Anti-Fibrosis Effect of Panax ginseng and Inula japonica Formula in Human Pulmonary Fibroblasts.

Panax ginseng Meyer and Inula japonica Thunb. are well established in traditional medicine and are known for their therapeutic properties in managing a range of ailments such as diabetes, asthma, and cancer. Although P. ginseng and I. japonica can alleviate pulmonary fibrosis (PF), the anti-fibrosis effect on PF by the combination of two herbal medicines remains unexplored. Therefore, this study explores this combined effect. In conditions that were not cytotoxic, MRC-5 cells underwent treatment using the formula combining P. ginseng and I. japonica (ISE081), followed by stimulation with transforming growth factor (TGF)-ß1, to explore the fibroblast-to-myofibroblast transition (FMT). After harvesting the cells, mRNA levels and protein expressions associated with inflammation and FMT-related markers were determined to evaluate the antiinflammation activities and antifibrosis effect of ISE081. Additionally, the anti-migratory effects of ISE081 were validated through a wound-healing assay. ISE081 remarkably reduced the mRNA levels of interleukin (IL)-6, IL-8, α-smooth muscle actin (SMA), and TGF-ß1 in MRC-5 cells and suppressed the α-SMA and fibronectin expressions, respectively. Furthermore, ISE081 inhibited Smad2/3 phosphorylation and wound migration of MRC-5 cells. Under the same conditions, comparing those of ISE081, P. ginseng did not affect the expression of α-SMA, fibronectin, and Smad2/3 phosphorylation, whereas I. japonica significantly inhibited them but with cytotoxicity. The results indicate that the synergistic application of P. ginseng and I. japonica enhances the anti-fibrotic properties in pulmonary fibroblasts and concurrently diminishes toxicity. Therefore, ISE081 has the potential as a prevention and treatment herbal medicine for PF.

Effects of Factors Influencing Scar Formation on the Scar Microbiome in Patients with Burns.

Skin microbiome dysbiosis has deleterious effects, and the factors influencing burn scar formation, which affects the scar microbiome composition, are unknown. Therefore, we investigated the effects of various factors influencing scar formation on the scar microbiome composition in patients with burns. We collected samples from the burn scar center and margin of 40 patients with burns, subgrouped by factors influencing scar formation. Scar microbiome composition-influencing factors were analyzed using univariate and multivariate analyses. Skin graft, hospitalization period, intensive care unit (ICU) admission, burn degree, sex, age, total body surface area burned (TBSA), time post-injury, transepidermal water loss, the erythrocyte sedimentation rate, and C-reactive protein levels were identified as factors influencing burn scar microbiome composition. Only TBSA and ICU admission were associated with significant differences in alpha diversity. Alpha diversity significantly decreased with an increase in TBSA and was significantly lower in patients admitted to the ICU than in those not admitted to the ICU. Furthermore, we identified microorganisms associated with various explanatory variables. Our cross-sectional systems biology study confirmed that various variables influence the scar microbiome composition in patients with burns, each of which is associated with various microorganisms. Therefore, these factors should be considered during the application of skin microbiota for burn scar management.

Does quorum quenching matter to microbial community dynamics in long-term membrane bioreactor operation?

Quorum quenching (QQ) has effectively prevented biofouling in membrane bioreactors (MBRs) employing isolated QQ bacterial strains. However, the influence of QQ on the microbial population still needs to be fully understood. This research aims to analyze the microbial population in MBRs over an extended period (>250 days) under different conditions, such as varying aeration intensities and doses of QQ bacteria, QQ media, and types of feed. Results show that no significant changes occurred in the structure and diversity of the microbial community in the mixed liquor and biofilm due to QQ treatment. Canonical correspondence analysis did reveal that the microbial communities were strongly influenced by feed types and phases. The microbial community composition varied between bacterial habitats (i.e., mixed liquor and biofilm), showing the two dominant phyla Proteobacteria and Bacteroidota in the former and Proteobacteria and Chloroflexi in the latter. The co-occurrence network analysis indicated that the biofilm (with 163 edges) in the MBR fed with real wastewater exhibited a more intricate network than the biofilm (with 53 edges) in the MBR fed with synthetic wastewater. With QQ, the biofilm exhibited more positive edges than negative ones. The phylogenetic investigation of communities showed that QQ barely affects functional gene-related quorum sensing (e.g., bacterial chemotaxis, motility proteins, and secretion) in mixed liquor but in biofilms at relatively large QQ doses (> 75 mg/L BH4). This research sheds light on the bacterial QQ's role in reducing MBR biofouling and provides crucial insights into its underlying mechanisms.

Sex differences in the skin microbiome of burn scars.

Sex differences are observed in various spectrums of skin diseases, and there are differences in wound healing rate. Herein, sex differences were identified for the newly healed skin microbiome of burn patients. Fifty-two skin samples (26 normal skin, 26 burn scars) were collected from 26 burn patients (12 male, 14 female) and microbiota analysis was performed. The correlation between skin microbiota and biomechanical properties of burn scars was also investigated. There were no significant differences in clinical characteristics between male and female patients. Considering the biomechanical properties of burn scars and normal skin around it performed before sample collection, the mean erythema level of men's normal skin was significantly higher than that of women, whereas the mean levels of melanin, transepidermal water loss and skin hydration showed no significant sex differences. The erythrocyte sedimentation rate was significantly higher in females than that in males. Alpha diversity showed no significant differences between normal skin and burn scars in the male group. However, the scar was significantly higher than that of normal skin in the female group. Microbial network analysis revealed that the male group had more complex microbial network than the female group. Additionally, in the male group, the edge density and clustering coefficient were higher in burn scars when compared to normal skin, than the female group. There were sex differences in the results of microbiome of normal skin and burn scars. Some of the altered microbiota have been correlated with the biomechanical properties of burn scars. In conclusion, sex difference in the burn scar microbiome was confirmed. These results suggest that burn treatment strategies should vary with sex.

Exploration of Potential Gut Microbiota-Derived Biomarkers to Predict the Success of Fecal Microbiota Transplantation in Ulcerative Colitis: A Prospective Cohort in Korea.

Background/Aims: Although fecal microbiota transplantation (FMT) has been proven as one of the promising treatments for patients with ulcerative colitis (UC), potential prognostic markers regarding the clinical outcomes of FMT remain elusive. Methods: We collected fecal samples of 10 participants undergoing FMT to treat UC and those from the corresponding donors. We categorized them into two groups: responders and nonresponders. Sequencing of the bacterial 16S rRNA gene was conducted on the samples to explore bacterial composition. Results: Analyzing the gut microbiota of patients who showed different outcomes in FMT presented a distinct microbial niche. Source tracking analysis showed the nonresponder group had a higher rate of preservation of donor microbiota, underscoring that engraftment degrees are not one of the major drivers for the success of FMT. At the phylum level, Bacteroidetes bacteria were significantly depleted (p<0.003), and three genera, including Enterococcus, Rothia, and Pediococcus, were enriched in the responder group before FMT (p=0.003, p=0.025, and p=0.048, respectively). Furthermore, we applied a machine learning algorithm to build a prediction model that might allow the prediction of FMT outcomes, which yielded an area under the receiver operating characteristic (ROC) curve of 0.844. Notably, the microbiota-based model was much better at predicting outcomes than the clinical features model (area under the ROC curve=0.531). Conclusions: This study is the first to suggest the significance of indigenous microbiota of recipients as a critical factor. The result highlights that bacterial composition should be evaluated before FMT to select suitable patients and achieve better efficiency.

Effect of a bioconverted product of Lotus corniculatus seed on the axillary microbiome and body odor.

The skin microbiome, especially the axillary microbiome, consists of odor-causing bacteria that decompose odorless sweat into malodor compounds, which contributes to the formation of body odor. Plant-derived products are a cheap source of bioactive compounds that are common ingredients in cosmetics. Microbial bioconversion of natural products is an ecofriendly and economical method for production of new or improved biologically active compounds. Therefore, in this study, we tested the potential of a Lactobacillus acidophilus KNU-02-mediated bioconverted product (BLC) of Lotus corniculatus seed to reduce axillary malodor and its effect on the associated axillary microbiota. A chemical profile analysis revealed that benzoic acid was the most abundant chemical compound in BLC, which increased following bioconversion. Moreover, BLC treatment was found to reduce the intensity of axillary malodor. We tested the axillary microbiome of 18 study participants, divided equally into BLC and placebo groups, and revealed through 16S rRNA gene sequencing that Staphylococcus, Corynebacterium, and Anaerococcus were the dominant taxa, and some of these taxa were significantly associated with axillary malodor. After one week of BLC treatment, the abundance of Corynebacterium and Anaerococcus, which are associated with well-known odor-related genes that produce volatile fatty acids, had significantly reduced. Likewise, the identified odor-related genes decreased after the application of BLC. BLC treatment enhanced the richness and network density of the axillary microbial community. The placebo group, on the other hand, showed no difference in the microbial richness, odor associated taxa, and predicted functional genes after a week. The results demonstrated that BLC has the potential to reduce the axillary malodor and the associated odor-causing bacteria, which makes BLC a viable deodorant material in cosmetic products.

Quorum Sensing System Affects the Plant Growth Promotion Traits of Serratia fonticola GS2.

Quorum sensing (QS) enables bacteria to organize gene expression programs, thereby coordinating collective behaviors. It involves the production, release, and population-wide detection of extracellular signaling molecules. The cellular processes regulated by QS in bacteria are diverse and may be used in mutualistic coordination or in response to changing environmental conditions. Here, we focused on the influence of the QS-dependent genes of our model bacterial strain Serratia fonticola GS2 on potential plant growth promoting (PGP) activities including indole-3-acetic acid (IAA) production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, and biofilm formation. Based on genomic and phenotypic experimental data we identified and investigated the function of QS genes in the genome of the model strain. Our gene deletion study confirmed the biological functionality of the QS auto-inducer (gloI) and receptor (gloR) on potential PGP activities of GS2. A transcriptomic approach was also undertaken to understand the role of QS genes in regulation of genes primarily involved in PGP activities (IAA, ACC deaminase activity, and biofilm formation). Both transcriptomic and phenotypic data revealed that the QS-deletion mutants had considerably less PGP activities, as compared to the wild type. In addition, in vivo plant experiments showed that plants treated with GS2 had significantly higher growth rates than plants treated with the QS-deletion mutants. Overall, our results showed how QS-dependent genes regulate the potential PGP activities of GS2. This information may be helpful in understanding the relationship between QS-dependent genes and the PGP activity of bacteria, which aid in the production of practical bio-fertilizers for plant growth promotion.

Ocean acidification alters bacterial communities on marine plastic debris.

The increasing quantity of plastic waste in the ocean is providing a growing and more widespread novel habitat for microbes. Plastics have taxonomically distinct microbial communities (termed the 'Plastisphere') and can raft these unique communities over great distances. In order to understand the Plastisphere properly it will be important to work out how major ocean changes (such as warming, acidification and deoxygenation) are shaping microbial communities on waste plastics in marine environments. Here, we show that common plastic drinking bottles rapidly become colonised by novel biofilm-forming bacterial communities, and that ocean acidification greatly influences the composition of plastic biofilm assemblages. We highlight the potential implications of this community shift in a coastal community exposed to enriched CO2 conditions.

Modulation of Gut Microbiota in Korean Navy Trainees following a Healthy Lifestyle Change.

Environmental factors can influence the composition of gut microbiota, but understanding the combined effect of lifestyle factors on adult gut microbiota is limited. Here, we investigated whether changes in the modifiable lifestyle factors, such as cigarette smoking, alcohol consumption, sleep duration, physical exercise, and body mass index affected the gut microbiota of Korean navy trainees. The navy trainees were instructed to stop smoking and alcohol consumption and follow a sleep schedule and physical exercise regime for eight weeks. For comparison, healthy Korean civilians, who had no significant change in lifestyles for eight weeks were included in this study. A total of 208 fecal samples were collected from navy trainees (n = 66) and civilians (n = 38) at baseline and week eight. Gut flora was assessed by sequencing the highly variable region of the 16S rRNA gene. The α-and ß -diversity of gut flora of both the test and control groups were not significantly changed after eight weeks. However, there was a significant difference among individuals. Smoking had a significant impact in altering α-diversity. Our study showed that a healthy lifestyle, particularly cessation of smoking, even in short periods, can affect the gut microbiome by enhancing the abundance of beneficial taxa and reducing that of harmful taxa.

In Situ Profiling of the Three Dominant Phyla Within the Human Gut Using TaqMan PCR for Pre-Hospital Diagnosis of Gut Dysbiosis.

A microbial imbalance called dysbiosis leads to inflammatory bowel disease (IBD), which can include ulcerative colitis (UC). Fecal microbiota transplantation (FMT), a novel therapy, has recently been successful in treating gut dysbiosis in UC patients. For the FMT technique to be successful, the gut microbiota of both the healthy donors and UC patients must be characterized. For decades, next-generation sequencing (NGS) has been used to analyze gut microbiota. Despite the popularity of NGS, the cost and time constraints make it difficult to use in emergency services and activities related to the periodic monitoring of microbiota profile alterations. Hence, in this study, we developed a multiplex TaqMan qPCR assay (MTq-PCR) with novel probes to simultaneously determine the relative proportions of the three dominant microbial phyla in the human gut: Bacteroidetes, Firmicutes, and Proteobacteria. The relative proportions of the three phyla in fecal samples of either healthy volunteers or UC patients were similar when assessed NGS and the MTq-PCR. Thus, our MTq-PCR assay could be a practical microbiota profiling alternative for diagnosing and monitoring gut dysbiosis in UC patients during emergency situations, and it could have a role in screening stool from potential FMT donors.

The first complete mitochondrial genome sequence of the korean endemic catfish Silurus microdorsalis (Actinopteri, Siluriformes, Siluridae).

The Silurus microdorsalis is known as Korean endemic slender catfish. Despite its value as a biological resource, there is no complete mitochondrial genome sequence. The complete mitochondrial genome consisted of 16,524 bp including 22 transfer RNA (tRNAs), 2 ribosomal RNA (rRNAs), 13 protein-coding genes (PCGs), and A + T rich region. The overall base composition of S. microdorsalis was A + T: 56.1%, C + G: 43.9%, apparently with slight AT bias. Phylogenetic relationship showed that S. microdorsalis was closely related to Silurus glanis.

Genome sequencing to develop Paenibacillus donghaensis strain JH8T (KCTC 13049T=LMG 23780T) as a microbial fertilizer and correlation to its plant growth-promoting phenotype.

Paenibacillus donghaensis JH8T (KCTC 13049T=LMG 23780T) is a Gram-positive, mesophilic, endospore-forming bacterium isolated from East Sea sediment at depth of 500m in Korea. The strain exhibited plant cell wall hydrolytic and plant growth promoting abilities. The complete genome of P. donghaensis strain JH8T contains 7602 protein-coding sequences and an average GC content of 49.7% in its chromosome (8.54Mbp). Genes encoding proteins related to the degradation of plant cell wall, nitrogen-fixation, phosphate solubilization, and synthesis of siderophore were existed in the P. donghaensis strain JH8T genome, indicating that this strain can be used as an eco-friendly microbial agent for increasing agricultural productivity.

The first complete mitochondrial genome sequence of the leucosiid crab Pyrhila pisum (Arthropoda, Decapoda, Leucosiidae).

Pyrhila pisum is known as leucosiid crab. So far, there is no study about whole mitochondrial genome in Leucosiidae family. Here, we report first the complete sequence of the mitochondrial genome from P. pisum, which is composed of 15,516 base pair encoding 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and A + T-rich region. The nucleotide composition of P. pisum was G + C: 25.5%, A + T: 74.5%, with a strong AT bias. In phylogenetic analysis using whole mitogenome, it was figured out that P. pisum was closely related to Sesarma neglectum but their family is different.