Characterization of ecotin homologs from Campylobacter rectus and Campylobacter showae

Uncovering the boundaries of Campylobacter species through large-scale phylogenetic and nucleotide identity analyses

Campylobacter species are typically helical shaped, Gram-negative, and non-spore-forming bacteria. Species in this genus include established foodborne and animal pathogens as well as emerging pathogens. The accumulation of genomic data from the Campylobacter genus has increased exponentially in recent years, accompanied by the discovery of putative new species. At present, the lack of a standardized species boundary complicates distinguishing established and novel species. We defined the Campylobacter genus core genome (500 loci) using publicly available Campylobacter complete genomes (n = 498) and constructed a core genome phylogeny using 2,193 publicly available Campylobacter genomes to examine inter-species diversity and species boundaries. Utilizing 8,440 Campylobacter genomes representing 33 species and 8 subspecies, we found species delineation based on an average nucleotide identity (ANI) cutoff of 94.2% is consistent with the core genome phylogeny. We identified 60 ANI genomic species that delineated Campylobacter species in concordance with previous comparative genetic studies. All pairwise ANI genomic species pairs had in silico DNA-DNA hybridization scores of less than 70%, supporting their delineation as separate species. We provide the tool Campylobacter Genomic Species typer (CampyGStyper) that assigns ANI genomic species to query genomes based on ANI similarities to medoid genomes from each ANI genomic species with an accuracy of 99.96%. The ANI genomic species definitions proposed here allow consistent species definition in the Campylobacter genus and will facilitate the detection of novel species in the future.IMPORTANCEIn recent years, Campylobacter has gained recognition as the leading cause of bacterial gastroenteritis worldwide, leading to a substantial rise in the collection of genomic data of the Campylobacter genus in public databases. Currently, a standardized Campylobacter species boundary at the genomic level is absent, leading to challenges in detecting emerging pathogens and defining putative novel species within this genus. We used a comprehensive representation of genomes of the Campylobacter genus to construct a core genome phylogenetic tree. Furthermore, we found an average nucleotide identity (ANI) of 94.2% as the optimal cutoff to define the Campylobacter species. Using this cutoff, we identified 60 ANI genomic species which provided a standardized species definition and nomenclature. Importantly, we have developed Campylobacter Genomic Species typer (CampyGStyper), which can robustly and accurately assign these ANI genomic species to Campylobacter genomes, thereby aiding pathogen surveillance and facilitating evolutionary and epidemiological studies of existing and emerging pathogens in the genus Campylobacter.

Ecotin: A versatile protease inhibitor of bacteria and eukaryotes

Serine protease inhibitors are a large family of proteins involved in important pathways and processes, such as inflammatory responses and blood clotting. Most are characterized by a precise mode of action, thereby targeting a narrow range of protease substrates. However, the serine-protease inhibitor ecotin is able to inhibit a broad range of serine proteases that display a wide range of specificities. This specificity is driven by special structural features which allow unique flexibility upon binding to targets. Although frequently observed in many human/animal-associated bacteria, ecotin homologs may also be found in plant-associated taxa and environmental species. The purpose of this review is to provide an update on the biological importance, role in host-microbe interactions, and evolutionary relationship between ecotin orthologs isolated from Eukaryotic and Prokaryotic species across the Tree of Life.

Uncovering the Oral Dysbiotic Microbiota as Masters of Neutrophil Responses in the Pathobiology of Periodontitis

Numerous bacterial species participate in the shift of the oral microbiome from beneficial to dysbiotic. The biggest challenge lying ahead of microbiologists, immunologists and dentists is the fact that the bacterial species act differently, although usually synergistically, on the host immune cells, including neutrophils, and on the surrounding tissues, making the investigation of single factors challenging. As biofilm is a complex community, the members interact with each other, which can be a key issue in future studies designed to develop effective treatments. To understand how a patient gets to the stage of the late-onset (previously termed chronic) periodontitis or develops other, in some cases life-threatening, diseases, it is crucial to identify the microbial composition of the biofilm and the mechanisms behind its pathogenicity. The members of the red complex (Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia) have long been associated as the cause of periodontitis and stayed in the focus of research. However, novel techniques, such as 16S clonal analysis, demonstrated that the oral microbiome diversity is greater than ever expected and it opened a new era in periodontal research. This review aims to summarize the current knowledge concerning bacterial participation beyond P. gingivalis and the red complex in periodontal inflammation mediated by neutrophils and to spread awareness about the associated diseases and pathological conditions.

Potential relationship between clinical symptoms and the root canal microbiomes of root filled teeth based on the next-generation sequencing

AIM

To determine the microorganism in root canal systems of root filled teeth with periapical disease and their relationship with clinical symptoms using next-generation sequencing.

METHODOLOGY

The roots of 10 extracted teeth were collected from 10 patients who presented with post-treatment apical periodontitis (PTAP; six with symptoms and four without symptoms). Each root was divided horizontally into two parts (apical and coronal segments) and cryo-pulverized. Microbial communities were detected using 16S rDNA hypervariable V3-V4 region. The diversity, principal coordinate analysis and linear discriminant analysis effect size were performed in the symptomatic and asymptomatic groups (apical and coronal parts respectively). A Mann-Whitney test and an analysis of similarities were applied for intergroup analysis, at a significance level of 5%.

RESULTS

A total of 23 phyla, 257 genera and 425 species were detected. Firmicutes was the most abundant phylum in all samples. Three phyla (Fusobacteria, Synergistetes and unidentified_Bacteria) and seven genera (Fusobacterium, Porphyromonas, Phocaeicola, Olsenella, Campylobacter, Tannerella and Fretibacterium) were significantly more abundant in the symptomatic patients (p < .05), whereas asymptomatic patients had more Sphingomonas. The species more significantly abundant in the symptomatic samples were Porphyromonas gingivalis, Phocaeicola abscessus, Campylobacter showae, Tannerella forsythia and Olsenella uli (p < .05).

CONCLUSIONS

A greater microbial diversity was observed in root filled teeth with PTAP compared to earlier reports. Several genera and species in root canal systems might be associated with clinical symptoms of PTAP.