Longitudinal study of the interplay between the skin barrier and facial microbiome over 1 year.

Skin is a diverse ecosystem that provides a habitat for microorganisms. The skin condition and the skin microbiome interact each other under diverse environmental conditions. This study was conducted on 10 study participants for a one-year, from September 2020 to August 2021, to investigate the variability of skin microbiome and skin biophysical parameters [TEWL, hydration, and elasticity (R5)] according to season, and to understand the interplay between skin microbiome and skin characteristics. We identified that Cutibacterium, Corynebacterium, Staphyloccocus, unclassified genus within Neisseriaceae, and Streptococcus were major skin microbial taxa at the genus level, and fluctuated with the seasons. Cutibacterium was more abundant in winter, while Corynebacterium, Staphylococcus, and Streptococcus were more abundant in summer. Notably, Cutibacterium and skin barrier parameter, TEWL, exhibited a co-decreasing pattern from winter to summer and showed a significant association between Cutibacterium and TEWL. Furthermore, functional profiling using KEGG provided clues on the impact of Cutibacterium on the host skin barrier. This study enhances our understanding of the skin microbiome and its interplay with skin characteristics and highlights the importance of seasonal dynamics in shaping skin microbial composition.

Bacteria detection and species identification at the single-cell level using super-resolution fluorescence imaging and AI analysis.

The skin microbiome is thought to play a critical role in maintaining skin health and protecting against infection. While most microorganisms that live on the skin are harmless or even beneficial, some can cause skin infections or other health problems, emphasizing the importance of diagnosis of the composition and diversity of the skin flora. However, conventional diagnostic methods for evaluation of the skin microbiome are not sensitive enough to detect bacteria at low concentrations and suffer from poor specificity, thus limiting early diagnosis of bacterial infections. In this study, we developed novel approaches for bacterial species detection and identification methods with single-cell sensitivity using super-resolution microscopy and AI-based image analysis: a protein quantification-based method and an AI-based bacterial image analysis method. We demonstrate that these methods can differentiate between common bacterial members of the skin flora, including Staphylococcus aureus and Staphylococcus epidermidis, and different ribotypes of Cutibacterium acnes, both in purified bacterial samples and in scaling skin samples. The advantages of these methods, including the lack of time-consuming amplification or purification steps and single-cell level detection sensitivity, allow early diagnosis of bacterial infections, even from bacterial samples at extremely low concentrations, thus showing promise as a next-generation platform for microbiome detection as single-cell diagnostics.

Visualizing extracellular vesicle biogenesis in gram-positive bacteria using super-resolution microscopy.

BACKGROUND: Recently, bacterial extracellular vesicles (EVs) have been considered to play crucial roles in various biological processes and have great potential for developing cancer therapeutics and biomedicine. However, studies on bacterial EVs have mainly focused on outer membrane vesicles released from gram-negative bacteria since the outermost peptidoglycan layer in gram-positive bacteria is thought to preclude the release of EVs as a physical barrier. RESULTS: Here, we examined the ultrastructural organization of the EV produced by gram-positive bacteria using super-resolution stochastic optical reconstruction microscopy (STORM) at the nanoscale, which has not been resolved using conventional microscopy. Based on the super-resolution images of EVs, we propose three major mechanisms of EV biogenesis, i.e., membrane blebbing (mechanisms 1 and 2) or explosive cell lysis (mechanism 3), which are different from the mechanisms in gram-negative bacteria, despite some similarities. CONCLUSIONS: These findings highlight the significant role of cell wall degradation in regulating various mechanisms of EV biogenesis and call for a reassessment of previously unresolved EV biogenesis in gram-positive bacteria.

Effect of the skincare product on facial skin microbial structure and biophysical parameters: A pilot study.

Daily use of cosmetics is known to affect the skin microbiome. This study aimed to determine the bacterial community structure and skin biophysical parameters following the daily application of a skincare product on the face. Twenty-five Korean women, who used the same skincare product for four weeks participated in the study. During this period, skin hydration, texture, sebum content, and pH were measured, and skin swab samples were collected on the cheeks. The microbiota was analyzed using the MiSeq system. Through these experiments, bacterial diversity in facial skin increased and the microbial community changed after four weeks of skincare product application. The relative abundance of Cutibacterium and Staphylococcus increased, significant changes in specific bacterial modules of the skin microbial network were observed, and skin hydration and texture improved. It was suggested that daily use of skincare products could affect the microbial structure of facial skin as well as the biophysical properties of the facial skin. These findings expand our understanding of the role of skincare products on the skin environment.

Analysis of Microbiota Structure and Potential Functions Influencing Spoilage of Fresh Beef Meat.

Beef is one of the most consumed food worldwide, and it is prone to spoilage by bacteria. This risk could be caused by resident microbiota and their alterations in fresh beef meat during processing. However, scarce information is available regarding potential spoilage factors due to resident microbiota in fresh beef meat. In this study, we analyzed the microbiota composition and their predicted functions on fresh beef meat. A total of 120 beef meat samples (60 fresh ground and 60 non-ground beef samples) were collected from three different sites in South Korea on different months, and the microbiota were analyzed by the MiSeq system. Our results showed that although the microbiota in beef meat were varied among sampling site and months, the dominant phyla were the same with shared core bacteria. Notably, psychrotrophic genera, related to spoilage, were detected in all samples, and their prevalence increased significantly in July. These genera could inhibit the growth of other microbes with using glucose by fermentation. The results of this study extend our understanding of initial microbiota in fresh beef meat and potential functions influencing spoilage and can be useful to develop the preventive measures to reduce the spoilage of beef meat products.

Influence of pathogen contamination on beef microbiota under different storage temperatures.

Outbreaks of food poisoning due to the consumption of contaminated beef from fast-food chains are becoming more frequent. Pathogen contamination in beef influences its spoilage as well as the development of foodborne illness. Thus, the influence of pathogen contamination on beef microbiota should be analyzed to evaluate food safety. We analyzed the influence of pathogen contamination on the shift in microbiota and the interactions between the pathogen and indigenous microbes in beef stored under different conditions. Sixty beef samples were stored at 25 °C and 4 °C for 24 h, and the shifts in microbiota were analyzed using the MiSeq system. The influence of pathogen contamination on microbiota was analyzed by artificial contamination experiments with Escherichia coli FORC_044, which was isolated from the stool of a food poisoning patient in Korea. The bacterial amounts and the proportion of Escherichia were higher when the beef was stored at 25 °C. Artificially contaminated Escherichia positively correlated with the indigenous microbes such as Pseudomonas, Brochothrix, Staphylococcus, Rahnella, and Rhizobium as determined by co-occurrence network analyses. Carnobacterium, a potential spoilage microbe, was negatively correlated with other microbes. The predicted functions of altered microbiota showed that the pathways related to the process of spoilage including biosynthesis of acetic acid and lactic acid increased over time. The shift in pathways was more pronounced in contaminated beef stored at 25 °C. Carnobacterium, Lactobacillus, and Escherichia were the main genera contributing to the shift in the relative abundance of functional genes involved in the various spoilage pathways. Our results indicated that pathogen contamination could influence beef microbiota and mediate spoilage. This study extends our understanding of the beef microbiota and provides insights into the role of pathogen and storage conditions in meat spoilage.

Erratum: Kim, J.; et al. Characterization of mcr-1-Harboring Plasmids from Pan Drug-Resistant Escherichia coli Strains Isolated from Retail Raw Chicken in South Korea. Microorganisms 2019, 7, 344.

The authors would like to make the following corrections to the published paper [...].

Characterization of mcr-1-Harboring Plasmids from Pan Drug-Resistant Escherichia coli Strains Isolated from Retail Raw Chicken in South Korea.

A number of studies from different countries have characterized mcr-1-harboring plasmids isolated from food; however, nothing has been reported about it in South Korea. In this study, we report the characterization of mcr-1 plasmids from pan drug-resistant (PDR) Escherichia coli strains isolated from retail food in the country. Colistin-resistant E. coli strains were isolated from retail raw chicken, and PCR was carried out to detect the mcr-1 gene. Whole genome sequencing of the mcr-1-positive strains was performed for further characterization. The results of whole genome sequencing revealed that all mcr-1 plasmids belonged to the IncI2 type. In addition to the mcr-1 plasmids, all of the isolates also carried additional plasmids possessing multiple antibiotic resistance genes, and the PDR was mediated by resistant plasmids except for fluoroquinolone resistance resulting from mutations in gyrA and parC. Interestingly, the mcr-1 plasmids were transferred by conjugation to other pathogenic strains including enterohemorrhagic E. coli (EHEC), enterotoxigenic E. coli (ETEC), enteroaggregative E. coli (EAEC), Salmonella, and Klebsiella at the frequencies of 10-3-10-6, 10-2-10-5, 10-4-10-5, 10-4-10-6, and 10-5-10-6, respectively. The results showed that mcr-1 plasmids can be easily transmitted to pathogenic bacteria by conjugation.