Article
Microbiology
Moussa Louati, Karima Hezbri, Maria del Carmen Montero-Calasanz, Manfred Rohde, Markus Goeker, Faten Ghodhbane-Gtari, Hans-Peter Klenk, Imen Nouioui, Maher Gtari
Summary: A new actinobacterium strain, Blastococcus tunisiensis sp. nov., was isolated from a limestone sample collected in Tunisia, which has distinct phenotypic and genotypic features.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
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
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
Biotechnology & Applied Microbiology
Andrey D. Prjibelski, Alla Mikheenko, Anoushka Joglekar, Alexander Smetanin, Julien Jarroux, Alla L. Lapidus, Hagen U. Tilgner
Summary: IsoQuant is a computational tool that uses intron graphs to accurately reconstruct transcripts with or without reference genome annotation. It reduces the false-positive rate by fivefold and 2.5-fold for Oxford Nanopore reference-based or reference-free mode, respectively, for novel transcript discovery. IsoQuant also improves performance for Pacific Biosciences data.
NATURE BIOTECHNOLOGY
(2023)
Article
Biochemical Research Methods
Dylan Chivian, Sean P. Jungbluth, Paramvir S. Dehal, Elisha M. Wood-Charlson, Richard S. Canon, Benjamin H. Allen, Mikayla M. Clark, Tianhao Gu, Miriam L. Land, Gavin A. Price, William J. Riehl, Michael W. Sneddon, Roman Sutormin, Qizhi Zhang, Robert W. Cottingham, Chris S. Henry, Adam P. Arkin
Summary: Uncultivated Bacteria and Archaea, which make up the majority of Earth's species, can now have their genomes extracted using shotgun sequencing. The U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform offers a series of analysis steps and data products to facilitate the recovery of high-quality metagenome-assembled genomes (MAGs) from microbiomes. This platform allows users to go from sequencing reads to MAGs, which can be further analyzed with other KBase capabilities.
Correction
Biochemical Research Methods
Dylan Chivian, Sean P. Jungbluth, Paramvir S. Dehal, Elisha M. Wood-Charlson, Richard S. Canon, Benjamin H. Allen, Mikayla M. Clark, Tianhao Gu, Miriam L. Land, Gavin A. Price, William J. Riehl, Michael W. Sneddon, Roman Sutormin, Qizhi Zhang, Robert W. Cottingham, Chris S. Henry, Adam P. Arkin
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)
Article
Microbiology
Markus Goeker, Aharon Oren
Summary: Observations show that adding a category should be done before informal names at that rank are widely used, based on the introduction of the phylum category into the International Code of Nomenclature of Prokaryotes (ICNP). An extrapolation from the number of validly published names under the ICNP at different categories suggests that adding kingdom and domain as separate principal ranks would be beneficial. By examining taxonomic activity and associated nomenclatural problems above the phylum level, it is confirmed that introducing these ranks would help stabilize prokaryotic nomenclature. Proposed amendments to the ICNP include the inclusion of kingdom and domain as additional categories.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Review
Microbiology
Pamela J. B. Brown, Jeff H. Chang, Clay Fuqua
Summary: Agrobacterium tumefaciens has been studied since the 17th century, when scientists started investigating the mechanisms behind its pathogenicity. Research over the years has revealed the genetic transfer mechanism by which A. tumefaciens causes crown gall and its significant applications in plant genetic manipulation.
JOURNAL OF BACTERIOLOGY
(2023)
Article
Geosciences, Multidisciplinary
Evgeny Abakumov, Timur Nizamutdinov, Alla Lapidus, Georgy Istigechev, Sergey Loiko
Summary: The Chernevaya taiga soils are characterized by a strong presence of stone-based matrix, organomineral aggregates, and high biological activity, indicating active material transformation and bioturbation in the region.
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)
Article
Cell Biology
Rekha Seshadri, Simon Roux, Katharina J. Huber, Dongying Wu, Sora Yu, Dan Udwary, Lee Call, Stephen Nayfach, Richard L. Hahnke, Rudiger Pukall, James R. White, Neha J. Varghese, Cody Webb, Krishnaveni Palaniappan, Lorenz C. Reimer, Joaquim Sarda, Jonathon Bertsch, Supratim Mukherjee, T. B. K. Reddy, Patrick P. Hajek, Marcel Huntemann, I-Min A. Chen, Alex Spunde, Alicia Clum, Nicole Shapiro, Zong-Yen Wu, Zhiying Zhao, Yuguang Zhou, Lyudmila Evtushenko, Sofie Thijs, Vincent Stevens, Emiley A. Eloe-Fadrosh, Nigel J. Mouncey, Yasuo Yoshikuni, William B. Whitman, Hans-Peter Klenk, Tanja Woyke, Markus Goeker, Nikos C. Kyrpides, Natalia N. Ivanova
Summary: The study presents a comprehensive analysis of actinobacterial diversity, showing that only a small portion of this diversity is represented by sequenced genomes. The comparison of gene functions reveals novel determinants of host-microbe interaction and environment-specific adaptations. The analysis of biosynthetic gene clusters highlights the role of horizontal gene transfer and gene loss in shaping secondary metabolite repertoire.
