Analysis of metagenomic data

Nature Reviews Methods Primers, Год журнала: 2025, Номер 5(1)

Опубликована: Янв. 23, 2025

Язык: Английский

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A roadmap for the functional annotation of protein families: a community perspective

Database, Год журнала: 2022, Номер 2022

Опубликована: Янв. 1, 2022

Over the last 25 years, biology has entered genomic era and is becoming a science of 'big data'. Most interpretations analyses rely on accurate functional annotations proteins encoded by more than 500 000 genomes sequenced to date. By different estimates, only half predicted carry an annotation, this percentage varies drastically between organismal lineages. Such large gap in knowledge hampers all aspects biological enterprise and, thereby, standing way reaching its full potential. A brainstorming meeting address issue funded National Science Foundation was held during 3-4 February 2022. Bringing together data scientists, biocurators, computational biologists experimentalists within same venue allowed for comprehensive assessment current state protein families. Further, major issues that were obstructing field identified discussed, which ultimately proposal solutions how move forward.

Язык: Английский

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Roadmap for the integration of environmental microbiomes in risk assessments under EFSA's remit

EFSA Supporting Publications, Год журнала: 2024, Номер 21(2)

Опубликована: Фев. 1, 2024

Scientific interest in the use of environmental microbiomes for risk assessment is rapidly growing, as exemplified by various EFSA opinions. In absence official regulatory guidelines on how to integrate assessment, aims this report are therefore determine whether microbiome studies can be used such purposes, and propose a roadmap integration assessments under EFSA's remit. The identifies current gaps (in terms knowledge from technical point view) barriers that might delay implementation methods, offers recommendations standardised (multi-)omics techniques purposes. Our main findings identified five priorities: (i) defining core (what it encompasses what made of, including identification bioindicators) assess impact any type disturbance; (ii) standardising methodologies protocols, sampling interpretation, guarantee comparability analyses; (iii) developing tools facilitate interpretation; (iv) collecting microbiome-based data shared, curated maintained databases; (v) setting up European Network Microbiome Laboratories reach an agreement standardise studies, interactions between researchers access or samples, actively include multiple stakeholders discussions involving assessment. There both short- longer-term priorities, all which highlight need mobilise concurrently different agencies institutions, well research. also points out capacity building training, acceptance emerging technology, communication issues. These will hopefully contribute elaboration widely accepted framework dealing with.

Язык: Английский

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Microbiology in the era of artificial intelligence: transforming medical and pharmaceutical microbiology

Biotechnology & Biotechnological Equipment, Год журнала: 2024, Номер 38(1)

Опубликована: Май 12, 2024

In this mini-review, we delve into the transformative impact of artificial intelligence (AI) and machine learning (ML) in field microbiology. The paper provides a brief overview various domains where AI is reshaping practices, including clinical diagnostics, drug vaccine discovery, public health management. Our discussion spotlights implementation convolutional neural networks for enhanced pathogen identification, advancements point-of-care emergence new antimicrobials to tackle resistant strains. application epidemiology, microbial ecology forensic microbiology also outlined, underscoring its proficiency deciphering complex interactions forecasting disease outbreaks. We critically examine challenges application, such as ensuring data quality overcoming algorithmic constraints, stress necessity interpretable models that align with medical ethical standards. address intricacies digitalization emphasizing need efficient management laboratory environments. Looking forward, identify key directions microbiology, particularly focusing on developing adaptable, self-updating their integration settings. conclude by highlighting AI's potential revolutionize microbiological diagnostics infection control, significantly influencing patient care health. This review serves an invitation explore showcasing role evolving current methodologies propelling future innovations.

Язык: Английский

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Modern microbiology: Embracing complexity through integration across scales

Cell, Год журнала: 2024, Номер 187(19), С. 5151 - 5170

Опубликована: Сен. 1, 2024

Язык: Английский

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Sensitive clustering of protein sequences at tree-of-life scale using DIAMOND DeepClust

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Янв. 25, 2023

Abstract The biosphere genomics era is transforming life science research, but existing methods struggle to efficiently reduce the vast dimensionality of protein universe. We present DIAMOND DeepClust, an ultra-fast cascaded clustering method optimized cluster 19 billion sequences currently defining biosphere. As a result, we detect 1.7 clusters which 32% hold more than one sequence. This means that 544 million represent 94% all known proteins, illustrating across tree can significantly accelerate comparative studies in Earth BioGenome era.

Язык: Английский

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Beyond the limits of the unassigned protist microbiome: inferring large-scale spatio-temporal patterns of Syndiniales marine parasites

ISME Communications, Год журнала: 2023, Номер 3(1)

Опубликована: Фев. 28, 2023

Abstract Marine protists are major components of the oceanic microbiome that remain largely unrepresented in culture collections and genomic reference databases. The exploration this uncharted protist diversity communities relies essentially on studying genetic markers from environment as taxonomic barcodes. Here we report across 6 large scale spatio-temporal planktonic surveys, half barcodes taxonomically unassigned at genus level, preventing a fine ecological understanding for numerous lineages. Among them, parasitic Syndiniales (Dinoflagellata) appear least described group. We have developed computational workflow, integrating diverse 18S rDNA gene metabarcoding datasets, order to infer large-scale patterns 100% similarity marker, overcoming limitation assignment. From spatial perspective, identified 2171 clusters, i.e., sequences with similarity, exclusively shared between Tropical/Subtropical Ocean Mediterranean Sea among all orders 25 ubiquitous clusters within studied marine regions. temporal over 3 time-series, highlighted 39 follow rhythmic recurrence best indicators parasite community’s variation. These withhold potential ecosystem change indicators, mirroring their associated host community responses. Our results underline importance structuring through space time, raising questions regarding host-parasite association specificity trophic mode persistent Syndiniales, while providing an innovative framework prioritizing taxa further description.

Язык: Английский

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Genomic adaptation of giant viruses in polar oceans

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Окт. 12, 2023

Despite being perennially frigid, polar oceans form an ecosystem hosting high and unique biodiversity. Various organisms show different adaptive strategies in this habitat, but how viruses adapt to environment is largely unknown. Viruses of phyla Nucleocytoviricota Mirusviricota are groups eukaryote-infecting large giant DNA with genomes encoding a variety functions. Here, by leveraging the Global Ocean Eukaryotic Viral database, we investigate biogeography functional repertoire these at global scale. We first confirm existence ecological barrier that clearly separates nonpolar viral communities, then demonstrate temperature drives dramatic changes virus-host network polar-nonpolar boundary. Ancestral niche reconstruction suggests adaptation conditions has occurred repeatedly over course evolution, polar-adapted modern ocean scattered across their phylogeny. Numerous genes specifically associated adaptation, although most homologues not identified as polar-adaptive eukaryotes. These results suggest cold environments changing repertoire, evolutionary strategy distinct from hosts.

Язык: Английский

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Refocusing the microbial rare biosphere concept through a functional lens

Trends in Ecology & Evolution, Год журнала: 2024, Номер 39(10), С. 923 - 936

Опубликована: Июль 9, 2024

Язык: Английский

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Barcoded overexpression screens in gut Bacteroidales identify genes with roles in carbon utilization and stress resistance

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Авг. 5, 2024

Abstract A mechanistic understanding of host-microbe interactions in the gut microbiome is hindered by poorly annotated bacterial genomes. While functional genomics can generate large gene-to-phenotype datasets to accelerate discovery, their applications study anaerobes have been limited. For instance, most gain-of-function screens gut-derived genes performed Escherichia coli and assayed a small number conditions. To address these challenges, we develop Barcoded Overexpression BActerial shotgun library sequencing (Boba-seq). We demonstrate power this approach assaying from diverse Bacteroidales overexpressed Bacteroides thetaiotaomicron . From hundreds experiments, identify new functions phenotypes for 29 important carbohydrate metabolism or tolerance antibiotics bile salts. Highlights include discovery d -glucosamine kinase, raffinose transporter, several routes that increase ceftriaxone salts through lipid biosynthesis. This be readily applied other strains additional phenotypic assays.

Язык: Английский

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