Article
Immunology
Brian M. Forde, Haakon Bergh, Thom Cuddihy, Krispin Hajkowicz, Trish Hurst, E. Geoffrey Playford, Belinda C. Henderson, Naomi Runnegar, Julia Clark, Amy Jennison, Susan Moss, Anna Hume, Hugo Leroux, Scott A. Beatson, David L. Paterson, Patrick N. A. Harris
Summary: This study implemented a program of routine sequencing of multi-drug resistant organisms and used custom analysis pipeline to automate reporting and support infection control interventions. The results showed the identification of transmission events within three hospitals, highlighting the feasibility of routine WGS for MDR pathogens.
CLINICAL INFECTIOUS DISEASES
(2023)
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
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
Biochemical Research Methods
Budi Permana, Scott A. Beatson, Brian M. Forde
Summary: GraphSNP is an interactive visualization tool that allows users to generate SNP distance networks, explore SNP distance distributions, identify clusters of related organisms, and reconstruct transmission routes.
BMC BIOINFORMATICS
(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)
Article
Genetics & Heredity
Young C. Song, Sophie I. Holland, Matthew Lee, Gao Chen, Frank E. Loffler, Michael J. Manefield, Philip Hugenholtz, Ulrike Kappler
Summary: In this study, a comparative analysis of 10 members of the Dehalobacteriia revealed that Dehalobacterium formicoaceticum is the only species capable of anaerobic fermentation of dichloromethane (DCM). Other species in this class do not possess this ability. Common traits of the Dehalobacteriia include the use of amino acids as carbon and energy sources, energy generation through electron-bifurcating protein complexes, and the presence of S-layer proteins. It was also found that D. formicoaceticum can use serine as a growth substrate in the absence of DCM, and the abundance of electron-bifurcating protein complexes and S-layer proteins is high during growth on DCM. Overall, the Dehalobacteriia are low-abundance fermentative scavengers in anoxic habitats.
MICROBIAL GENOMICS
(2023)
Article
Microbiology
Budi Permana, Patrick N. A. Harris, Naomi Runnegar, Margaret Lindsay, Belinda C. Henderson, E. G. Playford, David L. Paterson, Scott A. Beatson, Brian M. Forde
Summary: An outbreak of vanB-type VREfm ST78 occurred in a large tertiary Australian hospital. Whole-genome sequencing revealed a complex transmission route involving unknown environmental reservoirs. This genomic analysis provided detailed information on the local epidemiology of the outbreak strain and facilitated better targeted control measures for VREfm.
MICROBIOLOGY SPECTRUM
(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.
Review
Biochemistry & Molecular Biology
Jennifer Hosmer, Alastair G. McEwan, Ulrike Kappler
Summary: Acetate, as an important anti-inflammatory modulator, can affect host-microbe interactions, human health, inflammation, and outcomes of microbial infections. This mini-review provides a summary of the metabolic pathways of acetate in bacteria and human cells, the functions of acetate in bacterial cells, and the impact of microbially derived acetate on human immune function.
EMERGING TOPICS IN LIFE SCIENCES
(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)