BGC Atlas: a web resource for exploring the global chemical diversity encoded in bacterial genomes

被引：8

作者：

Bagci, Caner ^{[1
]}

Nuhamunada, Matin ^{[2
]}

Goyat, Hemant ^{[3
]}

Ladanyi, Casimir ^{[1
]}

Sehnal, Ludek ^{[1
]}

Blin, Kai ^{[2
]}

Kautsar, Satria A. ^{[4
]}

Tagirdzhanov, Azat ^{[5
,6
]}

Gurevich, Alexey ^{[5
,6
]}

Mantri, Shrikant ^{[3
]}

von Mering, Christian ^{[7
,8
]}

Udwary, Daniel ^{[4
]}

Medema, Marnix H. ^{[9
]}

Weber, Tilmann ^{[2
]}

Ziemert, Nadine ^{[1
,10
]}

机构：

[1] Univ Tubingen, Interfac Inst Microbiol & Infect Med Tubingen IMIT, Interfac Inst Biomed Informat IBMI, Translat Genome Min Nat Prod, Auf Morgenstelle 28, D-72076 Tubingen, Germany

[2] Tech Univ Denmark, Novo Nord Fdn Ctr Biosustainabil, Soltofts Plads,Bldg 220, DK-2800 Lyngby, Denmark

[3] Natl Agrifood Biotechnol Inst NABI, Computat Biol, Sect 81, Mohali 140306, Punjab, India

[4] DOE Joint Genome Inst, Lawrence Berkeley Natl Lab, 1 Cyclotron Rd, Berkeley, CA 94720 USA

[5] Helmholtz Ctr Infect Res HZI, Helmholtz Inst Pharmaceut Res Saarland HIPS, Campus E8 1, D-66123 Saarbrucken, Germany

[6] Saar & Saarland Univ, Ctr Bioinformat, Saarland Informat Campus,Campus E2 1, D-66123 Saarbrucken, Germany

[7] Univ Zurich, Dept Mol Life Sci, Winterthurerstr 190, CH-8057 Zurich, Switzerland

[8] Univ Zurich, Swiss Inst Bioinformat, Winterthurerstr 190, CH-8057 Zurich, Switzerland

[9] Wageningen Univ, Bioinformat Grp, Droevendaalsesteeg 1 Radix West, NL-6708PB Wageningen, Netherlands

[10] German Ctr Infect Res DZIF, Partner Site Tubingen, Auf Morgenstelle 28, D-72076 Tubingen, Germany

来源：

NUCLEIC ACIDS RESEARCH | 2024年 / 53卷 / D1期

关键词：

SECONDARY METABOLITES; REVEALS;

D O I：

10.1093/nar/gkae953

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Secondary metabolites are compounds not essential for an organism's development, but provide significant ecological and physiological benefits. These compounds have applications in medicine, biotechnology and agriculture. Their production is encoded in biosynthetic gene clusters (BGCs), groups of genes collectively directing their biosynthesis. The advent of metagenomics has allowed researchers to study BGCs directly from environmental samples, identifying numerous previously unknown BGCs encoding unprecedented chemistry. Here, we present the BGC Atlas (https://bgc-atlas.cs.uni-tuebingen.de), a web resource that facilitates the exploration and analysis of BGC diversity in metagenomes. The BGC Atlas identifies and clusters BGCs from publicly available datasets, offering a centralized database and a web interface for metadata-aware exploration of BGCs and gene cluster families (GCFs). We analyzed over 35 000 datasets from MGnify, identifying nearly 1.8 million BGCs, which were clustered into GCFs. The analysis showed that ribosomally synthesized and post-translationally modified peptides are the most abundant compound class, with most GCFs exhibiting high environmental specificity. We believe that our tool will enable researchers to easily explore and analyze the BGC diversity in environmental samples, significantly enhancing our understanding of bacterial secondary metabolites, and promote the identification of ecological and evolutionary factors shaping the biosynthetic potential of microbial communities. [GRAPHICS] .

引用

页码：D618 / D624

页数：7

共 31 条

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