FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies DOI Creative Commons
Arkadiy I. Garber, Kenneth H. Nealson, Akihiro Okamoto

et al.

Frontiers in Microbiology, Journal Year: 2020, Volume and Issue: 11

Published: Jan. 31, 2020

Iron is a micronutrient for nearly all life on Earth. It can be used as an electron donor and acceptor by iron-oxidizing iron-reducing microorganisms in variety of biological processes, including photosynthesis respiration. While it the fourth most abundant metal Earth's crust, iron often limiting growth oxic environments because readily oxidized precipitated. Much our understanding how compete utilize based laboratory experiments. However, advent next-generation sequencing surge publicly available sequence data has made possible to probe structure function microbial communities environment. To bridge gap between acquisition, redox cycling, storage, magnetosome formation model plethora from environmental studies, we have created comprehensive database hidden Markov models (HMMs) genes related reduction/oxidation Bacteria Archaea. Along with this database, present FeGenie, bioinformatics tool that accepts genome metagenome assemblies input uses HMM annotate provided datasets respect iron-related gene neighborhood. An important contribution efficient identification involved oxidation dissimilatory reduction, which been largely overlooked standard annotation pipelines. We validated FeGenie against selected set 28 isolate genomes showcase its utility exploring 27 metagenomes, 4 human oral biofilms, 17 candidate organisms, members phyla radiation. show accurately identifies isolates. Furthermore, analysis metagenomes using demonstrates repertoire abundance each environment correlated richness. will not replace reliability culture-dependent analyses physiology, provides reliable predictions derived up-to-date genetic markers. FeGenie's maintained continually updated new are discovered. freely available: https://github.com/Arkadiy-Garber/FeGenie.

Language: Английский

Fast and sensitive protein alignment using DIAMOND DOI
Benjamin Buchfink,

Chao Xie,

Daniel H. Huson

et al.

Nature Methods, Journal Year: 2014, Volume and Issue: 12(1), P. 59 - 60

Published: Nov. 17, 2014

Language: Английский

Citations

11088
Natural Products as Sources of New Drugs from 1981 to 2014 DOI Creative Commons
David Newman, Gordon M. Cragg

Journal of Natural Products, Journal Year: 2016, Volume and Issue: 79(3), P. 629 - 661

Published: Feb. 7, 2016

This contribution is a completely updated and expanded version of the four prior analogous reviews that were published in this journal 1997, 2003, 2007, 2012. In case all approved therapeutic agents, time frame has been extended to cover 34 years from January 1, 1981, December 31, 2014, for diseases worldwide, 1950 (earliest so far identified) 2014 antitumor drugs worldwide. As mentioned 2012 review, we have continued utilize our secondary subdivision "natural product mimic", or "NM", join original primary divisions designation botanical", "NB", those botanical "defined mixtures" now recognized as drug entities by U.S. FDA (and similar organizations). From data presented utilization natural products and/or their novel structures, order discover develop final entity, still alive well. For example, area cancer, over around 1940s end 175 small molecules approved, 131, 75%, are other than "S" (synthetic), with 85, 49%, actually being either directly derived therefrom. areas, influence structures quite marked, with, expected information, anti-infective dependent on structures. We wish draw attention readers rapidly evolving recognition significant number drugs/leads produced microbes microbial interactions "host whence it was isolated", therefore considered research should be significantly.

Language: Английский

Citations

5418
Natural products in drug discovery: advances and opportunities DOI Open Access
Atanas G. Atanasov, Sergey B. Zotchev, Verena M. Dirsch

et al.

Nature Reviews Drug Discovery, Journal Year: 2021, Volume and Issue: 20(3), P. 200 - 216

Published: Jan. 28, 2021

Language: Английский

Citations

3532
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking DOI Open Access
Mingxun Wang, Jeremy Carver, Vanessa V. Phelan

et al.

Nature Biotechnology, Journal Year: 2016, Volume and Issue: 34(8), P. 828 - 837

Published: Aug. 1, 2016

Language: Английский

Citations

3531
The re-emergence of natural products for drug discovery in the genomics era DOI

Alan L. Harvey,

RuAngelie Edrada‐Ebel, Ronald J. Quinn

et al.

Nature Reviews Drug Discovery, Journal Year: 2015, Volume and Issue: 14(2), P. 111 - 129

Published: Jan. 23, 2015

Language: Английский

Citations

2272
A new antibiotic kills pathogens without detectable resistance DOI
Losee L. Ling, Tanja Schneider, Aaron J. Peoples

et al.

Nature, Journal Year: 2015, Volume and Issue: 517(7535), P. 455 - 459

Published: Jan. 5, 2015

Language: Английский

Citations

2193
Antibacterial drug discovery in the resistance era DOI
Eric D. Brown, Gerard D. Wright

Nature, Journal Year: 2016, Volume and Issue: 529(7586), P. 336 - 343

Published: Jan. 1, 2016

Language: Английский

Citations

1973
Antibiotics: past, present and future DOI Creative Commons
Matthew I. Hutchings, Andrew W. Truman, Barrie Wilkinson

et al.

Current Opinion in Microbiology, Journal Year: 2019, Volume and Issue: 51, P. 72 - 80

Published: Oct. 1, 2019

The first antibiotic, salvarsan, was deployed in 1910. In just over 100 years antibiotics have drastically changed modern medicine and extended the average human lifespan by 23 years. discovery of penicillin 1928 started golden age natural product antibiotic that peaked mid-1950s. Since then, a gradual decline development evolution drug resistance many pathogens has led to current antimicrobial crisis. Here we give an overview history discovery, major classes where they come from. We argue future looks bright as new technologies such genome mining editing are discover products with diverse bioactivities. also report on state development, 45 drugs currently going through clinical trials pipeline, including several novel modes action phase 3 trials. Overall, there promising signs for but changes financial models required translate scientific advances into clinically approved antibiotics.

Language: Английский

Citations

1719
Discovery of microbial natural products by activation of silent biosynthetic gene clusters DOI
Peter J. Rutledge, Gregory L. Challis

Nature Reviews Microbiology, Journal Year: 2015, Volume and Issue: 13(8), P. 509 - 523

Published: June 29, 2015

Language: Английский

Citations

861
Lists of names of prokaryotic Candidatus taxa DOI Open Access
Aharon Oren, George M Garrity, Charles Thomas Parker

et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Journal Year: 2020, Volume and Issue: 70(7), P. 3956 - 4042

Published: July 1, 2020

We here present annotated lists of names Candidatus taxa prokaryotes with ranks between subspecies and class, proposed the mid-1990s, when provisional status was first established, end 2018. Where necessary, corrected are that comply current provisions International Code Nomenclature Prokaryotes its Orthography appendix. These lists, as well updated newly published additions corrections to be periodically in Journal Systematic Evolutionary Microbiology, may serve basis for valid publication if proposals expand type material naming also include gene sequences yet-uncultivated is accepted by Committee on Systematics Prokaryotes.

Language: Английский

Citations

832