Mining of novel secondary metabolite biosynthetic gene clusters from acid mine drainage

[1]  Huan Zhang,et al.  Metagenome sequencing and 768 microbial genomes from cold seep in South China Sea , 2022, Scientific data.

[2]  Lei Zhou,et al.  500 metagenome-assembled microbial genomes from 30 subtropical estuaries in South China , 2022, Scientific Data.

[3]  Jian Wang,et al.  Intracellular silicification by early-branching magnetotactic bacteria , 2022, Science advances.

[4]  Hui Jiang,et al.  ABO genotype alters the gut microbiota by regulating GalNAc levels in pigs , 2022, Nature.

[5]  Chuanlun Zhang,et al.  A holistic genome dataset of bacteria, archaea and viruses of the Pearl River estuary , 2022, Scientific data.

[6]  Donovan H. Parks,et al.  GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy , 2021, Nucleic Acids Res..

[7]  Xue-Wei Xu,et al.  An atlas of bacterial secondary metabolite biosynthesis gene clusters. , 2021, Environmental microbiology.

[8]  Aiping Lu,et al.  A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data , 2021, Computational and structural biotechnology journal.

[9]  M. Firestone,et al.  Methane-derived carbon flows into host–virus networks at different trophic levels in soil , 2021, Proceedings of the National Academy of Sciences.

[10]  K. Pollard,et al.  Caloric restriction disrupts the microbiota and colonization resistance , 2021, Nature.

[11]  Alexander M. Kloosterman,et al.  antiSMASH 6.0: improving cluster detection and comparison capabilities , 2021, Nucleic Acids Res..

[12]  P. Bork,et al.  Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation , 2021, Nucleic Acids Res..

[13]  J. Segre,et al.  Recovering prokaryotic genomes from host-associated, short-read shotgun metagenomic sequencing data , 2021, Nature Protocols.

[14]  Natalia N. Ivanova,et al.  Author Correction: A genomic catalog of Earth’s microbiomes , 2021, Nature biotechnology.

[15]  D. LaRowe,et al.  Trace gas oxidizers are widespread and active members of soil microbial communities , 2021, Nature Microbiology.

[16]  Pinaki Sar,et al.  Thermoplasmata and Nitrososphaeria as dominant archaeal members in acid mine drainage sediment of Malanjkhand Copper Project, India , 2021, Archives of microbiology.

[17]  Natalia N. Ivanova,et al.  Publisher Correction: A genomic catalog of Earth’s microbiomes , 2020, Nature biotechnology.

[18]  Carmen Li,et al.  Thermogenic hydrocarbon biodegradation by diverse depth-stratified microbial populations at a Scotian Basin cold seep , 2020, Nature Communications.

[19]  K. Kunstman,et al.  Characterization of an acid rock drainage microbiome and transcriptome at the Ely Copper Mine Superfund site , 2020, PloS one.

[20]  B. Stres,et al.  Computational Framework for High-Quality Production and Large-Scale Evolutionary Analysis of Metagenome Assembled Genomes , 2019, Molecular biology and evolution.

[21]  Marnix H. Medema,et al.  A computational framework to explore large-scale biosynthetic diversity , 2019, Nature Chemical Biology.

[22]  Lei Yan,et al.  Acidithiobacillus thiooxidans and its potential application , 2019, Applied Microbiology and Biotechnology.

[23]  Patricia P. Chan,et al.  tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes , 2019, bioRxiv.

[24]  S. Lee,et al.  antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline , 2019, Nucleic Acids Res..

[25]  M. V. van Loosdrecht,et al.  Recent advances in dissimilatory sulfate reduction: From metabolic study to application. , 2019, Water research.

[26]  Edoardo Pasolli,et al.  Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle , 2019, Cell.

[27]  N. Keller Fungal secondary metabolism: regulation, function and drug discovery , 2018, Nature Reviews Microbiology.

[28]  J. DiRuggiero,et al.  MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis , 2018, Microbiome.

[29]  A. Karkhane,et al.  Practical evaluation of 11 de novo assemblers in metagenome assembly. , 2018, Journal of microbiological methods.

[30]  Alexander J Probst,et al.  Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy , 2017, Nature Microbiology.

[31]  O. Tuovinen,et al.  Isolation, Characterization, and Metal Response of Novel, Acid-Tolerant Penicillium spp. from Extremely Metal-Rich Waters at a Mining Site in Transbaikal (Siberia, Russia) , 2018, Microbial Ecology.

[32]  Matthew Z. DeMaere,et al.  CAMISIM: simulating metagenomes and microbial communities , 2018, bioRxiv.

[33]  J. Seguin,et al.  A Comprehensive Overview of the Cyclodipeptide Synthase Family Enriched with the Characterization of 32 New Enzymes , 2018, Front. Microbiol..

[34]  Robert D. Finn,et al.  Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families , 2017, Nucleic Acids Res..

[35]  M. Megharaj,et al.  Microalgae–bacteria biofilms: a sustainable synergistic approach in remediation of acid mine drainage , 2017, Applied Microbiology and Biotechnology.

[36]  J. Siqueira,et al.  Recent Developments for Remediating Acidic Mine Waters Using Sulfidogenic Bacteria , 2017, BioMed research international.

[37]  Natalia N. Ivanova,et al.  Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea , 2017, Nature Biotechnology.

[38]  J. Banfield,et al.  dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication , 2017, The ISME Journal.

[39]  Philipp C. Münch,et al.  Characterisation of a stable laboratory co-culture of acidophilic nanoorganisms , 2017, Scientific Reports.

[40]  P. Pevzner,et al.  metaSPAdes: a new versatile metagenomic assembler. , 2017, Genome research.

[41]  M. Moutiez,et al.  Aminoacyl-tRNA-Utilizing Enzymes in Natural Product Biosynthesis. , 2017, Chemical reviews.

[42]  Hing-Fung Ting,et al.  MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices. , 2016, Methods.

[43]  Connor T. Skennerton,et al.  CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes , 2015, Genome research.

[44]  D. Holmes,et al.  Metagenomic analysis reveals adaptations to a cold-adapted lifestyle in a low-temperature acid mine drainage stream. , 2015, FEMS microbiology ecology.

[45]  Kunihiko Sadakane,et al.  MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph , 2014, Bioinform..

[46]  D. Paslier,et al.  16S rRNA and As-Related Functional Diversity: Contrasting Fingerprints in Arsenic-Rich Sediments from an Acid Mine Drainage , 2015, Microbial Ecology.

[47]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[48]  D. Johnson,et al.  Acidithiobacillus ferridurans sp. nov., an acidophilic iron-, sulfur- and hydrogen-metabolizing chemolithotrophic gammaproteobacterium. , 2013, International journal of systematic and evolutionary microbiology.

[49]  Sean R. Eddy,et al.  Infernal 1.1: 100-fold faster RNA homology searches , 2013, Bioinform..

[50]  W. Shu,et al.  Shifts in microbial community composition and function in the acidification of a lead/zinc mine tailings. , 2013, Environmental microbiology.

[51]  K. Williams,et al.  Proposal for a new class within the phylum Proteobacteria, Acidithiobacillia classis nov., with the type order Acidithiobacillales, and emended description of the class Gammaproteobacteria. , 2013, International journal of systematic and evolutionary microbiology.

[52]  Kai Blin,et al.  antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers , 2013, Nucleic Acids Res..

[53]  W. Shu,et al.  Contemporary environmental variation determines microbial diversity patterns in acid mine drainage , 2012, The ISME Journal.

[54]  Jianqiang Lin,et al.  Acidithiobacillus caldus Sulfur Oxidation Model Based on Transcriptome Analysis between the Wild Type and Sulfur Oxygenase Reductase Defective Mutant , 2012, PloS one.

[55]  A. D. Borthwick 2,5-Diketopiperazines: synthesis, reactions, medicinal chemistry, and bioactive natural products. , 2012, Chemical reviews.

[56]  Kevin J. Liu,et al.  RAxML and FastTree: Comparing Two Methods for Large-Scale Maximum Likelihood Phylogeny Estimation , 2011, PloS one.

[57]  Vincent J. Denef,et al.  AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature , 2010, The ISME Journal.

[58]  Paramvir S. Dehal,et al.  FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.

[59]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[60]  Adam P. Arkin,et al.  FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix , 2009, Molecular biology and evolution.

[61]  E. González-Toril,et al.  Acidithiobacillus ferrivorans, sp. nov.; facultatively anaerobic, psychrotolerant iron-, and sulfur-oxidizing acidophiles isolated from metal mine-impacted environments , 2009, Extremophiles.

[62]  A. Stierle,et al.  Berkeleydione and berkeleytrione, new bioactive metabolites from an acid mine organism. , 2004, Organic letters.

[63]  U. Schmidt,et al.  Enhancing phytoextraction: the effect of chemical soil manipulation on mobility, plant accumulation, and leaching of heavy metals. , 2003, Journal of environmental quality.