Journal of Microbiology

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Multi-omic profiling reveals the impact of keratinase kerZJ on mouse gut homeostasis: Xueqing Gan, Yijiao Wen, Si Chen, Famin Ke, Siyuan Liu, Zening Wang, Chunhua Zhang, Xuanting Wang, Qin Wang, Xiaowei Gao; J. Microbiol. 2025;63(12):e2509011. Published online December 31, 2025; DOI: https://doi.org/10.71150/jm.2509011

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Abstract PDF: Keratinase kerZJ is a multifunctional protease with potential as a feed additive and functional ingredient. Here we performed an integrated multi‑omics evaluation of its biosafety and impact on gut homeostasis in mice. Our findings confirm that kerZJ is well-tolerated, with no evidence of systemic toxicity or intestinal epithelial damage. Integrated transcriptomic and proteomic analyses revealed that kerZJ reinforces intestinal barrier integrity by upregulating extracellular matrix components, including collagen IV, and modulates mucosal immunity by enhancing B-cell activation and antimicrobial peptide defenses without inducing inflammation. Furthermore, kerZJ administration led to a significant upregulation of digestive enzymes and a dose-dependent increase in short-chain fatty acids production. Microbiome analysis showed that while high-dose kerZJ altered community composition, it enriched for beneficial taxa like Lactobacillaceae and did not induce dysbiosis. These results demonstrate that kerZJ safely enhances gut barrier function, promotes a favorable immune and metabolic environment, and fosters a resilient gut ecosystem, supporting its development as a safe feed additive and nutraceutical component.

Research Support, Non-U.S. Gov'ts

Proteomic Comparison between Salmonella Typhimurium and Salmonella Typhi: Yue Wang , Kuan-Yeh Huang , Yanan Huo; J. Microbiol. 2014;52(1):71-76. Published online January 4, 2014; DOI: https://doi.org/10.1007/s12275-014-3204-3

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The genus Salmonella contains more than 2500 serovars. While most cause the self-limiting gastroenteritis, a few serovars can elicit typhoid fever, a severe systemic infection. S. enterica subsp. enterica serovar Typhimurium and S. Typhi are the representatives of the gastroenteritis and typhoid fever types of Salmonella. In this study, we adopted Stable Isotope Labeling with Amino acids in Cell culture (SILAC) technology to quantitatively compare the proteomes of the two serovars. We found several proteins with serovar- specific expression, which could be developed as new biomarkers for clinical serotype diagnosis. We found that flagella and chemotaxis genes were down-regulated in S. Typhi in comparison with S. Typhimurium. We attributed this observation to the fact that the smooth cellular structure of S. Typhi may better fit its systemic lifestyle. Instead of known virulence factors that were located within Salmonella Pathogenecity Islands, a number of core genes, which were involved in metabolism and transport of carbohydrates and amino acids, showed differential expression between the two serovars. Further studies on the roles of these differentially- expressed genes in the pathogenesis should be undertaken.

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Proteomic Applications in Antimicrobial Resistance and Clinical Microbiology Studies

Ehsaneh Khodadadi, Elham Zeinalzadeh, Sepehr Taghizadeh, Bahareh Mehramouz, Fadhil S Kamounah, Ehsan Khodadadi, Khudaverdi Ganbarov, Bahman Yousefi, Milad Bastami, Hossein Samadi Kafil
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NOTE] Analysis of Cytoplasmic Membrane Proteome of Streptococcus pneumoniae by Shotgun Proteomic Approach: Chi-Won Choi , Sung-Ho Yun , Sang-Oh Kwon , Sun-Hee Leem , Jong-Soon Choi , Chi-Young Yun , Seung Il Kim; J. Microbiol. 2010;48(6):872-876. Published online January 9, 2011; DOI: https://doi.org/10.1007/s12275-010-0220-9

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Abstract PDF

In this study, cytoplasmic membrane proteins of S. pneumoniae strain R6 (ATCC BBA-255) were effectively separated from cell wall or extracellular proteins by sodium carbonate precipitation (SCP) and ultracentrifugation. Forty seven proteins were analyzed as cytoplasmic membrane proteins from the 260 proteins identified by the shotgun proteomic method using SDS-PAGE/LC/MS-MS. ABC transporters for metabolites such as metals, oligopeptides, phosphate, sugar, and amino acids, and membrane proteins involved in phosphotransferse systems, were identified as the predominant and abundant, cytoplasmic membrane proteins that would be essential for nutrient uptake, antibiotic resistance and virulence mechanisms. Our result supports that gel-based shotgun proteomics combined with sodium carbonate precipitation and ultracentrifugation is an effective method for analysis of cytoplasmic membrane proteins of S. pneumoniae.

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Application of Free-Flow Electrophoresis/2-Dimentional Gel Electrophoresis for Fractionation and Characterization of Native Proteome of Pseudomonas putida KT2440: Chi-Won Choi , Young S. Hong , Seung Il Kim; J. Microbiol. 2008;46(4):448-455. Published online August 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0063-9

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Abstract PDF

Free Flow Electrophoresis (FFE) is a liquid-based isoelectric focusing method. Unlike conventional in-gel fractionation of proteins, FFE can resolve proteins in their native forms and fractionation of subcellular compartments of the cell is also possible. To test the efficacy of the FFE method, the native cytosol proteome of a bacterium, Pseudomonas putida KT2440 was fractionated by FFE and the spectrum of protein elutes was characterized in association with 2-dimentional gel electrophoresis (2-DE). Major native proteins of P. putida KT2440 were eluted in the range of pH 4.8~6.0 in FFE, whereas the denatured proteome of P. putida KT2440 was widely distributed in the rage of pH 4~10 in the 2-DE analysis. In addition, one of the three FFE major fractions, which was eluted at pH 5.0, was further analyzed using 2-DE/MS-MS. Then, the pH range of identified proteins eluted in 2-DE/MS-MS was 4.72~5.89, indicating that observed pI values of native cytosolic proteomes in FFE were narrower than those of denatured cytosolic proteome. These results suggest that FFE fractionation and 2-DE/MS analysis may be useful tools for characterization of native proteomes of P. putida KT2440 and comparative analysis between denatured and native proteomes.

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Journal Article

The Physiological Role of CPR1 in Saccharomyces cerevisiae KNU5377 against Menadione Stress by Proteomics: Il Sup Kim , Hae Sun Yun , Sun Hye Kwak , Ing Nyol Jin; J. Microbiol. 2007;45(4):326-332.; DOI: https://doi.org/2565 [pii]

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Abstract PDF: In order to understand the functional role of CPR1 in Saccharomyces cerevisiae KNU5377 with regard to its multi-tolerance characteristics against high temperatures, inorganic acids, and oxidative stress conditions, whole cellular proteins were analyzed via liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS). This procedure was followed by two-dimensional (2-D) gel electrophoresis. Under menadione stress conditions, the 23 upregulated proteins were clearly identified only in the wildtype strain of KNU5377. Among the proteins, Sod1p, Tsa1p, Ahp1, Cpr1p, Cpr3, Ssb2p, and Hsp12p were identified as components of antioxidant systems or protein-folding related systems. The CPR1 protein could not be completely detected in the cpr1Δ mutant of KNU5377 and the other upregulated proteins in the wild-type strain evidenced a clear correlation with the results of immunoblot analysis. Moreover, a reduction in growth patterns (about 50%) could be observed in the cpr1Δ mutant, as compared with that of the wild-type strain under mild MD stress conditions. These results indicate that the upregulation of CPR1 may contribute to tolerance against MD as an inducer of oxidative stress.

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