[Objective] To study the inhibitory effect and mechanism of an antimicrobial peptide (A2M3) derived from alpha-2-macroglobulin identified in the human nasal cavity againstStaphylococcus aureus. [Methods] The mass spectrometry results of the human nasal liquid were analyzed, on the basis of which bioinformatic tools were used for the screening of potential antimicrobial peptides. The minimum inhibitory concentration (MIC) and time-kill curve of A2M3 againstS.aureus were determined by the microdilution method and plate colony counting method. Then, transmission electron microscopy, PI uptake assay, flow cytometry, and determination of nucleic acid protein leakage were employed to study the effects of A2M3 on the membrane integrity and permeability ofS.aureus. Finally, the effect of A2M3 on the genomic DNA ofS.aureus was investigated by the gel retardation assay and fluorescence spectroscopy. [Results] A2M3 showed an MIC of 125.0 µg/mL againstS.aureus and killed the bacteria completely within 3 h. A2M3 increased the cell membrane permeability to penetrate intoS.aureus cells, leading to leakage of nucleic acids and proteins as well as insertion into DNA base pairs to interfere with the gene function, resulting in the death of the cells. [Conclusion] The inhibitory mechanism of A2M3 againstS.aureus involves multiple targets. The antimicrobial peptide alters the permeability of the bacterial cell membrane and affects the gene function, thus exerting the inhibitory activity. The findings reveal that antimicrobial peptides could be screened and isolated from human body fluids for potential application.

[Objective] Colony extraction and counting is essential in agriculture, food, and health industries. Currently, most of the available algorithms for automatic counting of colonies use colony culture dishes and has poor applicability to colony count plates. In addition, the current technologies have good performance in conventional segmentation of adherent objects, while their accuracy remains to be improved for the segmentation and counting of adherent colonies due to the unique morphological characteristics of colonies. [Methods] To solve such problems, we proposed a colony segmentation and counting algorithm based on target color base and gradient direction matching. Firstly, the color feature of the colony in the image was used as a base to convert the image into a base space to enhance the difference between the colony and the background. Secondly, the gradient magnitude feature of the colony image was used to filter the gradient direction, and then the matching was performed through the gradient direction, thereby segmenting the adherent colonies. Finally, non-maximum suppression was employed to screen and count the colonies. [Results] Through experiments, the counting accuracy of the algorithm in this study reaches 98.00%, demonstrating its capability to meet practical requirements. [Conclusion] In the context of targeted segmentation and counting of colonies, the algorithm studied in this paper not only exhibits high counting accuracy but also demonstrates good robustness. This algorithm had not only high counting accuracy but also good robustness, producing excellent results in the colony segmentation and counting of colony count plates from different manufacturers. However, it showed decreased counting accuracy in the detection and segmentation of large-area targets. Therefore, this algorithm is suitable for the detection and segmentation of small targets such as colonies.

Mycobacterium tuberculosis (Mtb), the pathogen of tuberculosis (TB), threatens the health of millions of people worldwide. The pattern recognition receptors (PRRs) including DNA and RNA sensors on immune cells recognize the invaded Mtb to activate the innate immune system and induce the production of interferon-beta (IFN-β). IFN-β is a major effector cytokine in innate antiviral response, while its role in the host response to Mtb infection remains controversial. IFN-β induced by Mtb can promote bacterial growth and improve the bacterial survival in the host. However, IFN-β treatment before Mtb infection can protect the host from bacterial infection. Focusing on the PRR signaling pathways that can recognize Mtb and mediate the IFN-β production, this review expounds the role of IFN-β in mediating the regulation of immune function by Mtb, especially the mutual inhibitory effect between IFN-β and IL-1β, aiming to reveal the pathogenic mechanism of Mtb and facilitate future research and development of anti-TB drugs.

The prediction of bacteriophage host ranges is of great significance for the basic research and clinical application of bacteriophages. The conventional biological experimental methods are limited by the poor culturability of bacteriophages and strict cultivation conditions. The availability of massive genome or metagenome sequencing data provides the sequence signature of bacteriophages and bacteria. Therefore, intelligent computing serves as a feasible way to predict bacteriophage host ranges. This paper systematically reviews the studies about intelligent computing-based prediction of bacteriophage host ranges. Starting from the process of bacteriophage infecting bacteria, we describe the feature source and biological rationality of prediction models, analyze the typical intelligent models and their prediction principles, and list all the reference datasets, real-world datasets, and evaluation indicators. The review aims to improve the understanding on the mechanism of bacteriophages in invading bacterial hosts and promote the usage of bacteriophages as antibiotic substitutes in biological therapy.

Outer membrane vesicles (OMVs) are spherical structures secreted by Gram-negative bacteria, with diameters of 10–250 nm. OMVs have gradually been recognized as a novel secretion system capable of transporting various substances such as lipids, proteins, nucleic acids, cytotoxins, and signaling molecules. OMVs possess a range of biological functions, including inter-bacterial communication, transmission of pathogenic factors, resistance to adverse external environments, and modulation of immune responses. Due to the distinct biological characteristics of OMVs, the antibiotic resistance transmission mediated by bacterial OMVs, as well as the potential applications of OMVs, has garnered increasing attention in recent years. This paper reviews the origins and substance delivery functions of bacterial OMVs and the protective effects of OMVs on the bacteria exposed to antibiotics and in adverse environments. Furthermore, this paper summarizes the potential applications of bacterial OMVs in the treatment of diseases, aiming to enrich the knowledge about bacterial OMVs.

Guanosine tetraphosphate (ppGpp)/guanosine pentaphosphate (pppGpp) is a signaling molecule in the bacterial stringent response, whose synthesis and hydrolysis are controlled by the synthesis and hydrolysis activities of proteins in the RelA/SpoT homologue (RSH) family. The (p)ppGpp-mediated stringent response enhanced bacterial adaptation to nutrient deprivation and antibiotic resistance. In recent years, (p)ppGpp has been found to associate with bacterial growth, cell division, and antibiotic synthesis, which was an important global regulator in the bacteria. (p)ppGpp has many target sites in the cell, which allow it to regulate DNA replication, transcription, cell cycle, ribosome biosynthesis, and the expression of antibiotic synthesis gene clusters. However, how (p)ppGpp controls transcription and other metabolic processes depends on the bacterial species, and (p)ppGpp regulates the same processes in different bacteria species through different mechanisms. Therefore, this manuscript reviewed the types of (p)ppGpp synthetic and hydrolytic enzymes, the mechanisms of (p)ppGpp regulation on microbial metabolism and the cell cycle, as well as the regulation mechanisms of antibiotic synthesis and tolerance, which lays the foundation for bacterial resistance and cell physiology researches.

The type VI secretion system (T6SS) as a dynamic multi-protein complex has a clear division of labor among its components, transporting effector proteins to compete for bacterial growth. Studies have shown that T6SS mediates the competitiveness ofAcinetobacter baumannii in the microbial community and affects the drug resistance evolution and invasion in the host. Particularly, the valine-glycine repeat protein G (VgrG), the proline-alanine-alanine-arginine (PAAR), the hemolysin-coregulated protein (Hcp), and the effector-immunity (E-I) pair play a key role. Although T6SS has been extensively studied, there are few articles about its clinical application prospects, as this poses challenges to the identification, characterization, transport mechanism revealing, and other basic research on their functional proteins. We reviewed the research progress in the distribution, functional protein characteristics, and transport mechanism of T6SS inA.baumannii and provided evidence for its application based on the application cases of T6SS. This review aims to promote the research on the genes and functions of T6SS inA.baumannii and provide new targets and ideas for developing new anti-infective vaccines, screening suitable inhibitors, and producing engineered drug delivery tools.

Terpenoids, a group of natural products possessing diverse chemical structures and biological activities, have been widely used in the production of food additives, medicines, and cosmetics. Terpenoids are mainly produced by plants. With the rapid development of synthetic biology, heterologous production of terpenoids by engineered microbial strains is more economical and environmentally friendly compared with the conventional methods of extraction from plants and chemical synthesis. The catalytic activities of terpene synthases and the structural specificity of their products are pivotal for the heterologous biosynthesis of terpenoids. Directed evolution and rational design can be adopted to optimize the catalytic properties and product profile of target terpene synthases. However, this requires a feasible high-throughput method to screen mutant libraries. In recent years, various high-throughput screening methods have been developed to boost the sensitivity and efficiency in screening terpene synthases. We review recently established high-throughput screening methods for terpene synthases and briefly outline the principles and advantages and disadvantages of each method. Eventually, we envision the future directions of the application of high-throughput screening in the engineering of terpene synthases.

Using genomic data and bioinformatics methods has become an important approach to rapidly identify the genes and predict the phenotypes of bacterial antibiotic resistance. Dozens of antibiotic resistance databases have been established, providing information and auxiliary tools for the identification and prediction of bacterial antibiotic resistance. As the bacterial genome data and antibiotic resistance phenotype data are increasing, the correlation between them can be establishedvia big data and machine learning. Therefore, establishing efficient models predicting antibiotic resistance phenotypes has become a research hot topic. Focusing on the gene identification and phenotype prediction of bacterial antibiotic resistance, this review discusses the related databases, the theories and methods, the machine learning algorithms, and the prediction models. In addition, we made an outlook on the future prospects in this field, aiming to provide new ideas for the related studies.

[Objective] To explore the roles of phytochrome genesPaPhy1 andPaPhy2 in the sexual reproduction and asexual development ofPodospora anserina and decipher the regulatory mechanisms.[Methods] The homologous recombination method was employed to knock out the two phytochrome genes, and the resulting mutants, ΔPaPhy1 and ΔPaPhy2, were obtained. A double mutant, ΔPaPhy1ΔPaPhy2, was constructedvia genetic cross. We compared the sexual production, asexual development, growth rate, and reactive oxygen metabolism between the mutants and wild-type strains under different light conditions to reveal the main roles of the phytochrome genes inP.anserina.[Results] Blue light and white light induced the formation ofP.anserina ascospore shells. ΔPaPhy produced fewer ascospores in the light and showed prolonged life cycle.[Conclusion] Phytochrome genes are associated with the sexual reproduction ofP.anserina. The aging delay of ΔPaPhy is related to reactive oxygen metabolism. The results of this study provide new ideas for further exploring the mechanism of light in regulating the reproduction of filamentous fungi as well as anti-aging studies.