The oral microbiome: diversity, biogeography and human health

Nature Reviews Microbiology, Journal Year: 2023, Volume and Issue: 22(2), P. 89 - 104

Published: Sept. 12, 2023

Language: Английский

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MEGARes and AMR++, v3.0: an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using high-throughput sequencing

Nucleic Acids Research, Journal Year: 2022, Volume and Issue: 51(D1), P. D744 - D752

Published: Nov. 16, 2022

Antimicrobial resistance (AMR) is considered a critical threat to public health, and genomic/metagenomic investigations featuring high-throughput analysis of sequence data are increasingly common important. We previously introduced MEGARes, comprehensive AMR database with an acyclic hierarchical annotation structure that facilitates computational analysis, as well AMR++, customized bioinformatic pipeline specifically designed use MEGARes in for characterizing genes (ARGs) metagenomic data. Here, we present v3.0, published ARG sequences antimicrobial drugs, biocides, metals, AMR++ update our (available at MEGLab.org). Database annotations have been expanded include information regarding specific genomic locations single-nucleotide polymorphisms (SNPs) insertions and/or deletions (indels) when required by ARGs expression, the updated uses this check presence resistance-conferring genetic variants sequenced reads. This new encompasses 337 ARGs, whose could not be confirmed such manner. In 3.0, nodes ontology 4 compound types, 59 classes, 233 mechanisms 1448 gene groups classify 8733 accessions.

Language: Английский

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MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes

Peer Community Journal, Journal Year: 2023, Volume and Issue: 3

Published: March 24, 2023

Complex cellular functions are usually encoded by a set of genes in one or few organized genetic loci microbial genomes. Macromolecular System Finder (MacSyFinder) is program that uses these properties to model and then annotate This done integrating the identification each individual gene at level molecular system. We hereby present major release MacSyFinder (version 2) coded Python 3. The code was improved rationalized facilitate future maintainability. Several new features were added allow more flexible modelling systems. introduce intuitive comprehensive search engine identify all best candidate systems sub-optimal ones respect models' constraints. also novel macsydata companion tool enables easy installation broad distribution models developed for (macsy-models) from GitHub repositories. Finally, we have updated popular models: TXSScan protein secretion systems, TFFscan type IV filaments, CONJscan conjugative CasFinder CRISPR associated proteins. available at: https://github.com/gem-pasteur/macsyfinder https://github.com/macsy-models.

Language: Английский

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Identification of structural and regulatory cell-shape determinants in Haloferax volcanii

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Feb. 15, 2024

Abstract Archaea play indispensable roles in global biogeochemical cycles, yet many crucial cellular processes, including cell-shape determination, are poorly understood. Haloferax volcanii , a model haloarchaeon, forms rods and disks, depending on growth conditions. Here, we used combination of iterative proteomics, genetics, live-cell imaging to identify mutants that only form or disks. We compared the proteomes with wild-type cells across phases, thereby distinguishing between protein abundance changes specific cell shape those related phases. The results identified diverse set proteins, predicted transporters, transducers, signaling components, transcriptional regulators, as important for determination. Through phenotypic characterization deletion strains, established rod-determining factor A (RdfA) disk-determining (DdfA) required formation respectively. also structural an actin homolog plays role disk-shape morphogenesis, which named volactin. Using imaging, determined volactin’s localization showed its dynamic polymerization depolymerization. Our provide insights into archaeal possible implications understanding evolution morphology regulation domains.

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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Tissue-like multicellular development triggered by mechanical compression in archaea

Science, Journal Year: 2025, Volume and Issue: 388(6742), P. 109 - 115

Published: April 4, 2025

The advent of clonal multicellularity is a critical evolutionary milestone, seen often in eukaryotes, rarely bacteria, and only once archaea. We show that uniaxial compression induces haloarchaea, forming tissue-like structures. These archaeal tissues are mechanically molecularly distinct from their unicellular lifestyle, mimicking several eukaryotic features. Archaeal undergo multinucleate stage followed by tubulin-independent cellularization, orchestrated active membrane tension at cell size. After tissue junction elasticity becomes akin to animal tissues, giving rise two types—peripheral (Per) central scutoid (Scu) cells—with actin protein glycosylation polarity patterns. Our findings highlight the potential convergent evolution biophysical mechanism emergence multicellular systems across domains life.

Language: Английский

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Archaea methanogens are associated with cognitive performance through the shaping of gut microbiota, butyrate and histidine metabolism

Gut Microbes, Journal Year: 2025, Volume and Issue: 17(1)

Published: Feb. 5, 2025

The relationship between bacteria, cognitive function and obesity is well established, yet the role of archaeal species remains underexplored. We used shotgun metagenomics neuropsychological tests to identify microbial associated with cognition in a discovery cohort (IRONMET, n = 125). Interestingly, methanogen archaeas exhibited strongest positive associations cognition, particularly Methanobrevibacter smithii (M. smithii). Stratifying individuals by median-centered log ratios (CLR) M. (low high groups: LMs HMs) revealed that HMs better distinct gut bacterial profiles (PERMANOVA p 0.001), characterized increased levels Verrucomicrobia, Synergistetes Lentisphaerae reduced Bacteroidetes Proteobacteria. Several these were linked test scores. These findings replicated large-scale validation (Aging Imageomics, 942). Functional analyses an enrichment energy, butyrate, bile acid metabolism both cohorts. Global plasma metabolomics CIL LC-MS IRONMET identified methylhistidine, phenylacetate, alpha-linolenic linoleic acid, secondary 3-methylhistidine, phenylacetylgluamine, adrenic isolithocholic group. Phenylacetate also emerged Aging Imageomics performing untargeted HPLC-ESI-MS/MS metabolic profiling, while targeted profiling again as one most significant HMs. 3-Methylhistidine intense physical activity second (IRONMET-CGM, 116). Finally, FMT from donors improved flexibility, weight, altered SCFAs, histidine-, acid- phenylalanine-related metabolites dorsal striatum recipient mice. seems interact ecosystem affecting histidine, phenylalanine, impact on constituting promising therapeutic target enhance performance, especially subjects obesity.

Language: Английский

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Methanogenic archaea in the human gastrointestinal tract

Nature Reviews Gastroenterology & Hepatology, Journal Year: 2022, Volume and Issue: 19(12), P. 805 - 813

Published: Sept. 1, 2022

Language: Английский

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Factors shaping the abundance and diversity of the gut archaeome across the animal kingdom

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

Published: June 10, 2022

Archaea are common constituents of the gut microbiome humans, ruminants, and termites but little is known about their diversity abundance in other animals. Here, we analyse sequencing quantification data archaeal bacterial 16S rRNA genes from 250 species animals covering a large taxonomic spectrum. We detect presence archaea 175 animal belonging to invertebrates, fish, amphibians, birds, reptiles mammals. identify five dominant lineages, corresponding Methanobrevibacter, Methanosphaera, Methanocorpusculum, Methanimicrococcus "Ca. Methanomethylophilaceae". Some clades, notably within associated certain hosts, suggesting specific adaptations. The non-methanogenic lineage Nitrososphaeraceae (Thaumarchaeota) frequently present samples, although at low abundance, may have also adapted environment. Host phylogeny, diet type, fibre content, intestinal tract physiology major drivers archaeome overall more influenced by these factors than that bacteria. Methanogens reducing methyl-compounds with H

Language: Английский

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Considerations for constructing a protein sequence database for metaproteomics

Computational and Structural Biotechnology Journal, Journal Year: 2022, Volume and Issue: 20, P. 937 - 952

Published: Jan. 1, 2022

Mass spectrometry-based metaproteomics has emerged as a prominent technique for interrogating the functions of specific organisms in microbial communities, addition to total community function. Identifying proteins by mass spectrometry requires matching spectra fragmented peptide ions database protein sequences corresponding sample. This sequence determines which can be identified from measurement, and such taxonomic functional information that inferred measurement. Thus, construction directly impacts outcome any study. Several factors, source curation, need considered during maximize accurate identifications traceable species origin. In this review, we provide an overview existing strategies relevant studies have sought test validate these strategies. Based on review literature our experience decision tree best practices choosing implementing

Language: Английский

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