Although emerging evidence revealed that the gut microbiome served as a tool and as biomarkers for predicting and detecting specific cancer or illness, it is yet unknown if vaginal microbiome-derived bacterial markers can be used as a predictive model to predict the severity of CIN. In this study, we sequenced V3 region of 16S rRNA gene on vaginal swab samples from 66 participants (24 CIN 1−, 42 CIN 2+ patients) and investigated the taxonomic composition. The vaginal microbial diversity was not significantly different between the CIN 1− and CIN 2+ groups. However, we observed Lactobacillus amylovorus dominant type (16.7%), which does not belong to conventional community state type (CST). Moreover, a minimal set of 33 bacterial species was identified to maximally differentiate CIN 2+ from CIN 1− in a random forest model, which can distinguish CIN 2+ from CIN 1− (area under the curve (AUC) = 0.952). Among the 33 bacterial species, Lactobacillus iners was selected as the most impactful predictor in our model. This finding suggests that the random forest model is able to predict the severity of CIN and vaginal microbiome may play a role as biomarker.

Background and Purpose: Fecal microbiota transplantation (FMT) has emerged for the therapeutic treatment of recurrent Clostridioides difficile infection (rCDI) with concurrent inflammatory bowel disease (IBD). As the first Iranian population cohort, we examined how gut microbiota and their functional profiles change in Iranian rCDI patients with underlying IBD before and after FMT. Patients and Methods: FMT was performed to eight IBD patients via colonoscopy. Profiles of gut microbiota from donors and recipients were investigated using 16S rRNA gene sequence analysis. Results: Patients experienced no IBD flare-ups or other adverse effects, and all recovered to full health. Moreover, all rCDI patients lacked the Bacteroidetes present in donor samples. After FMT, the proportion of Bacteroidetes increased until a normal range was achieved. More specifically, the relative abundance of Prevotella was found to increase significantly following FMT. Prevotella was also found to correlate negatively with inflammation metrics, suggesting that Prevotella may be a key factor for resolving CDI and IBD. Gut microbiota diversity was found to increase following FMT, while dysbiosis decreased. However, the similarity of microbial communities of host and recipients did not increase, and wide variation in the extent of donor stool engraftment indicated that the gut bacterial communities of recipients do not shift towards those of donors. Conclusion: FMT leads to significant alterations of the community structure of gut bacteria in rCDI patients with IBD. The change in relative abundance of Proteobacteria and bacterial diversity indicated that FMT promotes recovery from intestinal permeability and inflammation in rCDI patients. Moreover, strong negative correlation between Prevotella and inflammation index, and decreased dysbiosis index advocate that the improvement of CDI is possibly due to gut microbiome alteration. Collectively, our findings show that FMT would be a promising therapy to help reprogram the gut microbiome of Iranian rCDI patients with IBD.

Panax ginseng is a well-known medicinal plant that achieves strong resistance against plant pathogens while growing in the wild. Due to the high market demand for ginseng as a health food source, ginseng cultivation is prevalent in South Korea. However, continuous monocropping creates problems like irregular growth or vulnerability to crop diseases. Quorum sensing (QS) deals with the intracellular communication of bacteria and plays a role in dynamic changes in the soil microbiome. Here, we investigated how acyl-homoserine lactone (AHL) signaling molecules in QS (C8, C10, and C12) improve plant growth and induce shifts in the soil microbiome. To assess the effects, we recorded root and shoot growth of ginseng seedlings and checked the changes in the soil microbiome during different time points (0, 2, 4, and 8) after 8 weeks of growth. We observed that soils treated with N-decanoyl-L-homoserine lactone (C10) showed the most pronounced effects. Very striking was that C10 had the lowest alpha diversity. Using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2), we observed a high number of QS-related functional genes, with the highest count occurring in the untreated planted soil (W). Together with the known direct and beneficial effects of AHLs on plant development, AHLs treated mono-cropped soil showed trends in the microbiome community.

The population of the Korean fir, Abies koreana, is declining at an accelerating rate, and the average mortality rate in 2019 exceeded 36.43% on Mt. Hallasan in Jeju Island, Republic of Korea. Several prior studies have reported different reasons with various interpretations, indicating that additional data, such as data on microbial communities that promote plant growth and resistance to abiotic stresses, are required to understand the phenomenon further. This is the first investigation that documents the changes in the soil microbial and fungal community and soil physicochemical properties resulting from the death of the Korean fir. In our case, high throughput sequencing data have been provided for the soil microbiome and mycobiome of Korean fir trees, identifying the microbial composition differences before and after the decline in the health of Korean fir trees. The results showed that the soil fungal community was considerably shaped in response to the decline in the health of Korean fir rather than the soil bacterial community. The decline in health or the death of Korean fir trees contributed to the decrease in diversity and dominance of symbiotic fungi such as Russula, Sebacina, and Phenoliferia in the forest ecosystem. It also weakened the complexity and ecological competition of the fungal co-occurrence network. Structural equation modeling showed that the death of Korean fir was strongly associated with the concentrations of soil nutrients such as available phosphorus (P2O5) and potassium ion (K+) concentrations and low moisture content, adversely affecting the symbiotic relationship with ectomycorrhizal fungi. Our findings shed light on the critical taxa of mycobiome of live and dead A. koreana plants and their relationship with ecological edaphic factors, highlighting their potential role as biomarkers for the death of Korean fir.

Conceptualization to utilize microbial composition as a prediction tool has been widely applied in human cohorts, yet the potential capacity of soil microbiota as a diagnostic tool to predict plant phenotype remains unknown. Here, we collected 130 soil samples which are 54 healthy controls and 76 ginseng rusty roots (GRRs). Alpha diversities including Shannon, Simpson, Chao1, and phylogenetic diversity were significantly decreased in GRR (P < 0.05). Moreover, we identified 30 potential biomarkers. The optimized markers were obtained through fivefold cross-validation on a support vector machine and yielded a robust area under the curve of 0.856. Notably, evaluation of multi-index classification performance including accuracy, F1-score, and Kappa coefficient also showed robust discriminative capability (90.99%, 0.903, and 0.808). Taken together, our results suggest that the disease affects the microbial community and offers the potential ability of soil microbiota to identifying farms at the risk of GRR.