The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery

ACS Central Science, Journal Year: 2019, Volume and Issue: 5(11), P. 1824 - 1833

Published: Nov. 14, 2019

Despite rapid evolution in the area of microbial natural products chemistry, there is currently no open access database containing all microbially produced product structures. Lack availability these data preventing implementation new technologies science. Specifically, development computational strategies for compound characterization and identification are being hampered by lack a comprehensive known compounds against which to compare experimental data. The creation an access, community-maintained structures would enable discovery improve interoperability existing resources. However, spread unevenly throughout historical scientific literature, including both journal articles international patents. These documents have standard format, often not digitized as machine readable text, publicly available. Further, none associated structure files (e.g., MOL, InChI, or SMILES), instead images This makes extraction formatting relevant formidable challenge. Using combination manual curation automated mining approaches we created (The Natural Products Atlas, www.npatlas.org) that includes 24 594 contains referenced structure, names, source organisms, isolation references, total syntheses, instances structural reassignment. accompanied interactive web portal permits searching substructure, physical properties. Web site also provides mechanisms visualizing chemical space dashboards displaying author timeline tools offer powerful knowledge base with central interface property-based presents viewpoints on diversity products. Atlas has been developed under FAIR principles (Findable, Accessible, Interoperable, Reusable) integrated other emerging databases, Minimum Information About Biosynthetic Gene Cluster (MIBiG) repository, Global Social Molecular Networking (GNPS) platform. It designed community-supported resource provide repository from microorganisms first comprehensive, this type. expected will modalities accelerate process complex libraries.

Language: Английский

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gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models

Genome biology, Journal Year: 2021, Volume and Issue: 22(1)

Published: March 10, 2021

Genome-scale metabolic models of microorganisms are powerful frameworks to predict phenotypes from an organism's genotype. While manual reconstructions laborious, automated often fail recapitulate known processes. Here we present gapseq ( https://github.com/jotech/gapseq ), a new tool pathways and automatically reconstruct microbial using curated reaction database novel gap-filling algorithm. On the basis scientific literature experimental data for 14,931 bacterial phenotypes, demonstrate that outperforms state-of-the-art tools in predicting enzyme activity, carbon source utilisation, fermentation products, interactions within communities.

Language: Английский

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Past, present and future of the boundaries of the Pseudomonas genus: Proposal of Stutzerimonas gen. Nov

Systematic and Applied Microbiology, Journal Year: 2021, Volume and Issue: 45(1), P. 126289 - 126289

Published: Dec. 6, 2021

Language: Английский

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Weighting by Gene Tree Uncertainty Improves Accuracy of Quartet-based Species Trees

Molecular Biology and Evolution, Journal Year: 2022, Volume and Issue: 39(12)

Published: Oct. 6, 2022

Abstract Phylogenomic analyses routinely estimate species trees using methods that account for gene tree discordance. However, the most scalable inference methods, which summarize independently inferred to obtain a tree, are sensitive hard-to-avoid errors introduced in estimation step. This dilemma has created much debate on merits of concatenation versus summary and practical obstacles more widely exclusion concatenation. The successful attempt at making resilient noisy been contracting low support branches from trees. Unfortunately, this approach requires arbitrary thresholds poses new challenges. Here, we introduce threshold-free weighting schemes quartet-based inference, metric used popular method ASTRAL. By reducing impact quartets with or long terminal (or both), provides stronger theoretical guarantees better empirical performance than unweighted Our simulations show improves accuracy across many conditions reduces gap discordance high noise. On data, congruence increases support. Together, our results weighting, enabled by optimization algorithm introduce, utility can reduce incongruence often observed analytical pipelines.

Language: Английский

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Phylogenetic Distribution of Secondary Metabolites in the Bacillus subtilis Species Complex

mSystems, Journal Year: 2021, Volume and Issue: 6(2)

Published: March 15, 2021

Microbes produce a plethora of secondary (or specialized) metabolites that, although not essential for primary metabolism, benefit them to survive in the environment, communicate, and influence cell differentiation. Biosynthetic gene clusters (BGCs), responsible production these metabolites, are readily identifiable on bacterial genome sequences. Understanding phylogeny distribution BGCs helps us predict natural product synthesis ability new isolates. Here, we examined 310 genomes from

Language: Английский

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The Planctomycetia: an overview of the currently largest class within the phylum Planctomycetes

Antonie van Leeuwenhoek, Journal Year: 2022, Volume and Issue: 115(2), P. 169 - 201

Published: Jan. 17, 2022

Language: Английский

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Recent Progress of Reclassification of the Genus Streptomyces

Microorganisms, Journal Year: 2023, Volume and Issue: 11(4), P. 831 - 831

Published: March 24, 2023

The genus Streptomyces is a representative group of actinomycetes and one the largest taxa in bacteria, including approximately 700 species with validly published names. Since classification was mainly based on phenotypic characteristics old days, many members needed to be reclassified according recent molecular-based taxonomies. Recent developments analysis methods availability whole genome sequences type strains enables researchers reclassify these phylogenetically complex large scale. This review introduces reclassifications reported past decade. Appropriately 34 were transferred other genera, such as Kitasatospora, Streptacidiphilus, Actinoalloteichus recently proposed new genera. As result 14 subspecies, includes only four subspecies at present practice. A total 63 later heterotypic synonyms previously recognized 24 reports. strong relationships between secondary metabolite-biosynthetic gene clusters become clarified, appropriate classifications this will not contribute systematics, but also provide significant information when searching for useful bioactive substances.

Language: Английский

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Antibiotics from rare actinomycetes, beyond the genus Streptomyces

Current Opinion in Microbiology, Journal Year: 2023, Volume and Issue: 76, P. 102385 - 102385

Published: Oct. 5, 2023

Throughout the golden age of antibiotic discovery, Streptomyces have been unsurpassed for their ability to produce bioactive metabolites. Yet, this success has hampered by rediscovery. As we enter a new stage biodiscovery, omics data and existing scientific repositories can enable informed choices on biodiversity that may yield novel antibiotics. Here, focus chemical potential rare actinomycetes, defined as bacteria within order Actinomycetales, but not belonging genus Streptomyces. They are named such due less-frequent isolation under standard laboratory practices, yet there is increasing evidence suggest these biologically diverse genera harbour considerable biosynthetic diversity. In review, examples successful more concentrated biodiscovery efforts, survey representation actinomycete taxa, compared with Streptomyces, across natural product in addition its potential. This followed an overview clinically useful drugs produced actinomycetes considerations future efforts. There much learn about underexplored mounting suggests they fruitful avenue discovery antimicrobials.

Language: Английский

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EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets

BMC Bioinformatics, Journal Year: 2023, Volume and Issue: 24(1)

Published: Oct. 14, 2023

Genome-scale phylogenetic analysis based on core gene sets is routinely used in microbiological research. However, the techniques are still not approachable for individuals with little bioinformatics experience. Here, we present EasyCGTree, a user-friendly and cross-platform pipeline to reconstruct genome-scale maximum-likehood (ML) tree using supermatrix (SM) supertree (ST) approaches.EasyCGTree was implemented Perl programming languages built collection of published reputable programs. All programs were precompiled as standalone executable files contained EasyCGTree package. It can run after installing language environment. Several profile hidden Markov models (HMMs) prepared advance construct HMM database (PHD) that enclosed package available homolog searching. Customized also be build added PHD via EasyCGTree. Taking 43 genomes genus Paracoccus testing data set, consensus (a variant typical SM), SM, ST trees inferred successfully, SM compared those pipelines UBCG bcgTree, metrics cophenetic correlation coefficients (CCC) Robinson-Foulds distance (topological distance). The results suggested infer nearly identical topology (distance < 0.1) accuracy (CCC > 0.99) two pipelines.EasyCGTree an all-in-one automatic from input phylogenomic guaranteed accuracy, much easier install use than reference pipelines. In addition, conveniently explore prokaryotic evolutionary signals different perspective. version 4 freely Linux Windows users at Github ( https://github.com/zdf1987/EasyCGTree4 ).

Language: Английский

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Pangenome analysis reveals the genetic basis for taxonomic classification of the Lactobacillaceae family

Food Microbiology, Journal Year: 2023, Volume and Issue: 115, P. 104334 - 104334

Published: July 8, 2023

Lactobacillaceae represent a large family of important microbes that are foundational to the food industry. Many genome sequences strains now available, enabling us conduct comprehensive pangenome analysis this family. We collected 3591 high-quality genomes from public sources and found that: 1) they contained enough for 26 species perform pangenomic analysis, 2) normalized Heap's coefficient λ (a measure openness) was have an average value 0.27 (ranging 0.07 0.37), 3) openness correlated with abundance genomic location transposons mobilomes, 4) each divided into core, accessory, rare genomes, highlight species-specific properties (such as motility restriction-modification systems), 5) Lactiplantibacillus plantarum (which highest number amongst studied) nine distinct phylogroups, 6) mining revealed richness detected biosynthetic gene clusters, functions ranging antimicrobial probiotic preservation, but ∼93% were unknown function. This study provides first in-depth comparative pangenomics

Language: Английский

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