Modeling and Simulation


Publications (5)

Comparative Genomic Insights into the Evolution of <i>Halobacteria</i> -Associated “ <i>Candidatus</i> Nanohaloarchaeota”

Citation
Zhao et al. (2022). mSystems
Names
Ca. Nanohaloarchaeota
Subjects
Biochemistry Computer Science Applications Ecology, Evolution, Behavior and Systematics Genetics Microbiology Modeling and Simulation Molecular Biology Physiology
Abstract
The DPANN superphylum is a group of archaea widely distributed in various habitats. They generally have small cells and have a symbiotic lifestyle with other archaea.

Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database

Citation
Pallen et al. (2022). International Journal of Systematic and Evolutionary Microbiology 72 (9)
Subjects
Ecology, Evolution, Behavior and Systematics General Medicine Microbiology Modeling and Simulation
Abstract
Thousands of new bacterial and archaeal species and higher-level taxa are discovered each year through the analysis of genomes and metagenomes. The Genome Taxonomy Database (GTDB) provides hierarchical sequence-based descriptions and classifications for new and as-yet-unnamed taxa. However, bacterial nomenclature, as currently configured, cannot keep up with the need for new well-formed names. Instead, microbiologists have been forced to use hard-to-remember alphanumeric placeholder labels. Here, we exploit an approach to the generation of well-formed arbitrary Latinate names at a scale sufficient to name tens of thousands of unnamed taxa within GTDB. These newly created names represent an important resource for the microbiology community, facilitating communication between bioinformaticians, microbiologists and taxonomists, while populating the emerging landscape of microbial taxonomic and functional discovery with accessible and memorable linguistic labels.

Reevaluation of the Phylogenetic Diversity and Global Distribution of the Genus “ <i>Candidatus</i> Accumulibacter”

Citation
Petriglieri et al. (2022). mSystems 7 (3)
Names
Ca. Accumulibacter
Subjects
Biochemistry Computer Science Applications Ecology, Evolution, Behavior and Systematics Genetics Microbiology Modeling and Simulation Molecular Biology Physiology
Abstract
“ Candidatus Accumulibacter” is the most studied PAO, with a primary role in biological nutrient removal. However, the species-level taxonomy of this lineage is convoluted due to the use of different phylogenetic markers or genome sequencing approaches. Here, we redefined the phylogeny of these organisms, proposing a comprehensive approach which could be used to address the classification of other diverse and uncultivated lineages.

Deciphering Symbiotic Interactions of “ Candidatus Aenigmarchaeota” with Inferred Horizontal Gene Transfers and Co-occurrence Networks

Citation
Li et al. (2021). mSystems 6 (4)
Names
Ca. Aenigmarchaeota
Subjects
Biochemistry Computer Science Applications Ecology, Evolution, Behavior and Systematics Genetics Microbiology Modeling and Simulation Modelling and Simulation Molecular Biology Physiology
Abstract
Recent advances in sequencing technology promoted the blowout discovery of super tiny microbes in the Diapherotrites , Parvarchaeota , Aenigmarchaeota , Nanoarchaeota , and Nanohaloarchaeota (DPANN) superphylum. However, the unculturable properties of the majority of microbes impeded our investigation of their behavior and symbiotic lifestyle in the corresponding community.