Longitudinal Analysis of the Microbial Community on the Surface of Bloodstains Under Different Environmental Conditions in Areas with Minimal Human Interference.

The association between human metabolites and the environmental microbiome has primarily been investigated in relation to disease. In this study, the associations between environmental conditions and microbial communities on the surface of bloodstains were analyzed from a forensic science approach. The composition of microbial communities can be affected by numerous variables. After exposing bloodstains to two different environments with limited airflow and human interference, the microbial communities of the bloodstain surfaces were subjected to longitudinal analysis. Various microbes showed increasing or decreasing trends at the phylum and species level. The microbes identified in this study are usually found in soil, freshwater, and seawater and are known to exhibit unique properties, such as sporulation. Longitudinal variation in temperature and humidity were associated with various changes and correlations with the blood surface microbial community. Understanding these changes could introduce a new perspective to forensic science and could be used to develop a forensic tool used at crime scenes to analyze blood stains in more detail.

Increasing correlation between oral and gastric microbiota during gastric carcinogenesis.

BACKGROUND/AIMS: Recent research has increasingly focused on the role of the gastric microbiome in the development of gastric cancer. We aimed to investigate the changes in the microbiome during gastric carcinogenesis in structural and functional aspects, with a specific focus on the association between oral and gastric microbiomes. METHODS: We collected saliva, gastric juice, and gastric tissue samples from 141 patients at different stages of gastric carcinogenesis and processed them for microbiome analysis using 16S rRNA gene profiling. The alpha and beta diversities were analyzed, and the differences in microbiome composition and function profiles were analyzed among the groups, as well as the correlation between changes in the oral and gastric microbiomes during carcinogenesis. RESULTS: We observed significant differences in microbial diversity and composition between the disease and control groups, primarily in the gastric juice. Specific bacterial strains, including Schaalia odontolytica, Streptococcus cristatus, and Peptostreptococcus stomatis, showed a significant increase in abundance in the gastric juice in the low-grade dysplasia and gastric cancer groups. Notably, the correlation between the oral and gastric microbiota compositions, increased as the disease progressed. Predictive analysis of the metagenomic functional profiles revealed changes in functional pathways that may be associated with carcinogenesis (ABC transport and two-component systems). CONCLUSION: During gastric carcinogenesis, the abundance of oral commensals associated with cancer increased in the stomach. The similarity in microbial composition between the stomach and oral cavity also increased, implying a potential role of oral-gastric bacterial interactions in gastric cancer development.

Metabolic pathway prediction of core microbiome based on enterotype and orotype.

Introduction: Identification of key microbiome components has been suggested to help address the maintenance of oral and intestinal health in humans. The core microbiome is similar in all individuals, whereas the diverse microbiome varies across individuals, based on their unique lifestyles and phenotypic and genotypic determinants. In this study, we aimed to predict the metabolism of core microorganisms in the gut and oral environment based on enterotyping and orotyping. Materials and methods: Gut and oral samples were collected from 83 Korean women aged 50 years or older. The extracted DNA was subjected to next-generation sequencing analysis of 16S rRNA hypervariable regions V3-V4. Results: Gut bacteria were clustered into three enterotypes, while oral bacteria were clustered into three orotypes. Sixty-three of the core microbiome between the gut and oral population were correlated, and different metabolic pathways were predicted for each type. Eubacterium_g11, Actinomyces, Atopobium, and Enterococcus were significantly positively correlated between the gut and oral abundance. The four bacteria were classified as type 3 in orotype and type 2 in enterotype. Conclusion: Overall, the study suggested that collapsing the human body's multidimensional microbiome into a few categories may help characterize the microbiomes better and address health issues more deeply.

Next-Generation Sequencing Results Vary Between Cultured and Uncultured Microbes.

Next-generation sequencing (NGS) technology has led to innovations in environmental metagenomics and investigations involving humans and microbes. However, it is necessary to analyze the components that will affect analysis of the method upon processing a large amount of information. In particular, the processing method after sample collection affects the NGS results, and it is necessary to check for inaccurate results. Here, we show that the microbial communities obtained from fingertip samples differ from those obtained from fingertips remaining on mobile phones and desks, when cultured or not for 24 h. We also confirmed changes in microbial communities in fingertip samples from desks incubated for 2, 4, 8, 16, and 24 h. Samples of prints from mobile phones that are considerably vulnerable to external factors were not analyzed. Ratios of Firmicutes and Bacillus were, respectively, increased in cultures at the phylum and species levels. Collectively, we identified bacterial species that can aid in determining whether a sample has been cultured. In addition, although microbial communities differed depending on sample types, we confirmed changes after culture for 4 and 8 h. However, since this study is a sample limited to three types, it is necessary to analyze other types of samples in the same way and check whether they are applicable to all types. This strategy can verify the suitability of samples for deriving informative results from cultured or uncultured bacterial communities.

Microbial analyses of blood spot surfaces collected from a laboratory and the bathroom of a female single-person household under different environmental conditions.

Many people spend most of their time indoors, thereby exposing themselves to indoor environmental microbial communities that might interact with the human microbiota. These potential interactions have only been considered for personal identification; however, accumulating evidence indicates that these microbial interactions are potentially implicated with the identification of human interactions and location-specific factors including time and seasonal variations in the microbial community. To augment the potential of metagenomics-based forensic tools, we compared the composition of microbial communities in blood spot surfaces from healthy adults placed in different environments, such as in the bathroom of a female single-person household and on a laboratory, which were sampled across seasons and time points. The laboratory samples showed more changes in the bacterial community over time owing to the higher number of individuals using the laboratory, whereas the microbial communities in the bathroom samples remained relatively stable over time. Moreover, the two locations could be distinguished according to their specific bacterial community compositions. Variations were also observed related to changes in temperature and humidity, allowing for prediction of season-based microbial community. These findings offer a new perspective regarding the use of microbial community analysis in forensic science.

Association between Altered Blood Parameters and Gut Microbiota after Synbiotic Intake in Healthy, Elderly Korean Women.

Synbiotics intake can alter the composition of intestinal microbes beneficially. We aimed to detect the changes in the intestinal microbiomes of 37 healthy elderly Korean women after the intake of a synbiotic drink. This was a longitudinal study controlled with a temporal series, including a control period of 3 weeks before intake, synbiotic intake for 3 weeks, and a washout period of 3 weeks. Fecal microbiota composition was analyzed by sequencing the V3-V4 hypervariable regions of 16S rRNA. Physical fecal activity increased with improvement in fecal shape. Thirty intestinal bacterial taxa were observed to change only after the intake period. In particular, Ellagibacter appeared only after ingestion. In addition, the abundance of Terrisporobacter showed a positive correlation with C-reactive protein, triglyceride. Lachnospiraceae_uc, Eubacterium_g5, and Blautia had a positive correlation with creatinine, whereas PAC001100_g had a negative correlation with creatinine. Short-term (3 weeks) intake of symbiotic organisms changes the composition of the gut microbiota in healthy elderly Korean women.

OmpA of Klebsiella pneumoniae ATCC 13883 induces pyroptosis in HEp-2 cells, leading to cell-cycle arrest and apoptosis.

Klebsiella pneumoniae is an opportunistic pathogenic bacterium that commonly causes pneumonia in elderly people. OmpA, a toxin that is highly expressed in the outer membrane of the bacterium, is one of the primary factors implicated in the pulmonary pathogenesis of K. pneumoniae. To evaluate the associated pyroptosis mechanism of infection, the ompA gene was cloned, and the protein was expressed, extracted, and used to treat human larynx epithelial cells. We observed that OmpA induces reactive oxygen species production and cell-cycle arrest in the G2/M phase in host cells, leading to subsequent apoptosis. Moreover, OmpA was found to induce IL-1ß and IL-18 production in host cells, resulting in caspase-1 activation, which simultaneously stimulated pyroptosis, thus leading to the death of the host cells. We next sought to examine differential gene expression via RNA sequencing to better elucidate the mechanisms associated with these cellular changes, and found that genes associated with these pathways were more highly expressed in OmpA-treated cells than in K. pneumoniae-infected cells. Thus, cell-cycle arrest, apoptosis, and pyroptosis may serve as the primary defenses employed by host cells against OmpA. These results provide novel insights into the host defense against K. pneumoniae infection.

Comparison of Swabbing Solution Volume and gDNA Extraction Kits on DNA Recovery from Rigid Surface.

For bacteria sampling studies, various collection methods have been used to identify bacteria. To obtain accurate information about bacteria, high quality samples should be obtained. In order to obtain a high quality sample, a stable and large number of DNA copies must be collected. This study compared the efficiency of different methods of bacterial gDNA extraction and bacteria collection according to swabbing solution volumes and types. The efficiency of bacterial genomic DNA extraction was compared using a AccuPrep® Genomic DNA Extraction kit, a QIAamp® DNA Mini kit, and a MOBIO® DNeasy PowerSoil kit. The DNA Mini kit was shown to extract the highest amount of gDNA, and sub-experiments were conducted using this kit. Phosphate-buffered saline and phosphate-buffered saline with 0.1% Tween 20 were used as collection solutions of various volumes (0, 40, 50, 60, 70, 80, 90, 100, 110, and 120 µL) using cotton swabs. Bacteria collection efficiency was highest when 70 µL PBS was used. The target strains collected in this experiment were Staphylococcus aureus and Escherichia coli, and these were quantified using the number of colony-forming units, DNA concentrations, and the number of DNA copies. These results can be used to efficiently bacterial collection for experiments in various fields.

Development of a novel DsRed-NLS vector with a monopartite classical nuclear localization signal.

The nuclear localization signal (NLS) marks proteins for transport to the nucleus and is used in various applications in many fields. NLSs are used to achieve efficient and stable transport of biomolecules. Previously, commercial vectors used in NLS studies contained three iterations of the NLS sequence, but these sequences can affect experimental results and alter protein function. Here, we investigated a new vector using a single classical NLS sequence with a mutation in pDsRed2-C1-wt to reduce experimental artifacts. In the newly constructed pDsRed2-C1-1NLS vector, the NLS sequence is placed near the multiple cloning sites of pDsRed2-C1-wt, and the multiple cloning site region was designed to facilitate insertion of the desired gene by site-directed mutagenesis. Fluorescent protein expression in the nucleus can be visually confirmed. The results show that the fluorescent protein was bound to the transport protein. The constructed vector had a cell survival rate of 89-95% and a transfection efficiency of 39-56% when introduced into animal cells, which are similar to those of other NLS vectors. Additionally, the constructed NLS vector can be used to demonstrate complementary binding between target proteins, and that the target protein is transported by the NLS transport system. Especially, we show that the vector can be useful for experiments involving the S100A10 gene. In addition, the constructed vector is useful for studies of genes and proteins that show potential for gene therapy or drug delivery applications.

Changes in Gene Expression in Human Epithelial and Mast Cells in Response to Vesicles from Klebsiella pneumonia ATCC 13883.

We investigated alterations in the expression of immune-related genes in epithelial cells and mast cells treated with outer membrane vesicles (OMVs) derived from Klebsiella pneumoniae (KpOMVs). Previous studies have shown that OMVs contain substances that enable their delivery to host cells and induce an immune response. Our results indicate an increase in expression of genes such as IL-8, IL-1b, MIP-1α, HMOX1, HSPA1A, and IL-24 in epithelial cells and mast cells treated with KpOMVs. The pathogenicity of KpOMVs was confirmed by measuring the changes in the expression of these immune-related genes.

Influence of swabbing solution and swab type on DNA recovery from rigid environmental surfaces.

Determination of the metagenome has become an important component of forensic identification, which requires efficient environmental sampling techniques. Therefore, in this study, we compared the efficiency of sample collection using swabbing with cotton swabs and three types of medical swabs (S7, S22, S24) along with three different solutions: phosphate-buffered saline (PBS), 1% Tween 20 + 1% glycerol in PBS (TG), and GS commercial solution (Noble Bio, Hwaseong, Republic of Korea). Combinations of the three solutions with the three types of swabs were tested at different volumes (cotton swab, S7: 0, 30, 50, 70 µL; S22, S24: 0, 70, 100, 130 µL). Escherichia coli and Staphylococcus aureus were selected as representative environmental microbial samples, and the number of colony-forming units (CFUs), DNA concentration, and DNA copy numbers were compared across groups. The sampling process had a clear effect on the efficiency of extraction, which allowed for determination of a more efficient sample sampling method. In particular, cotton swabs showed 2-10-fold greater CFUs of both species than the medical swabs, and resulted in significantly greater amounts of extracted DNA. TG was found to be the most efficient solution for bacterial DNA extraction, with higher CFUs and DNA obtained than with the other three solutions at all volumes tested. This study highlights the need for a standardized sampling method that can be applied to all environmental samples, especially for microbial quantification, and provides valuable reference data for the efficient collection of environmental samples for metagenomic analyses in microbial-based forensic assessments.