Multi-level analysis of the gut–brain axis shows autism spectrum disorder-associated molecular and microbial profiles

Nature Neuroscience, Journal Year: 2023, Volume and Issue: 26(7), P. 1208 - 1217

Published: June 26, 2023

Autism spectrum disorder (ASD) is a neurodevelopmental characterized by heterogeneous cognitive, behavioral and communication impairments. Disruption of the gut-brain axis (GBA) has been implicated in ASD although with limited reproducibility across studies. In this study, we developed Bayesian differential ranking algorithm to identify ASD-associated molecular taxa profiles 10 cross-sectional microbiome datasets 15 other datasets, including dietary patterns, metabolomics, cytokine human brain gene expression profiles. We found functional architecture along GBA that correlates heterogeneity phenotypes, it amino acid, carbohydrate lipid predominantly encoded microbial species genera Prevotella, Bifidobacterium, Desulfovibrio Bacteroides changes, restrictive patterns pro-inflammatory The revealed age-matched sex-matched cohorts not present sibling-matched cohorts. also show strong association between temporal changes composition phenotypes. summary, propose framework leverage multi-omic from well-defined investigate how influences ASD.

Language: Английский

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Examining the healthy human microbiome concept

Nature Reviews Microbiology, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 23, 2024

Language: Английский

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Challenges in capturing the mycobiome from shotgun metagenome data: lack of software and databases

Microbiome, Journal Year: 2025, Volume and Issue: 13(1)

Published: March 7, 2025

The mycobiome, representing the fungal component of microbial communities, is increasingly acknowledged as an integral part gut microbiome. However, research in this area remains relatively limited. characterization mycobiome taxa from metagenomic data heavily reliant on quality software and databases. In study, we evaluated feasibility profiling using existing bioinformatics tools simulated data. We identified seven claiming to perform taxonomic assignment shotgun sequences. One these was outdated required substantial modifications code be functional thus excluded. To evaluate accuracy identification relative abundance remaining (Kraken2, MetaPhlAn4, EukDetect, FunOMIC, MiCoP, HumanMycobiomeScan), constructed 18 mock communities varying species richness levels. comprised up 165 belonging phyla Ascomycota Basidiomycota, commonly found microbiomes. Of tools, FunOMIC HumanMycobiomeScan needed source run. Notably, only one species, Candida orthopsilosis, consistently by all across where it included. Increasing community improved precision Kraken2 genus, family MetaPhlAn4 accurately genera present most species. top three for overall both estimation were respectively. Adding 90% 99% bacterial background did not significantly impact tools' performance. Among whole genome reference HMS, MiCoP), MiCoP exhibited highest when same database used. Our survey mycobiome-specific revealed a very limited selection such their poor robustness due error-prone software, along with significant lack comprehensive databases enabling mycobiome. None implemented fully agreed profiles. recognized but EukDetect provided predictions that closest correct compositions.

Language: Английский

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Current Uses and Future Perspectives of Genomic Technologies in Clinical Microbiology

Antibiotics, Journal Year: 2023, Volume and Issue: 12(11), P. 1580 - 1580

Published: Oct. 30, 2023

Recent advancements in sequencing technology and data analytics have led to a transformative era pathogen detection typing. These developments not only expedite the process, but also render it more cost-effective. Genomic analyses of infectious diseases are swiftly becoming standard for analysis control. Additionally, national surveillance systems can derive substantial benefits from genomic data, as they offer profound insights into epidemiology emergence antimicrobial-resistant strains. Antimicrobial resistance (AMR) is pressing global public health issue. While clinical laboratories traditionally relied on culture-based antimicrobial susceptibility testing, integration AMR holds immense promise. Genomic-based furnish swift, consistent, highly accurate predictions phenotypes specific strains or populations, all while contributing invaluable surveillance. Moreover, genome assumes pivotal role investigation hospital outbreaks. It aids identification infection sources, unveils genetic connections among isolates, informs strategies The One Health initiative, with its focus intricate interconnectedness humans, animals, environment, seeks develop comprehensive approaches disease surveillance, control, prevention. When integrated epidemiological systems, forecast expansion bacterial populations species transmissions. Consequently, this provides evolution relationships pathogens, hosts, environment.

Language: Английский

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Integrating the milk microbiome signatures in mastitis: milk-omics and functional implications

World Journal of Microbiology and Biotechnology, Journal Year: 2025, Volume and Issue: 41(2)

Published: Jan. 18, 2025

Mammalian milk contains a variety of complex bioactive and nutritional components microorganisms. These microorganisms have diverse compositions functional roles that impact host health disease pathophysiology, especially mastitis. The advent use high throughput omics technologies, including metagenomics, metatranscriptomics, metaproteomics, metametabolomics, as well culturomics in microbiome studies suggest strong relationships between phenotype signatures While single undoubtedly contributed to our current understanding mastitis, they often provide limited information, targeting only biological viewpoint which is insufficient system-wide information necessary for elucidating the footprints molecular mechanisms driving mastitis dysbiosis. Therefore, integrating multi-omics approach research could generate new knowledge, improve structural ecosystem, insights sustainable control management.

Language: Английский

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Revisiting the ecological significance, composition, and functions of plant microbiome: a review

New Zealand Journal of Crop and Horticultural Science, Journal Year: 2025, Volume and Issue: unknown, P. 1 - 33

Published: Jan. 30, 2025

Plants have evolved alongside a diverse array of microorganisms, playing crucial roles in supporting plant growth and health. Considerable knowledge now exists regarding the composition dynamics microbiota, along with functional capabilities individual community members. Given significance microbiome challenges crop farming faces, there is pressing necessity to translate microbial techniques into practical applications. Various approaches enhance are available. However, success applying inoculants field often inconsistent, necessitating improvements. Farming practices genetic makeup can also impact microbiota functioning. Consequently, selecting suitable agronomic breeding strategies that plant-microbiome interactions becomes maximising benefits microbiota. To conclude, exploiting new generation inoculants, adopting microbiota-based farm management approaches, developing improved lines promising avenues optimise utilisation microbiome. This paper provides comprehensive review importance functions plant-associated microbes explains concepts use

Language: Английский

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Refining microbiome diversity analysis by concatenating and integrating dual 16S rRNA amplicon reads

npj Biofilms and Microbiomes, Journal Year: 2025, Volume and Issue: 11(1)

Published: April 12, 2025

Understanding the role of human gut microbiota in health and disease requires insights into its taxonomic composition functional capabilities. This study evaluates whether concatenating paired-end reads enhances data output for microbiome analysis compared to merging approach across various regions 16S rRNA gene. We assessed this both mock communities Korean cohorts with or without ulcerative colitis. Our results indicate that using direct joining method V1-V3 V6-V8 improves resolution (ME) post-sequencing data. While predicting microbial function based on sequencing has inherent limitations, integrating from enhanced predictions. was confirmed by whole metagenome (WMS) cohorts, where our improved taxa detection lost ME method. Thus, we propose integrated dual technique serves as a valuable tool research bridging gap between amplicon WMS.

Language: Английский

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Infection and the microbiome in bronchiectasis

European Respiratory Review, Journal Year: 2024, Volume and Issue: 33(173), P. 240038 - 240038

Published: July 1, 2024

Bronchiectasis is marked by bronchial dilatation, recurrent infections and significant morbidity, underpinned a complex interplay between microbial dysbiosis immune dysregulation. The identification of distinct endophenotypes have refined our understanding its pathogenesis, including heterogeneous disease mechanisms that influence treatment prognosis responses. Next-generation sequencing (NGS) has revolutionised the way we view airway microbiology, allowing insights into “unculturable”. Understanding bronchiectasis microbiome through targeted amplicon and/or shotgun metagenomics provided key information on host immunity, central feature progression. rapid increase in translational clinical studies now provides scope for application precision medicine better efficacy interventions aimed at restoring balance modulating Holistic integration these driving an evolving paradigm shift bronchiectasis, which includes critical role unique with clinical, inflammatory, immunological metabolic factors. Here, review current state infection provide views future directions this field.

Language: Английский

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Multiple indicators of gut dysbiosis predict all-cause and cause-specific mortality in solid organ transplant recipients

Gut, Journal Year: 2024, Volume and Issue: 73(10), P. 1650 - 1661

Published: July 2, 2024

Gut microbiome composition is associated with multiple diseases, but relatively little known about its relationship long-term outcome measures. While gut dysbiosis has been linked to mortality risk in the general population, overall survival specific diseases not extensively studied. In current study, we present results from an in-depth analysis of between and all-cause cause-specific setting solid organ transplant recipients (SOTR).

Language: Английский

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Metagenomic analyses of gut microbiome composition and function with age in a wild bird; little change, except increased transposase gene abundance

ISME Communications, Journal Year: 2025, Volume and Issue: 5(1)

Published: Jan. 1, 2025

Abstract Studies on wild animals, mostly undertaken using 16S metabarcoding, have yielded ambiguous evidence regarding changes in the gut microbiome (GM) with age and senescence. Furthermore, variation GM function has rarely been studied such populations, despite metabolic characteristics potentially being associated host senescent declines. Here, we used 7 years of repeated sampling individuals shotgun metagenomic sequencing to investigate taxonomic functional Seychelles warblers (Acrocephalus sechellensis) age. Our results suggest that species richness declines terminal year, this decline occurring consistently across all ages. Taxonomic composition also shifted However, identified occurred linearly (or even mainly during early prior onset senescence species) little accelerated change later life or their year. Therefore, are not linked Interestingly, found a significant increase abundance group transposase genes age, which may accumulate passively due increased transposition induced as result stressors arise These findings reveal but senescence, vertebrate provide blueprint for future studies

Language: Английский

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