A microbial sea of possibilities: current knowledge and prospects for an improved understanding of the fish microbiome

Reviews in Aquaculture, Год журнала: 2019, Номер 12(2), С. 1101 - 1134

Опубликована: Авг. 13, 2019

Abstract The mucosal surfaces of fish represent an important barrier that supports and regulates a diverse array microbial assemblages contributes to the overall health fitness host. For farmed species, knowledge how these host–microbial systems adapt respond various stressors is pivotal for managing health, nutrition optimizing productivity in aquaculture. While our understanding communities factors shape them now suggest balanced microbiota critical healthy functioning fish, mechanisms behind interactions are still poorly understood. Much existing research has focused on characterizing taxonomic diversity different across body (e.g. skin, gills gastrointestinal tract), response changing nutrition, environmental conditions. However, specific functional contributions (or members) remain elusive, especially or diseased fish. Here, we review current their interplay likely involvement with We also seek address identify gaps explore future prospects improving

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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‘Multi-omics’ data integration: applications in probiotics studies

npj Science of Food, Год журнала: 2023, Номер 7(1)

Опубликована: Июнь 5, 2023

Abstract The concept of probiotics is witnessing increasing attention due to its benefits in influencing the host microbiome and modulation immunity through strengthening gut barrier stimulation antibodies. These benefits, combined with need for improved nutraceuticals, have resulted extensive characterization leading an outburst data generated using several ‘omics’ technologies. recent development system biology approaches microbial science paving way integrating from different omics techniques understanding flow molecular information one level other clear on regulatory features phenotypes. limitations tendencies a ‘single omics’ application ignore influence processes justify ‘multi-omics’ selections action host. Different techniques, including genomics, transcriptomics, proteomics, metabolomics lipidomics, used studying their are discussed this review. Furthermore, rationale multi-omics integration platforms supporting analyses was also elucidated. This review showed that useful selecting functions microbiome. Hence, recommend approach holistically

Язык: Английский

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Deciphering the gut microbiome of grass carp through multi-omics approach

Microbiome, Год журнала: 2024, Номер 12(1)

Опубликована: Янв. 3, 2024

Abstract Background Aquaculture plays an important role in global protein supplies and food security. The ban on antibiotics as feed additive proposes urgent need to develop alternatives. Gut microbiota roles the metabolism immunity of fish has potential give rise novel solutions for challenges confronted by culture. However, our understanding gut microbiome is still lacking. Results We identified 575,856 non-redundant genes metagenomic sequencing intestinal content samples grass carp. Taxonomic functional annotation gene catalogue revealed specificity carp compared with mammals. Co-occurrence analysis indicated exclusive relations between genera belonging Proteobacteria Fusobacteria/Firmicutes/Bacteroidetes , suggesting two independent ecological groups microbiota. association pattern expression modules liver was consistently opposite that Fusobacteria Firmicutes Bacteroidetes implying differential functionality / . Therefore, were considered groups, i.e., Functional Group 1: 2: Further differ genetic capacity carbohydrate utilization, virulence factors, antibiotic resistance. Finally, we proposed ratio “Functional 2/Functional 1” can be used a biomarker efficiently reflects structural characteristics Conclusions resource investigating Multi-omics provides insights into implications main phyla comprise shed lights targets regulation.

Язык: Английский

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Unraveling host regulation of gut microbiota through the epigenome–microbiome axis

Trends in Microbiology, Год журнала: 2024, Номер 32(12), С. 1229 - 1240

Опубликована: Июнь 5, 2024

Recent studies of dynamic interactions between epigenetic modifications a host organism and the composition or activity its associated gut microbiota suggest an opportunity for to shape microbiome through alterations that lead changes in gene expression noncoding RNA activity. We use insights from microbiota-induced review potential epigenetically regulate microbiome, which bidirectional 'epigenome–microbiome axis' emerges. This axis embeds environmentally induced variation, may influence adaptive evolution host–microbe interactions. furthermore present our perspective on how epigenome–microbiome can be understood investigated within holo-omic framework with applications applied health food sciences.

Язык: Английский

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Holo-Omics: Integrated Host-Microbiota Multi-omics for Basic and Applied Biological Research

iScience, Год журнала: 2020, Номер 23(8), С. 101414 - 101414

Опубликована: Июль 25, 2020

From ontogenesis to homeostasis, the phenotypes of complex organisms are shaped by bidirectional interactions between host and their associated microbiota. Current technology can reveal many such combining multi-omic data from both hosts microbes. However, exploring full extent these requires careful consideration study design for efficient generation optimal integration derived (meta)genomics, (meta)transcriptomics, (meta)proteomics, (meta)metabolomics. In this perspective, we introduce holo-omic approach that incorporates microbiota domains untangle interplay two. We revisit recent literature on biomolecular host-microbe discuss implementation current limitations approach. anticipate application contribute opening new research avenues discoveries in biomedicine, biotechnology, agricultural aquacultural sciences, nature conservation, as well basic ecological evolutionary research.

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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Disentangling host–microbiota complexity through hologenomics

Nature Reviews Genetics, Год журнала: 2021, Номер 23(5), С. 281 - 297

Опубликована: Окт. 21, 2021

Язык: Английский

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Holo-omics for deciphering plant-microbiome interactions

Microbiome, Год журнала: 2021, Номер 9(1)

Опубликована: Март 24, 2021

Abstract Host-microbiome interactions are recognized for their importance to host health. An improved understanding of the molecular underpinnings host-microbiome relationships will advance our capacity accurately predict fitness and manipulate interaction outcomes. Within plant microbiome research field, unlocking functional between plants microbial partners is next step effectively using improve fitness. We propose that strategies pair datasets—referred here as holo-omics—provide a powerful approach hypothesis development advancement in this area. discuss several experimental design considerations present case study highlight potential holo-omics generate more holistic perspective networks within system. In addition, we biggest challenges conducting studies; specifically, lack vetted analytical frameworks, publicly available tools, required technical expertise process integrate heterogeneous data. Finally, conclude with on appropriate use-cases studies, need downstream validation, new techniques hold promise field. argue utilizing characterize can provide important opportunities broadening system-level understandings significantly inform approaches improving health

Язык: Английский

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Early life microbial exposures shape the Crassostrea gigas immune system for lifelong and intergenerational disease protection

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

Опубликована: Июнь 4, 2022

Abstract Background The interaction of organisms with their surrounding microbial communities influences many biological processes, a notable example which is the shaping immune system in early life. In Pacific oyster, Crassostrea gigas , role environmental community on maturation — and, importantly, protection from infectious disease still an open question. Results Here, we demonstrate that life exposure durably improves oyster survival when challenged pathogen causing mortality syndrome (POMS), both exposed generation and subsequent one. Combining microbiota, transcriptomic, genetic, epigenetic analyses, show induced changes marks reprogramming gene expression leading to long-term intergenerational against POMS. Conclusions We anticipate this likely extends additional pathogens may prove be important new strategy for safeguarding aquaculture efforts disease. tag videobyte/videoabstract section

Язык: Английский

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