Conjugative type IV secretion systems enable bacterial antagonism that operates independently of plasmid transfer.

Bacterial cooperation and antagonism mediated by secretion systems are among the ways in which bacteria interact with one another. Here we report the discovery of an antagonistic property of a type IV secretion system (T4SS) sourced from a conjugative plasmid, RP4, using engineering approaches. We scrutinized the genetic determinants and suggested that this antagonistic activity is independent of molecular cargos, while we also elucidated the resistance genes. We further showed that a range of Gram-negative bacteria and a mixed bacterial population can be eliminated by this T4SS-dependent antagonism. Finally, we showed that such an antagonistic property is not limited to T4SS sourced from RP4, rather it can also be observed in a T4SS originated from another conjugative plasmid, namely R388. Our results are the first demonstration of conjugative T4SS-dependent antagonism between Gram-negative bacteria on the genetic level and provide the foundation for future mechanistic studies.

Mining the Metabolic Capacity of Clostridium sporogenes Aided by Machine Learning.

Anaerobes dominate the microbiota of the gastrointestinal (GI) tract, where a significant portion of small molecules can be degraded or modified. However, the enormous metabolic capacity of gut anaerobes remains largely elusive in contrast to aerobic bacteria, mainly due to the requirement of sophisticated laboratory settings. In this study, we employed an in silico machine learning platform, MoleculeX, to predict the metabolic capacity of a gut anaerobe, Clostridium sporogenes, against small molecules. Experiments revealed that among the top seven candidates predicted as unstable, six indeed exhibited instability in C. sporogenes culture. We further identified several metabolites resulting from the supplementation of everolimus in the bacterial culture for the first time. By utilizing bioinformatics and in vitro biochemical assays, we successfully identified an enzyme encoded in the genome of C. sporogenes responsible for everolimus transformation. Our framework thus can potentially facilitate future understanding of small molecules metabolism in the gut, further improve patient care through personalized medicine, and guide the development of new small molecule drugs and therapeutic approaches.

Specific residues and conformational plasticity define the substrate specificity of short-chain dehydrogenases/reductases.

Short-chain dehydrogenases/reductases (SDRs) are one of the most prevalent enzyme families distributed among the sequenced microorganisms. Despite the presence of a conserved catalytic tetrad and high structural similarity, these enzymes exhibit different substrate specificities. The insufficient knowledge regarding the amino acids underlying substrate specificity hinders the understanding of the SDRs' roles in diverse and significant biological processes. Here, we performed bioinformatic analysis, molecular modeling, and mutagenesis studies to identify the key residues that regulate the substrate specificities of two homologous microbial SDRs (i.e., DesE and KduD). Further, we investigated the impact of altering the physicochemical properties of these amino acids on enzyme activity. Interestingly, molecular dynamics simulations also suggest a critical role of enzyme conformational flexibility in substrate recognition and catalysis. Overall, our findings improve the understanding of microbial SDR substrate specificity and shed light on future rational design of more efficient and effective biocatalysts.

Identification of Gut Bacterial Enzymes for Keto-Reductive Metabolism of Xenobiotics.

Human gastrointestinal microbiota are known for the keto-reductive metabolism of small-molecule pharmaceuticals; however, the responsible enzymes remain poorly understood. Through in vitro biochemical assays, we report the identification of enzymes encoded in the genome of Clostridium bolteae that can reduce the ketone groups of nabumetone, hydrocortisone, and tacrolimus. The homologues to a newly identified enzyme (i.e., DesE) are potentially widely distributed in the gut microbiome. The selected enzymes display different levels of activities against additional chemicals such as two dietary compounds (i.e., raspberry ketone and zingerone), chemotherapeutic drug doxorubicin, and its aglycone metabolite doxorubicinone. Thus, our results expand the repertoire of enzymes that can reduce the ketone groups in small molecules and could serve as the basis for future personalized medicine approaches.

Screwdriver aspiration during implant surgery: case report and literature review / 口腔疾病防治

Objective @#To discuss and summarize the preventive measures and treatment methods for aspiration/ingestion during dental procedures.@*Methods @# One case of aspiration during an implant operation was reported, and the literature on aspiration/ingestion during oral procedures was reviewed.@*Results@#An implant screwdriver accidentally slipped into the mouth of the patient during implant surgery. The patient experienced no obvious discomfort except a few coughs. The surgeon and assistant paused the procedure immediately to search for the screwdriver, but it was not found. The patient declared that there was no special abnormality, such as breathing disorder or chest distress, so we considered that the foreign body was ingestion. After the implant surgery was completed, no foreign body was found in the stomach via gastroscopy. Chest X-ray and CT showed a dense metal shadow in the lower lobe of the left lung. Under local anesthesia, bronchoscopy and biopsy forceps were used by respiratory physicians to clip out the foreign body. After removal of the foreign body, the patient had no obvious discomfort but a slight cough. Cephalexin and metronidazole were given for three days to prevent infection. Three days later, the patient had no complaints of respiratory discomfort. After reviewing the literature, we found that the operation should be paused immediately after aspiration/ingestion occurs during dental procedures and that the dental chair should be laid down to prevent the foreign body from descending deeper, which may increase the difficulty of removal and cause gastrointestinal and respiratory tract injury. The position of the foreign body should be determined by imaging examination, and the corresponding means to remove the foreign body should be performed.@*Conclusion @# Patients may have no obvious symptoms after aspiration/ingestion during dental procedures, and the foreign body can be removed after imaging examination.