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Keystone species are thought to play a critical role in determining the structure and function of microbial communities. As they are important candidates for microbiome-targeted interventions, the identification and characterization of keystones is a pressing research goal. Both empirical as well as computational approaches to identify keystones have been proposed, and in particular correlation network analysis is frequently utilized to interrogate sequencing-based microbiome data. Here, we apply an established method for identifying putative keystone taxa in correlation networks. We develop a robust workflow for network construction and systematically evaluate the effects of taxonomic resolution on network properties and the identification of keystone taxa. We are able to identify correlation network keystone species and genera, but could not detect taxa with high keystone potential at lower taxonomic resolution. Based on the correlation patterns observed, we hypothesize that the identified putative keystone taxa have a stabilizing effect that is exerted on correlated taxa. Correlation network analysis further revealed subcommunities present in the dataset that are remarkably similar to previously described patterns. The interrogation of available metatranscriptomes also revealed distinct transcriptional states present in all putative keystone taxa. These results suggest that keystone taxa may have stabilizing properties in a subset of community members rather than global effects. The work presented here contributes to the understanding of correlation network keystone taxa and sheds light on their potential ecological significance., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2024 Bauchinger, Seki and Berry.)

Veillonella atypica is a nonmotile, nonsporulating anaerobic bacteria commonly found in various human biofilms. V. atypica FB0054 was isolated from the gastrointestinal tract of marathon runners, who have increased amounts of this species after athletic events. Interestingly, the consumption of this strain by rodents has been shown to increase their treadmill endurance, leading to the hypothesis that consumption of this species may improve athletic performance in humans as well. Further evaluation, in humans, of the usefulness of this strain should be preceded by safety studies. Therefore, the genotoxic and subchronic toxicological potential was evaluated as a contribution to this effort. Genotoxicity investigation was performed using the in vivo comet assay and in vivo mammalian micronucleus assay due to the anaerobic characteristic of the strain. A 90-day, repeated-dose oral toxicity study was performed in rats up to 2200 mg/kg bw/d to investigate general toxicity and identify any target organs. Mitsuoka buffer, a solution shown to preserve the viability of anaerobic bacteria, was used as the vehicle. All three studies revealed no toxicological effects from exposure to FB0054 was isolated from the gastrointestinal tract of marathon runners, who have increased amounts of this species after athletic events. Interestingly, the consumption of this strain by rodents has been shown to increase their treadmill endurance, leading to the hypothesis that consumption of this species may improve athletic performance in humans as well. Further evaluation, in humans, of the usefulness of this strain should be preceded by safety studies. Therefore, the genotoxic and subchronic toxicological potential was evaluated as a contribution to this effort. Genotoxicity investigation was performed using the in vivo comet assay and in vivo mammalian micronucleus assay due to the anaerobic characteristic of the strain. A 90-day, repeated-dose oral toxicity study was performed in rats up to 2200 mg/kg bw/d to investigate general toxicity and identify any target organs. Mitsuoka buffer, a solution shown to preserve the viability of anaerobic bacteria, was used as the vehicle. All three studies revealed no toxicological effects from exposure to FB0054 at the highest doses tested., (© 2022 John Wiley & Sons Ltd.)

Veillonella atypica is a bacterium that is present in the gut and the oral cavity of mammals and plays diverse roles in different niches. A recent study demonstrated that Veillonella is highly associated with marathon running and approved that V. atypica gavage improves treadmill run time in mice, revealing that V. atypica has a high biotechnological potential in improving athlete performance. However, a comprehensive analysis of the genetic diversity, function traits, and genome editing method of V. atypica remains elusive. In the present study, we conducted a systemically comparative analysis of the genetic datasets of nine V. atypica strains. The pan-genome of V. atypica consisted of 2,065 homologous clusters and exhibited an open pan-genome structure. A phylogenetic analysis of V. atypica with two different categories revealed that V. atypica OK5 was the most distant from the other eight V. atypica strains. A total of 43 orthologous genes were identified as CAZyme genes and grouped into 23 CAZyme families. The CAZyme components derived from accessory clusters contributed to the differences in the ability of the nine V. atypica strains to utilize carbohydrates. An integrated analysis of the metabolic pathways of V. atypica suggested that V. atypica strains harbored vancomycin resistance and were involved in several biosynthesis pathways of secondary metabolites. The V. atypica strains harbored four main Cas proteins, namely, CAS-Type IIIA, CAS-Type IIA, CAS-Type IIC, and CAS-Type IIID. This pilot study provides an in-depth understanding of and a fundamental knowledge about the biology of V. atypica that allow the possibility to increase the biotechnological potential of this bacterium., (Copyright © 2020 Han, Liu, Chen, Wang and Zhang.)

Aims and Objective: Oral biofilms in denture wearers are populated with a large number of bacteria, a few of which have been associated with medical conditions such as sepsis and infective endocarditis (IE). The present study was designed to investigate the relative presence of pathogenic bacteria in biofilms of denture wearers specifically those that are associated with IE., Methods: Biofilm samples from 88 denture wearers were collected and processed to extract total genomic DNA. Eight of these samples were subjected to 16S rRNA gene sequencing analysis to first identify the general bacterial occurrence pattern. This was followed by species-specific quantitative polymerase chain reaction (qPCR) on entire batch of 88 samples to quantify the relative copy numbers of IE-associated pathogens., Results: 16S rRNA gene analysis of eight biofilm samples identified bacteria from Firmicutes , Actinobacteria , Proteobacteria, Bacteroidetes , and Fusobacteria species. Interestingly, Streptococcus mutans , Veillonella atypica , and Granulicatella adiacens from Firmicutes , all known to be associated with early-onset sepsis and IE was present in five of eight biofilm samples. The other three samples carried bacteria from genus Proteobacteria with Neisseria flava and Neisseria mucosa , which are known to be commensals, as dominant species. Species-specific qPCR of S. mutans V. atypica , and G. adiacens on 88 biofilm DNA samples identified the presence of S. mutans in 83%, V. atypica in 79%, and G. adiacens in 76% of samples., Conclusion: The findings from the present study demonstrate co-occurrence of S. mutans , V. atypica , and G. adiacens in a majority of denture wearers, which is clinically significant as elderly patients with compromised immune system are more prone to develop IE. To the best of our knowledge, the co-occurrence of S. mutans , V. atypica , and G. adiacens is being reported for the first time in biofilms of denture wearers., Competing Interests: There are no conflicts of interest.