Journal of Microbiology

Protocol

Protocol for efficient recovery of high-quality DNA from microbiome of marine invertebrates: Yeong-Jun Park, Jae Kyu Lim, Yeon-Ju Lee, Kae Kyoung Kwon; J. Microbiol. 2025;63(9):e2507003. Published online September 30, 2025; DOI: https://doi.org/10.71150/jm.2507003

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Abstract PDF: Marine organisms often form symbiotic relationships with various microorganisms to adapt and thrive in harsh environments. These symbiotic microbes contribute to host survival by providing nutrition, modulating the hosts’ immune system, and supporting overall physiological stability. Advances in high-throughput sequencing technologies have enabled a deeper understanding of the structure and function of symbiotic microbial communities, as well as host-microbe interactions. Notably, symbiotic bacteria associated with marine invertebrates such as corals and sponges are recognized as a potential source of useful bioactive compounds, including antibiotics and enzymes. However, obtaining high-quality microbial DNA from host tissues still remains a technical challenge due to the presence of unknown substances. This study focuses on optimizing sample preparation and DNA extraction procedures and additional purification to improve the recovery of microbial DNA while minimizing host DNA contamination. Comparison between several methods was conducted using sponge samples to evaluate DNA quality and microbial recovery. A sample designated as 2110BU-001 was collected from the east coast of the Republic of Korea and used for culture-independent microbial cell isolation. Total bacterial DNA was extracted by using a manual Phenol-Chloroform protocol and three commercial kits. DNA extracted using the standard manual method showed both the highest yield and the largest fragment size. However, PCR (Polymerase chain reaction) test showed that quality of manually extracted DNA was not enough for sequencing. Therefore, the quality of DNA was improved through additional purification steps. Briefly, host eukaryotic cells were removed by mechanical process and almost only bacterial DNA was successfully obtained by combination of manual extraction method and further purification processes. The established protocol was successfully introduced to extraction of metagenomic DNA from mussel and jellyfish microbiomes, indicating that it can be widely applied to various marine organisms.

Full articles

Microbial signatures in oral sites of patients with primary Sjögren’s syndrome: Association with salivary gland hypofunction: Sarah Kamounah, Arjun Sarathi, Christiane Elisabeth Sørensen, Manimozhiyan Arumugam, Anne Marie Lynge Pedersen; J. Microbiol. 2025;63(6):e2501030. Published online June 30, 2025; DOI: https://doi.org/10.71150/jm.2501030

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Abstract PDF Supplementary Material: This study aimed to determine if the microbiota in four different oral sites and the oral health status differ between patients with primary Sjögren’s syndrome (pSS), non-pSS sicca symptoms, and healthy controls. All participants underwent an interview and clinical oral examination. Stimulated whole saliva (SWS), supragingival plaque (SGP), buccal mucosa tissue (BLM), and tongue scrape (TGS) samples from 23 pSS patients, 36 patients with sicca symptoms, not fulfilling the classification criteria for pSS (non-pSS sicca), and 21 age-matched healthy controls (HC) were analyzed using V3–V4 16S rRNA gene amplicon sequencing, and determination of amplicon sequence variants (ASVs). PSS and non-pSS sicca patients did not differ with respect to oral health status, saliva flow rates, abundance of predominant genera, relative abundance on genus level or bacterial diversity in any of the oral sites. Both patient groups differed significantly from the healthy control group in the abundance of 61 ASVs across all sites. The alpha-diversity was lower in SGP from non-pSS sicca patients (p = 0.019), and in TGS from pSS patients (p = 0.04). The proportion of variation in the beta-diversity across all four sites could be explained by the diagnosis (pSS, non-pSS sicca, and HC). However, subgrouping of patients according to their stimulated salivary flow rates (SWS > 0.7 ml/min versus SWS ≤ 0.7 ml/min), revealed significantly different abundance of three ASVs in SWS, 11 in SGP, and six in TGS. Our findings suggest that hyposalivation rather than pSS itself modifies the microbial composition in oral site-specific patterns leading to oral diseases.

Microbiome therapeutic PMC72 through reverse translational research in gout: Mohammed Solayman Hossain, Hoonhee Seo, Kyung-Ann Lee, Asad ul-Haq, Sukyung Kim, Sujin Jo, Md Abdur Rahim, Hanieh Tajdozian, Fatemeh Ghorbanian, Youjin Yoon, Indrajeet Barman, Md Sarower Hossen Shuvo, Hyun-Sook Kim, Ho-Yeon Song; J. Microbiol. 2025;63(5):e2501002. Published online May 27, 2025; DOI: https://doi.org/10.71150/jm.2501002

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Abstract PDF Supplementary Material: Gout is an inflammatory arthritis resulting from the deposition of monosodium urate crystals. Urate-lowering therapies for gout have limitations, including side effects and limited efficacy, highlighting the need for novel therapeutic approaches to improve patient outcomes. In this context, our research team conducted a microbiome analysis of fecal samples from healthy individuals and gout patients, identifying Bifidobacterium as a key biomarker. Subsequently, we isolated and identified this strain, B. longum PMC72, and demonstrated its efficacy in a gout mouse model. In potassium oxonate (PO)-induced hyperuricemia mice, PMC72 significantly alleviated nausea, gait disturbances, ankle inflammation, and improved renal health. These effects were associated with marked reductions in oxidative stress markers, including serum uric acid, blood urea nitrogen, hepatic xanthine oxidase, and malondialdehyde (MDA) levels in serum, liver, and joint samples, as well as the downregulation of inflammation and uric acid transport-related gene expression in kidney samples. These benefits were comparable to those treated with Febuxostat, a standard urate-lowering therapy for gout. Furthermore, gut microbiome analysis revealed that PMC72 restored dysbiosis induced by hyperuricemia, contrasting with the reduced microbial diversity observed with febuxostat alone, and showed a complete recovery to eubiosis when combined with Febuxostat. These findings position PMC72 as a promising microbial therapeutic candidate for gout management, demonstrating significant development potential and serving as a benchmark for reverse translational microbiome-based therapeutic research.

Research Article

Synbiotic combination of fructooligosaccharides and probiotics ameliorates the metabolic dysfunction-associated steatotic liver disease: Sang Yoon Lee, Su-Been Lee, Goo-Hyun Kwon, Seol Hee Song, Jeong Ha Park, Min Ju Kim, Jung A Eom, Kyeong Jin Lee, Sang Jun Yoon, Hyunjoon Park, Sung-Min Won, Jin-Ju Jeong, Ki-Kwang Oh, Young Lim Ham, Gwang Ho Baik, Dong Joon Kim, Satya Priya Sharma, Ki Tae Suk; J. Microbiol. 2025;63(2):e2411002. Published online February 27, 2025; DOI: https://doi.org/10.71150/jm.2411002

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Abstract PDF

Synbiotics have become a new-age treatment tool for limiting the progression of metabolic dysfunction-associated steatotic liver disease; however, inclusive comparisons of various synbiotic treatments are still lacking. Here, we have explored and evaluated multiple synbiotic combinations incorporating three distinctive prebiotics, lactitol, lactulose and fructooligosaccharides. Of the synbiotic treatments evaluated, a combination of fructooligosaccharides and probiotics (FOS+Pro) exhibited superior protection against western diet-induced liver degeneration. This synbiotic (FOS+Pro) combination resulted in the lowest body weight gains, liver weights and liver/body weight ratios. The FOS+Pro synbiotic combination substantially alleviated liver histopathological markers and reduced serum AST and cholesterol levels. FOS+Pro ameliorated hepatic inflammation by lowering expression of proinflammatory markers including TNF-α, IL-1β, IL-6, and CCL2. FOS+Pro significantly improved steatosis by restricting the expression of lipid metabolic regulators (ACC1, FAS) and lipid transporters (CD36) in the liver. These findings are critical in suggesting that synbiotic treatments are capable of restraining western diet-induced metabolic dysfunction in the liver. Additionally, this study demonstrated that adding probiotic strains amplified the effectiveness of fructooligosaccharides but not all prebiotics.

Citations

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Therapeutic Potential of Probiotics in Metabolic Dysfunction-Associated Steatohepatitis: A Comprehensive Review
Xueying Wang, Zhiying Wei, Qing Xiang, Lijie Tang, Weichun Xie
Microorganisms.2025; 13(8): 1894. CrossRef
Profiling oligosaccharide components in Polygonatum kingianum with potential anti-NAFLD activity using UPLC-Orbitrap-MS/MS technology
Hong Guo, Rui Yao, Jing Fan, Ying Wang, Lingzhi Zhang, Hua Sun, Xiaohan Guo, Jianbo Yang, Jingzhe Pu, Yazhong Zhang, Baozhong Duan, Jia Chen, Wenguang Jing, Xianlong Cheng, Feng Wei
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Yue Li, Dayong Ren
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Minireview

Advances in functional analysis of the microbiome: Integrating metabolic modeling, metabolite prediction, and pathway inference with Next-Generation Sequencing data: Sungwon Jung; J. Microbiol. 2025;63(1):e.2411006. Published online January 24, 2025; DOI: https://doi.org/10.71150/jm.2411006

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Abstract PDF

This review explores current advancements in microbiome functional analysis enabled by next-generation sequencing technologies, which have transformed our understanding of microbial communities from mere taxonomic composition to their functional potential. We examine approaches that move beyond species identification to characterize microbial activities, interactions, and their roles in host health and disease. Genome-scale metabolic models allow for in-depth simulations of metabolic networks, enabling researchers to predict microbial metabolism, growth, and interspecies interactions in diverse environments. Additionally, computational methods for predicting metabolite profiles offer indirect insights into microbial metabolic outputs, which is crucial for identifying biomarkers and potential therapeutic targets. Functional pathway analysis tools further reveal microbial contributions to metabolic pathways, highlighting alterations in response to environmental changes and disease states. Together, these methods offer a powerful framework for understanding the complex metabolic interactions within microbial communities and their impact on host physiology. While significant progress has been made, challenges remain in the accuracy of predictive models and the completeness of reference databases, which limit the applicability of these methods in under-characterized ecosystems. The integration of these computational tools with multi-omic data holds promise for personalized approaches in precision medicine, allowing for targeted interventions that modulate the microbiome to improve health outcomes. This review highlights recent advances in microbiome functional analysis, providing a roadmap for future research and translational applications in human health and environmental microbiology.

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Microbiota, chronic inflammation, and health: The promise of inflammatome and inflammatomics for precision medicine and health care
Huan Zhang, Bing Jun Yang Lee, Tong Wang, Xuesong Xiang, Yafang Tan, Yanping Han, Yujing Bi, Fachao Zhi, Xin Wang, Fang He, Seppo J. Salminen, Baoli Zhu, Ruifu Yang
hLife.2025; 3(7): 307. CrossRef
Study on the Rhizosphere Soil Microbial Diversity of Five Common Orchidaceae Species in the Transitional Zone Between Warm Temperate and Subtropical Regions
Jingjing Du, Shengqian Guo, Xiaohang Li, Zhonghu Geng, Zhiliang Yuan, Xiqiang Song
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Cherelle Atallah, Ayline El Abiad, Marita El Abiad, Mantoura Nakad, Jean Claude Assaf
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Marco Antonio Pita-Galeana, Martin Ruhle, Lucía López-Vázquez, Guillermo de Anda-Jáuregui, Enrique Hernández-Lemus
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Research Article

Characteristics of skin microbiome associated with disease severity in systemic sclerosis: Kyung-Ann Lee, Asad Ul-Haq, Hoonhee Seo, Sujin Jo, Sukyung Kim, Ho-Yeon Song, Hyun-Sook Kim; J. Microbiol. 2025;63(1):e.2409018. Published online January 24, 2025; DOI: https://doi.org/10.71150/jm.2409018

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Abstract PDF Supplementary Material

Systemic sclerosis (SSc) is a chronic autoimmune disorder characterised by skin fibrosis and internal organ involvement. Disruptions in the microbial communities on the skin may contribute to the onset of autoimmune diseases that affect the skin. However, current research on the skin microbiome in SSc is lacking. This study aimed to investigate skin microbiome associated with disease severity in SSc. Skin swabs were collected from the upper limbs of 46 healthy controls (HCs) and 36 patients with SSc. Metagenomic analysis based on the 16S rRNA gene was conducted and stratified by cutaneous subtype and modified Rodnan skin score (mRSS) severity. Significant differences in skin bacterial communities were observed between the HCs and patients with SSc, with further significant variations based on subtype and mRSS severity. The identified biomarkers were Bacteroides and Faecalibacterium for patients with diffuse cutaneous SSc with high mRSS (≥ 10) and Mycobacterium and Parabacteroides for those with low mRSS (< 10). Gardnerella, Abies, Lactobacillus, and Roseburia were the biomarkers in patients with limited cutaneous SSc (lcSS) and high mRSS, whereas Coprococcus predominated in patients with lcSS and low mRSS. Cutaneous subtype analysis identified Pediococcus as a biomarker in the HCs, whereas mRSS analysis revealed the presence of Pseudomonas in conjunction with Pediococcus. In conclusion, patients with SSc exhibit distinct skin microbiota compared with healthy controls. Bacterial composition varies by systemic sclerosis cutaneous subtype and skin thickness.

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Microbiome therapeutic PMC72 through reverse translational research in gout
Mohammed Solayman Hossain, Hoonhee Seo, Kyung-Ann Lee, Asad ul-Haq, Sukyung Kim, Sujin Jo, Md Abdur Rahim, Hanieh Tajdozian, Fatemeh Ghorbanian, Youjin Yoon, Indrajeet Barman, Md Sarower Hossen Shuvo, Hyun-Sook Kim, Ho-Yeon Song
Journal of Microbiology.2025; 63(5): e2501002. CrossRef
Alterations of the skin microbiome in multiple system atrophy: a pilot study
Daji Chen, Lang Sun, Linlin Wan, Zhao Chen, LinLiu Peng, Jinzi Peng, Riwei Ouyang, Xiafei Long, Kefang Du, Xiao Dong, Xiaokang Wu, Xinying Xiao, Ruqing He, Rong Qiu, Beisha Tang, Hong Jiang
npj Parkinson's Disease.2025;[Epub] CrossRef

Journal Article

Description of Streptococcus dentalis sp. nov., Streptococcus gingivalis sp. nov., and Streptococcus lingualis sp. nov., Isolated from Human Oral Cavities: Beom-Jin Goo, Young-Sik Choi, Do-Hun Gim, Su-Won Jeong, Jee-Won Choi, Hojun Sung, Jae-Yun Lee, Jin-Woo Bae; J. Microbiol. 2024;62(11):973-983. Published online November 12, 2024; DOI: https://doi.org/10.1007/s12275-024-00178-1

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Abstract PDF

We isolated three novel strains, S1^T, S2^T, and S5^T, from human oral cavities and identified them as distinct novel species. All these strains are facultatively anaerobic, Gram-stain-positive, and non-flagellated bacteria. Their optimal growth conditions for these strains were observed in Columbia broth (CB) at 37 °C, pH 7.0, and in the absence of NaCl. Phylogenetic analyses, employing the 16S rRNA gene and whole-genome sequencing, confirmed that all three strains belong to the genus Streptococcus. The 16S rRNA gene sequences of strains S1^T, S2^T, and S5^T showed the highest similarities to Streptococcus parasanguinis, 98.57%, 99.05%, and 99.05%, respectively, and the orthologous average nucleotide identity (OrthoANI) values between the three strains and S. parasanguinis were 93.82%, 93.67%, and 94.04%, respectively. The pairwise OrthoANI values between the novel strains were 94.37% (S1^T-S2^T), 95.03% (S2^T-S5^T), and 94.71% (S1^T-S5^T). All strains had C_20:1 ω9c and summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c) as major cellular fatty acids. Additionally, diphosphatidylglycerol (DPG) and hydroxyphosphatidylethanolamine (OH-PE) were identified as major polar lipids. Menaquinone was undetected in all strains. The results from the phylogenetic, phenotypic, chemotaxonomic, and genotypic analyses collectively indicated that strains S1^T, S2^T, and S5^T represent three distinct novel species within the genus Streptococcus, and we propose the names Streptococcus dentalis sp. nov. for strain S1^T (= KCTC 21234^T = JCM 36526^T), Streptococcus gingivalis sp. nov. for strain S2^T (= KCTC 21235^T = JCM 36527^T), and Streptococcus lingualis sp. nov. for strain S5^T (= KCTC 21236^T = JCM 36528^T).

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Validation List no. 223. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef

Reviews

Microbiome-Mucosal Immunity Nexus: Driving Forces in Respiratory Disease Progression: Young Chae Park, Soo Yeon Choi, Yunah Cha, Hyeong Won Yoon, Young Min Son; J. Microbiol. 2024;62(9):709-725. Published online September 6, 2024; DOI: https://doi.org/10.1007/s12275-024-00167-4

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Abstract PDF

The importance of the complex interplay between the microbiome and mucosal immunity, particularly within the respiratory tract, has gained significant attention due to its potential implications for the severity and progression of lung diseases. Therefore, this review summarizes the specific interactions through which the respiratory tract-specific microbiome influences mucosal immunity and ultimately impacts respiratory health. Furthermore, we discuss how the microbiome affects mucosal immunity, considering tissue-specific variations, and its capacity in respiratory diseases containing asthma, chronic obstructive pulmonary disease, and lung cancer. Additionally, we investigate the external factors which affect the relationship between respiratory microbiome and mucosal immune responses. By exploring these intricate interactions, this review provides valuable insights into the potential for microbiome-based interventions to modulate mucosal immunity and alleviate the severity of respiratory diseases.

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The impact of environmental factors on respiratory tract microbiome and respiratory system diseases
Yutao Ge, Guo Tang, Yawen Fu, Peng Deng, Rong Yao
European Journal of Medical Research.2025;[Epub] CrossRef
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Meng’en Liao, Jianpeng Cai, Feng Zhu, Yuanbo Lan, Tianqi Xu, Jingxin Guo, Quanlin Xue, Yilong Wen, Fan Zou, Yu Zhang, Shiliang Zhang, Yan Yan, Jingwen Ai, Jie Cui, Wenhong Zhang
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Lactobacillus salivarius HHuMin-U attenuates vulvovaginal candidiasis via vaginal epithelial immune enhancement mediated by NF-κB activation
Juwon Choi, Jay-Young Jo, Ji Su Lee, Joe Eun Son, Sun Young Kim, Hye Eun Lee, Yeong-Je Seong, Keon Heo, Yongbaek Kim, Myeong Soo Park, Sanguine Byun
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Enrico Garaci, Marilena Pariano, Emilia Nunzi, Claudio Costantini, Marina Maria Bellet, Cinzia Antognelli, Matteo Antonio Russo, Luigina Romani
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Understanding the Diversity and Roles of the Ruminal Microbiome: Gi Beom Keum, Sriniwas Pandey, Eun Sol Kim, Hyunok Doo, Jinok Kwak, Sumin Ryu, Yejin Choi, Juyoun Kang, Sheena Kim, Hyeun Bum Kim; J. Microbiol. 2024;62(3):217-230. Published online April 25, 2024; DOI: https://doi.org/10.1007/s12275-024-00121-4

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Abstract PDF

The importance of ruminal microbiota in ruminants is emphasized, not only as a special symbiotic relationship with ruminants but also as an interactive and dynamic ecosystem established by the metabolites of various rumen microorganisms. Rumen microbial community is essential for life maintenance and production as they help decompose and utilize fber that is difcult to digest, supplying about 70% of the energy needed by the host and 60–85% of the amino acids that reach the small intestine. Bacteria are the most abundant in the rumen, but protozoa, which are relatively large, account for 40–50% of the total microorganisms. However, the composition of these ruminal microbiota is not conserved or constant throughout life and is greatly infuenced by the host. It is known that the initial colonization of calves immediately after birth is mainly infuenced by the mother, and later changes depending on various factors such as diet, age, gender and breed. The initial rumen microbial community contains aerobic and facultative anaerobic bacteria due to the presence of oxygen, but as age increases, a hypoxic environment is created inside the rumen, and anaerobic bacteria become dominant in the rumen microbial community. As calves grow, taxonomic diversity increases, especially as they begin to consume solid food. Understanding the factors afecting the rumen microbial community and their efects and changes can lead to the early development and stabilization of the microbial community through the control of rumen microorganisms, and is expected to ultimately help improve host productivity and efciency.

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Dawit Adisu Tadese, James Mwangi, Lei Luo, Hao Zhang, Xiaoshan Huang, Brenda B. Michira, Shengwen Zhou, Peter Muiruri Kamau, Qiumin Lu, Ren Lai
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International Symposium on Ruminant Physiology: Stochastic and deterministic factors that shape the rumen microbiome
Samodha C. Fernando, Seidu Adams, Andrew Lakamp, Matthew L. Spangler
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Application of Microbiome‑Based Therapies in Chronic Respiratory Diseases: Se Hee Lee, Jang Ho Lee, Sei Won Lee; J. Microbiol. 2024;62(3):201-216. Published online April 18, 2024; DOI: https://doi.org/10.1007/s12275-024-00124-1

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Abstract PDF

The application of microbiome-based therapies in various areas of human disease has recently increased. In chronic respiratory disease, microbiome-based clinical applications are considered compelling options due to the limitations of current treatments. The lung microbiome is ecologically dynamic and afected by various conditions, and dysbiosis is associated with disease severity, exacerbation, and phenotype as well as with chronic respiratory disease endotype. However, it is not easy to directly modulate the lung microbiome. Additionally, studies have shown that chronic respiratory diseases can be improved by modulating gut microbiome and administrating metabolites. Although the composition, diversity, and abundance of the microbiome between the gut and lung are considerably diferent, modulation of the gut microbiome could improve lung dysbiosis. The gut microbiome infuences that of the lung via bacterial-derived components and metabolic degradation products, including short-chain fatty acids. This phenomenon might be associated with the cross-talk between the gut microbiome and lung, called gut-lung axis. There are multiple alternatives to modulate the gut microbiome, such as prebiotics, probiotics, and postbiotics ingestion and fecal material transplantation. Several studies have shown that high-fber diets, for example, present benefcial efects through the production of short-chain fatty acids. Additionally, genetically modifed probiotics to secrete some benefcial molecules might also be utilized to treat chronic respiratory diseases. Further studies on microbial modulation to regulate immunity and potentiate conventional pharmacotherapy will improve microbiome modulation techniques, which will develop as a new therapeutic area in chronic respiratory diseases.

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Skin Deep: The Potential of Microbiome Cosmetics: Ju Hee Han, Hei Sung Kim; J. Microbiol. 2024;62(3):181-199. Published online April 16, 2024; DOI: https://doi.org/10.1007/s12275-024-00128-x

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Abstract PDF

The interplay between the skin microbiome and its host is a complex facet of dermatological health and has become a critical focus in the development of microbiome cosmetics. The skin microbiome, comprising various microorganisms, is essential from birth, develops over the lifespan, and performs vital roles in protecting our body against pathogens, training the immune system, and facilitating the breakdown of organic matter. Dysbiosis, an imbalance of these microorganisms, has been implicated in a number of skin conditions such as acne, atopic dermatitis, and skin cancer. Recent scientific findings have spurred cosmetic companies to develop products that preserve and enhance the skin's microbial diversity balance. These products may incorporate elements like prebiotics, probiotics, and postbiotics, which are beneficial for the skin microbiome. Beyond topical products, there's increasing interest in ingestible beauty supplements (i.e. oral probiotics), highlighting the connection between the gut and skin. This review examines the influence of the microbiome on skin health and the emerging trends of microbiome skincare products.

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Biological and Chemical Approaches for Controlling Harmful Microcystis Blooms: Wonjae Kim, Yerim Park, Jaejoon Jung, Che Ok Jeon, Masanori Toyofuku, Jiyoung Lee, Woojun Park; J. Microbiol. 2024;62(3):249-260. Published online April 8, 2024; DOI: https://doi.org/10.1007/s12275-024-00115-2

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Abstract PDF

The proliferation of harmful cyanobacterial blooms dominated by Microcystis aeruginosa has become an increasingly serious problem in freshwater ecosystems due to climate change and eutrophication. Microcystis-blooms in freshwater generate compounds with unpleasant odors, reduce the levels of dissolved O₂, and excrete microcystins into aquatic ecosystems, potentially harming various organisms, including humans. Various chemical and biological approaches have thus been developed to mitigate the impact of the blooms, though issues such as secondary pollution and high economic costs have not been adequately addressed. Red clays and H₂O₂ are conventional treatment methods that have been employed worldwide for the mitigation of the blooms, while novel approaches, such as the use of plant or microbial metabolites and antagonistic bacteria, have also recently been proposed. Many of these methods rely on the generation of reactive oxygen species, the inhibition of photosynthesis, and/or the disruption of cellular membranes as their mechanisms of action, which may also negatively impact other freshwater microbiota. Nevertheless, the underlying molecular mechanisms of anticyanobacterial chemicals and antagonistic bacteria remain unclear. This review thus discusses both conventional and innovative approaches for the management of M. aeruginosa in freshwater bodies.

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The Microbiome Matters: Its Impact on Cancer Development and Therapeutic Responses: In‑Young Chung, Jihyun Kim, Ara Koh; J. Microbiol. 2024;62(3):137-152. Published online April 8, 2024; DOI: https://doi.org/10.1007/s12275-024-00110-7

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Abstract PDF

In the evolving landscape of cancer research, the human microbiome emerges as a pivotal determinant reshaping our understanding of tumorigenesis and therapeutic responses. Advanced sequencing technologies have uncovered a vibrant microbial community not confned to the gut but thriving within tumor tissues. Comprising bacteria, viruses, and fungi, this diverse microbiota displays distinct signatures across various cancers, with most research primarily focusing on bacteria. The correlations between specifc microbial taxa within diferent cancer types underscore their pivotal roles in driving tumorigenesis and infuencing therapeutic responses, particularly in chemotherapy and immunotherapy. This review amalgamates recent discoveries, emphasizing the translocation of the oral microbiome to the gut as a potential marker for microbiome dysbiosis across diverse cancer types and delves into potential mechanisms contributing to cancer promotion. Furthermore, it highlights the adverse efects of the microbiome on cancer development while exploring its potential in fortifying strategies for cancer prevention and treatment.

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Journal Articles

Genetic and Functional Characterization of a Salicylate 1‑monooxygenase Located on an Integrative and Conjugative Element (ICE) in Pseudomonas stutzeri AJR13: Igor Ivanovski , Gerben J. Zylstra; J. Microbiol. 2023;61(12):1025-1032. Published online December 15, 2023; DOI: https://doi.org/10.1007/s12275-023-00093-x

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Abstract PDF

Pseudomonas stutzeri strain AJR13 was isolated for growth on the related compounds biphenyl (BPH) and diphenylmethane (DPM). The BPH and DPM degradative pathway genes are present on an integrative and conjugative element (ICE) in the chromosome. Examination of the genome sequence of AJR13 revealed a gene encoding a salicylate 1-monooxygenase (salA) associated with the ICE even though AJR13 did not grow on salicylate. Transfer of the ICE to the well-studied Pseudomonas putida KT2440 resulted in a KT2440 strain that could grow on salicylate. Knockout mutagenesis of the salA gene on the ICE in KT2440 eliminated the ability to grow on salicylate. Complementation of the knockout with the cloned salA gene restored growth on salicylate. Transfer of the cloned salA gene under control of the lac promoter to KT2440 resulted in a strain that could grow on salicylate. Heterologous expression of the salA gene in E. coli BL21 DE3 resulted in the production of catechol from salicylate, confirming that it is indeed a salicylate 1-monooxygenase. Interestingly, transfer of the cloned salA gene under control of the lac promoter to AJR13 resulted in a strain that could now grow on salicylate, suggesting that gene expression for the downstream catechol pathway is intact.

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Analysis of Benzoate 1,2‐Dioxygenase Identifies Shared Electron Transfer Components With DxnA1A2 in Rhizorhabdus wittichii RW1
Igor Ivanovski, Suha Eleya, Gerben J. Zylstra
Journal of Basic Microbiology.2025;[Epub] CrossRef

Quantitative Analysis of RNA Polymerase Slippages for Production of P3N‑PIPO Trans‑frame Fusion Proteins in Potyvirids: Dongjin Choi , Yoonsoo Hahn; J. Microbiol. 2023;61(10):917-927. Published online October 16, 2023; DOI: https://doi.org/10.1007/s12275-023-00083-z

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Abstract PDF

Potyvirids, members of the family Potyviridae, produce the P3N-PIPO protein, which is crucial for the cell-to-cell transport of viral genomic RNAs. The production of P3N-PIPO requires an adenine (A) insertion caused by RNA polymerase slippage at a conserved GAA AAA A ( GA6) sequence preceding the PIPO open reading frame. Presently, the slippage rate of RNA polymerase has been estimated in only a few potyvirids, ranging from 0.8 to 2.1%. In this study, we analyzed publicly available plant RNA-seq data and identified 19 genome contigs from 13 distinct potyvirids. We further investigated the RNA polymerase slippage rates at the GA6 motif. Our analysis revealed that the frequency of the A insertion variant ranges from 0.53 to 4.07% in 11 potyviruses (genus Potyvirus). For the two macluraviruses (genus Macluravirus), the frequency of the A insertion variant was found to be 0.72% and 10.96% respectively. Notably, the estimated RNA polymerase slippage rates for 12 out of the 13 investigated potyvirids were reported for the first time in this study. Our findings underscore the value of plant RNA-seq data for quantitative analysis of potyvirid genome variants, specifically at the GA6 slippage site, and contribute to a more comprehensive understanding of the RNA polymerase slippage phenomenon in potyvirids.

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Discovery of novel tepovirus genomes with a nucleic acid-binding protein homolog by systematic analysis of plant transcriptome data
Dongjin Choi, Hyerin Park, Seungwoo Baek, Myeung Seok Choi, Sylvain Legay, Gea Guerriero, Jean-François Hausman, Yoonsoo Hahn
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Veronika Hýsková, Kateřina Bělonožníková, Josef Chmelík, Hana Hoffmeisterová, Noemi Čeřovská, Tomáš Moravec, Helena Ryšlavá
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