Project description:Background: Pantoea ananatis LMG 2665T synthesizes and utilizes acyl homoserine lactones (AHLs) for signaling. In this strain, short chain AHLs (C4 to C8) are produced by the EanI/R quorum sensing (QS) system that is involved in pathogenicity and biofilm formation. The complete set of genes regulated by the EanI/R system in P. ananatis LMG 2665T is still not fully known. In the present study, RNA-seq was used to analyze the transcriptome profiles controlled by the EanI/R system in this strain by comparing the wild type strain and its QS mutant 2665T ean∆I/R during lag and log stages. The RNA seq data was validated by RT qPCR. Results: The results showed that the EanI/R regulon in P. ananatis LMG 2665T comprised 144 genes, constituting 3.3% of the whole transcriptome under the experimental conditions in this study. The majority of genes regulated by the EanI/R system included genes for flagella assembly, bacterial chemotaxis, pyruvate metabolism, two component system, metabolic pathways, microbial metabolism and biosynthesis of secondary metabolites. Conclusions: This is the first study to identify the EanI/R QS regulon in P. ananatis LMG 2665T. Functional analysis of genes regulated the EanI/R system in LMG 2665T could help unveil genes that play a vital role in pathogenesis and survival strategies of this pathogen.
Project description:Nanosynbacter lyticus type strain TM7x was the first cultivated member of the broadly prevelent, but poorly udnerstood Candidate Phylum Radiation super-phylum. TM7x was shown to be an obligate epibiont with a host range including Schaalia odontolyticus strain XH001. The process of infecting a naive host goes through multiple phases, from an initial binding and interaction phase we call the initial encounter, to a rapid die off of infected host cells, killing phase, followed by regrowth of the host cells, regrowth phase, and finally a stable symbiosis between the species, stable symbiosis.To obtain a better understanding of the process by which these species establish a stable symbiosis, we measured the transcriptome using RNA sequencing across the course of infection. We sampled infected host, XH001/TM7x, during the initial interaction, regrowth, and after attaining stable symbiosis, as well as naive host controls grown under the same culture conditions.
Project description:ObjectiveRecent advancements in genome-based taxonomic classification propose the reclassification of certain Actinomyces species into new genera, including Schaalia. Schaalia odontolytica, the type species within this genus, is frequently found in the human oral cavity and has been associated with actinomycotic lesions. Currently, only two complete genomes of S. odontolytica strains have been reported. Recognizing the limited research on subspecies-level variation of S. odontolytica, we conducted genome sequencing of strain KHUD_008, isolated from a Korean periodontitis patient's subgingival biofilm. Additionally, we performed a comparative genome analysis using previously sequenced genomes of strain XH001 and strain FDAARGOS_732, both derived from the human oral cavity.Data descriptionPacific Biosciences Sequel II sequencing generated 15,904 and 76,557 raw sequencing sub-reads, which were integrated to assemble the de novo genome using the Microbial Genome Analysis pipeline in the Single-Molecule Real-Time Analysis. The genome assembly completeness, assessed by Benchmarking Universal Single-Copy Orthologs, reached 99.2%. The genome is 2,389,595 bp with a GC content of 66.37%, and contains 2,002 protein-coding genes, 9 rRNAs, and 48 tRNA. Comparative analysis with two previously sequenced strains revealed many strain-specific genes in KHUD_008, primarily related to envelope biogenesis and replication/recombination/repair processes.
Project description:Here, we report the draft, nearly complete genome sequence of the human oral actinobacterium Schaalia odontolytica strain ORNL0103, which was isolated in association with "Candidatus Saccharibacteria" HMT352 strain ORNL0105. The genome was sequenced using a combination of Pacific Biosciences and Illumina platforms and encodes 1,948 proteins and 60 RNAs.