Article
Microbiology
Adyasha Panda, Salim T. Islam, Gaurav Sharma
Summary: In this article, Lloyd and Tahon criticize the proposed changes in bacterial phylum nomenclature and highlight several pitfalls of the new framework. They suggest new names for key bacterial phyla while keeping the archaeal phylum names. These changes aim to achieve a consistent and chaos-free nomenclature for researchers.
Article
Microbiology
Adyasha Panda, Salim T. Islam, Gaurav Sharma
Summary: This article criticizes the proposed changes in bacterial phylum nomenclature by the International Committee on Systematics of Prokaryotes and discusses the potential problems and suggestions for improvement.
Review
Biochemistry & Molecular Biology
Lotus A. Lofgren, Jason E. Stajich
Summary: Fungi play essential roles in global ecosystems and biodiversity, influencing ecosystem cycling and ecological diversity. Despite limited understanding of the fungal world, the recognition and conservation of fungal diversity are crucial for maintaining fungal resources, predicting the development of fungal diseases, and understanding ecosystem cycling.
Review
Microbiology
Erik Munson, Karen C. Carroll
Summary: Understanding novel prokaryotic taxon discovery and nomenclature revisions is crucial for clinical microbiology laboratory practice, infectious disease epidemiology, and microbial pathogenesis studies. Recent summaries of taxonomic designations and revisions have included changes in several bacterial genera, highlighting the need for further efforts to determine their clinical relevance and support.
JOURNAL OF CLINICAL MICROBIOLOGY
(2021)
Review
Microbiology
Zachary Ardern, Sagarika Chakraborty, Florian Lenk, Anne-Kristin Kaster
Summary: Annotating protein sequences is crucial for understanding microbial diversity and potential applications, but traditional methods are limited by the vast amount of 'omics' data. Hypothetical proteins (HPs) are a knowledge gap with hidden potential. Artificial intelligence (AI) and machine learning algorithms offer opportunities to leverage 'Big Data' for comprehensive genome annotations. This review explores the aims, methods, and recent research examples of protein annotation, with a focus on machine and deep learning algorithms.
FEMS MICROBIOLOGY REVIEWS
(2023)
Editorial Material
Microbiology
Sybren de Hoog, Thomas J. Walsh, Sarah A. Ahmed, Ana Alastruey-Izquierdo, Barbara D. Alexander, Maiken Cavling Arendrup, Esther Babady, Feng-Yan Bai, Joan-Miquel Balada-Llasat, Andrew Borman, Anuradha Chowdhary, Andrew Clark, Robert C. Colgrove, Oliver A. Cornely, Tanis C. Dingle, Philippe J. Dufresne, Jeff Fuller, Jean-Pierre Gangneux, Connie Gibas, Heather Glasgow, Yvonne Graeser, Jacques Guillot, Andreas H. Groll, Gerhard Haase, Kimberly Hanson, Amanda Harrington, David L. Hawksworth, Randall T. Hayden, Martin Hoenigl, Vit Hubka, Kristie Johnson, Julianne V. Kus, Ruoyu Li, Jacques F. Meis, Michaela Lackner, Fanny Lanternier, Sixto M. Leal Jr, Francesca Lee, Shawn R. Lockhart, Paul Luethy, Isabella Martin, Kyung J. Kwon-Chung, Wieland Meyer, M. Hong Nguyen, Luis Ostrosky-Zeichner, Elizabeth Palavecino, Preeti Pancholi, Peter G. Pappas, Gary W. Procop, Scott A. Redhead, Daniel D. Rhoads, Stefan Riedel, Bryan Stevens, Kaede Ota Sullivan, Paschalis Vergidis, Emmanuel Roilides, Amir Seyedmousavi, Lili Tao, Vania A. Vicente, Roxana G. Vitale, Qi-Ming Wang, Nancy L. Wengenack, Lars Westblade, Nathan Wiederhold, Lewis White, Christina M. Wojewoda, Sean X. Zhang
Summary: The rapid pace of name changes of medically important fungi creates challenges for clinical laboratories and clinicians. Suggestions are made to reduce the number of name changes and provide diagnostic markers. It is recommended to maintain stability at the genus level and report both overarching species and molecular siblings. An open access online database of all medically important fungi names is essential, and new name changes should be reviewed routinely by a standing committee.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Article
Plant Sciences
Giulio Barone, Gianniantonio Domina, Fabrizio Bartolucci, Gabriele Galasso, Lorenzo Peruzzi
Summary: Senecio squalidus, a plant species of the Asteraceae family, consists of nine subspecies. A comprehensive study was conducted to examine the nomenclatural types of this taxonomic group, resulting in the designation of 14 lectotypes. Field investigations and nomenclatural analysis led to the acceptance of 10 species and the proposal of two new names.
Review
Food Science & Technology
Theresa J. Smith, Kristin M. Schill, Charles H. D. Williamson
Summary: Botulinum neurotoxins are a group of protein toxins with similar structures and activities, produced by different bacteria. The nomenclature of these toxins and bacteria has been evolving, which is crucial for accurate reporting of information.
Article
Business, Finance
Ian W. R. Martin, Stefan Nagel
Summary: Modern investors face a high-dimensional prediction problem with thousands of observable variables potentially influencing forecasts. This study reevaluates conventional wisdom on market efficiency in light of this fact. The findings suggest that returns can be predicted in cross-section if the number of asset characteristics is comparable to the number of assets, despite investors optimally using information in real time. In-sample tests and out-of-sample tests exhibit different results.
JOURNAL OF FINANCIAL ECONOMICS
(2022)
Review
Microbiology
Sara D. Lawhon, Claire R. Burbick, Erik Munson, Elizabeth Thelen, Amanda Zapp, Anastasia Wilson
Summary: The study describes the discovery of new taxa in the microbial world of domestic animals in 2022 and discusses the implications of these changes. The newly discovered species include Moraxella nasovis, which causes respiratory disease in sheep, novel members of Campylobacteraceae associated with spotty liver disease in chickens, and diverse organisms from the microbiota of dogs, pigs, honeybees, and other important pollinators. The findings also highlight the presence of diseases in cattle, such as mastitis, endocarditis, orchitis, and endometritis, as well as the identification of a new species, Pseudochrobactrum algeriense, isolated from the mammary lymph nodes of cows.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
A. Muthama Muasya, Isabel Larridon
Summary: The generic delimitations in the Ficinia Clade of tribe Cypereae are revisited, highlighting the paraphyly of Isolepis and the new combinations made within the Ficinia genus based on nuclear and plastid data.
Article
Biology
Robert Poulin, Cameron McDougall, Bronwen Presswell
Summary: This study investigated the naming trends of nearly 2900 new species of parasitic helminths described in the past two decades. The findings suggest that the likelihood of new species being given names that convey information about them or not depends on the higher taxonomic group to which the parasite or its host belongs. Furthermore, there is a consistent gender bias among species named after eminent scientists, with male scientists being immortalized more frequently than female scientists. The study also reveals an increasing tendency to name new species after family members or close friends.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Review
Biotechnology & Applied Microbiology
Wilson Wen Bin Goh, Chern Han Yong, Limsoon Wong
Summary: Batch effects are technical biases that can affect the analysis of high-throughput biotechnological data. Mitigating batch effects effectively depends on the specific context. The emergence of high-resolution technologies presents new challenges in measuring and reducing batch effects. The increased complexity of next-generation biotechnological data poses challenges for batch effect management, even with the advancement of machine learning and artificial intelligence.
TRENDS IN BIOTECHNOLOGY
(2022)
Review
Mathematics, Interdisciplinary Applications
Zhongbo Bai, Xiaomei Bai
Summary: With the rapid growth of information technology and sports, analyzing sports information has become an increasingly challenging issue. This paper introduces the background, management methods, analysis techniques, applications, and research issues of sports big data, providing researchers with a broader understanding and potential research directions in this field. Sports big data contains rich information such as athletes, coaches, and can be further explored using various data analysis technologies.
Article
Public, Environmental & Occupational Health
Roshanak Nateghi, Terje Aven
Summary: This article contributes to the debate on big data risk analysis by clarifying its definition, attributes, and methods, emphasizing the advantages of big data over traditional approaches. Additionally, it highlights the significant contributions of big data to risk assessment and stresses the importance of explicitly considering the strength of knowledge in risk analysis.
Article
Microbiology
Zhaobin Huang, Yuanyuan Huang, Qiliang Lai, Aharon Oren, Wanpeng Wang
Summary: A new bacterial strain GM2-3-6-6(T) was isolated from a mangrove sediment, and it represents a novel species of a novel genus, named Paracrocinitomix mangrovi gen. nov., sp. nov. Additionally, two new families, Phaeocystidibacteraceae fam. nov. and Owenweeksiaceae fam. nov., are proposed based on phylogenetic and genomic analysis.
ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY
(2023)
Article
Oncology
Jacoba Isobella Bromfield, Philip Hugenholtz, Ian Hector Frazer, Kiarash Khosrotehrani, Janin Chandra
Summary: Cutaneous squamous cell carcinoma (cSCC) and actinic keratosis (AK) are significant global health burdens, with chronic UV exposure being a major risk factor. However, recent studies have shown that skin microbiome dysbiosis, particularly an overabundance of Staphylococcus aureus (S. aureus), may also be associated with AK and cSCC development. S. aureus-derived toxins can cause DNA damage and chronic upregulation of proinflammatory cytokines, contributing to carcinogenesis. Removing S. aureus and restoring a healthy microbiome presents a potential therapeutic opportunity, with topical probiotics being a possible non-invasive treatment option.
FRONTIERS IN ONCOLOGY
(2023)
Article
Engineering, Environmental
Xiaole Yin, Xi Chen, Xiao-Tao Jiang, Ying Yang, Bing Li, Marcus Ho-Hin Shum, Tommy T. Y. Lam, Gabriel M. Leung, Joan Rose, Concepcion Sanchez-Cid, Timothy M. Vogel, Fiona Walsh, Thomas U. Berendonk, Janet Midega, Chibuzor Uchea, Dominic Frigon, Gerard D. Wright, Carlos Bezuidenhout, Renata C. Picao, Shaikh Z. Ahammad, Per Halkjaer Nielsen, Philip Hugenholtz, Nicholas J. Ashbolt, Gianluca Corno, Despo Fatta-Kassinos, Helmut Buergmann, Heike Schmitt, Chang-Jun Cha, Amy Pruden, Kornelia Smalla, Eddie Cytryn, Yu Zhang, Min Yang, Yong-Guan Zhu, Arnaud Dechesne, Barth F. Smets, David W. Graham, Michael R. Gillings, William H. Gaze, Celia M. Manaia, Mark C. M. van Loosdrecht, Pedro J. J. Alvarez, Martin J. Blaser, James M. Tiedje, Edward Topp, Tong Zhang
Summary: Surveillance of antibiotic resistance genes (ARGs) in environmental sectors is increasingly conducted to complement studies in human and animal sectors. However, comparing and synthesizing results from different studies using different test methods and bioinformatic analysis approaches pose substantial challenges. This article suggests a universal unit (ARG copy per cell) for reporting biological measurements of ARGs in order to improve comparability. By comparing commonly used quantification units, this study proposes a step towards standardization.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Review
Chemistry, Multidisciplinary
Stefan Krco, Samuel J. J. Davis, Pallav Joshi, Liam A. A. Wilson, Marcelo Monteiro Pedroso, Andrew Douw, Christopher J. J. Schofield, Philip Hugenholtz, Gerhard Schenk, Marc T. T. Morris
Summary: Beta-lactams are widely used antibiotics with broad efficacy and low toxicity. However, resistance to these antibiotics has become a major global health threat, with many bacteria using beta-lactamases to inactivate them. Metallo-beta-lactamases (MBLs), which employ metal ions in catalysis, are particularly problematic due to the lack of effective inhibitors.
FRONTIERS IN CHEMISTRY
(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
Evolutionary Biology
Tom A. Williams, Adrian A. Davin, Benoit Morel, Lenard L. Szantho, Anja Spang, Alexandros Stamatakis, Philip Hugenholtz, Gergely J. Szollosi
Summary: ALE and GeneRax are reliable methods for probabilistic gene tree-species tree reconciliation. They accurately infer gene duplication, transfer, and loss events based on gene vs. species tree discordance. These methods have been used to root species trees and infer ancestral gene repertoires. While there have been criticisms of their reliability, our assessment shows that they are accurate when applied to simulated data and are generally in agreement with alternative methodological approaches on empirical data. ALE and related approaches are promising tools for studying genome evolution.
GENOME BIOLOGY AND EVOLUTION
(2023)
Correction
Biotechnology & Applied Microbiology
Daniel McDonald, Yueyu Jiang, Metin Balaban, Kalen Cantrell, Qiyun Zhu, Antonio Gonzalez, James T. Morton, Giorgia Nicolaou, Donovan H. Parks, Soren M. Karst, Mads Albertsen, Philip Hugenholtz, Todd DeSantis, Se Jin Song, Andrew Bartko, Aki S. Havulinna, Pekka Jousilahti, Susan Cheng, Michael Inouye, Teemu Niiranen, Mohit Jain, Veikko Salomaa, Leo Lahti, Siavash Mirarab, Rob Knight
NATURE BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Daniel McDonald, Yueyu Jiang, Metin Balaban, Kalen Cantrell, Qiyun Zhu, Antonio Gonzalez, James T. T. Morton, Giorgia Nicolaou, Donovan H. H. Parks, Soren M. Karst, Mads Albertsen, Philip Hugenholtz, Todd DeSantis, Se Jin Song, Andrew Bartko, Aki S. S. Havulinna, Pekka Jousilahti, Susan Cheng, Michael Inouye, Teemu Niiranen, Mohit Jain, Veikko Salomaa, Leo Lahti, Siavash Mirarab, Rob Knight
Summary: In this study, a unified reference tree called Greengenes2 was introduced to reconcile genomic and 16S rRNA databases. Through inserting sequences into a whole-genome phylogeny, the results showed that 16S rRNA and shotgun metagenomic data generated from the same samples agreed in principal coordinates space, taxonomy, and phenotype effect size when analyzed with the same tree.
NATURE BIOTECHNOLOGY
(2023)
Article
Biochemical Research Methods
Alex Chklovski, Donovan H. Parks, Ben J. J. Woodcroft, Gene W. Tyson
Summary: This work presents CheckM2, a machine learning-based tool for predicting the genome quality of isolated, single-cell, and metagenome-assembled genomes. CheckM2 outperforms existing tools in accuracy and computational speed, as demonstrated by synthetic and experimental data. CheckM2's database can be rapidly updated with new high-quality reference genomes, even for taxa represented by only a single genome. It accurately predicts the genome quality of MAGs from novel lineages, including those with reduced genome size.
Correction
Genetics & Heredity
Young C. Song, Sophie I. Holland, Matthew Lee, Gao Chen, Julian Zaugg, Frank E. Loeffler, Michael J. Manefield, Philip Hugenholtz, Ulrike Kappler
MICROBIAL GENOMICS
(2023)
Article
Biology
Joyce Zhou, Joel A. Boyd, Bozica Nyeverecz, Charlotte Vivian, Nicola Angel, David L. A. Wood, Philip Hugenholtz, Gene W. Tyson, Lutz Krause, Paraic O. Cuiv
Summary: A novel bacterium, Candidatus Intestinicoccus colisanans, was isolated and its whole genome was sequenced. The study aims to gain insights into the functional potential of this bacterium and its role in modulating host health and well-being.
BMC RESEARCH NOTES
(2023)
Article
Microbiology
Maria Chuvochina, Aaron J. Mussig, Pierre-Alain Chaumeil, Adam Skarshewski, Christian Rinke, Donovan H. Parks, Philip Hugenholtz
Summary: The Genome Taxonomy Database (GTDB) is a taxonomic framework that redefines prokaryotic taxa based on systematic criteria. This has led to changes in existing classifications, including union of taxa and changes in rank. To reduce confusion, we propose names and descriptions for 329 GTDB-defined prokaryotic taxa, with 223 suitable for validation under the International Code of Nomenclature of Prokaryotes (ICNP) and 49 under the Code of Nomenclature of Prokaryotes described from Sequence Data (SeqCode). Additionally, 57 taxa that do not meet validation criteria are proposed as Candidatus.
FEMS MICROBIOLOGY LETTERS
(2023)
