Peach gummosis disease has been identified as a serious challenge in Korean agriculture and has developed to become a major cause of agricultural productivity losses. However, treatments for gummosis have not been systemically established and studies of the microbiome closely related to this plant disease are lacking. Therefore, we analyzed the bacterial and fungal communities in the bark and rhizosphere soil of healthy peach trees and those with gummosis. Through high-throughput sequencing, we obtained unprecedented insights into the bacterial and fungal dynamics of each group, including their diversity and taxonomic classification, as well as network analyses. We found that the presence of gummosis drives a significantly higher alpha diversity in the bark bacterial community. Peach gummosis bark mycobiomes included greater numbers of opportunistic pathogens such as Ascochyta, Botryosphaeria, Saccharomyces, Nectriaceae_NA, Trametes, and Valsaceae_NA. However, the microbiome also included bacteria beneficial to plant growth and the production of polysaccharides—namely, 1174-901-12, Catenibacterium, Cutibacterium, Friedmanniella, Methylobacterium-Methylorubrum, Pseudomonas, Rhodobacter, and Sphingomonas. Furthermore, we confirmed that gummosis induced a more complex structure in the bark microbiome network. We conclude that the findings of this study provide a valuable aid in profiling the overall peach tree microbial ecosystem, which can be utilized to develop precise biomarkers for the early diagnosis of gummosis.

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.

Owing to the emergence and improvement of high-throughput technology and the associated reduction in costs, next-generation sequencing (NGS) technology has made large-scale sampling and sequencing possible. With the large volume of data produced, the processing and downstream analysis of data are important for ensuring meaningful results and interpretation. Problems in data analysis may be encountered if researchers have little experience in using programming languages, especially if they are clinicians and beginners in the field. A strategy for solving this problem involves ensuring easy access to commercial software and tools. Here, we observed the current status of free web-based tools for microbiome analysis that can help users analyze and handle microbiome data effortlessly. We limited our search to freely available web-based tools and identified MicrobiomeAnalyst, Mian, gcMeta, VAMPS, and Microbiome Toolbox. We also highlighted the various analyses that each web tool offers, how users can analyze their data using each web tool, and noted some of their limitations. From the abovementioned list, gcMeta, VAMPS, and Microbiome Toolbox had several issues that made the analysis more difficult. Over time, as more data are generated and accessed, more users will analyze microbiome data. Thus, the availability of free and easily accessible web tools can enable the easy use and analysis of microbiome data, especially for those users with less experience in using command-line interfaces.

Odor emissions from animal manure present a significant environmental challenge in livestock farming, impacting air quality and farm sustainability. Traditional methods, such as chemical additives and manure treatment, can be costly, labor-intensive, and less eco-friendly. Therefore, this study investigated the effectiveness of microbial feed additives in reducing these odors. Conducted over three months in 2022 on a Korean beef cattle farm with 20 cattle, the experiment involved feeding a mixture of four microbial strains—Bacillus subtilis KNU-11, Lactobacillus acidophilus KNU-02, Lactobacillus casei KNU-12, and Saccharomyces cerevisiae KNU-06. Manure samples were collected from an experimental group (n = 9) and a control group (n = 11), with microbial community changes assessed through 16S ribosomal RNA gene amplicon sequencing. The results demonstrated significant reductions in specific odorous compounds in the experimental group compared to the control group: ammonia decreased by 64.1%, dimethyl sulfide by 81.3%, butyric acid by 84.6%, and isovaleric acid by 49.8%. Additionally, there was a notable shift in the microbiome, with an increase in the relative abundance of Ruminococcaceae and Prevotellaceae microbes associated with fiver degradation and fermentation, while the control group had higher levels of Bacteroidota and Spirochaetota, which are linked to pathogenicity. This study demonstrates that probiotics effectively alter intestinal microbiota to enhance microorganisms associated with odor mitigation, offering a promising and more sustainable approach to reducing odor emissions in livestock farming.

Livestock odors are unavoidable problems in modern industrial society. We foresaw a role for fermented organic wastes in controlling odorous gases. In this study, we applied fermented coffee grounds to the floor area of a dairy cow barn and assessed alterations in odor compounds and a microbial shift over a period of three weeks. The treatment dramatically reduced ten odor compounds (more than 50%), highlighting the utility of fermented coffee grounds as an excellent product to reduce odors derived from cow manure. By the end of the treatment, the microbial consortium showed increases in rare families whose prevalence and abundance before the treatment had been low. Network analysis manifested 23 bacterial families dominant in fermented coffee grounds, negatively connected with odorous compounds, indicating potential odor-reducing bacterial families. This study provides an insight into using bacteria at the community level as a treatment to solve an environmental issue; simultaneously, it suggests proper usage of organic wastes by recycling them as fermenters for beneficial bacteria.

Ex situ conservation is used to protect endangered wildlife. As captive and wild long-tailed gorals are known to be similar, individuals under ex situ conservation can be reintroduced into nature. However, there is no appropriate indicator to evaluate them. Here, we amplified the internal transcribed spacer 2 (ITS2) region and compared the gut ecological information (eco-information) of captive and wild long-tailed gorals. We validated the existing ITS86F and ITS4 universal primers using reference sequences of the National Center for Biotechnology Information (NCBI) and improved their matching rates. We compared the gut eco-information of captive and wild long-tailed gorals obtained through experiments using the improved primer pair and found that the gut ecological diversity of captive gorals was low. Based on this, we suggested that the gut eco-information can be used as an evaluation index before reintroducing captive long-tailed gorals. Furthermore, we identified four plant types from the gut eco-information of wild long-tailed gorals, which can be the additional food sources to enhance the reduced intestinal ecological diversity of the captive animals.