Isolation of potentially novel species expands the genomic and functional diversity of Lachnospiraceae DOI Creative Commons
Xiaoqian Lin, Tongyuan Hu,

Zhinan Wu

et al.

iMeta, Journal Year: 2024, Volume and Issue: 3(2)

Published: Feb. 13, 2024

Abstract The Lachnospiraceae family holds promise as a source of next‐generation probiotics, yet comprehensive delineation its diversity is lacking, hampering the identification suitable strains for future applications. To address this knowledge gap, we conducted an in‐depth genomic and functional analysis 1868 high‐quality genomes, combining data from public databases with our new isolates. This set represented 387 colonization‐selective species‐level clusters, which eight genera multilineage clusters. Pan‐genome analysis, single‐nucleotide polymorphism (SNP) identification, probiotic predictions revealed that species taxonomy, habitats, geography together shape Lachnospiraceae. Moreover, analyses associations atherosclerotic cardiovascular disease (ACVD) inflammatory bowel (IBD) indicated several potentially novel possess capacity to reduce abundance opportunistic pathogens, thereby imparting potential health benefits. Our findings shed light on untapped enabling knowledge‐based selection development probiotics holding improving human management.

Language: Английский

Alkalihalobacterium elongatum gen. nov. sp. nov.: An Antibiotic-Producing Bacterium Isolated From Lonar Lake and Reclassification of the Genus Alkalihalobacillus Into Seven Novel Genera DOI Creative Commons
Amaraja Joshi,

Sonia Thite,

Prachi Karodi

et al.

Frontiers in Microbiology, Journal Year: 2021, Volume and Issue: 12

Published: Oct. 11, 2021

A Gram-stain positive, long, rod-shaped, motile, and spore-forming bacterium (MEB199

Language: Английский

Citations

184
eggNOG 6.0: enabling comparative genomics across 12 535 organisms DOI Creative Commons
Ana Hernández-Plaza, Damian Szklarczyk, Jorge Botas

et al.

Nucleic Acids Research, Journal Year: 2022, Volume and Issue: 51(D1), P. D389 - D394

Published: Nov. 18, 2022

The eggNOG (evolutionary gene genealogy Non-supervised Orthologous Groups) database is a bioinformatics resource providing orthology data and comprehensive functional information for organisms from all domains of life. Here, we present major update the website (version 6.0), which increases number covered to 12 535 reference species, expands annotations, implements new functionality. In total, 6.0 provides hierarchy over 17M orthologous groups (OGs) computed at 1601 taxonomic levels, spanning 10 756 bacterial, 457 archaeal 1322 eukaryotic organisms. OGs have been thoroughly annotated using recent knowledge databases, including KEGG, Gene Ontology, UniProtKB, BiGG, CAZy, CARD, PFAM SMART. also offers phylogenetic trees OGs, maximising utility versatility end users while allowing researchers investigate evolutionary history speciation duplication events as well distribution terms within each OG. Furthermore, contains functionality mine with ease, possibility generating profiles multiple across species or identifying single-copy custom levels. available http://eggnog6.embl.de.

Language: Английский

Citations

154
Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics DOI Creative Commons
Tao Yang, Rong Liu, Yingfeng Luo

et al.

Nature Genetics, Journal Year: 2022, Volume and Issue: 54(10), P. 1553 - 1563

Published: Sept. 22, 2022

Abstract Complete and accurate reference genomes annotations provide fundamental resources for functional genomics crop breeding. Here we report a de novo assembly annotation of pea cultivar ZW6 with contig N50 8.98 Mb, which features 243-fold increase in length evident improvements the continuity quality sequence complex repeat regions compared existing one. Genome diversity 118 cultivated wild demonstrated that Pisum abyssinicum is separate species different from P. fulvum sativum within . Quantitative trait locus analyses uncovered two known Mendel’s genes related to stem ( Le/le ) seed shape R/r as well some candidate pod form studied by Mendel. A pan-genome 116 accessions was constructed, pan-genes preferred showed distinct enrichment, indicating potential value them breeding future.

Language: Английский

Citations

105
Personalized bacteriophage therapy outcomes for 100 consecutive cases: a multicentre, multinational, retrospective observational study DOI Creative Commons
Jean‐Paul Pirnay,

Sarah Djebara,

Griet Steurs

et al.

Nature Microbiology, Journal Year: 2024, Volume and Issue: 9(6), P. 1434 - 1453

Published: June 4, 2024

Abstract In contrast to the many reports of successful real-world cases personalized bacteriophage therapy (BT), randomized controlled trials non-personalized products have not produced expected results. Here we present outcomes a retrospective observational analysis first 100 consecutive BT difficult-to-treat infections facilitated by Belgian consortium in 35 hospitals, 29 cities and 12 countries during period from 1 January 2008 30 April 2022. We assessed how often positive clinical outcome (general efficacy) performed regression identify functional relationships. The most common indications were lower respiratory tract, skin soft tissue, bone infections, involved combinations 26 bacteriophages 6 defined cocktails, individually selected sometimes pre-adapted target causative bacterial pathogens. Clinical improvement eradication targeted bacteria reported for 77.2% 61.3% respectively. our dataset cases, was 70% less probable when no concomitant antibiotics used (odds ratio = 0.3; 95% confidence interval 0.127–0.749). vivo selection resistance vitro bacteriophage–antibiotic synergy documented 43.8% (7/16 patients) 90% (9/10) evaluated patients, observed combination antibiotic re-sensitization reduced virulence bacteriophage-resistant isolates that emerged BT. Bacteriophage immune neutralization 38.5% (5/13) screened patients. Fifteen adverse events reported, including seven non-serious drug reactions suspected be linked While is limited uncontrolled nature these data, it indicates can effective with inform design future trials. BT100 study, ClinicalTrials.gov registration: NCT05498363 .

Language: Английский

Citations

101
Discovery of antimicrobial peptides in the global microbiome with machine learning DOI Creative Commons
Célio Dias Santos Júnior, Marcelo D. T. Torres, Yiqian Duan

et al.

Cell, Journal Year: 2024, Volume and Issue: 187(14), P. 3761 - 3778.e16

Published: June 5, 2024

Novel antibiotics are urgently needed to combat the antibiotic-resistance crisis. We present a machine-learning-based approach predict antimicrobial peptides (AMPs) within global microbiome and leverage vast dataset of 63,410 metagenomes 87,920 prokaryotic genomes from environmental host-associated habitats create AMPSphere, comprehensive catalog comprising 863,498 non-redundant peptides, few which match existing databases. AMPSphere provides insights into evolutionary origins including by duplication or gene truncation longer sequences, we observed that AMP production varies habitat. To validate our predictions, synthesized tested 100 AMPs against clinically relevant drug-resistant pathogens human gut commensals both in vitro vivo. A total 79 were active, with 63 targeting pathogens. These active exhibited antibacterial activity disrupting bacterial membranes. In conclusion, identified nearly one million an open-access resource for antibiotic discovery.

Language: Английский

Citations

88
Cell-type profiling in salamanders identifies innovations in vertebrate forebrain evolution DOI
Jamie Woych, Alonso Ortega Gurrola, Astrid Deryckere

et al.

Science, Journal Year: 2022, Volume and Issue: 377(6610)

Published: Sept. 1, 2022

The evolution of advanced cognition in vertebrates is associated with two independent innovations the forebrain: six-layered neocortex mammals and dorsal ventricular ridge (DVR) sauropsids (reptiles birds). How these arose vertebrate ancestors remains unclear. To reconstruct forebrain tetrapods, we built a cell-type atlas telencephalon salamander Pleurodeles waltl . Our molecular, developmental, connectivity data indicate that parts sauropsid DVR trace back to tetrapod ancestors. By contrast, pallium devoid cellular molecular characteristics mammalian yet shares similarities entorhinal cortex subiculum. findings chart series resulted emergence DVR.

Language: Английский

Citations

75
Short- and long-read metagenomics expand individualized structural variations in gut microbiomes DOI Creative Commons
Liang Chen, Na Zhao, Yīmíng Bào

et al.

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

Published: June 8, 2022

In-depth profiling of genetic variations in the gut microbiome is highly desired for understanding its functionality and impacts on host health disease. Here, by harnessing long read advantage provided Oxford Nanopore Technology (ONT), we characterize fine-scale structural (SVs) hundreds microbiomes from healthy humans. ONT reads dramatically improve quality metagenomic assemblies, enable reliable detection a large, expanded set variation types (notably including large insertions inversions). We find SVs are distinct between individuals stable within an individual, representing fingerprints that shape strain-level differentiations function species, complicating associations to metabolites phenotypes such as blood glucose. In summary, our study strongly emphasizes incorporating into analyses expands scope variations, enables microbiome, their intricate correlations with metabolome.

Language: Английский

Citations

71
Microbiome composition modulates secondary metabolism in a multispecies bacterial community DOI Creative Commons
Marc G. Chevrette, Chris S. Thomas, Amanda Hurley

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(42)

Published: Oct. 10, 2022

Bacterial secondary metabolites are a major source of antibiotics and other bioactive compounds. In microbial communities, these molecules can mediate interspecies interactions responses to environmental change. Despite the importance in human health ecology, little is known about their roles regulation context multispecies communities. simplified model rhizosphere composed Bacillus cereus , Flavobacterium johnsoniae Pseudomonas koreensis we show that dynamics metabolism depend on community species composition interactions. Comparative metatranscriptomics metametabolomics reveal abundance transcripts biosynthetic gene clusters (BGCs) metabolomic molecular features differ between monocultures or dual cultures tripartite community. both two- three-member cocultures, P. modified expression BGCs for zwittermicin, petrobactin, B. F. johnsoniae, whereas BGC transcriptional response itself was minimal. Pairwise cocultures with displayed unique appear be derivatives lokisin, suggesting metabolic handoffs species. Deleting koreenceine, another metabolite, altered transcript metabolite profiles across community, including substantial up-regulation petrobactin bacillibactin koreenceine represses siderophore production. Results from this bacterial chemical output identity capacity coculture partners, microbiome may shape nature.

Language: Английский

Citations

71
cGLRs are a diverse family of pattern recognition receptors in innate immunity DOI Creative Commons
Yao Li, Kailey M. Slavik,

Hunter C. Toyoda

et al.

Cell, Journal Year: 2023, Volume and Issue: 186(15), P. 3261 - 3276.e20

Published: June 27, 2023

Cyclic GMP-AMP synthase (cGAS) is an enzyme in human cells that controls immune response to cytosolic DNA. Upon binding DNA, cGAS synthesizes a nucleotide signal 2′3′-cGAMP activates STING-dependent downstream immunity. Here, we discover cGAS-like receptors (cGLRs) constitute major family of pattern recognition innate Building on recent analysis Drosophila, identify >3,000 cGLRs present nearly all metazoan phyla. A forward biochemical screening 150 animal reveals conserved mechanism signaling including dsDNA and dsRNA ligands synthesis isomers the signals cGAMP, c-UMP-AMP, c-di-AMP. Combining structural biology vivo coral oyster animals, explain how distinct enables control discrete cGLR-STING pathways. Our results reveal as widespread establish molecular rules govern

Language: Английский

Citations

60
A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources DOI Creative Commons
Bin Ma, Caiyu Lu, Yiling Wang

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Nov. 11, 2023

Abstract Soil harbors a vast expanse of unidentified microbes, termed as microbial dark matter, presenting an untapped reservoir biodiversity and genetic resources, but has yet to be fully explored. In this study, we conduct large-scale excavation soil matter by reconstructing 40,039 metagenome-assembled genome bins (the SMAG catalogue) from 3304 metagenomes. We identify 16,530 21,077 species-level (SGBs) unknown SGBs (uSGBs), which expand archaeal bacterial diversity across the tree life. also illustrate pivotal role uSGBs in augmenting microbiome’s functional landscape intra-species diversity, providing large proportions 43,169 biosynthetic gene clusters 8545 CRISPR-Cas genes. Additionally, determine that contributed 84.6% previously unexplored viral-host associations catalogue. The catalogue provides useful genomic resource for further studies investigating resources.

Language: Английский

Citations

59