Salmon gut microbiota correlates with disease infection status: potential for monitoring health in farmed animals

Animal Microbiome, Год журнала: 2021, Номер 3(1)

Опубликована: Апрель 20, 2021

Infectious diseases cause significant production losses in aquaculture every year. Since the gut microbiota plays an essential role regulating host immune system, health and physiology, altered compositions are often associated with a diseased status. However, few studies have examined association between disease severity degree of dysbiosis, especially when is not site primary infection. Moreover, there lack knowledge on whether bath treatment formalin, disinfectant commonly used to treat external infections, might affect microbiome as consequence formalin ingestion. Here we investigate, through 16S rRNA gene metabarcoding, changes distal composition captive-reared cohort 80 Atlantic salmon (Salmo salar L.), bacterial skin infection due natural outbreak subsequent treatment.We identified Tenacibaculum dicentrarchi causative pathogen show that presented different from healthy individuals. A new, yet undescribed, Mycoplasma genus characterized salmon, while sick fish observed increase terms relative abundance Aliivibrio sp., strain regarded opportunistic. We also noticed positive correlation weight sp. abundance, potentially indicating beneficial effect for its host. treated was more similar those than ones.We conclude infections potential indirectly affecting microbiota. As such, optimization procedures should account that. Formalin optimal solution holistic perspective, since observe fish. suggest coupling probiotic aimed at re-establishing community. Lastly, weight, therefore encourage further investigations towards utilization biomarker monitoring other farmed species.

Язык: Английский

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A multi-omics approach unravels metagenomic and metabolic alterations of a probiotic and synbiotic additive in rainbow trout (Oncorhynchus mykiss)

Microbiome, Год журнала: 2022, Номер 10(1)

Опубликована: Янв. 30, 2022

Abstract Background Animal protein production is increasingly looking towards microbiome-associated services such as the design of new and better probiotic solutions to further improve gut health sustainability. Here, we investigate functional effects bacteria-based pro- synbiotic feed additives on functions in relation growth performance commercially important rainbow trout ( Oncorhynchus mykiss ). We combine complementary insights from multiple omics datasets content samples, including 16S bacterial profiling, whole metagenomes, untargeted metabolomics, metagenome-assembled genomes (MAGs) their molecular interactions with host metabolism. Results Our findings reveal that (I) changed microbiome reared had a significantly reduced relative abundance salmonid related Candidatus Mycoplasma salmoninae both mid distal content, (II) genome resolved metagenomics revealed alterations microbial arginine biosynthesis terpenoid backbone synthesis pathways were directly associated presence salmoninae, (III) differences composition intestinal microbiota among types significant changes metabolomic landscape, lipids lipid-like metabolites, amino acids, bile steroid-related metabolites. Conclusion results demonstrate how use multi-omics complex host-microbiome enable us evaluate potential probiotics compared studies only measure overall or characterise environments.

Язык: Английский

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Genome-resolved metagenomics suggests a mutualistic relationship between Mycoplasma and salmonid hosts

Communications Biology, Год журнала: 2021, Номер 4(1)

Опубликована: Май 14, 2021

Abstract Salmonids are important sources of protein for a large proportion the human population. Mycoplasma species major constituent gut microbiota salmonids, often representing majority microbiota. Despite frequent reported dominance salmonid-related species, little is known about phylogenomic placement, functions and potential evolutionary relationships with their salmonid hosts. In this study, we utilise 2.9 billion metagenomic reads generated from 12 samples three different host to I) characterise curate first metagenome-assembled genomes (MAGs) dominating intestines II) establish phylogeny these candidate III) perform comprehensive pangenomic analysis , IV) decipher putative functionalities MAGs reveal specific expected benefit host. Our data provide basis future studies examining composition function

Язык: Английский

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Differential response of digesta- and mucosa-associated intestinal microbiota to dietary insect meal during the seawater phase of Atlantic salmon

Animal Microbiome, Год журнала: 2021, Номер 3(1)

Опубликована: Янв. 7, 2021

Abstract Background Intestinal digesta is commonly used for studying responses of microbiota to dietary shifts, yet evidence accumulating that it represents an incomplete view the intestinal microbiota. The present work aims investigate differences between digesta- and mucosa-associated in Atlantic salmon ( Salmo salar ) how they may respond differently perturbations. In a 16-week seawater feeding trial, were fed either commercially-relevant reference diet or insect meal containing ~ 15% black soldier fly Hermetia illucens larvae meal. distal profiled by 16S rRNA gene sequencing. Results Regardless diet, we observed substantial Microbial richness diversity much higher than mucosa. altered resulting microbial diversity. effect, however, depended on sample origin. Digesta-associated showed more pronounced changes Multivariate association analyses identified two mucosa-enriched taxa, Brevinema andersonii Spirochaetaceae , associated with expression genes related immune barrier function intestine, respectively. Conclusions Our data show mucosa harbor communities clear differences. While insects increased both microbiota, seems resilient variations composition. To fully unveil response changes, concurrent profiling recommended whenever feasible. Specific taxa enriched are function. Detailed studies needed ecological functional significance dwelling

Язык: Английский

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Microbiota in intestinal digesta of Atlantic salmon (Salmo salar), observed from late freshwater stage until one year in seawater, and effects of functional ingredients: a case study from a commercial sized research site in the Arctic region

Animal Microbiome, Год журнала: 2021, Номер 3(1)

Опубликована: Янв. 28, 2021

Abstract Background The importance of the gut microbiota for health and wellbeing is well established humans some land animals. supposedly as important fish, but existing knowledge has many gaps, in particular fish Arctic areas. This study addressed dynamics Atlantic salmon digesta-associated assemblage its associations with host responses from freshwater to seawater life stages under large-scale, commercial conditions region Norway, explored effects functional ingredients. was characterized by 16S rRNA gene sequencing distal intestinal digesta at four time points: 2 weeks before transfer (in May, FW); 4 after June, SW1); November (SW2), April (SW3) following year. Two series diets were fed, varying throughout observation nutrient composition according requirements one without (Ref diet), other ingredients (Test diet). ingredients, i.e. nucleotides, yeast cell walls, prebiotic essential fatty acids, supplemented single or mixtures based on strategies feed company. Results Overall, showed higher microbial richness lactic acid bacteria (LAB) abundance transfer, while Simpson’s diversity decreased period. At SW1, slightly different those FW, dominated genera Lactobacillus Photobacterium . As progressed towards SW2 SW3, Mycoplasma became more prominent, a corresponding decline genus overall bacterial profiles these points clear distinction FW. A significant effect (a mixture walls acids) observed SW2, where Test-fed lower richness, Shannon’s diversity, LAB abundance. multivariate association analysis identified differentially abundant taxa, especially Megasphaera , be significantly associated immune barrier expressions, plasma nutrients. Conclusions profile varied during period, dominating time. biomarkers. Functional modulated an ongrowing stage.

Язык: Английский

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A systematic review of advances in intestinal microflora of fish

Fish Physiology and Biochemistry, Год журнала: 2021, Номер 47(6), С. 2041 - 2053

Опубликована: Ноя. 8, 2021

Язык: Английский

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Longitudinal transmission of bacterial and fungal communities from seed to seed in rice

Communications Biology, Год журнала: 2022, Номер 5(1)

Опубликована: Авг. 1, 2022

Abstract Vertical transmission of microbes is crucial for the persistence host-associated microbial communities. Although vertical seed has been reported from diverse plants, ecological mechanisms and dynamics communities parent to progeny remain scarce. Here we reveal veiled mechanism governing bacterial fungal in rice across two consecutive seasons. We identify 29 34 members transmitted generations. Abundance-based regression models allow classify colonization types microbes. find that they are late colonizers dominating each community at ripening stage. Ecological further show observed temporal patterns affected by niche change neutrality. Source-sink modeling reveals parental seeds stem endosphere major origins This study gives empirical evidence as an continuum during seed-to-seed transmission.

Язык: Английский

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Co-diversification of an intestinal Mycoplasma and its salmonid host

The ISME Journal, Год журнала: 2023, Номер 17(5), С. 682 - 692

Опубликована: Фев. 17, 2023

Abstract Understanding the evolutionary relationships between a host and its intestinal resident bacteria can transform how we understand adaptive phenotypic traits. The interplay hosts their inevitably affects environment and, thereby, living conditions of both microbiota. Thereby this co-existence likely influences fitness host. Whether leads to co-diversification in animals is largely unexplored, mainly due complexity microbial communities often low selection. We present gut metagenome from wild Atlantic salmon (Salmo salar), new organism model with an microbiota well-described population structure, making it well-suited for investigating co-evolution. Our data reveal strong selection core dominated by single Mycoplasma species. found clear structure nucleotide variability populations conforming expectations co-evolution bacteria. results show that stable has evolved salmonid while potentially providing traits populations, including defence mechanisms, biosynthesis essential amino acids, metabolism B vitamins. highlight as novel studying vertebrate

Язык: Английский

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Network analysis reveals significant joint effects of microplastics and tetracycline on the gut than the gill microbiome of marine medaka

Journal of Hazardous Materials, Год журнала: 2022, Номер 442, С. 129996 - 129996

Опубликована: Сен. 14, 2022

Язык: Английский

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

Microbiome, Год журнала: 2023, Номер 11(1)

Опубликована: Ноя. 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.

Язык: Английский

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