Review
Biotechnology & Applied Microbiology
Franziska Hemmerling, Joern Piel
Summary: Bacteria are a rich source of natural products with potential therapeutic applications. Advances in sequencing technology and computational tools have revealed diverse and chemically distinct natural products in previously unstudied bacteria, which have important implications for drug discovery.
NATURE REVIEWS DRUG DISCOVERY
(2022)
Review
Chemistry, Multidisciplinary
Duncan J. Kountz, Emily P. Balskus
Summary: The genomic era has revolutionized the discovery and investigation of microbial biochemistry, providing researchers with vast amounts of sequence data to explore biochemical functions and mechanisms, as well as novel enzymes and metabolites. By analyzing genomic context and understanding enzyme mechanisms, new microbial metabolic activities, enzymes, and metabolites can be discovered at an accelerated pace. The canonical organization of microbial genomes into gene clusters presents a unique opportunity for the utilization of genomic data, allowing for effective chemical discovery in microbial systems by leveraging functional and physiological relationships between genes within gene clusters.
ACCOUNTS OF CHEMICAL RESEARCH
(2021)
Article
Biology
Eshani Aggarwal, Srishti Chauhan, Dipti Sareen
Summary: As we approach the post-antibiotic era with global antimicrobial resistance on the rise, the discovery of new antibiotics becomes crucial. Thiopeptides, a structurally complex class of natural products, show antimicrobial activity against gram-positive pathogens. By employing genome mining, new thiopeptide biosynthetic gene clusters have been identified, offering potential for expanding the medicinal diversity of NPs.
JOURNAL OF BIOSCIENCES
(2021)
Article
Microbiology
Roberto Sanchez-Navarro, Matin Nuhamunada, Omkar S. Mohite, Kenneth Wasmund, Mads Albertsen, Lone Gram, Per H. Nielsen, Tilmann Weber, Caitlin M. Singleton
Summary: Microorganisms produce a wide variety of secondary metabolites, many of which are yet to be discovered. In this study, the authors assessed the genetic potential of microbes in wastewater treatment plants using genome mining and discovered numerous biosynthetic gene clusters, most of which likely encode novel compounds. The study also highlights the importance of long-read sequencing for assembling complete biosynthetic gene clusters.
Article
Biochemistry & Molecular Biology
Mingyang Liu, Yun Li, Hongzhe Li
Summary: Researchers developed a deep learning method, e-DeepBGC, for detecting BGCs and their biosynthetic classes in bacterial genomes. Compared to previous methods, e-DeepBGC can accurately identify BGCs and improve the sensitivity of BGC detection while reducing false positive rates. The researchers applied e-DeepBGC to a large dataset of bacterial genomes and summarized the functional classes and distribution of predicted BGCs in different bacterial phyla.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Microbiology
Athina Gavriilidou, Satria A. Kautsar, Nestor Zaburannyi, Daniel Krug, Rolf Mueller, Marnix H. Medema, Nadine Ziemert
Summary: By analyzing a large number of bacterial genomes and metagenome assembled genomes (MAGs), it was found that only about 3% of the potential natural products encoded in bacterial genomes have been characterized. The study also identified the genus level as an appropriate taxonomic rank for comparing the biosynthetic diversity of secondary metabolites, with Streptomyces bacteria encoding the largest diversity. Additionally, less-studied taxa such as Weeksellaceae, Myxococcaceae, Pleurocapsa, and Nostocaceae were found to have the potential to produce diverse secondary metabolites that require further investigation.
NATURE MICROBIOLOGY
(2022)
Review
Microbiology
Tanim Arpit Singh, Ajit Kumar Passari, Anjana Jajoo, Sheetal Bhasin, Vijai Kumar Gupta, Abeer Hashem, Abdulaziz A. Alqarawi, Elsayed Fathi Abd-Allah
Summary: Advancements in genome sequencing, metabolomics, and bioinformatics have provided a plethora of information about actinobacterial physiology and genetic regulation, enhancing our understanding of their ability to synthesize bioactive molecules. Developments in genomic approaches have opened new opportunities to discover and manipulate novel antibiotic gene clusters.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemical Research Methods
Jarno N. Alanko, Jaakko Vuohtoniemi, Tommi Maklin, Simon J. Puglisi
Summary: Themisto is a scalable colored k-mer index that works for large collections of microbial reference genomes. It outperforms competing tools in terms of indexing efficiency and pseudoalignment quality.
Review
Biotechnology & Applied Microbiology
Lei Li
Summary: Microbial natural products and their analogues have been widely used as pharmaceutical agents, especially for infectious diseases and cancer. However, the development of new structural classes with innovative chemistry and modes of action is urgently needed to combat antimicrobial resistance and other public health problems. Advances in next-generation sequencing technologies and computational tools present new opportunities to explore untapped microbial biosynthetic potential and discover millions of secondary metabolites. This review emphasizes the challenges associated with discovering new chemical entities, the rich reservoirs provided by unexplored sources, and emerging synthetic biotechnologies for large-scale and rapid drug discovery.
BIOTECHNOLOGY ADVANCES
(2023)
Article
Biochemistry & Molecular Biology
Erik Mingyar, Lucas Muhling, Andreas Kulik, Anika Winkler, Daniel Wibberg, Jorn Kalinowski, Kai Blin, Tilmann Weber, Wolfgang Wohlleben, Evi Stegmann
Summary: By introducing regulator genes into streptomycetes, silent biosynthetic gene clusters can be activated to produce specific compounds.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Mihir Mongia, Romel Baral, Abhinav Adduri, Donghui Yan, Yudong Liu, Yuying Bian, Paul Kim, Bahar Behsaz, Hosein Mohimani
Summary: Microbial natural products are an important source of bioactive compounds for drug discovery, and nonribosomal peptides (NRPs) are a diverse class of NRPs that include antibiotics, immunosuppressants, anticancer agents, toxins, siderophores, pigments, and cytostatics. Prediction of the chemical structure and properties of NRPs, especially those composed of nonstandard amino acids, remains a challenge. In this article, we evaluated various machine learning algorithms and features for predicting the specificity of NRPs and showed that the extra trees model with one-hot encoding features outperforms existing approaches. Additionally, we developed novel techniques for predicting various properties of potentially novel amino acids found in A-domains using unsupervised clustering.
Article
Chemistry, Medicinal
Ton That Huu Dat, Georg Steinert, Nguyen Thi Kim Cuc, Pham Viet Cuong, Hauke Smidt, Detmer Sipkema
Summary: Recent reviews have shown that sponge-associated bacteria are valuable sources of structurally diverse secondary metabolites with potent biological activities, making these microbial communities promising for new drug candidates. However, accessing the overall diversity of secondary metabolite biosynthetic potential in bacteria is challenging due to the difficulty in culturing the majority of bacteria in the laboratory. This study investigates the diversity of secondary metabolite biosynthetic gene clusters in metagenomes of bacterial communities associated with three different sponge species and identifies numerous potential gene clusters for the production of novel compounds.
Review
Microbiology
Kalindi D. Morgan
Summary: This mini-review summarizes the use of nitrogen-15 in bacterial and fungal natural product discovery and biosynthetic characterization. Nitrogen-15 is an important element in various bioactive and structurally intriguing natural products. It can be detected utilizing two-dimensional nuclear magnetic resonance and mass spectrometry, and can also be added to growth media for stable isotope feeding. The use of nitrogen-15 stable isotope feeding has provided additional strategies for the biosynthetic characterization of natural products.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Chemistry, Organic
Ji Hyeon Im, Daniel Shin, Yeon Hee Ban, Woong Sub Byun, Eun Seo Bae, Donghoon Lee, Young Eun Du, Jinsheng Cui, Yun Korea, Sang-Jip Nam, Sangwon Cha, Sang Kook Lee, Yeo Joon Yoon, Dong-Chan Oh
Summary: A new cycloaromatized enediyne, jejucarboside A, was discovered from a marine actinomycete strain through a genomic and spectroscopic signature-based search. Its structure was determined using various analytical methods, and a putative biosynthesis pathway was proposed through genomic analysis. Jejucarboside A exhibited cytotoxicity against colon carcinoma cells.
Article
Multidisciplinary Sciences
Zuodong Sun, Cooper S. Jamieson, Masao Ohashi, K. N. Houk, Yi Tang
Summary: This study reports the discovery of a norbornene synthase SdnG and its role in the biosynthesis of the antifungal natural product sordarin. The reconstitution of sordarin biosynthesis reveals a concise oxidative strategy used by Nature to transform a hydrocarbon precursor into a highly functionalized substrate for SdnG. It was found that SdnG generates the norbornene core of sordarin and accelerates the intramolecular Diels-Alder reaction.
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
Gina Chaput, Jacob Ford, Lani DeDiego, Achala Narayanan, Wing Yin Tam, Meghan Whalen, Marcel Huntemann, Alicia Clum, Alex Spunde, Manoj Pillay, Krishnaveni Palaniappan, Neha Varghese, Natalia Mikhailova, I-Min Chen, Dimitrios Stamatis, T. B. K. Reddy, Ronan O'Malley, Chris Daum, Nicole Shapiro, Natalia Ivanova, Nikos C. Kyrpides, Tanja Woyke, Tijana Glavina del Rio, Kristen M. DeAngelis
Summary: In this study, a novel bacterium strain 159R belonging to the genus Sodalis was successfully isolated from temperate forest soil. It has the capability to depolymerize lignin and can survive in anaerobic conditions. Its application potential in lignocellulosic biofuel production is promising.
MICROBIOLOGY SPECTRUM
(2022)
Article
Multidisciplinary Sciences
Jean-Marie Volland, Silvina Gonzalez-Rizzo, Olivier Gros, Tomas Tyml, Natalia Ivanova, Frederik Schulz, Danielle Goudeau, Nathalie H. Elisabeth, Nandita Nath, Daniel Udwary, Rex R. Malmstrom, Chantal Guidi-Rontani, Susanne Bolte-Kluge, Karen M. Davies, Maitena R. Jean, Jean-Louis Mansot, Nigel J. Mouncey, Esther R. Angert, Tanja Woyke, Shailesh Date
Summary: Through various cellular and genomic techniques, we investigated the bacterium Candidatus (Ca.) Thiomargarita magnifica and found that it has extremely long cell length and unique features that challenge traditional concepts of bacterial cells, indicating evolutionary complexity in the Thiomargarita lineage.
Article
Biochemistry & Molecular Biology
Uri Neri, Yuri I. Wolf, Simon Roux, Antonio Pedro Camargo, Benjami Lee, Darius Kazlauskas, I. Min Chen, Natalia Ivanova, Lisa Zeigler Allen, David Paez-Espino, Donald A. Bryant, Devaki Bhaya, Mart Krupovic, Valerian V. Dolja, Nikos C. Kyrpides, Eugene Koonin, Uri Gophna
Summary: High-throughput RNA sequencing allows us to explore the diversity of RNA viruses on Earth. By analyzing diverse metatranscriptomes and RNA-dependent RNA polymerases, we discovered a 5-fold increase in the known diversity of RNA viruses, as well as new protein domains and virus-host interactions. Additionally, we identified two new bacteriophage phyla and potential new classes and orders.
Article
Biochemistry & Molecular Biology
Supratim Mukherjee, Dimitri Stamatis, Cindy Tianqing Li, Galina Ovchinnikova, Jon Bertsch, Jagadish Chandrabose Sundaramurthi, Mahathi Kandimalla, Paul A. Nicolopoulos, Alessandro Favognano, I-Min A. Chen, Nikos C. Kyrpides, T. B. K. Reddy
Summary: The Genomes OnLine Database (GOLD) continues to serve as a flagship genomic metadata repository, providing freely available projects and metadata for large-scale comparative genomics analysis. New features and components have been added in the latest GOLD v.9 version.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Tina Keller-Costa, Lydia Kozma, Sandra G. Silva, Rodolfo Toscan, Jorge Goncalves, Asuncion Lago-Leston, Nikos C. Kyrpides, Ulisses Nunes da Rocha, Rodrigo Costa
Summary: This study is the first to recover metagenome-assembled genomes (MAGs) from dominant symbionts of octocorals, including previously unculturable Endozoicomonadaceae, Ca. Thioglobaceae, and Metamycoplasmataceae symbionts. The study identified a global role for Endozoicomonadaceae symbionts in octocorals in processing chitin, the most abundant natural polysaccharide in the oceans. Niche partitioning, metabolic specialization, and adaptation to low oxygen conditions among prokaryotic symbionts contribute to the plasticity and adaptability of the octocoral holobiont in changing marine environments.
Article
Microbiology
Bryan T. Piatkowski, Dana L. Carper, Alyssa A. Carrell, I-Min A. Chen, Alicia Clum, Chris Daum, Emiley A. Eloe-Fadrosh, Daniel Gilbert, Gustaf Granath, Marcel Huntemann, Sara S. Jawdy, Ingeborg Jenneken Klarenberg, Joel E. Kostka, Nikos C. Kyrpides, Travis J. Lawrence, Supratim Mukherjee, Mats B. Nilsson, Krishnaveni Palaniappan, Dale A. Pelletier, Christa Pennacchio, T. B. K. Reddy, Simon Roux, A. Jonathan Shaw, Denis Warshan, Tatjana Zivkovic, David J. Weston
Summary: This study presents 49 metagenome assemblies of the microbiome associated with Sphagnum (peat moss) collected from various temperature conditions across Europe. These data will facilitate further research on the impact of climate change on plant-microbe symbiosis, ecology, and ecosystem functioning in northern peatland ecosystems.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
Article
Microbiology
Joana Fernandes Couceiro, Tina Keller-Costa, Nikos C. Kyrpides, Tanja Woyke, William B. Whitman, Rodrigo Costa
Summary: In this study, we report the genome sequences of three Aquimarina megaterium strains isolated from the octocoral Euniceila labiata. We uncover their coding potential for versatile carbon metabolism and biosynthesis of natural products belonging to the polyketide, nonribosomal peptide, and terpene compound classes.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
Article
Biochemistry & Molecular Biology
Benjamin D. Lee, Uri Neri, Simon Roux, Yuri I. Wolf, Antonio Pedro Camargo, Mart Krupovic, Peter Simmonds, Nikos Kyrpides, Uri Gophna, Valerian V. Dolja, Eugene V. Koonin
Summary: We developed a computational pipeline to identify viroid-like cccRNAs and found a 5-fold increase in the number of identified elements compared to previous studies. The presence of viroid-like cccRNAs in diverse transcriptomes and ecosystems suggests that their host range is broader than currently known.
Article
Ecology
Antonio P. Camargo, Rafael S. C. de Souza, Juliana Jose, Isabel R. Gerhardt, Ricardo A. Dante, Supratim Mukherjee, Marcel Huntemann, Nikos C. Kyrpides, Marcelo F. Carazzolle, Paulo Arruda
Summary: The grassland ecosystem of Brazilian campos rupestres has low concentrations of phosphorus and nitrogen, yet supports a high plant diversity. This study explores the taxonomic profile and functional potential of microbial communities associated with two plant species of the campos rupestres. The results show that the soil and rock communities associated with these plants share a core group of efficient colonizers enriched in certain bacterial families. The microbial populations associated with plant roots have a genetic repertoire for organic compound intake, phosphorus and nitrogen turnover, highlighting their role in nutrient availability.
Article
Biochemistry & Molecular Biology
Antonio Pedro Camargo, Stephen Nayfach, I-Min A. Chen, Krishnaveni Palaniappan, Anna Ratner, Ken Chu, Stephan J. Ritter, T. B. K. Reddy, Supratim Mukherjee, Frederik Schulz, Lee Call, Russell Y. Neches, Tanja Woyke, Natalia N. Ivanova, Emiley A. Eloe-Fadrosh, Nikos C. Kyrpides, Simon Roux
Summary: Viruses play critical roles in all microbiomes and their genomic diversity and impacts on biological processes are extensively explored through metagenomics. IMG/VR is a platform providing access to a large collection of viral sequences along with functional annotation and metadata. The latest version, IMG/VR v4, contains over 15 million virus genomes and genome fragments.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
I-Min A. Chen, Ken Chu, Krishnaveni Palaniappan, Anna Ratner, Jinghua Huang, Marcel Huntemann, Patrick Hajek, Stephan J. Ritter, Cody Webb, Dongying Wu, Neha J. Varghese, T. B. K. Reddy, Supratim Mukherjee, Galina Ovchinnikova, Matt Nolan, Rekha Seshadri, Simon Roux, Axel Visel, Tanja Woyke, Emiley A. Eloe-Fadrosh, Nikos C. Kyrpides, Natalia N. Ivanova
Summary: The Integrated Microbial Genomes & Microbiomes system (IMG/M) at the Department of Energy Joint Genome Institute (JGI) provides support for comparative analysis of various genomes, metagenomes, and metatranscriptomes. It includes datasets from JGI, as well as imported datasets from public sources and user-submitted datasets. In recent years, efforts have been made to improve annotation pipeline, upgrade reference database versions, and add new analysis functionalities.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Multidisciplinary Sciences
Supratim Mukherjee, Krishnaveni Palaniappan, Rekha Seshadri, Ken Chu, Anna Ratner, Jinghua Huang, Marcel Huntemann, Patrick Hajek, Stephan Ritter, Cody Webb, Dongying Wu, Neha Varghese, Dimitri Stamatis, Cindy Tianqing Li, Galina Ovchinnikova, Robert M. Bowers, Antonio Pedro Camargo, Stephen Nayfach, Frederik Schulz, Simon Roux, Tanja Woyke, Emiley A. Eloe-Fadrosh, Natalia N. Ivanova, Nikos C. Kyrpides, I. -Min A. Chen, T. B. K. Reddy
Summary: The DOE Joint Genome Institute has developed and maintains computational resources and databases, including Genome OnLine Database (GOLD) and Integrated Microbial Genomes (IMG), for -omics-based scientific research. GOLD is a sequencing project and metadata management system, providing well-curated associated metadata critical for sequence data interpretation. IMG is an omics data management system enabling comparative analysis of microbial genomes, metagenomes, and metatranscriptomics. It contains a large number of datasets and offers advanced search and comparative analysis tools. These publicly accessible systems also support private user data submission and integration for annotation and comparative analysis.
JOURNAL OF THE INDIAN INSTITUTE OF SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Antonio Pedro Camargo, Lee Call, Simon Roux, Stephen Nayfach, Marcel Huntemann, Krishnaveni Palaniappan, Anna Ratner, Ken Chu, Supratim Mukherjeep, T. B. K. Reddy, I-Min A. Chen, Natalia N. Ivanova, Emiley A. Eloe-Fadrosh, Tanja Woyke, David A. Baltrus, Salvador Castaneda-Barba, Fernando de la Cruz, Barbara E. Funnell, James P. J. Hall, Aindrila Mukhopadhyay, Eduardo P. C. Rocha, Thibault Stalder, Eva Top, Nikos C. Kyrpides
Summary: This study introduces the IMG/PR database, which collects a large number of plasmid sequences from various microbiome samples and provides rich metadata and multiple browsing methods.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Mathematical & Computational Biology
Supratim Mukherjee, Galina Ovchinnikova, Dimitri Stamatis, Cindy Tianqing Li, I-Min A. Chen, Nikos C. Kyrpides, T. B. K. Reddy
Summary: The power of next-generation sequencing has led to a massive increase in projects aiming to understand the diversity of complex microbial environments. However, the lack of standardized reporting standards for microbiome data and samples poses a challenge for follow-up studies. The Genomes OnLine Database (GOLD) has developed a standardized naming system for microbiome samples to address this issue and has continued to enrich the research community with well-curated and understandable names for metagenomes and metatranscriptomes. This naming system should be adopted as a best practice to improve the interoperability and reusability of microbiome data.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2023)