Publications (3219)

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Indications for a genetic basis for big bacteria and description of the giant cable bacterium Candidatus Electrothrix gigas sp. nov

Citation
Geelhoed et al. (2023). Microbiology Spectrum
Names (2)
Ca. Electrothrix gigas Ca. Electrothrix
Subjects
Cell Biology Ecology General Immunology and Microbiology Genetics Infectious Diseases Microbiology (medical) Physiology
Abstract
ABSTRACT Bacterial cells can vary greatly in size, from a few hundred nanometers to hundreds of micrometers in diameter. Filamentous cable bacteria also display substantial size differences, with filament diameters ranging from 0.4 to 8 µm. We analyzed the genomes of cable bacterium filaments from 11 coastal environments of which the resulting 23 new genomes represent 10 novel species-level clades of Candidatus Electrothrix and two clades that putatively represent novel genus-level diversity. Fluorescence in situ hybridization with a species-level probe showed that large-sized cable bacteria belong to a novel species with the proposed name Ca . Electrothrix gigas. Comparative genome analysis suggests genes that play a role in the construction or functioning of large cable bacteria cells: the genomes of Ca . Electrothrix gigas encode a novel actin-like protein as well as a species-specific gene cluster encoding four putative pilin proteins and a putative type II secretion platform protein, which are not present in other cable bacteria. The novel actin-like protein was also found in a number of other giant bacteria, suggesting there could be a genetic basis for large cell size. This actin-like protein (denoted big bacteria protein, Bbp) may have a function analogous to other actin proteins in cell structure or intracellular transport. We contend that Bbp may help overcome the challenges of diffusion limitation and/or morphological complexity presented by the large cells of Ca . Electrothrix gigas and other giant bacteria. IMPORTANCE In this study, we substantially expand the known diversity of marine cable bacteria and describe cable bacteria with a large diameter as a novel species with the proposed name Candidatus Electrothrix gigas. In the genomes of this species, we identified a gene that encodes a novel actin-like protein [denoted big bacteria protein (Bbp)]. The bbp gene was also found in a number of other giant bacteria, predominantly affiliated to Desulfobacterota and Gammaproteobacteria, indicating that there may be a genetic basis for large cell size. Thus far, mostly structural adaptations of giant bacteria, vacuoles, and other inclusions or organelles have been observed, which are employed to overcome nutrient diffusion limitation in their environment. In analogy to other actin proteins, Bbp could fulfill a structural role in the cell or potentially facilitate intracellular transport.

Complete genomes of mutualistic bacterial co-symbionts “ Candidatus Sulcia muelleri” and “ Candidatus Nasuia deltocephalinicola” of the rice green leafhopper Nephotettix cincticeps

Citation
Moriyama et al. (2023). Microbiology Resource Announcements 12 (9)
Names (2)
Ca. Sulcia muelleri Ca. Nasuia deltocephalinicola
Subjects
Genetics Immunology and Microbiology (miscellaneous) Molecular Biology
Abstract
ABSTRACT The genomes of obligate bacterial co-symbionts of the green rice leafhopper Nephotettix cincticeps , which is notorious as an agricultural pest, were determined. The streamlined genomes of “ Candidatus Sulcia muelleri” and “ Candidatus Nasuia deltocephalinicola” exhibited complementary metabolic pathways for synthesizing essential nutrients that contribute to host adaptation.

Complete genome sequence of “ Candidatus Phytoplasma pruni” PR2021, an uncultivated bacterium associated with poinsettia ( Euphorbia pulcherrima )

Citation
Pei et al. (2023). Microbiology Resource Announcements 12 (9)
Names (1)
Ca. Phytoplasma pruni
Subjects
Genetics Immunology and Microbiology (miscellaneous) Molecular Biology
Abstract
ABSTRACT The complete genome sequence of “ Candidatus Phytoplasma pruni” strain PR2021, which consists of one 705,138 bp circular chromosome and one 4,757 bp circular plasmid, is presented in this work. This bacterium is associated with poinsettia ( Euphorbia pulcherrima ) cultivar “Princettia Pink.”

Ecophysiology and interactions of a taurine-respiring bacterium in the mouse gut

Citation
Ye et al. (2023). Nature Communications 14 (1)
Names (2)
“Taurinivorans” “Taurinivorans muris”
Subjects
General Biochemistry, Genetics and Molecular Biology General Chemistry General Physics and Astronomy Multidisciplinary
Abstract
AbstractTaurine-respiring gut bacteria produce H2S with ambivalent impact on host health. We report the isolation and ecophysiological characterization of a taurine-respiring mouse gut bacterium. Taurinivorans muris strain LT0009 represents a new widespread species that differs from the human gut sulfidogen Bilophila wadsworthia in its sulfur metabolism pathways and host distribution. T. muris specializes in taurine respiration in vivo, seemingly unaffected by mouse diet and genotype, but is dependent on other bacteria for release of taurine from bile acids. Colonization of T. muris in gnotobiotic mice increased deconjugation of taurine-conjugated bile acids and transcriptional activity of a sulfur metabolism gene-encoding prophage in other commensals, and slightly decreased the abundance of Salmonella enterica, which showed reduced expression of galactonate catabolism genes. Re-analysis of metagenome data from a previous study further suggested that T. muris can contribute to protection against pathogens by the commensal mouse gut microbiota. Together, we show the realized physiological niche of a key murine gut sulfidogen and its interactions with selected gut microbiota members.

Ecogenomics and cultivation reveal distinctive viral-bacterial communities in the surface microlayer of a Baltic Sea slick

Citation
Rahlff et al. (2023). ISME Communications 3 (1)
Names (1)
“Alishewanella slickus”
Subjects
General Medicine
Abstract
AbstractVisible surface films, termed slicks, can extensively cover freshwater and marine ecosystems, with coastal regions being particularly susceptible to their presence. The sea-surface microlayer (SML), the upper 1-mm at the air-water interface in slicks (herein slick SML) harbors a distinctive bacterial community, but generally little is known about SML viruses. Using flow cytometry, metagenomics, and cultivation, we characterized viruses and bacteria in a brackish slick SML in comparison to non-slick SML as well as seawater below slick and non-slick areas (subsurface water = SSW). Size-fractionated filtration of all samples distinguished viral attachment to hosts and particles. The slick SML contained higher abundances of virus-like particles, prokaryotic cells, and dissolved organic carbon compared to non-slick SML and SSW. The community of 428 viral operational taxonomic units (vOTUs), 426 predicted as lytic, distinctly differed across all size fractions in the slick SML compared to non-slick SML and SSW. Specific metabolic profiles of bacterial metagenome-assembled genomes and isolates in the slick SML included a prevalence of genes encoding motility and carbohydrate-active enzymes (CAZymes). Several vOTUs were enriched in slick SML, and many virus variants were associated with particles. Nine vOTUs were only found in slick SML, six of them being targeted by slick SML-specific clustered-regularly interspaced short palindromic repeats (CRISPR) spacers likely originating from Gammaproteobacteria. Moreover, isolation of three previously unknown lytic phages for Alishewanella sp. and Pseudoalteromonas tunicata, abundant and actively replicating slick SML bacteria, suggests that viral activity in slicks contributes to biogeochemical cycling in coastal ecosystems.

Metagenomics Revealed a New Genus ‘Candidatus Thiocaldithrix dubininis’ gen. nov., sp. nov. and a New Species ‘Candidatus Thiothrix putei’ sp. nov. in the Family Thiotrichaceae, Some Members of Which Have Traits of Both Na+- and H+-Motive Energetics

Citation
Ravin et al. (2023). International Journal of Molecular Sciences 24 (18)
Names (2)
Ca. Thiothrix putei Ca. Thiocaldithrix dubininis
Subjects
Catalysis Computer Science Applications General Medicine Inorganic Chemistry Molecular Biology Organic Chemistry Physical and Theoretical Chemistry Spectroscopy
Abstract
Two metagenome-assembled genomes (MAGs), GKL-01 and GKL-02, related to the family Thiotrichaceae have been assembled from the metagenome of bacterial mat obtained from a sulfide-rich thermal spring in the North Caucasus. Based on average amino acid identity (AAI) values and genome-based phylogeny, MAG GKL-01 represented a new genus within the Thiotrichaceae family. The GC content of the GKL-01 DNA (44%) differed significantly from that of other known members of the genus Thiothrix (50.1–55.6%). We proposed to assign GKL-01 to a new species and genus ‘Candidatus Thiocaldithrix dubininis’ gen. nov., sp. nov. GKL-01. The phylogenetic analysis and estimated distances between MAG GKL-02 and the genomes of the previously described species of the genus Thiothrix allowed assigning GKL-02 to a new species with the proposed name ‘Candidatus Thiothrix putei’ sp. nov. GKL-02 within the genus Thiothrix. Genome data first revealed the presence of both Na+-ATPases and H+-ATPases in several Thiothrix species. According to genomic analysis, bacteria GKL-01 and GKL-02 are metabolically versatile facultative aerobes capable of growing either chemolithoautotrophically or chemolithoheterotrophically in the presence of hydrogen sulfide and/or thiosulfate or chemoorganoheterotrophically.

Complete genome sequence of “ Candidatus Phytoplasma cynodontis” GY2015, a plant pathogen associated with Bermuda grass white leaf disease in Taiwan

Citation
Cho et al. (2023). Microbiology Resource Announcements
Names (1)
Ca. Phytoplasma cynodontis
Subjects
Genetics Immunology and Microbiology (miscellaneous) Molecular Biology
Abstract
ABSTRACT The complete genome sequence of “ Candidatus Phytoplasma cynodontis” strain GY2015, which consists of one 498,922-bp circular chromosome, is presented in this work. This uncultivated plant-pathogenic bacterium is associated with Bermuda grass white leaf disease in Taoyuan, Taiwan.