Bifidobacterium and Lactobacillus improve inflammatory bowel disease in zebrafish of different ages by regulating the intestinal mucosal barrier and microbiota

Life Sciences, Journal Year: 2023, Volume and Issue: 324, P. 121699 - 121699

Published: April 14, 2023

Language: Английский

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The role of animal hosts in shaping gut microbiome variation

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2024, Volume and Issue: 379(1901)

Published: March 18, 2024

Millions of years co-evolution between animals and their associated microbial communities have shaped diversified the nature relationship. Studies continue to reveal new layers complexity in host–microbe interactions, fate which depends on a variety different factors, ranging from neutral processes environmental factors local dynamics. Research is increasingly integrating ecosystem-based approaches, metagenomics mathematical modelling disentangle individual contribution ecological microbiome evolution. Within this framework, host are known be among dominant drivers composition animal species. However, extent they shape assembly evolution remains unclear. In review, we summarize our understanding how drive these dynamics conserved vary across taxa. We conclude by outlining key avenues for research highlight need implementation modifications existing theory fully capture host-associated microbiomes. This article part theme issue ‘Sculpting microbiome: determine respond colonization’.

Language: Английский

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Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Nov. 17, 2022

Abstract Fish are the most diverse and widely distributed vertebrates, yet little is known about microbial ecology of fishes nor biological environmental factors that influence fish microbiota. To identify explain diversity patterns in a geographical subset marine fish, we analyzed microbiota (gill tissue, skin mucus, midgut digesta hindgut digesta) from 101 species Southern California fishes, spanning 22 orders, 55 families 83 genera, representing ~25% local diversity. We compare alpha, beta gamma while establishing method to estimate biomass associated with these host surfaces. show body site strongest driver lowest gill larger, pelagic fishes. Patterns phylosymbiosis observed across gill, hindgut. In quantitative synthesis vertebrate hindguts (569 species), also mammals have highest when controlling for number percent unique taxa. The composite dataset will be useful researchers biologists interested ecology, applications aquaculture fisheries management.

Language: Английский

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Signatures of dysbiosis in fish microbiomes in the context of aquaculture

Reviews in Aquaculture, Journal Year: 2023, Volume and Issue: 16(2), P. 706 - 731

Published: Oct. 26, 2023

Abstract Fish microbiome plays an important role in maintaining host homeostasis, with many bacterial functions directly linked to fitness. research is advancing fast, especially the context of aquaculture where several stressors are known disrupt stability host‐associated bacteria, prompting dysbiosis. Therefore, understanding signatures dysbiosis different fish mucosae and their association such fundamental set up efficient health‐monitoring strategies, as well sound objective working hypothesis for future research. Herein, we reviewed studies that employed culture‐independent approaches assess effects disease, chemotherapeutics water quality changes on diversity metrics gut, skin gill microbiomes. We conclude increases abundance potential pathogens community structure reliable indicators fish. The gut emerged being highly susceptible salinity chemotherapeutics, whereas external microbiota seems be more caused by disease temperature changes. Our analysis showed treatments tetracyclines florfenicol likely elicit severe compared quinolones disinfectants cause lesser disturbance microbiome. Bacterial diseases also frequently (enteritis particular), parasitic far less deleterious. Regarding impacts quality, only reasonably studied. Recent developments metagenomics, include a fast turn‐around time results, can used detect homeostasis during critical periods production, assisting management.

Language: Английский

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Host species and habitat shape fish-associated bacterial communities: phylosymbiosis between fish and their microbiome

Microbiome, Journal Year: 2023, Volume and Issue: 11(1)

Published: Nov. 20, 2023

While many studies have reported that the structure of gut and skin microbiota is driven by both species-specific habitat-specific factors, relative importance host-specific versus environmental factors in wild vertebrates remains poorly understood. The aim this study was to determine diversity composition fish skin, gut, surrounding water bacterial communities (hereafter referred as microbiota) assess extent which host habitat phylogeny predict similarity. Skin swabs samples from 334 belonging 17 species were sampled three Laurentian Great Lakes (LGLs) habitats (Detroit River, Lake Erie, Ontario). We also collected filtered at time collection. analyzed community using 16S metabarcoding tested for variation.We found distinct microbiota, although more closely resembled microbiota. (sample location), habitat, diet, shape promote divergence or convergence Since significantly affected (separately effects), we phylosymbiosis pairwise phylogenetic distance dissimilarity. significant effects on dissimilarity, consistent with perhaps reflecting longstanding co-evolutionary relationship between their microbiomes.Analyzing mucus across diverse complex natural ecosystems such LGLs provides insights into potential microbiome, ultimately health, host. Video Abstract.

Language: Английский

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Tilapia aquaculture, emerging diseases, and the roles of the skin microbiomes in health and disease

Aquaculture International, Journal Year: 2023, Volume and Issue: 31(5), P. 2945 - 2976

Published: April 25, 2023

Abstract Aquaculture is playing an increasingly important role in global food security, especially for low-income and food-deficit countries. The majority of aquaculture production occurs freshwater earthen ponds tilapia has quickly become one the most widely adopted culture species these systems. Tilapia are now farmed over 140 countries facilitated by their ease production, adaptability to a wide range environmental conditions, fast growth, high nutritional value. Typically, have been considered hardy, disease resilient species; however, increasing with subsequent threats industry as intensified. In this review, we discuss focus on Bangladesh top producing countries, highlight problems associated treatment approaches them, including misuse antimicrobials. We address key missing component understanding health processes sustainable aquaculture, specifically played microbiome. Here examine importance microbiome supporting health, focused symbiotic microbial community fish skin mucosal surface, abiotic biotic factors that influence microbiome, shifts diseased states. also identify conserved taxa microbiomes may be used indicators status offering new opportunities mitigate manage optimize growing conditions farming practices.

Language: Английский

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The intestinal digesta microbiota of tropical marine fish is largely uncultured and distinct from surrounding water microbiota

npj Biofilms and Microbiomes, Journal Year: 2024, Volume and Issue: 10(1)

Published: Feb. 19, 2024

Studying the gut microbes of marine fishes is an important part conservation as many fish species are increasingly threatened by extinction. The microbiota only a small fraction more than 32,000 known has been investigated. In this study we analysed intestinal digesta composition 50 different wild from tropical waters. Our results show that harbour distinct surrounding water and location, domestication status, host intrinsic factors strongly associated with composition. Furthermore, vast majority (~97%) fish-associated microorganisms do not have any cultured representative. Considering impact on health physiology, these findings underpin call to also preserve species, especially those may be exposed habitat destruction.

Language: Английский

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Fish gut microbiome and its application in aquaculture and biological conservation

Frontiers in Microbiology, Journal Year: 2025, Volume and Issue: 15

Published: Jan. 7, 2025

Understanding the diversity and function of fish gut microbiomes has advanced substantially, yet many aspects remain poorly understood, particularly interplay among microbiota, host species, environmental factors in context conservation. This review explores composition abundance bacterial communities key aquaculture groups-cyprinids, ictalurids (catfish), salmonids, cichlids (tilapia)-alongside model organism zebrafish, across diverse geographic regions. The findings highlight habitats species as primary determinants microbiome structure, offering a global perspective on these microbial communities. Across all groups, phyla Firmicutes, Fusobacteria, Proteobacteria consistently dominated, while temperate, sub-equatorial, sub-tropical regions exhibited highest diversity, underscoring contribution taxonomic factors. farm-raised shows significant divergence from that wild-caught fish, reflecting impacts ecological management differences. dynamic responses microbiota is vital for guiding conservation efforts, safeguarding aquatic biodiversity, advancing sustainable practices. Future research should leverage innovative techniques integrative approaches, both experimental theoretical, to uncover functional roles predict their changes. Expanding coverage will be critical creating comprehensive framework inform strategies. Collectively, this highlights transformative potential addressing challenges biology.

Language: Английский

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Ecological Specialization Within a Carnivorous Fish Family Is Supported by a Herbivorous Microbiome Shaped by a Combination of Gut Traits and Specific Diet

Frontiers in Marine Science, Journal Year: 2021, Volume and Issue: 8

Published: Feb. 15, 2021

Animals have been developing key associations with micro-organisms through evolutionary processes and ecological diversification. Hence, in some host clades, phylogenetic distance between hosts is correlated to dissimilarity microbiomes, a pattern called phylosymbiosis. Teleost fishes, despite being the most diverse ancient group of vertebrates, received little attention from microbiome perspective our understanding its determinants currently limited. In this study, we assessed gut 12 co-occurring species teleost representing large breadth diversity originating single family (i.e., Sparidae). We tested how history, diet composition morphological traits are related fish microbiome. Despite having different there no phylosymbiosis signal family, but length had strong influence on revealed that only specialized herbivorous diet, Sarpa salpa 3.3 times longer than carnivorous such long favor presence anaerobic bacteria typical microbiomes. dietary uniqueness paired both unique anatomy

Language: Английский

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Important role of endogenous microbial symbionts of fish gills in the challenging but highly biodiverse Amazonian blackwaters

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: July 6, 2023

Abstract Amazonian blackwaters are extremely biodiverse systems containing some of Earth’s most naturally acidic, dissolved organic carbon -rich and ion‐poor waters. Physiological adaptations fish facing these ionoregulatory challenges unresolved but could involve microbially-mediated processes. Here, we characterize the physiological response 964 fish-microbe from four blackwater Teleost species along a natural hydrochemical gradient, using dual RNA-Seq 16 S rRNA gill samples. We find that host transcriptional responses to species-specific, occasionally include overexpression Toll-receptors integrins associated interkingdom communication. Blackwater microbiomes characterized by transcriptionally-active betaproteobacterial cluster potentially interfering with epithelial permeability. explore further interactions analyzing transcriptomes axenic zebrafish larvae exposed sterile, non-sterile inverted (non-native bacterioplankton) blackwater. survive poorly when sterile/inverted Overall, our results suggest critical role for endogenous symbionts in physiology.

Language: Английский

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