Journal of Microbiology

Research article

Application of NaCl-supplemented antimicrobial susceptibility testing conditions to marine bacterial isolates: Daegyu Lee, Jin Lee, Hye Won Hong, Tatsuya Unno, Dukki Han; J. Microbiol. 2026;64(9):e2606005. Published online September 30, 2026; DOI: https://doi.org/10.71150/jm.2606005

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Abstract PDF Supplementary Material: Antimicrobial resistance (AMR) in marine environments remains difficult to assess under standard antimicrobial susceptibility testing conditions, which may not adequately reflect the physiological requirements of marine-derived bacteria. In this study, we applied NaCl-supplemented susceptibility testing conditions to bacterial isolates recovered from coastal environments and marine organism guts to evaluate their practical applicability and limitations. A total of 927 isolates were obtained from lagoon, seawater, soil, and gut samples of abalone, crab, eel, halibut, and salmon. Of these, 365 isolates grew on standard Mueller–Hinton (MH) medium, whereas 562 isolates were not evaluable under standard MH conditions. Taxonomic analysis showed that the isolate collection was dominated by Proteobacteria and Firmicutes, with Vibrio as the most abundant genus. Disk diffusion assays of the 365 MH-grown isolates revealed differences in screening-level reduced susceptibility profiles among sample groups, and putative multidrug resistance was frequently observed in Vibrio isolates from abalone and seawater. For isolates not evaluable under standard MH conditions, minimum inhibitory concentration (MIC) analysis was performed using 2% NaCl-supplemented MH broth. Under these conditions, 115 isolates showed stable growth and distinct antibiotic-dependent MIC profiles. Chloramphenicol and tetracycline inhibited most isolates at relatively low concentrations, whereas reduced susceptibility to penicillin was relatively high in isolates from seawater, abalone, and eel. Overall, these findings suggest that standard MH conditions alone may be insufficient for evaluating antibiotic responses in marine- and brackish-origin bacteria, and that 2% NaCl-supplemented MH broth can serve as a practical supplementary condition for selected marine-derived isolates.

Research article

Long-read sequencing reveals putatively mobilizable resistance genes and multi-drug resistance plasmids underestimated by short-read metagenomics: Dabin Jeon, Tatsuya Unno; J. Microbiol. 2026;64(8):e2605007. Published online August 26, 2026; DOI: https://doi.org/10.71150/jm.2605007

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Abstract PDF Supplementary Material: While shotgun metagenomics is often used to profile antibiotic resistome in gut microbial communities, few studies have investigated if the choice of sequencing platform and assembly strategy affect what mobile genetic elements and antimicrobial resistance genes are recovered. In this study, we compared three platforms (Illumina, Oxford Nanopore, and PacBio HiFi) and seven assembly strategies on gut metagenomes from cattle, pig, and human as case studies. Long-read assemblies recovered 5- to 7-fold more plasmid sequence than Illumina in cattle and pig (mean 17.0 Mb vs. 3.1 Mb), while Illumina performed comparably in the less diverse human gut where high per-species coverage enabled effective short-read plasmid assembly. Long reads also detected more resistance genes on plasmid contigs. Hybrid assembly results depended on the algorithm: scaffolding-based OPERA-MS preserved long-read contiguity and recovered more plasmid-borne resistance genes, while the short-read-centric metaSPAdes hybrid mode produced fragmented assemblies. After collapsing haplotype redundancy, PacBio HiFi identified 2 and 49 unique multi-drug resistance plasmid lineages in cattle and pig, respectively. On the other hand, only 2 and 4 were identified from Illumina. Long reads also placed far more ARGs in a putative mobilization context (50–73%) compared to 14–21% for short reads. Platform and assembly strategy are thus key variables in mobilome and resistome characterization and should be accounted for in antimicrobial resistance surveillance.

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.

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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

Microbial source tracking using metagenomics and other new technologies: Shahbaz Raza , Jungman Kim , Michael J. Sadowsky , Tatsuya Unno; J. Microbiol. 2021;59(3):259-269. Published online February 10, 2021; DOI: https://doi.org/10.1007/s12275-021-0668-9

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Abstract PDF

The environment is under siege from a variety of pollution sources. Fecal pollution is especially harmful as it disperses pathogenic bacteria into waterways. Unraveling origins of mixed sources of fecal bacteria is difficult and microbial source tracking (MST) in complex environments is still a daunting task. Despite the challenges, the need for answers far outweighs the difficulties experienced. Advancements in qPCR and next generation sequencing (NGS) technologies have shifted the traditional culture-based MST approaches towards culture independent technologies, where communitybased MST is becoming a method of choice. Metagenomic tools may be useful to overcome some of the limitations of community-based MST methods as they can give deep insight into identifying host specific fecal markers and their association with different environments. Adoption of machine learning (ML) algorithms, along with the metagenomic based MST approaches, will also provide a statistically robust and automated platform. To compliment that, ML-based approaches provide accurate optimization of resources. With the successful application of ML based models in disease prediction, outbreak investigation and medicine prescription, it would be possible that these methods would serve as a better surrogate of traditional MST approaches in future.

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Article

Intervention with kimchi microbial community ameliorates obesity by regulating gut microbiota: Seong-Eun Park , Sun Jae Kwon , Kwang-Moon Cho , Seung-Ho Seo , Eun-Ju Kim , Tatsuya Unno , So-Hyeon Bok , Dae-Hun Park , Hong-Seok Son; J. Microbiol. 2020;58(10):859-867. Published online September 2, 2020; DOI: https://doi.org/10.1007/s12275-020-0266-2

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Abstract PDF

The objective of this study was to evaluate anti-obesity effects of kimchi microbial community (KMC) on obesity and gut microbiota using a high fat diet-induced mouse model compared to effects of a single strain. Administration of KMC decreased body weight, adipose tissue, and liver weight gains. Relative content of Muribaculaceae in the gut of the KMCtreated group was higher than that in the high-fat diet (HFD) group whereas relative contents of Akkermansiaceae, Coriobacteriaceae, and Erysipelotrichaceae were lower in KMCtreated group. Metabolic profile of blood was found to change differently according to the administration of KMC and a single strain of Lactobacillus plantarum. Serum metabolites significantly increased in the HFD group but decreased in the KMC-treated group included arachidic acid, stearic acid, fumaric acid, and glucose, suggesting that the administration of KMC could influence energy metabolism. The main genus in KMC was not detected in guts of mice in KMC-treated group. Since the use of KMC has advantages in terms of safety, it has potential to improve gut microbial community for obese people.

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Article

Metagenomic analysis reveals the prevalence and persistence of antibiotic- and heavy metal-resistance genes in wastewater treatment plant: Sachin Kumar Gupta , Hanseob Shin , Dukki Han , Hor-Gil Hur , Tatsuya Unno; J. Microbiol. 2018;56(6):408-415. Published online June 1, 2018; DOI: https://doi.org/10.1007/s12275-018-8195-z

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Abstract PDF

The increased antibiotic resistance among microorganisms has resulted into growing interest for investigating the wastewater treatment plants (WWTPs) as they are reported to be the major source in the dissemination of antibiotic resistance genes (ARGs) and heavy metal resistance genes (HMRGs) in the environment. In this study, we investigated the prevalence and persistence of ARGs and HMRGs as well as bacterial diversity and mobile genetic elements (MGEs) in influent and effluent at the WWTP in Gwangju, South Korea, using high-throughput sequencing based metagenomic approach. A good number of broad-spectrum of resistance genes (both ARG and HMRG) were prevalent and likely persistent, although large portion of them were successfully removed at the wastewater treatment process. The relative abundance of ARGs and MGEs was higher in effluent as compared to that of influent. Our results suggest that the resistance genes with high abundance and bacteria harbouring ARGs and MGEs are likely to persist more through the treatment process. On analyzing the microbial community, the phylum Proteobacteria, especially potentially pathogenic species belonging to the genus Acinetobacter, dominated in WWTP. Overall, our study demonstrates that many ARGs and HMRGs may persist the treatment processes in WWTPs and their association to MGEs may contribute to the dissemination of resistance genes among microorganisms in the environment.

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Review

Current understanding of microbiota- and dietary-therapies for treating inflammatory bowel disease: Taekil Eom , Yong Sung Kim , Chang Hwan Choi , Michael J. Sadowsky , Tatsuya Unno; J. Microbiol. 2018;56(3):189-198. Published online February 28, 2018; DOI: https://doi.org/10.1007/s12275-018-8049-8

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Abstract PDF

Inflammatory bowel disease (IBD) is a result of chronic inflammation caused, in some part, by dysbiosis of intestinal microbiota, mainly commensal bacteria. Gut dysbiosis can be caused by multiple factors, including abnormal immune responses which might be related to genetic susceptibility, infection, western dietary habits, and administration of antibiotics. Consequently, the disease itself is characterized as having multiple causes, etiologies, and severities. Recent studies have identified > 200 IBD risk loci in the host. It has been postulated that gut microbiota interact with these risk loci
result
ing in dysbiosis, and this subsequently leads to the development of IBD. Typical gut microbiota in IBD patients are characterized with decrease in species richness and many of the commensal, and beneficial, fecal bacteria such as Firmicutes and Bacteroidetes and an increase or bloom of Proteobacteria. However, at this time, cause and effect relationships have not been rigorously established. While treatments of IBD usually includes medications such as corticosteroids, 5-aminosalicylates, antibiotics, immunomodulators, and anti- TNF agents, restoration of gut dysbiosis seems to be a safer and more sustainable approach. Bacteriotherapies (now called microbiota therapies) and dietary interventions are effective way to modulate gut microbiota. In this review, we summarize factors involved in IBD and studies attempted to treat IBD with probiotics. We also discuss the potential use of microbiota therapies as one promising approach in treating IBD. As therapies based on the modulation of gut microbiota becomes more common, future studies should include individual gut microbiota differences to develop personalized therapy for IBD.

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Probiotics: If It Does Not Help It Does Not Do Any Harm. Really?
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Micronized Cells of the Probiotic Strain Bifidobacterium lactis BS01 Activate Monocyte Polarization
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