Journal of Microbiology

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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.

Journal Article

Pat- and Pta-mediated protein acetylation is required for horizontallyacquired virulence gene expression in Salmonella Typhimurium: Hyojeong Koo , Eunna Choi , Shinae Park , Eun-Jin Lee , Jung-Shin Lee; J. Microbiol. 2022;60(8):823-831. Published online May 27, 2022; DOI: https://doi.org/10.1007/s12275-022-2095-y

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Salmonella Typhimurium is a Gram-negative facultative pathogen that causes a range of diseases, from mild gastroenteritis to severe systemic infection in a variety of animal hosts. S. Typhimurium regulates virulence gene expression by a silencing mechanism using nucleoid-associated proteins such as Histone-like Nucleoid Structuring protein (H-NS) silencing. We hypothesize that the posttranslational modification, specifically protein acetylation, of proteins in gene silencing systems could affect the pathogenic gene expression of S. Typhimurium. Therefore, we created acetylation-deficient mutant by deleting two genes, pat and pta, which are involved in the protein acetylation pathway. We observed that the pat and pta deletion attenuates mouse virulence and also decreases Salmonella’s replication within macrophages. In addition, the Δpat Δpta strain showed a decreased expression of the horizontally-acquired virulence genes, mgtC, pagC, and ugtL, which are highly expressed in low Mg2+. The decreased virulence gene expression is possibly due to higher H-NS occupancy to those promoters because the pat and pta deletion increases H-NS occupancy whereas the same mutation decreases occupancy of RNA polymerase. Our results suggest that Pat- and Pta-mediated protein acetylation system promotes the expression of virulence genes by regulating the binding affinity of H-NS in S. Typhimurium.

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Multi-Lasso Peptide-Based Synergistic Nanocomposite: A High-Stability, Broad-Spectrum Antimicrobial Agent with Potential for Combined Antibacterial Therapy
Yu Li, Jinyu Zhang, Ke Wei, Di Zhou, Zepeng Wang, Zhiwei Zeng, Yu Han, Weisheng Cao
ACS Nano.2024; 18(45): 31435. CrossRef

Randomized Controlled Trial

Ulmus macrocarpa Hance extract modulates intestinal microbiota in healthy adults: a randomized, placebo-controlled clinical trial: Kwangmin Kim , Karpagam Veerappan , Nahyun Woo , Bohyeon Park , Sathishkumar Natarajan , Hoyong Chung , Cheolmin Kim , Junhyung Park; J. Microbiol. 2021;59(12):1150-1156. Published online October 26, 2021; DOI: https://doi.org/10.1007/s12275-021-1329-8

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Abstract

The stem and root bark of Ulmus macrocarpa Hance has been used as traditional pharmacological agent against inflammation related disorders. The objective of this study was to explore the impact of Ulmus macrocarpa Hance extract (UME) on human gut microbiota. A randomized placebo-controlled clinical study was conducted in healthy adults. The study subjects were given 500 mg/day of UME or placebo orally for 4 weeks. Eighty fecal samples were collected at baseline and 4 weeks of UME or placebo intervention. The gut microbiota variation was evaluated by 16S rRNA profiling. The microbial response was highly personalized, and no statistically significant differences was observed in both species richness and abundance. The number of bacterial species identified in study subjects ranged from 86 to 182 species. The analysis for taxonomical changes revealed an increase in Eubacterium ventriosum, Blautia faecis, Ruminococcus gnavus in the UME group. Functional enrichment of bacterial genes showed an increase in primary and secondary bile acid biosynthesis in UME group. Having known from previous studies Eubacterium regulated bile acid homeostasis in protecting gut microbial architecture and immunity, we suggest that UME supplementation might enhance host immunity by modulating gut microbiota. This is the first stage study and forthcoming clinical studies with larger participants are needed to confirm these findings.

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Catechin and flavonoid glycosides from the Ulmus genus: Exploring their nutritional pharmacology and therapeutic potential in osteoporosis and inflammatory conditions
Chanhyeok Jeong, Chang Hyung Lee, Jiwon Seo, Jung Han Yoon Park, Ki Won Lee
Fitoterapia.2024; 178: 106188. CrossRef
Comparative transcriptomes of four Elm species provide insights into the genetic features and adaptive evolution of Ulmus spp.
Shijie Wang, Lihui Zuo, Yichao Liu, Lianxiang Long, Jianghao Wu, Mengting Yuan, Jinmao Wang, Minsheng Yang
Forest Ecology and Management.2024; 553: 121560. CrossRef
Dietary Supplementation with Popped Amaranth Modulates the Gut Microbiota in Low Height-for-Age Children: A Nonrandomized Pilot Trial
Oscar de Jesús Calva-Cruz, Cesaré Ovando-Vázquez, Antonio De León-Rodríguez, Fabiola Veana, Eduardo Espitia-Rangel, Samuel Treviño, Ana Paulina Barba-de la Rosa
Foods.2023; 12(14): 2760. CrossRef
Potential lipid-lowering effects of Ulmus macrocarpa Hance extract in adults with untreated high low-density lipoprotein cholesterol concentrations: A randomized double-blind placebo-controlled trial
Ye Li Lee, Sang Yeoup Lee
Frontiers in Medicine.2022;[Epub] CrossRef
Research progress on the relationship between intestinal microecology and intestinal bowel disease
Qianhui Fu, Tianyuan Song, Xiaoqin Ma, Jian Cui
Animal Models and Experimental Medicine.2022; 5(4): 297. CrossRef
The current status of old traditional medicine introduced from Persia to China
Jinmin Shi, Yifan Yang, Xinxin Zhou, Lijun Zhao, Xiaohua Li, Abdullah Yusuf, Mohaddeseh S. M. Z. Hosseini, Fatemeh Sefidkon, Xuebo Hu
Frontiers in Pharmacology.2022;[Epub] CrossRef

Journal Articles

Incomplete autophagy promotes the replication of Mycoplasma hyopneumoniae: Zhaodi Wang† , Yukang Wen† , Bingqian Zhou , Yaqin Tian , Yaru Ning , Honglei Ding; J. Microbiol. 2021;59(8):782-792. Published online July 5, 2021; DOI: https://doi.org/10.1007/s12275-021-1232-3

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Abstract

Autophagy is an important cellular homeostatic mechanism for recycling of degradative proteins and damaged organelles. Autophagy has been shown to play an important role in cellular responses to bacteria and bacterial replication. However, the role of autophagy in Mycoplasma hyopneumoniae infection and the pathogenic mechanism is not well characterized. In this study, we showed that M. hyopneumoniae infection significantly increases the number of autophagic vacuoles in host cells. Further, we found significantly enhanced expressions of autophagy marker proteins (LC3-II, ATG5, and Beclin 1) in M. hyopneumoniae-infected cells. Moreover, immunofluorescence analysis showed colocalization of P97 protein with LC3 during M. hyopneumoniae infection. Interestingly, autophagic flux marker, p62, accumulated with the induction of infection. Conversely, the levels of p62 and LC3-II were decreased after treatment with 3-MA, inhibiting the formation of autophagosomes, during infection. In addition, accumulation of autophagosomes promoted the expression of P97 protein and the survival of M. hyopneumoniae in PK- 15 cells, as the replication of M. hyopneumoniae was downregulated by adding 3-MA. Collectively, these findings provide strong evidence that M. hyopneumoniae induces incomplete autophagy, which in turn enhances its reproduction in host cells. These findings provide novel insights into the interaction of M. hyopneumoniae and host.

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Research Progress on Immune Evasion of Mycoplasma hyopneumoniae
Bin Jiang, Ying Zhang, Gaojian Li, Yanping Quan, Jianhong Shu, Huapeng Feng, Yulong He
Microorganisms.2024; 12(7): 1439. CrossRef
The Role of Pyroptosis and Autophagy in Ischemia Reperfusion Injury
Huijie Zhao, Yihan Yang, Xinya Si, Huiyang Liu, Honggang Wang
Biomolecules.2022; 12(7): 1010. CrossRef
Mycoplasma bovis inhibits autophagy in bovine mammary epithelial cells via a PTEN/PI3K-Akt-mTOR-dependent pathway
Maolin Xu, Yang Liu, Tuerdi Mayinuer, Yushan Lin, Yue Wang, Jian Gao, Dong Wang, John P. Kastelic, Bo Han
Frontiers in Microbiology.2022;[Epub] CrossRef
Incomplete autophagy promotes the proliferation of Mycoplasma hyopneumoniae through the JNK and Akt pathways in porcine alveolar macrophages
Yukang Wen, Zhengkun Chen, Yaqin Tian, Mei Yang, Qingshuang Dong, Yujiao Yang, Honglei Ding
Veterinary Research.2022;[Epub] CrossRef

Instruction of microbiome taxonomic profiling based on 16S rRNA sequencing: Hyojung Kim , Sora Kim , Sungwon Jung; J. Microbiol. 2020;58(3):193-205. Published online February 27, 2020; DOI: https://doi.org/10.1007/s12275-020-9556-y

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Abstract

Recent studies on microbiome highlighted their importance in various environments including human, where they are involved in multiple biological contexts such as immune mechanism, drug response, and metabolism. The rapid increase of new findings in microbiome research is partly due to the technological advances in microbiome identification, including the next-generation sequencing technologies. Several applications of different next-generation sequencing platforms exist for microbiome identification, but the most popular method is using short-read sequencing technology to profile targeted regions of 16S rRNA genes of microbiome because of its low-cost and generally reliable performance of identifying overall microbiome compositions. The analysis of targeted 16S rRNA sequencing data requires multiple steps of data processing and systematic analysis, and many software tools have been proposed for such procedures. However, properly organizing and using such software tools still require certain level of expertise with computational environments. The purpose of this article is introducing the concept of computational analysis of 16S rRNA sequencing data to microbiologists and providing easy-to-follow and step-by-step instructions of using recent software tools of microbiome analysis. This instruction may be used as a quick guideline for general next-generation sequencing-based microbiome studies or a template of constructing own software pipelines for customized analysis.

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Yin-Cheng Chen, Yin-Yuan Su, Tzu-Yu Chu, Ming-Fong Wu, Chieh-Chun Huang, Chen-Ching Lin
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Interaction between cecal microbiota and liver genes of laying ducks with different residual feed intake
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Rhizocompartments and environmental factors affect microbial composition and variation in native plants: Myung-Suk Kang , Moonsuk Hur , Soo-Je Park; J. Microbiol. 2019;57(7):550-561. Published online June 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8646-1

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Abstract

Molecular analysis based on large-scale sequencing of the plant microbiota has revealed complex relationships between plants and microbial communities, and environmental factors such as soil type can influence these relationships. However, most studies on root-associated microbial communities have focused on model plants such as Arabidopsis, rice or crops. Herein, we examined the microbiota of rhizocompartments of two native plants, Sedum takesimense Nakai and Campanula takesimana Nakai, using archaeal and bacterial 16S rRNA gene amplicon profiling, and assessed relationships between environmental factors and microbial community composition. We identified 390 bacterial genera, including known plant-associated genera such as Pseudomonas, Flavobacterium, Bradyrhizobium and Rhizobium, and uncharacterized clades such as DA101 that might be important in root-associated microbial communities in bulk soil. Unexpectedly, Nitrososphaera clade members were abundant, indicating functional association with roots. Soil texture/type has a greater impact on microbial community composition in rhizocompartments than chemical factors. Our results provide fundamental knowledge on microbial diversity, community and correlations with environmental factors, and expand our understanding of the microbiota in rhizocompartments of native plants.

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Ammonium bicarbonate alleviates apple replant disease: Inhibiting Fusarium and improving soil environment
Mei Wang, Li Xiang, Weixiao Tang, Xuesen Chen, Chuanrong Li, Chengmiao Yin, Zhiquan Mao
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Regulation of root-associated microbiomes and root exudates by different tobacco species
Mengli Gu, Jingjing Jin, Peng Lu, Shizhou Yu, Huan Su, Haihong Shang, Zhixiao Yang, Jianfeng Zhang, Peijian Cao, Jiemeng Tao
Chemical and Biological Technologies in Agriculture.2024;[Epub] CrossRef
MAPK Cascades in Plant Microbiota Structure and Functioning
Thijs Van Gerrewey, Hoo Sun Chung
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Viviana Rodríguez Rivera, Yendi E. Navarro-Noya, Luc Dendooven, Marco Luna Guido
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Full Issue PDF

Phytobiomes Journal.2020; 4(2): 103. CrossRef
Tomato-Associated Archaea Show a Cultivar-Specific Rhizosphere Effect but an Unspecific Transmission by Seeds
Julian Taffner, Alessandro Bergna, Tomislav Cernava, Gabriele Berg
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Weiyi Liu, Fang Wang, Yanmei Sun, Lei Yang, Huihai Chen, Weijie Liu, Bin Zhu, Chaomao Hui, Shiwei Wang
Journal of Microbiology.2020; 58(11): 906. CrossRef

Highly diverse endophytes in roots of Cycas bifida (Cycadaceae), an ancient but endangered gymnosperm: Ying Zheng , Tzen-Yuh Chiang , Chao-Li Huang , Xun Gong; J. Microbiol. 2018;56(5):337-345. Published online May 2, 2018; DOI: https://doi.org/10.1007/s12275-018-7438-3

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Abstract

As an ancient seed plant, cycads are one of the few gymnosperms that develop a root symbiosis with cyanobacteria, which has allowed cycads to cope with harsh geologic and climatic conditions during the evolutionary process. However, the endophytic microbes in cycad roots remain poorly identified. In this study, using next-generation sequencing techniques, we investigated the microbial diversity and composition of both the coralloid and regular roots of Cycas bifida (Dyer) K.D. Hill. Highly diverse endophytic communities were observed in both the coralloid and regular roots. Of the associated bacteria, the top five families were the Nostocaceae, Sinobacteraceae, Bradyrhizobiaceae, Bacillaceae, and Hyphomicrobiaceae. The Nectriaceae, Trichocomaceae, and Incertae sedis were the predominant fungal families in all root samples. A significant difference in the endophytic bacterial community was detected between coralloid roots and regular roots, but no difference was observed between the fungal communities in the two root types. Cyanobacteria were more dominant in coralloid roots than in regular roots. The divergence of cycad root structures and the modified physiological processes may have contributed to the abundance of cyanobionts in coralloid roots. Consequently, the colonization of cyanobacteria inhibits the assemblage of other endophytes. Our results contribute to an understanding of the species diversity and composition of the cycad-endophyte microbiome and provide an abbreviated list of potential ecological roles of the core microbes present.

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Diversity of fungi associated with roots of Calanthe orchid species in Korea: Myung Soo Park , John A. Eimes , Sang Hoon Oh , Hwa Jung Suh , Seung-Yoon Oh , Seobihn Lee , Ki Hyeong Park , Hyuk Joon Kwon , Soo-Young Kim , Young Woon Lim; J. Microbiol. 2018;56(1):49-55. Published online January 4, 2018; DOI: https://doi.org/10.1007/s12275-018-7319-9

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Abstract

While symbiotic fungi play a key role in the growth of endangered Calanthe orchid species, the relationship between fungal diversity and Calanthe species remains unclear. Here, we surveyed root associated fungal diversity of six Calanthe orchid species by sequencing the internal transcribed spacer (ITS) region using 454 pyrosequencing. Our results revealed that Paraboeremia and Coprinopsis are dominant fungal genera among Calanthe species. In terms of overall relative abundance, Paraboeremia was the most common fungal genus associated with Calanthe roots, followed by Coprinopsis. Overall fungal diversity showed a significant degree of variation depending on both location and Calanthe species. In terms of number of different fungal genera detected within Calanthe species, C. discolor had the most diverse fungal community, with 10 fungal genera detected. This study will contribute toward a better understanding of those fungi that are required for successful cultivation and conservation of Korean Calanthe species.

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