taxonomy
Observation | Ecological and Evolutionary ScienceNovel Effective Bacillus cereus Group Species “Bacillus clarus” Is Represented by Antibiotic-Producing Strain ATCC 21929 Isolated from SoilThe 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...
Commentary | Applied and Environmental ScienceMetagenome Proteins and Database ContaminationContinued 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.
Perspective | Ecological and Evolutionary ScienceNo to Neocosmospora: Phylogenomic and Practical Reasons for Continued Inclusion of the Fusarium solani Species Complex in the Genus FusariumThis 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...
Research Article | Applied and Environmental ScienceQuantitatively Partitioning Microbial Genomic Traits among Taxonomic Ranks across the Microbial Tree of LifeRecently, 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...
Research Article | Ecological and Evolutionary ScienceDictyostelid Cellular Slime Molds from Christmas Island, Indian OceanReported 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...
Research Article | Ecological and Evolutionary ScienceTaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic ResolutionMicrobial 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...
Perspective | Clinical Science and EpidemiologyImportance of Resolving Fungal Nomenclature: the Case of Multiple Pathogenic Species in the Cryptococcus GenusCryptococcosis 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.
Research Article | Clinical Science and EpidemiologyFirst Case of Actinomycetoma in France Due to a Novel Nocardia Species, Nocardia boironii sp. novBacterial 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...