, QU Health, Qatar University, P.O. Box 2713 Doha, Qatar; (L.K.); (H.N.); (M.U.S.); (H.A.)
| | - Maha Al-Asmakh
- Department of Biomedical Science, College of Health Sciences, QU Health, Qatar University, P.O. Box 2713 Doha, Qatar; (L.K.); (H.N.); (M.U.S.); (H.A.)
- Biomedical Research Center, QU Health, Qatar University, P.O. Box 2713 Doha, Qatar
- Correspondence: ; Tel.: +974-4403-4789
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Xie S, Zhou A, Xu N, Feng Y, Pan Z, Junaid M, Wang J, Zou J. Benzo[a]pyrene induces microbiome dysbiosis and inflammation in the intestinal tracts of western mosquitofish (Gambusia affinis) and zebrafish (Danio rerio). FISH & SHELLFISH IMMUNOLOGY 2020; 105:24-34. [PMID: 32592928 DOI: 10.1016/j.fsi.2020.06.041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/23/2020] [Accepted: 06/18/2020] [Indexed: 06/11/2023]
Abstract
Benzo[a]pyrene (BaP) is one of the most well studied carcinogenic polycyclic aromatic hydrocarbons (PAHs) that has been associated with a wide range of toxic effects in aquatic organisms. In the present study, the mosquitofish and zebrafish were exposed to BaP (100 μg/L) for 15 days. We analyzed the intestinal microbial community of mosquitofish and zebrafish using 16S rRNA gene amplicon sequencing and also performed transcriptional profiling of the inflammation pathway related genes in the intestinal tissues. Our results showed that BaP exposure induced similar changes to the composition of microbial community in mosquitofish and zebrafish. At the phylum level, the abundance of Proteobacteria decreased while the abundance of Firmicutes increased following BaP exposure. At the genus level, a common pathogenic genus staphylococcus significantly increased in the BaP treatment groups, compared to the control (DMSO, ~0.001% v/v). In addition, it was observed that BaP significantly increased the mRNA level of il1β in both mosquitofish and zebrafish. The transcript levels of il6, il8, il10 and ifnphi1 were significantly increased in zebrafish, however not in mosquitofish, following Bap exposure. Our findings suggest that BaP could induce microbiota dysbiosis and inflammation in the intestine of mosquitofish and zebrafish.
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Affiliation(s)
- Shaolin Xie
- College of Marine Science, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China; Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, South China Agricultural University, Guangzhou, 510642, PR China
| | - Aiguo Zhou
- College of Marine Science, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China; Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, South China Agricultural University, Guangzhou, 510642, PR China
| | - Nan Xu
- Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Yongyong Feng
- College of Marine Science, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
| | - Zhengkun Pan
- College of Marine Science, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
| | - Muhammad Junaid
- Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Jun Wang
- College of Marine Science, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China.
| | - Jixing Zou
- College of Marine Science, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China.
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Gerardo NM, Hoang KL, Stoy KS. Evolution of animal immunity in the light of beneficial symbioses. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190601. [PMID: 32772666 DOI: 10.1098/rstb.2019.0601] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Immune system processes serve as the backbone of animal defences against pathogens and thus have evolved under strong selection and coevolutionary dynamics. Most microorganisms that animals encounter, however, are not harmful, and many are actually beneficial. Selection should act on hosts to maintain these associations while preventing exploitation of within-host resources. Here, we consider how several key aspects of beneficial symbiotic associations may shape host immune system evolution. When host immunity is used to regulate symbiont populations, there should be selection to evolve and maintain targeted immune responses that recognize symbionts and suppress but not eliminate symbiont populations. Associating with protective symbionts could relax selection on the maintenance of redundant host-derived immune responses. Alternatively, symbionts could facilitate the evolution of host immune responses if symbiont-conferred protection allows for persistence of host populations that can then adapt. The trajectory of immune system evolution will likely differ based on the type of immunity involved, the symbiont transmission mode and the costs and benefits of immune system function. Overall, the expected influence of beneficial symbiosis on immunity evolution depends on how the host immune system interacts with symbionts, with some interactions leading to constraints while others possibly relax selection on immune system maintenance. This article is part of the theme issue 'The role of the microbiome in host evolution'.
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Affiliation(s)
- Nicole M Gerardo
- Department of Biology, Emory University, O. Wayne Rollins Research Center, 1510 Clifton Road, Atlanta, GA 30322, USA
| | - Kim L Hoang
- Department of Biology, Emory University, O. Wayne Rollins Research Center, 1510 Clifton Road, Atlanta, GA 30322, USA
| | - Kayla S Stoy
- Department of Biology, Emory University, O. Wayne Rollins Research Center, 1510 Clifton Road, Atlanta, GA 30322, USA
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40
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Bhagat J, Zang L, Nishimura N, Shimada Y. Zebrafish: An emerging model to study microplastic and nanoplastic toxicity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 728:138707. [PMID: 32361115 DOI: 10.1016/j.scitotenv.2020.138707] [Citation(s) in RCA: 198] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/12/2020] [Accepted: 04/13/2020] [Indexed: 05/23/2023]
Abstract
Microplastics (MPs) and nanoplastics (NPs) have received global concern due to its widespread contamination, ingestion in aquatic organisms and the ability to cross the biological barrier. However, our understanding of its bioaccumulation, toxicity, and interaction with other environmental pollutants is limited. Zebrafish is increasingly used to study the bioaccumulation and toxicity of environmental contaminants because of their small size, ease of breed, short life cycle and inexpensive maintenance. The transparent nature of zebrafish embryo and larvae provides excellent experimental advantages over other model organisms in studying the localization of fluorescent-labeled MPs/NPs particles. Zebrafish outplays the traditional rodent models with the availability of transgenic lines, high-throughput sequencing and genetic similarities to humans. All these characteristics provide an unprecedented opportunity to investigate the toxicity of MPs/NPs and associated contaminants. This review summarizes the existing literature on MPs/NPs research in zebrafish and suggests a path forward for future research.
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Affiliation(s)
- Jacky Bhagat
- Graduate School of Regional Innovation Studies, Mie University, Tsu, Mie 514-8507, Japan; Mie University Zebrafish Drug Screening Center, Tsu, Mie 514-8507, Japan
| | - Liqing Zang
- Graduate School of Regional Innovation Studies, Mie University, Tsu, Mie 514-8507, Japan; Mie University Zebrafish Drug Screening Center, Tsu, Mie 514-8507, Japan
| | - Norihiro Nishimura
- Graduate School of Regional Innovation Studies, Mie University, Tsu, Mie 514-8507, Japan; Mie University Zebrafish Drug Screening Center, Tsu, Mie 514-8507, Japan
| | - Yasuhito Shimada
- Mie University Zebrafish Drug Screening Center, Tsu, Mie 514-8507, Japan; Department of Integrative Pharmacology, Mie University Graduate School of Medicine, Tsu, Mie 514-8507, Japan; Department of Bioinformatics, Mie University Advanced Science Research Promotion Center, Tsu, Mie 514-8507, Japan.
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41
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Ruiz-Rodríguez M, Scheifler M, Sanchez-Brosseau S, Magnanou E, West N, Suzuki M, Duperron S, Desdevises Y. Host Species and Body Site Explain the Variation in the Microbiota Associated to Wild Sympatric Mediterranean Teleost Fishes. MICROBIAL ECOLOGY 2020; 80:212-222. [PMID: 31932881 DOI: 10.1007/s00248-020-01484-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 01/06/2020] [Indexed: 05/10/2023]
Abstract
Microorganisms are an important component in shaping the evolution of hosts and as such, the study of bacterial communities with molecular techniques is shedding light on the complexity of symbioses between bacteria and vertebrates. Teleost fish are a heterogeneous group that live in a wide variety of habitats, and thus a good model group to investigate symbiotic interactions and their influence on host biology and ecology. Here we describe the microbiota of thirteen teleostean species sharing the same environment in the Mediterranean Sea and compare bacterial communities among different species and body sites (external mucus, skin, gills, and intestine). Our results show that Proteobacteria is the dominant phylum present in fish and water. However, the prevalence of other bacterial taxa differs between fish and the surrounding water. Significant differences in bacterial diversity are observed among fish species and body sites, with higher diversity found in the external mucus. No effect of sampling time nor species individual was found. The identification of indicator bacterial taxa further supports that each body site harbors its own characteristic bacterial community. These results improve current knowledge and understanding of symbiotic relationships among bacteria and their fish hosts in the wild since the majority of previous studies focused on captive individuals.
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Affiliation(s)
- M Ruiz-Rodríguez
- Biologie Intégrative des Organismes Marins, BIOM, Sorbonne Université, CNRS, Observatoire Océanologique de Banyuls-sur-Mer. Avenue Pierre Fabre., F-66650, Banyuls/Mer, France.
| | - M Scheifler
- Biologie Intégrative des Organismes Marins, BIOM, Sorbonne Université, CNRS, Observatoire Océanologique de Banyuls-sur-Mer. Avenue Pierre Fabre., F-66650, Banyuls/Mer, France
| | - S Sanchez-Brosseau
- Biologie Intégrative des Organismes Marins, BIOM, Sorbonne Université, CNRS, Observatoire Océanologique de Banyuls-sur-Mer. Avenue Pierre Fabre., F-66650, Banyuls/Mer, France
| | - E Magnanou
- Biologie Intégrative des Organismes Marins, BIOM, Sorbonne Université, CNRS, Observatoire Océanologique de Banyuls-sur-Mer. Avenue Pierre Fabre., F-66650, Banyuls/Mer, France
| | - N West
- FR3724, Sorbonne Université, CNRS, Observatoire Océanologique de Banyuls-sur-Mer. Avenue Pierre Fabre., F-66650, Banyuls/Mer, France
| | - M Suzuki
- FR3724, Sorbonne Université, CNRS, Observatoire Océanologique de Banyuls-sur-Mer. Avenue Pierre Fabre., F-66650, Banyuls/Mer, France
| | - S Duperron
- Molécules de Communication et Adaptation des Micro-organismes, MCAM, Muséum National d'Histoire Naturelle, CNRS, 12 rue Buffon, Paris, France
| | - Y Desdevises
- Biologie Intégrative des Organismes Marins, BIOM, Sorbonne Université, CNRS, Observatoire Océanologique de Banyuls-sur-Mer. Avenue Pierre Fabre., F-66650, Banyuls/Mer, France
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Derome N, Filteau M. A continuously changing selective context on microbial communities associated with fish, from egg to fork. Evol Appl 2020; 13:1298-1319. [PMID: 32684960 PMCID: PMC7359827 DOI: 10.1111/eva.13027] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 02/06/2023] Open
Abstract
Fast increase of fish aquaculture production to meet consumer demands is accompanied by important ecological concerns such as disease outbreaks. Meanwhile, food waste is an important concern with fish products since they are highly perishable. Recent aquaculture and fish product microbiology, and more recently, microbiota research, paved the way to a highly integrated approach to understand complex relationships between host fish, product and their associated microbial communities at health/disease and preservation/spoilage frontiers. Microbial manipulation strategies are increasingly validated as promising tools either to replace or to complement traditional veterinary and preservation methods. In this review, we consider evolutionary forces driving fish microbiota assembly, in particular the changes in the selective context along the production chain. We summarize the current knowledge concerning factors governing assembly and dynamics of fish hosts and food microbial communities. Then, we discuss the current microbial community manipulation strategies from an evolutionary standpoint to provide a perspective on the potential for risks, conflict and opportunities. Finally, we conclude that to harness evolutionary forces in the development of sustainable microbiota manipulation applications in the fish industry, an integrated knowledge of the controlling abiotic and especially biotic factors is required.
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Affiliation(s)
- Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
- Département de BiologieUniversité LavalQuébecQCCanada
| | - Marie Filteau
- Département de BiologieUniversité LavalQuébecQCCanada
- Département des Sciences des alimentsInstitut sur la nutrition et les aliments fonctionnels (INAF)Université LavalQuébecQCCanada
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Ikeda-Ohtsubo W, López Nadal A, Zaccaria E, Iha M, Kitazawa H, Kleerebezem M, Brugman S. Intestinal Microbiota and Immune Modulation in Zebrafish by Fucoidan From Okinawa Mozuku ( Cladosiphon okamuranus). Front Nutr 2020; 7:67. [PMID: 32671088 PMCID: PMC7327095 DOI: 10.3389/fnut.2020.00067] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/20/2020] [Indexed: 12/11/2022] Open
Abstract
Fucoidan represents fucose-rich sulfated polysaccharides derived from brown seaweeds, which exerts various biological activities applicable for functional foods and therapeutic agents. The objective of the present study was to investigate in vivo effects of fucoidan extracted from Okinawa mozuku (Cladosiphon okamuranus), common edible seaweed in Japan, on immune responses and microbiota composition in zebrafish. We treated larvae and adult zebrafish with Okinawa mozuku (OM) fucoidan by immersion (100 and 500 μg/mL, 3 days) and by feeding (3 weeks), respectively. The effect of OM fucoidan on immune responses in zebrafish larvae was evaluated by live imaging of neutrophils and macrophages as well as quantitative polymerase chain reaction of pro- and anti-inflammatory cytokine genes. Whole microbiota of zebrafish larvae and intestinal microbiota of adult zebrafish treated with OM fucoidan were analyzed by Illumina MiSeq pair-end sequencing of the V3–V4 region of 16S rRNA genes. Fucoidan treatment only slightly affected the composition of the larvae microbiota and the number of neutrophils and macrophages, while pro- and anti-inflammatory cytokine gene expression levels were upregulated in the larvae treated with 500 μg/mL OM fucoidan. In contrast, feeding of OM fucoidan clearly altered the intestinal microbiota composition of adult zebrafish, which was characterized by the emergence and predominance of multiple bacterial operational taxonomic units (OTUs) affiliated with Rhizobiaceae and Comamonadaceae at the expense of E. coli-related Enterobacteriaceae, the dominant OTUs throughout the studied samples. These changes were accompanied by decreased expression levels of pro-inflammatory cytokine il1b in the intestines of the adult zebrafish. Our current study provides the first insights into in vivo modulatory effects of fucoidan on microbiota and immune responses of unchallenged zebrafish, which underscores the potential of fucoidan to play a modulatory role in the diet–microbiota–host interplay.
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Affiliation(s)
- Wakako Ikeda-Ohtsubo
- Cell Biology and Immunology Group, Department of Animal Sciences, Wageningen University and Research, Wageningen, Netherlands.,Host-Microbe Interactomics Group, Department of Animal Sciences, Wageningen University and Research, Wageningen, Netherlands.,Laboratory of Animal Products Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan.,Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Adrià López Nadal
- Cell Biology and Immunology Group, Department of Animal Sciences, Wageningen University and Research, Wageningen, Netherlands
| | - Edoardo Zaccaria
- Host-Microbe Interactomics Group, Department of Animal Sciences, Wageningen University and Research, Wageningen, Netherlands
| | | | - Haruki Kitazawa
- Laboratory of Animal Products Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan.,Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Michiel Kleerebezem
- Host-Microbe Interactomics Group, Department of Animal Sciences, Wageningen University and Research, Wageningen, Netherlands
| | - Sylvia Brugman
- Cell Biology and Immunology Group, Department of Animal Sciences, Wageningen University and Research, Wageningen, Netherlands.,Host-Microbe Interactomics Group, Department of Animal Sciences, Wageningen University and Research, Wageningen, Netherlands
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Stagaman K, Sharpton TJ, Guillemin K. Zebrafish microbiome studies make waves. Lab Anim (NY) 2020; 49:201-207. [PMID: 32541907 DOI: 10.1038/s41684-020-0573-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 05/18/2020] [Indexed: 12/16/2022]
Abstract
Zebrafish have a 50-year history as a model organism for studying vertebrate developmental biology and more recently have emerged as a powerful model system for studying vertebrate microbiome assembly, dynamics and function. In this Review, we discuss the strengths of the zebrafish model for both observational and manipulative microbiome studies, and we highlight some of the important insights gleaned from zebrafish gut microbiome research.
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Affiliation(s)
- Keaton Stagaman
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
| | - Thomas J Sharpton
- Department of Microbiology, Oregon State University, Corvallis, OR, USA.,Department of Statistics, Oregon State University, Corvallis, OR, USA
| | - Karen Guillemin
- Institute of Molecular Biology, University of Oregon, Eugene, OR, USA. .,Humans and the Microbiome Program, CIFAR, Toronto, Ontario, Canada.
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45
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Kohl KD. Ecological and evolutionary mechanisms underlying patterns of phylosymbiosis in host-associated microbial communities. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190251. [PMID: 32200746 PMCID: PMC7133527 DOI: 10.1098/rstb.2019.0251] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2019] [Indexed: 02/06/2023] Open
Abstract
Phylosymbiosis, where similarities in host-associated microbial communities recapitulate the phylogeny of their hosts, is a newly recognized yet pervasive pattern in the field of host-microbe interactions. While phylosymbiosis has been documented across many systems, we still have a poor understanding of the mechanisms that underlie this emergent pattern. Host selection of the microbiome is a widely cited mechanism, yet other basic ecological and evolutionary processes (dispersal, drift and diversification) may also be at play. This paper discusses the roles that each of these processes and their interactions may play in yielding phylosymbiotic signals across hosts. Finally, this paper will identify open questions and methods that are required to better understand the relative contributions of these basic processes to phylosymbiosis. Given that phylosymbiosis has been shown to relate to functional components of host fitness, understanding the processes that contribute to these patterns will be important for our understanding of the ecology and evolution of host-microbe interactions. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.
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Affiliation(s)
- Kevin D. Kohl
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
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46
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Tropical pitcher plants (Nepenthes) act as ecological filters by altering properties of their fluid microenvironments. Sci Rep 2020; 10:4431. [PMID: 32157122 PMCID: PMC7064508 DOI: 10.1038/s41598-020-61193-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 02/18/2020] [Indexed: 01/13/2023] Open
Abstract
Characteristics of host species can alter how other, interacting species assemble into communities by acting as ecological filters. Pitchers of tropical pitcher plants (Nepenthes) host diverse communities of aquatic arthropods and microbes in nature. This plant genus exhibits considerable interspecific diversity in morphology and physiology; for example, different species can actively control the pH of their pitcher fluids and some species produce viscoelastic fluids. Our study investigated the extent to which Nepenthes species differentially regulate pitcher fluid traits under common garden conditions, and the effects that these trait differences had on their associated communities. Sixteen species of Nepenthes were reared together in the controlled environment of a glasshouse using commonly-sourced pH 6.5 water. We analyzed their bacterial and eukaryotic communities using metabarcoding techniques, and found that different plant species differentially altered fluid pH, viscosity, and color, and these had strong effects on the community structure of their microbiota. Nepenthes species can therefore act as ecological filters, cultivating distinctive microbial communities despite similar external conditions, and blurring the conceptual line between biotic and abiotic filters.
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47
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Metagenomic Shotgun Analyses Reveal Complex Patterns of Intra- and Interspecific Variation in the Intestinal Microbiomes of Codfishes. Appl Environ Microbiol 2020; 86:AEM.02788-19. [PMID: 31953333 PMCID: PMC7054092 DOI: 10.1128/aem.02788-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 01/06/2020] [Indexed: 12/12/2022] Open
Abstract
The composition of the intestinal microbial community associated with teleost fish is influenced by a diversity of factors, ranging from internal factors (such as host-specific selection) to external factors (such as niche occupation). These factors are often difficult to separate, as differences in niche occupation (e.g., diet, temperature, or salinity) may correlate with distinct evolutionary trajectories. Here, we investigate four gadoid species with contrasting levels of evolutionary separation and niche occupation. Using metagenomic shotgun sequencing, we observed distinct microbiomes among two Atlantic cod (Gadus morhua) ecotypes (NEAC and NCC) with distinct behavior and habitats. In contrast, interspecific patterns of variation were more variable. For instance, we did not observe interspecific differentiation between the microbiomes of coastal cod (NCC) and Norway pout (Trisopterus esmarkii), whose lineages underwent evolutionary separation over 20 million years ago. The observed pattern of microbiome variation in these gadoid species is therefore most parsimoniously explained by differences in niche occupation. The relative importance of host-specific selection or environmental factors in determining the composition of the intestinal microbiome in wild vertebrates remains poorly understood. Here, we used metagenomic shotgun sequencing of individual specimens to compare the levels of intra- and interspecific variation of intestinal microbiome communities in two ecotypes (NEAC and NCC) of Atlantic cod (Gadus morhua) that have distinct behavior and habitats and three Gadidae species that occupy a range of ecological niches. Interestingly, we found significantly diverged microbiomes among the two Atlantic cod ecotypes. Interspecific patterns of variation are more variable, with significantly diverged communities for most species’ comparisons, apart from the comparison between coastal cod (NCC) and Norway pout (Trisopterus esmarkii), whose community compositions are not significantly diverged. The absence of consistent species-specific microbiomes suggests that external environmental factors, such as temperature, diet, or a combination thereof, comprise major drivers of the intestinal community composition of codfishes. IMPORTANCE The composition of the intestinal microbial community associated with teleost fish is influenced by a diversity of factors, ranging from internal factors (such as host-specific selection) to external factors (such as niche occupation). These factors are often difficult to separate, as differences in niche occupation (e.g., diet, temperature, or salinity) may correlate with distinct evolutionary trajectories. Here, we investigate four gadoid species with contrasting levels of evolutionary separation and niche occupation. Using metagenomic shotgun sequencing, we observed distinct microbiomes among two Atlantic cod (Gadus morhua) ecotypes (NEAC and NCC) with distinct behavior and habitats. In contrast, interspecific patterns of variation were more variable. For instance, we did not observe interspecific differentiation between the microbiomes of coastal cod (NCC) and Norway pout (Trisopterus esmarkii), whose lineages underwent evolutionary separation over 20 million years ago. The observed pattern of microbiome variation in these gadoid species is therefore most parsimoniously explained by differences in niche occupation.
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48
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Schwob G, Cabrol L, Poulin E, Orlando J. Characterization of the Gut Microbiota of the Antarctic Heart Urchin (Spatangoida) Abatus agassizii. Front Microbiol 2020; 11:308. [PMID: 32184772 PMCID: PMC7058685 DOI: 10.3389/fmicb.2020.00308] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/11/2020] [Indexed: 12/25/2022] Open
Abstract
Abatus agassizii is an irregular sea urchin species that inhabits shallow waters of South Georgia and South Shetlands Islands. As a deposit-feeder, A. agassizii nutrition relies on the ingestion of the surrounding sediment in which it lives barely burrowed. Despite the low complexity of its feeding habit, it harbors a long and twice-looped digestive tract suggesting that it may host a complex bacterial community. Here, we characterized the gut microbiota of specimens from two A. agassizii populations at the south of the King George Island in the West Antarctic Peninsula. Using a metabarcoding approach targeting the 16S rRNA gene, we characterized the Abatus microbiota composition and putative functional capacity, evaluating its differentiation among the gut content and the gut tissue in comparison with the external sediment. Additionally, we aimed to define a core gut microbiota between A. agassizii populations to identify potential keystone bacterial taxa. Our results show that the diversity and the composition of the microbiota, at both genetic and predicted functional levels, were mostly driven by the sample type, and to a lesser extent by the population location. Specific bacterial taxa, belonging mostly to Planctomycetacia and Spirochaetia, were differently enriched in the gut content and the gut tissue, respectively. Predictive functional profiles revealed higher abundance of specific pathways, as the sulfur cycle in the gut content and the amino acid metabolism, in the gut tissue. Further, the definition of a core microbiota allowed to obtain evidence of specific localization of bacterial taxa and the identification of potential keystone taxa assigned to the Desulfobacula and Spirochaeta genera as potentially host selected. The ecological relevance of these keystone taxa in the host metabolism is discussed.
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Affiliation(s)
- Guillaume Schwob
- Laboratorio de Ecología Molecular, Instituto de Ecología y Biodiversidad, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Laboratorio de Ecología Microbiana, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Léa Cabrol
- Laboratorio de Ecología Molecular, Instituto de Ecología y Biodiversidad, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Aix Marseille University, Univ Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, Marseille, France
| | - Elie Poulin
- Laboratorio de Ecología Molecular, Instituto de Ecología y Biodiversidad, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Julieta Orlando
- Laboratorio de Ecología Microbiana, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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49
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Uren Webster TM, Rodriguez-Barreto D, Castaldo G, Gough P, Consuegra S, Garcia de Leaniz C. Environmental plasticity and colonisation history in the Atlantic salmon microbiome: A translocation experiment. Mol Ecol 2020; 29:886-898. [PMID: 32011775 PMCID: PMC7078932 DOI: 10.1111/mec.15369] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 01/11/2020] [Accepted: 01/29/2020] [Indexed: 12/20/2022]
Abstract
Microbial communities associated with the gut and the skin are strongly influenced by environmental factors, and can rapidly adapt to change. Historical processes may also affect the microbiome. In particular, variation in microbial colonisation in early life has the potential to induce lasting effects on microbial assemblages. However, little is known about the relative extent of microbiome plasticity or the importance of historical colonisation effects following environmental change, especially for nonmammalian species. To investigate this we performed a reciprocal translocation of Atlantic salmon between artificial and semi-natural conditions. Wild and hatchery-reared fry were transferred to three common garden experimental environments for 6 weeks: standard hatchery conditions, hatchery conditions with an enriched diet, and simulated wild conditions. We characterized the faecal and skin microbiome of individual fish before and after the environmental translocation, using a BACI (before-after-control-impact) design. We found evidence of extensive microbiome plasticity for both the gut and skin, with the greatest changes in alpha and beta diversity associated with the largest changes in environment and diet. Microbiome richness and diversity were entirely determined by environment, with no detectable effects of fish origin, and there was also a near-complete turnover in microbiome structure. However, we also identified, for the first time in fish, evidence of historical colonisation effects reflecting early-life experience, including ASVs characteristic of captive rearing. These results have important implications for host adaptation to local selective pressures, and highlight how conditions experienced during early life can have a long-term influence on the microbiome and, potentially, host health.
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Affiliation(s)
- Tamsyn M Uren Webster
- Centre for Sustainable Aquatic Research, College of Science, Swansea University, Swansea, UK
| | | | - Giovanni Castaldo
- Centre for Sustainable Aquatic Research, College of Science, Swansea University, Swansea, UK
| | - Peter Gough
- Cynrig Fish Culture Unit, Natural Resources Wales, Llanfrynach, UK
| | - Sofia Consuegra
- Centre for Sustainable Aquatic Research, College of Science, Swansea University, Swansea, UK
| | - Carlos Garcia de Leaniz
- Centre for Sustainable Aquatic Research, College of Science, Swansea University, Swansea, UK
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50
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López Nadal A, Ikeda-Ohtsubo W, Sipkema D, Peggs D, McGurk C, Forlenza M, Wiegertjes GF, Brugman S. Feed, Microbiota, and Gut Immunity: Using the Zebrafish Model to Understand Fish Health. Front Immunol 2020; 11:114. [PMID: 32117265 PMCID: PMC7014991 DOI: 10.3389/fimmu.2020.00114] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 01/16/2020] [Indexed: 12/12/2022] Open
Abstract
Aquafeed companies aim to provide solutions to the various challenges related to nutrition and health in aquaculture. Solutions to promote feed efficiency and growth, as well as improving the fish health or protect the fish gut from inflammation may include dietary additives such as prebiotics and probiotics. The general assumption is that feed additives can alter the fish microbiota which, in turn, interacts with the host immune system. However, the exact mechanisms by which feed influences host-microbe-immune interactions in fish still remain largely unexplored. Zebrafish rapidly have become a well-recognized animal model to study host-microbe-immune interactions because of the diverse set of research tools available for these small cyprinids. Genome editing technologies can create specific gene-deficient zebrafish that may contribute to our understanding of immune functions. Zebrafish larvae are optically transparent, which allows for in vivo imaging of specific (immune) cell populations in whole transgenic organisms. Germ-free individuals can be reared to study host-microbe interactions. Altogether, these unique zebrafish features may help shed light on the mechanisms by which feed influences host-microbe-immune interactions and ultimately fish health. In this review, we first describe the anatomy and function of the zebrafish gut: the main surface where feed influences host-microbe-immune interactions. Then, we further describe what is currently known about the molecular pathways that underlie this interaction in the zebrafish gut. Finally, we summarize and critically review most of the recent research on prebiotics and probiotics in relation to alterations of zebrafish microbiota and immune responses. We discuss the advantages and disadvantages of the zebrafish as an animal model for other fish species to study feed effects on host-microbe-immune interactions.
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Affiliation(s)
- Adrià López Nadal
- Cell Biology and Immunology Group, Wageningen University and Research, Wageningen, Netherlands.,Aquaculture and Fisheries Group, Wageningen University and Research, Wageningen, Netherlands
| | - Wakako Ikeda-Ohtsubo
- Laboratory of Animal Products Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Detmer Sipkema
- Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - David Peggs
- Skretting Aquaculture Research Centre, Stavanger, Norway
| | - Charles McGurk
- Skretting Aquaculture Research Centre, Stavanger, Norway
| | - Maria Forlenza
- Cell Biology and Immunology Group, Wageningen University and Research, Wageningen, Netherlands
| | - Geert F Wiegertjes
- Aquaculture and Fisheries Group, Wageningen University and Research, Wageningen, Netherlands
| | - Sylvia Brugman
- Cell Biology and Immunology Group, Wageningen University and Research, Wageningen, Netherlands
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