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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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AbstractAbstract
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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  • Bacteria and fungi of the lung: allies or enemies?
    Enrico Garaci, Marilena Pariano, Emilia Nunzi, Claudio Costantini, Marina Maria Bellet, Cinzia Antognelli, Matteo Antonio Russo, Luigina Romani
    Frontiers in Pharmacology.2024;[Epub]     CrossRef
Metabolic Interaction Between Host and the Gut Microbiota During High‑Fat Diet‑Induced Colorectal Cancer
Chaeeun Lee, Seungrin Lee, Woongjae Yoo
J. Microbiol. 2024;62(3):153-165.   Published online April 16, 2024
DOI: https://doi.org/10.1007/s12275-024-00123-2
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AbstractAbstract
Colorectal cancer (CRC) is the second-highest cause of cancer-associated mortality among both men and women worldwide. One of the risk factors for CRC is obesity, which is correlated with a high-fat diet prevalent in Western dietary habits. The association between an obesogenic high-fat diet and CRC has been established for several decades; however, the mechanisms by which a high-fat diet increases the risk of CRC remain unclear. Recent studies indicate that gut microbiota strongly infuence the pathogenesis of both high-fat diet-induced obesity and CRC. The gut microbiota is composed of hundreds of bacterial species, some of which are implicated in CRC. In particular, the expansion of facultative anaerobic Enterobacteriaceae, which is considered a microbial signature of intestinal microbiota functional imbalance (dysbiosis), is associated with both high-fat diet-induced obesity and CRC. Here, we review the interaction between the gut microbiome and its metabolic byproducts in the context of colorectal cancer (CRC) during high-fat diet-induced obesity. In addition, we will cover how a high-fat diet can drive the expansion of genotoxin-producing Escherichia coli by altering intestinal epithelial cell metabolism during gut infammation conditions.

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  • Wheat β-glucan reduces obesity and hyperlipidemia in mice with high-fat and high-salt diet by regulating intestinal flora
    Min Li, Qingshan Wang, Xiuwei Zhang, Kaikai Li, Meng Niu, Siming Zhao
    International Journal of Biological Macromolecules.2025; 288: 138754.     CrossRef
  • Microbial Metabolites-induced Epigenetic Modifications for Inhibition of Colorectal Cancer: Current Status and Future Perspectives
    Vaibhav Singh, Ekta Shirbhate, Rakesh Kore, Subham Vishwakarma, Shadiya Parveen, Ravichandran Veerasamy, Amit K Tiwari, Harish Rajak
    Mini-Reviews in Medicinal Chemistry.2025; 25(1): 76.     CrossRef
  • Molecular Mechanisms of Skatole-Induced Inflammatory Responses in Intestinal Epithelial Caco-2 Cells: Implications for Colorectal Cancer and Inflammatory Bowel Disease
    Katsunori Ishii, Kazuma Naito, Dai Tanaka, Yoshihito Koto, Koichi Kurata, Hidehisa Shimizu
    Cells.2024; 13(20): 1730.     CrossRef
  • Research Progress on the Relationship between Intestinal Flora and Gastrointestinal Malignancy
    军 陈
    Advances in Clinical Medicine.2024; 14(11): 262.     CrossRef
  • Host-Associated Microbiome
    Woo Jun Sul
    Journal of Microbiology.2024; 62(3): 135.     CrossRef
Journal Article
Salicibibacter cibarius sp. nov. and Salicibibacter cibi sp. nov., two novel species of the family Bacillaceae isolated from kimchi
Young Joon Oh , Joon Yong Kim , Seul Ki Lim , Min-Sung Kwon , Hak-Jong Choi
J. Microbiol. 2021;59(5):460-466.   Published online April 28, 2021
DOI: https://doi.org/10.1007/s12275-021-0513-1
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AbstractAbstract
To date, all species in the genus Salicibibacter have been isolated in Korean commercial kimchi. We aimed to describe the taxonomic characteristics of two strains, NKC5-3T and NKC21-4T, isolated from commercial kimchi collected from various regions in the Republic of Korea. Cells of these strains were rod-shaped, Gram-positive, aerobic, oxidase- and catalase- positive, non-motile, halophilic, and alkalitolerant. Both strains, unlike other species of the genus Salicibibacter, could not grow without NaCl. Strains NKC5-3T and NKC21-4T could tolerate up to 25.0% (w/v) NaCl (optimum 10%) and grow at pH 7.0–10.0 (optimum 8.5) and 8.0–9.0 (optimum 8.5), respectively; they showed 97.1% 16S rRNA gene sequence similarity to each other and were most closely related to S. kimchii NKC1-1T (97.0% and 96.8% similarity, respectively). The genome of strain NKC5-3T was nearly 4.6 Mb in size, with 4,456 protein-coding sequences (CDSs), whereas NKC21-4T genome was nearly 3.9 Mb in size, with 3,717 CDSs. OrthoANI values between the novel strains and S. kimchii NKC1-1T were far lower than the species demarcation threshold. NKC5-3T and NKC21-4T clustered together to form branches that were distinct from the other Salicibibacter species. The major fatty acids in these strains were anteiso-C15:0 and anteiso-C17:0, and the predominant menaquinone was menaquinone-7. The polar lipids of NKC5-3T included diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), and five unidentified phospholipids (PL), and those of NKC21-4T included DPG, PG, seven unidentified PLs, and an unidentified lipid. Both isolates had DPG, which is the first case in the genus Salicibibacter. The genomic G + C content of strains NKC5-3T and NKC21-4T was 44.7 and 44.9 mol%, respectively. Based on phenotypic, genomic, phylogenetic, and chemotaxonomic analyses, strains NKC5-3T (= KACC 22040T = DSM 111417T) and NKC21-4T (= KACC 22041T = DSM 111418T) represent two novel species of the genus Salicibibacter, for which the names Salicibibacter cibarius sp. nov. and Salicibibacter cibi sp. nov. are proposed.

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  • Valid publication of new names and new combinations effectively published outside the IJSEM
    Aharon Oren, George M. Garrity
    International Journal of Systematic and Evolutionary Microbiology .2021;[Epub]     CrossRef
Reviews
Rediscovery of antimicrobial peptides as therapeutic agents
Minkyung Ryu , Jaeyeong Park , Ji-Hyun Yeom , Minju Joo , Kangseok Lee
J. Microbiol. 2021;59(2):113-123.   Published online February 1, 2021
DOI: https://doi.org/10.1007/s12275-021-0649-z
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AbstractAbstract
In recent years, the occurrence of antibiotic-resistant pathogens is increasing rapidly. There is growing concern as the development of antibiotics is slower than the increase in the resistance of pathogenic bacteria. Antimicrobial peptides (AMPs) are promising alternatives to antibiotics. Despite their name, which implies their antimicrobial activity, AMPs have recently been rediscovered as compounds having antifungal, antiviral, anticancer, antioxidant, and insecticidal effects. Moreover, many AMPs are relatively safe from toxic side effects and the generation of resistant microorganisms due to their target specificity and complexity of the mechanisms underlying their action. In this review, we summarize the history, classification, and mechanisms of action of AMPs, and provide descriptions of AMPs undergoing clinical trials. We also discuss the obstacles associated with the development of AMPs as therapeutic agents and recent strategies formulated to circumvent these obstacles.

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REVIEW] The Ruminococci: key symbionts of the gut ecosystem
Alex J. La Reau , Garret Suen
J. Microbiol. 2018;56(3):199-208.   Published online February 28, 2018
DOI: https://doi.org/10.1007/s12275-018-8024-4
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AbstractAbstract
Mammalian gut microbial communities form intricate mutualisms with their hosts, which have profound implications on overall health. One group of important gut microbial mutualists are bacteria in the genus Ruminococcus, which serve to degrade and convert complex polysaccharides into a variety of nutrients for their hosts. Isolated decades ago from the bovine rumen, ruminococci have since been cultured from other ruminant and non-ruminant sources, and next-generation sequencing has further shown their distribution to be widespread in a diversity of animal hosts. While most ruminococci that have been studied are those capable of degrading cellulose, much less is known about non-cellulolytic, nonruminant- associated species, such as those found in humans. Furthermore, a mechanistic understanding of the role of Ruminococcus spp. in their respective hosts is still a work in progress. This review highlights the broad work done on species within the genus Ruminococcus with respect to their physiology, phylogenetic relatedness, and their potential impact on host health.

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  • Causal Link between Gut Microbiota, Neurophysiological States, and Bone Diseases: A Comprehensive Mendelian Randomization Study
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  • Evaluation of Antioxidant Capacity and Gut Microbiota Modulatory Effects of Different Kinds of Berries
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  • Altered Immunoglobulin Repertoire and Decreased IgA Somatic Hypermutation in the Gut during Chronic HIV-1 Infection
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  • Saccharomyces cerevisiae boulardiiCNCM I-1079 supplementation in finishing male pigs helps to cope with heat stress through feeding behaviour and gut microbiota modulation
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  • Specific Alterations of Gut Microbiota in Chinese Patients with Hypertension: A Systematic Review and Meta-Analysis
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  • 2-Hydroxy-4-(Methylthio) Butanoic Acid Isopropyl Ester Supplementation Altered Ruminal and Cecal Bacterial Composition and Improved Growth Performance of Finishing Beef Cattle
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  • Integrated Fecal Microbiome and Metabolomics Reveals a Novel Potential Biomarker for Predicting Tibial Dyschondroplasia in Chickens
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  • How to Maintain a Healthy Gut Microbiome in Children with Cancer? Gut Microbiome Association with Diet in Children with Solid Tumors Postchemotherapy
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  • Seasonal and geographical differences in the ruminal microbial and chloroplast composition of sika deer (Cervus nippon) in Japan
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  • Analysis of Faecal Microbiota and Small ncRNAs in Autism: Detection of miRNAs and piRNAs with Possible Implications in Host–Gut Microbiota Cross-Talk
    Federica Chiappori, Francesca Anna Cupaioli, Arianna Consiglio, Noemi Di Nanni, Ettore Mosca, Vito Flavio Licciulli, Alessandra Mezzelani
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  • Microbiota Composition of Mucosa and Interactions between the Microbes of the Different Gut Segments Could Be a Factor to Modulate the Growth Rate of Broiler Chickens
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  • Comparative Analysis of Gut Microbial Composition and Functions in Przewalski’s Gazelle (Procapra przewalskii) From Various Habitats
    Jingjie Zhang, Hongmei Gao, Feng Jiang, Daoxin Liu, Yuansheng Hou, Xiangwen Chi, Wen Qin, Pengfei Song, Zhenyuan Cai, Tongzuo Zhang
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    Ashok K. Sharma, Sam Davison, Barbora Pafco, Jonathan B. Clayton, Jessica M. Rothman, Matthew R. McLennan, Marie Cibot, Terence Fuh, Roman Vodicka, Carolyn Jost Robinson, Klara Petrzelkova, Andres Gomez
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    Erwin A. Paz, Eng Guan Chua, Shamshad Ul Hassan, Johan C. Greeff, Dieter G. Palmer, Shimin Liu, Binit Lamichhane, Néstor Sepúlveda, Junhua Liu, Chin Yen Tay, Graeme B. Martin
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  • Albuca Bracteate Polysaccharides Synergistically Enhance the Anti-Tumor Efficacy of 5-Fluorouracil Against Colorectal Cancer by Modulating β-Catenin Signaling and Intestinal Flora
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  • Fecal Metabolome Signature in the HIV-1 Elite Control Phenotype: Enrichment of Dipeptides Acts as an HIV-1 Antagonist but a Prevotella Agonist
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Microbial ecology in Hydra: Why viruses matter
Thomas C.G. Bosch , Juris A. Grasis , Tim Lachnit
J. Microbiol. 2015;53(3):193-200.   Published online March 3, 2015
DOI: https://doi.org/10.1007/s12275-015-4695-2
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AbstractAbstract
While largely studied because of their harmful effects on human health, there is growing appreciation that viruses are also important members of the animal holobiont. This review highlights recent findings on viruses associated with Hydra and related Cnidaria. These early evolutionary diverging animals not only select their bacterial communities but also select for viral communities in a species-specific manner. The majority of the viruses associating with these animals are bacteriophages. We demonstrate that the animal host and its virome have evolved into a homeostatic, symbiotic relationship and propose that viruses are an important part of the Hydra holobiont by controlling the species-specific microbiome. We conclude that beneficial virus-bacterial-host interactions should be considered as an integral part of animal development and evolution.

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