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

Temporal changes in culturable fungal community composition with their plastic degradation capacities in the marine plastisphere through mesocosm experiments: Sumin Jo, Ji Seon Kim, Wonjun Lee, Chang Wan Seo, Young Woon Lim; J. Microbiol. 2026;64(8):e2605011. Published online August 31, 2026; DOI: https://doi.org/10.71150/jm.2605011

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Abstract PDF Supplementary Material: Plastic waste in marine environments provides novel habitats for diverse organisms, forming distinct microbial ecosystems known as the ‘plastisphere’. Although bacteria of the plastisphere have been widely studied, the role of fungi in plastisphere formation and plastic degradation remains largely unexplored. Thus, we investigated temporal changes in culturable fungal community composition on three common plastic types—high-density polyethylene, low-density polyethylene, and polypropylene—across the early (seven days) and mature (30 days) plastisphere developmental stages through a marine mesocosm experiment. In total, 436 fungal strains were isolated and identified as belonging to 179 taxa, with Penicillium, Cladosporium, Trichoderma, Aspergillus, and Fusarium as the dominant genera. Temporal shifts in the species richness of the dominant genera were observed: Cladosporium showed higher species richness at the early stage, whereas that of Trichoderma increased at the mature stage. Plastic degradation assays revealed that 54.6% of the strains exhibited measurable degradation capacity, with patterns varying by plastic type rather than fungal developmental stage. Scanning electron microscope observations revealed surface damage patterns including cracks, pitting, and erosion on the plastic surfaces. These findings provide novel insights into the composition and functional heterogeneity of culturable fungal communities in the marine plastisphere and suggest that plastisphere fungi play diverse ecological roles beyond direct plastic degradation.

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.

Research article

Development and analytical evaluation of a microneutralization cytopathic effect assay for human adenovirus type 55-specific neutralizing antibodies: Dae-Im Jung, Yunjeong Park, Jung-ah Choi, Soon-Hwan Kwon, Jun Young Lee, Manki Song, Sang Hwan Seo; J. Microbiol. 2026;64(7):e2604007. Published online July 6, 2026; DOI: https://doi.org/10.71150/jm.2604007

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Abstract PDF Supplementary Material: Reliable quantification of neutralizing antibodies (nAb) against human adenovirus type 55 (HAdV-55) is critical for the evaluation of emerging vaccine candidates. While the plaque reduction neutralization test (PRNT) is currently the reference standard, its utility for large-scale studies is limited by low throughput, labor-intensive plaque counting, and prolonged assay times. In this study, we established and analytically validated a microneutralization assay based on cytopathic effect (MN-CPE) as a scalable alternative for HAdV-55-specific nAb quantification. Comparative performance analysis revealed that both assays maintain high dilution linearity, with coefficients of determination (R²) of 0.988 for MN-CPE and 0.9926 for PRNT. Relative accuracy assessments using high-, middle-, and low-titer reference sera demonstrated acceptable responses across the dynamic range. Notably, the MN-CPE assay allowed for the definition of a negative-control acceptance range, providing a distinct statistical advantage over PRNT, where negative-control values were consistently zero. Furthermore, both assays successfully detected HAdV-55-specific nAbs in immunized cynomolgus macaques, with no cross-reactivity observed against other HAdV types such as HAdV-4. These findings indicate that the MN-CPE assay is analytically comparable to PRNT and serves as a practical, relatively high-capacity alternative for HAdV-55 neutralization testing in clinical and preclinical vaccine research.

Article

Genomic landscape reveals the dominance of self-catalytic, high-copy group II introns in PMU-deficient complete genomes of PWB phytoplasmas: Kiran Kirdat, Malad Mubarak, Pradeep Choudhary, Shivaji Sathe, Amit Yadav; J. Microbiol. 2026;64(4):e2511004. Published online March 19, 2026; DOI: https://doi.org/10.71150/jm.2511004

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Abstract PDF Supplementary Material: Phytoplasmas are wall-less obligate parasites of plants and insects. Several phytoplasma strains within the Peanut Witches’ Broom (PWB; 16SrII) group are associated with significant disease losses across diverse crops and weeds. We present complete, single contig genome assemblies for two Indian parthenium phyllody strains, ‘Candidatus Phytoplasma asiaticum’ PR34 and ‘Ca. P. australasiaticum’ PR08, generated through host DNA depletion and hybrid Illumina–Nanopore sequencing. Both genomes display characteristic features of reductive evolution (∼614 kb and 589 kb, respectively) but show notable differences from previously sequenced PWB phytoplasmas. In contrast to most of PMU-rich phytoplasma genomes, neither PR34 nor PR08 retains intact Potential Mobile Units. Instead, both harbor numerous open reading frames encoding group II intron reverse transcriptase/ maturase proteins, predominantly of the mitochondrial-like type, with PR34 containing 52 and PR08 28 such loci that together constitute > 4% of each genome. These observations support the hypothesis that intron-associated processes may contribute to genome variability in the absence of canonical PMUs. Comparative analyses support the classification of PR34 as a distinct species within the PWB complex and reveal both conserved Sec-dependent effectors (SAP05, SAP11, and SAP54/PHYL1) and lineage-specific secreted proteins with predicted nuclear localization. Additional retained features include functional sodA genes and multiple truncated HlyB-like transporters. Collectively, these high-quality genomes illustrate a genomic configuration in which extensive genome reduction and loss of PMUs coexist with the retention of core virulence factors and an expanded repertoire of group II introns, providing a framework for future investigation of genome plasticity in phytoplasmas.

Article

Mucilaginibacter florum sp. nov., isolated from the flower of Coreopsis grandiflora and Mucilaginibacter oryzagri sp. nov., isolated from rice paddy soil in Korea: Parthiban Subramanian, Jun Heo, Daseul Lee, Seunghwan Kim, Hyorim Choi, Yunhee Choi, Yiseul Kim; J. Microbiol. 2025;63(12):e2509014. Published online December 31, 2025; DOI: https://doi.org/10.71150/jm.2509014

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Abstract PDF Supplementary Material

Two aerobic, Gram-stain-negative, non-motile and rod-shaped bacterial strains designated GGG-R5^T and M4-18^T were isolated from flowers of golden wave (Coreopsis grandiflora) and rice paddy soil, respectively in the Republic of Korea. Both strains were pigmented and produced flexirubin-type pigments. Based on phylogenetic analysis using 16S rRNA gene sequence, both strains were placed within the genus Mucilaginibacter with M. agri R11^T and M. jinjuensis YC7004^T both being the closest relatives to GGG-R5^T (97.7%) and in case of M4-18^T, M. ginsenosidivorax KHI28^T (98.5%) was the nearest neighbor. Characteristic to genus Mucilaginibacter, the major cellular fatty acids in both strains were iso-C_15:0, iso-C_{17:0 3-OH}, summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c); menaquinone-7 was the major menaquinone and phosphatidylethanolamine was the major polar lipid observed. Comparison of genome sequences with the other members of Mucilaginibacter indicated orthologous average nucleotide identity (orthoANI) at 73.3–73.5% for GGG-R5^T and 78.9–88.5% for M4-18^T. Digital DNA-DNA hybridization (dDDH) values ranged at 19.1–19.7% between GGG-R5^T and its neighbor species. In case of M4-18^T, the observed range was at 21.9–36.6%. Considering the 16S rRNA similarity, orthoANI and dDDH values as well as comparison of phenotypic and chemotaxonomic characteristics indicated that both strains belonged to genus Mucilaginibacter but were distinctly distinguishable from previously described species. The strains GGG-R5^T and M4-18^T, therefore represent distinct novel species for which names Mucilaginibacter florum GGG-R5^T and Mucilaginibacter oryzagri M4-18^T are proposed. The type strains are GGG-R5^T (= KACC 22063^T = JCM 36590^T) and M4-18^T (= KACC 22773^T = JCM 35894^T).

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Validation List no. 230: valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2026;[Epub] CrossRef

Article

Characterization of novel bacteriophages for effective phage therapy against Vibrio infections in aquaculture: Kira Moon, Sangdon Ryu, Seung Hui Song, Se Won Chun, Nakyeong Lee, Aslan Hwanhwi Lee; J. Microbiol. 2025;63(5):e2502009. Published online May 27, 2025; DOI: https://doi.org/10.71150/jm.2502009

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Abstract PDF Supplementary Material

The widespread use of antibiotics in aquaculture has led to the emergence of multidrug-resistant pathogens and environmental concerns, highlighting the need for sustainable, eco-friendly alternatives. In this study, we isolated and characterized three novel bacteriophages from aquaculture effluents in Korean shrimp farms that target the key Vibrio pathogens, Vibrio harveyi, and Vibrio parahaemolyticus. Bacteriophages were isolated through environmental enrichment and serial purification using double-layer agar assays. Transmission electron microscopy revealed that the phages infecting V. harveyi, designated as vB_VhaS-MS01 and vB_VhaS-MS03, exhibited typical Siphoviridae morphology with long contractile tails and icosahedral heads, whereas the phage isolated from V. parahaemolyticus (vB_VpaP-MS02) displayed Podoviridae characteristics with an icosahedral head and short tail.

Whole-genome sequencing produced complete, circularized genomes of 81,710 bp for vB_VhaS-MS01, 81,874 bp for vB_VhaS-MS03, and 76,865 bp for vB_VpaP-MS02, each showing a modular genome organization typical of Caudoviricetes. Genomic and phylogenetic analyses based on the terminase large subunit gene revealed that although vB_VhaS-MS01 and vB_VhaS-MS03 were closely related, vB_VpaP-MS02 exhibited a distinct genomic architecture that reflects its unique morphology and host specificity. Collectively, these comparative analyses demonstrated that all three phages possess genetic sequences markedly different from those of previously reported bacteriophages, thereby establishing their novelty. One-step growth and multiplicity of infection (MOI) experiments demonstrated significant differences in replication kinetics, such as burst size and lytic efficiency, among the phages, with vB_VhaS-MS03 maintaining the most effective bacterial control, even at an MOI of 0.01. Additionally, host range assays showed that vB_VhaS-MS03 possessed a broader spectrum of activity, supporting its potential use as a stand-alone agent or key component of phage cocktails. These findings highlight the potential of region-specific phage therapy as a targeted and sustainable alternative to antibiotics for controlling Vibrio infections in aquaculture.

Citations

Citations to this article as recorded by

Revolutionizing seafood safety with bacteriophages: emerging technologies and applications
Nigar Sultana Meghla, Soo-Jin Jung, Md Furkanur Rahaman Mizan, Syeda Roufun Nesa, IkSoon Kang, Sang-Do Ha
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Qin Lu, Xinxin Jin, Zui Wang, Rongrong Zhang, Yunqing Guo, Qiao Hu, Wenting Zhang, Tengfei Zhang, Qingping Luo
Frontiers in Microbiology.2026;[Epub] CrossRef
Characterization and genomic analysis of a novel Vibrio harveyi Vibrio phage LRZ
Zhengyu Yang, Hui Ge, Nan Chen, Yongrui Zhang, Huina Wei, Jinbo Hu, Chao Fan, Yilei Wang, Ziping Zhang
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Frontiers in Veterinary Science.2026;[Epub] CrossRef
Preliminary in vitro characterization and lytic dynamics of three novel siphovirus-like bacteriophages targeting extensively drug-resistant Vibrio alginolyticus V79
Van-Thanh Vo, Nguyen Chi Thom, Bui Thanh Liem, Truong Thi Bich Van
Israeli Journal of Aquaculture - Bamidgeh.2026;[Epub] CrossRef
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Review

Synthetic biology strategies for sustainable bioplastic production by yeasts: Huong-Giang Le, Yongjae Lee, Sun-Mi Lee; J. Microbiol. 2025;63(3):e2501022. Published online March 28, 2025; DOI: https://doi.org/10.71150/jm.2501022

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