Journal of Microbiology

Research article

A retrospective metagenomic analysis of fecal microbiota transplantation donors from five countries: Safety considerations for donor screening and core microbiome profiles of qualified donors: Sha-Sha Li, Yun-Hui Niu, Hong-Jing Yu; J. Microbiol. 2026;64(9):e2604010. Published online September 30, 2026; DOI: https://doi.org/10.71150/jm.2604010

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Abstract PDF Supplementary Material: Fecal microbiota transplantation (FMT) has been successfully applied on clinical aspects, but its clinical outcomes remain unpredictable due to inconsistent donor screening protocols across hospitals, institutions, and countries. Hence, a retrospective analysis of metagenomic data from published studies on FMT donors via a unified bioinformatics workflow might contribute to the understanding of the safety considerations for donor screening and the fecal microbial profiles of qualified donors. In this study, we reanalyzed metagenomic data of 475 screened donor fecal samples from 24 studies spanning China, the USA, Canada, New Zealand, and the Netherlands. The genomic safety risks were evaluated by profiling antibiotic resistance genes (ARGs) and virulence factors (VFs), the results of which showed that no major toxin-associated virulence genes, such as Shiga toxin, Shiga-like toxin, or botulinum neurotoxin (BoNTs) genes harbored in the detected Escherichia coli, Clostridium butyricum, and Streptococcus pneumoniae, but several high-risk ARGs remained insufficiently addressed. The distribution of ARG-harboring bacteria in eligible FMT donors was country-specific. The alpha-diversity and microbial community structure were comparable between donor fecal samples from China and the USA. Interestingly, the core microbiome in fecal samples from Canada, the Netherlands, and New Zealand formed a single guild, while that from China and the USA formed two guilds, with predominantly positive intra-guild and negative inter-guild correlations, indicating that the co-abundance patterns of the core microbiome were conserved among certain countries. Furthermore, an exploratory retrospective classifier was developed based on core microbiome profiles to distinguish eligible FMT donors from general healthy individuals. These results provide evidence for integrating metagenomic sequencing into future FMT donor screening strategies.

Resource

SimpleMicrobiome: An integrated web-based platform for streamlined microbiome data analysis and visualization: Seong-In Na, Juhee Kim, So-Yeon Kim, Jin Park, Yong-Joon Cho; J. Microbiol. 2026;64(9):e2606011. Published online September 18, 2026; DOI: https://doi.org/10.71150/jm.2606011

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Abstract PDF Supplementary Material: Microbiome studies require multiple analytical steps after initial sequence processing. These steps commonly include data harmonization, preprocessing, taxonomic profiling, diversity analysis, differential abundance testing, predictive modeling, network inference, and preparation of publication-ready outputs. Although robust packages are available for many of these tasks, routine use often depends on command-line workflows, repeated data reformatting, and method-specific scripting. These requirements can limit accessibility for experimental researchers and complicate consistent analysis across interdisciplinary teams. We developed SimpleMicrobiome, a web-based R Shiny platform that integrates established microbiome analysis methods into a single interactive downstream workflow. The application accepts standard abundance, taxonomy, and metadata tables, supports interactive preprocessing and sample filtering, and provides modules for taxa profile visualization, alpha and beta diversity analysis, ANCOM-BC2 and MaAsLin2 differential abundance testing, Random Forest modeling with SHAP-based interpretation, microbial association network inference using SparCC and SPIEC-EASI through NetCoMi, correlation heatmaps, and dbRDA/CAP-style association biplots. The platform is implemented as a modular Shiny application so that preprocessing choices are propagated across downstream analyses, results can be exported as figures and tables, and the same application can be run through the public server, source-code installation, or a Docker image.
SimpleMicrobiome consolidates major downstream microbiome analysis tasks in an accessible browser-based environment while retaining links to established analytical frameworks. The platform may reduce technical barriers for non-programming users, improve consistency across exploratory and reporting-oriented analyses, and support collaborative microbiome research. The public application is available at https://simplemicrobiome.mglab.org, the source code is available at https://github.com/yjcho2252/SimpleMicrobiome, and a Docker image for local deployment is available at https://hub.docker.com/r/mglab2252/simplemicrobiome.

Research article

Adipose tissue-derived stem cell exosomes enhance skin barrier function and show exploratory associations with the skin mycobiome in aging skin: Bo-Yun Choi, Hye-Jin Kim, Myeong Jae Kim, Yoon Jin Roh, Ji Yeon Hong, Kui Young Park, Woo Jun Sul; J. Microbiol. 2026;64(6):e2603020. Published online June 30, 2026; DOI: https://doi.org/10.71150/jm.2603020

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Abstract PDF Supplementary Material: Skin aging increases transepidermal water loss (TEWL), reduces elasticity, and perturbs the skin microbiome. Adipose tissue-derived stem cell exosomes (ASCE) show regenerative potential; however, their clinical effects on skin physiology and microbiome remain unclear. We conducted a split-face, randomized controlled trial in 16 adults aged ≥ 40 years with visible facial aging. One facial side received ultrasound-assisted transdermal delivery of a human ASCE-containing solution (HACS), whereas the other side received normal saline, at two-week intervals for three sessions. Biophysical outcomes (TEWL, stratum corneum hydration, and elasticity parameters R2/R5/R7) were assessed at baseline and week 2, 4, and 8. Wrinkles, pigmentation, and sebum levels were quantified using Mark-Vu imaging, and the Physician’s Global Aesthetic Improvement Scale (PGAIS) and patient satisfaction assessment scores were recorded. Skin swabs from ten participants were subjected to 16S rRNA and ITS1 sequencing. HACS treatment significantly reduced TEWL (p = 0.006 at week 2; p = 0.009 at week 8) and increased hydration (p < 0.001 at all time points) with a significant increase in elasticity (R2/R5/R7 values, p < 0.001). Both the PGAIS and patient satisfaction scores were significantly higher on the experimental side. Bacterial α/β-diversity remained largely unchanged, and no bacterial taxa remained significantly associated with skin parameters after FDR correction. In contrast, several fungal taxa showed significant positive associations with skin parameters after FDR correction, detectable only on the HACS-treated side. No significant adverse events were observed. HACS improved barrier function, elasticity, and aesthetic outcomes, whereas microbiome analyses suggested a modest fungal response associated with treatment-related skin changes in aging skin.

Protocol

16S-Pipeline: A comprehensive web-based platform for end-to-end 16S rRNA amplicon sequencing analysis: Tatsuya Unno; J. Microbiol. 2026;64(5):e2603014. Published online May 14, 2026; DOI: https://doi.org/10.71150/jm.2603014

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Abstract PDF Supplementary Material

16S rRNA gene amplicon sequencing is the most widely used approach for characterizing microbial communities, yet analyzing such data requires navigating a fragmented landscape of bioinformatics tools with distinct installation requirements, parameter settings, and data formats. Here we present 16S-Pipeline, an open-source, web-based platform that provides a complete workflow from raw FASTQ files to publication-ready statistical analyses. 16S-Pipeline automatically detects sequencing type (paired-end, single-end, long-read), variable region, and sequencing platform (Illumina, PacBio HiFi, Nanopore), then performs quality filtering, primer trimming, amplicon sequence variant (ASV) inference via DADA2, taxonomy assignment against SILVA v138.1, phylogenetic tree construction, and optional functional prediction via PICRUSt2. Downstream analyses include alpha and beta diversity, taxonomic composition visualization, differential abundance testing using five complementary methods (ALDEx2, DESeq2, ANCOM-BC2, LinDA, MaAsLin2) with consensus reporting, and KEGG pathway mapping. Built-in NCBI SRA integration enables downloading public datasets for re-analysis and generates submission metadata spreadsheets for data deposition. The interactive web interface built on FastAPI and Plotly Dash enables researchers to perform complex microbiome analyses without command-line expertise. 16S-Pipeline is freely available at https://github.com/tatsu1207/16S-Pipeline under the MIT License.

Citations

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Bat guano contamination of karst spring water revealed by an automated microbial source tracking pipeline: Integrating amplicon sequencing and shotgun metagenomics
Tatsuya Unno, Geon Choi, Jae-Hyeon Oh, Jun Heo, Dukki Han, Jeonghwan Jang, Soyeon Park, Jae-Yeon Kang, Jangwon Seo
Water Research X.2026; 32: 100582. CrossRef

Review

Emerging synthetic biology-assisted technologies for overcoming antibiotic resistance: CRISPR-Cas, bacteriophage, microbiome, and metabolic engineering-based solutions: Yujeong Oh, Hyunjin Lee, Sungho Jang; J. Microbiol. 2026;64(3):e2512002. Published online March 31, 2026; DOI: https://doi.org/10.71150/jm.2512002

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