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  • Articles
    • Latest Articles
    • COVID-19 Research and News from ASM Journals
    • mSphere of Influence: Commentaries from Early Career Microbiologists
    • Archive
  • Topics
    • Applied and Environmental Science
    • Clinical Science and Epidemiology
    • Ecological and Evolutionary Science
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taxonomy

  • Open Access
    Novel Effective <span class="named-content genus-species" id="named-content-1">Bacillus cereus</span> Group Species “<em>Bacillus clarus</em>” Is Represented by Antibiotic-Producing Strain ATCC 21929 Isolated from Soil
    Observation | Ecological and Evolutionary Science
    Novel Effective Bacillus cereus Group Species “Bacillus clarus” Is Represented by Antibiotic-Producing Strain ATCC 21929 Isolated from Soil

    The B. cereus group comprises numerous closely related lineages with various degrees of pathogenic potential and industrial relevance. Species-level taxonomic classification of B. cereus group strains is important for risk evaluation and communication but remains challenging. Biochemical and...

    Marysabel Méndez Acevedo, Laura M. Carroll, Manjari Mukherjee, Emma Mills, Lingzi Xiaoli, Edward G. Dudley, Jasna Kovac
  • Open Access
    Metagenome Proteins and Database Contamination
    Commentary | Applied and Environmental Science
    Metagenome Proteins and Database Contamination

    Continued influx of metagenome-derived proteins with misannotated taxonomy into conventional databases, including RefSeq, threatens to eliminate the value of taxonomy identifiers. To prevent this, urgent efforts should be undertaken by submitters of metagenomic data sets as well as by database managers.

    Irina R. Arkhipova
  • Open Access
    No to <em>Neocosmospora</em>: Phylogenomic and Practical Reasons for Continued Inclusion of the <span class="named-content genus-species" id="named-content-1">Fusarium solani</span> Species Complex in the Genus <em>Fusarium</em>
    Perspective | Ecological and Evolutionary Science
    No to Neocosmospora: Phylogenomic and Practical Reasons for Continued Inclusion of the Fusarium solani Species Complex in the Genus Fusarium

    This article is to alert medical mycologists and infectious disease specialists of recent name changes of medically important species of the filamentous mold Fusarium. Fusarium species can cause localized and life-threating infections in humans. Of the 70 Fusarium species that have been reported to cause infections, close to one-third are members of the...

    Kerry O’Donnell, Abdullah M. S. Al-Hatmi, Takayuki Aoki, Balázs Brankovics, José F. Cano-Lira, Jeffrey J. Coleman, G. Sybren de Hoog, Antonio Di Pietro, Rasmus J. N. Frandsen, David M. Geiser, Connie F. C. Gibas, Josep Guarro, Hye-Seon Kim, H. Corby Kistler, Imane Laraba, John F. Leslie, Manuel S. López-Berges, Erik Lysøe, Jacques F. Meis, Michel Monod, Robert H. Proctor, Martijn Rep, Carmen Ruiz-Roldán, Adnan Šišić, Jason E. Stajich, Emma T. Steenkamp, Brett A. Summerell, Theo A. J. van der Lee, Anne D. van Diepeningen, Paul E. Verweij, Cees Waalwijk, Todd J. Ward, Brian L. Wickes, Nathan P. Wiederhold, Michael J. Wingfield, Ning Zhang, Sean X. Zhang
  • Open Access
    Quantitatively Partitioning Microbial Genomic Traits among Taxonomic Ranks across the Microbial Tree of Life
    Research Article | Applied and Environmental Science
    Quantitatively Partitioning Microbial Genomic Traits among Taxonomic Ranks across the Microbial Tree of Life

    Recently, there has been great progress in defining a complete taxonomy of bacteria and archaea, which has been enabled by improvements in DNA sequencing technology and new bioinformatic techniques. A new, algorithmically defined microbial tree of life describes those linkages, relying solely on genetic data, which raises the issue of how microbial traits relate to taxonomy. Here, we adopted cluster of orthologous group functional...

    Taylor M. Royalty, Andrew D. Steen
  • Open Access
    Dictyostelid Cellular Slime Molds from Christmas Island, Indian Ocean
    Research Article | Ecological and Evolutionary Science
    Dictyostelid Cellular Slime Molds from Christmas Island, Indian Ocean

    Reported here are the results of a study for dictyostelids carried out on Christmas Island, Indian Ocean. Six isolates representing four species of dictyostelid cellular slime molds were obtained from two of the four localities from which samples were collected on the island. Two of the species (Dictyostelium insulinativitatis and D. barbarae) belong to the Dictyosteliaceae, genus Dictyostelium, and are new to...

    Pu Liu, Yue Zou, Wenxiu Li, Yu Li, Xinru Li, Songhao Che, Steven L. Stephenson
  • Open Access
    TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution
    Research Article | Ecological and Evolutionary Science
    TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution

    Microbial communities drive ecosystem processes, but microbial community composition analyses using 16S rRNA gene amplicon data sets are limited by the lack of fine-resolution taxonomy classifications. Coarse taxonomic groupings at the phylum, class, and order levels lump ecologically distinct organisms together. To avoid this, many researchers define operational taxonomic units (OTUs) based on clustered sequences, sequence variants, or...

    Robin R. Rohwer, Joshua J. Hamilton, Ryan J. Newton, Katherine D. McMahon
  • Open Access
    Importance of Resolving Fungal Nomenclature: the Case of Multiple Pathogenic Species in the <em>Cryptococcus</em> Genus
    Perspective | Clinical Science and Epidemiology
    Importance of Resolving Fungal Nomenclature: the Case of Multiple Pathogenic Species in the Cryptococcus Genus

    Cryptococcosis is a major fungal disease caused by members of the Cryptococcus gattii and Cryptococcus neoformans species complexes. After more than 15 years of molecular genetic and phenotypic studies and much debate, a proposal for a taxonomic revision was made.

    Ferry Hagen, H. Thorsten Lumbsch, Valentina Arsic Arsenijevic, Hamid Badali, Sebastien Bertout, R. Blake Billmyre, M. Rosa Bragulat, F. Javier Cabañes, Mauricio Carbia, Arunaloke Chakrabarti, Sudha Chaturvedi, Vishnu Chaturvedi, Min Chen, Anuradha Chowdhary, Maria-Francisca Colom, Oliver A. Cornely, Pedro W. Crous, Maria S. Cuétara, Mara R. Diaz, Ana Espinel-Ingroff, Hamed Fakhim, Rama Falk, Wenjie Fang, Patricia F. Herkert, Consuelo Ferrer Rodríguez, James A. Fraser, Josepa Gené, Josep Guarro, Alexander Idnurm, María-Teresa Illnait-Zaragozi, Ziauddin Khan, Kantarawee Khayhan, Anna Kolecka, Cletus P. Kurtzman, Katrien Lagrou, Wanqing Liao, Carlos Linares, Jacques F. Meis, Kirsten Nielsen, Tinashe K. Nyazika, Weihua Pan, Marina Pekmezovic, Itzhack Polacheck, Brunella Posteraro, Flavio de Queiroz Telles, Orazio Romeo, Manuel Sánchez, Ana Sampaio, Maurizio Sanguinetti, Pojana Sriburee, Takashi Sugita, Saad J. Taj-Aldeen, Masako Takashima, John W. Taylor, Bart Theelen, Rok Tomazin, Paul E. Verweij, Retno Wahyuningsih, Ping Wang, Teun Boekhout
  • Open Access
    First Case of Actinomycetoma in France Due to a Novel <em>Nocardia</em> Species, <em>Nocardia boironii</em> sp. nov
    Research Article | Clinical Science and Epidemiology
    First Case of Actinomycetoma in France Due to a Novel Nocardia Species, Nocardia boironii sp. nov

    Bacterial mycetoma is an endemic infection in areas with tropical and subtropical climates. Thus, its presence in temperate climate areas remains rare. We report here the first case of autochthonous actinomycetoma in continental France originating from a Nocardia species other than N. brasiliensis, namely, Nocardia boironii. Considering the history...

    Jacques M. Gilquin, Brigitte Riviere, Valme Jurado, Bernard Audouy, Jean-Baptiste Kouatche, Emmanuelle Bergeron, Delphine Mouniée, Thierry Molina, Philippe Faure, Cesáreo Saiz-Jimenez, Verónica Rodríguez-Nava
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