Journal of Microbiology

Research Article

Lactic acid bacteria from Ethiopian traditional beverage, Tella: technological and metabolic profiles for industrial application: Gashaw Assefa Yehuala, Jaein Choe, Nurelegne Tefera Shibeshi, Kumsa Delessa, Asnake Desalegn, Mi-Kyung Park; J. Microbiol. 2025;63(1):e.2409008. Published online December 20, 2024; DOI: https://doi.org/10.71150/jm.2409008

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Abstract PDF: Tella is a traditional beverage widely accepted by consumers, despite the lack of product consistency owing to its reliance on natural fermentation. This study aimed to identify potential industrial lactic acid bacteria (LAB) starter cultures based on their technological properties. Seven LAB strains isolated from Tella were characterized for their carbohydrate utilization, salt content, temperature, and acid tolerances, growth and acidification rates, and metabolite profiles. Most strains efficiently utilized various carbohydrates, with Lactiplantibacillus plantarum TDM41 showing exceptional versatility. The strains exhibited similar growth characteristics. Principal component analysis of stress tolerance properties revealed that L. plantarum TDM41, Pediococcus pentosaceus TAA01, and Leuconostoc mesenteroides TDB22 exhibited superior tolerance ability. Strong acidification properties were detected in the L. plantarum TDM41, P. pentosaceus TAA01, and Leuconostoc mesenteroides TDB22 strains after 24 h incubation at 30°C. L. plantarum TDM41 displayed the fastest acidification rate throughout the analysis period. All LAB strains produced significant amounts of diverse organic acids, including lactic acid, citric acid, acetic acid, malic acid, and succinic acid, with lactic acid being the primary acid produced by each strain. Overall, strains L. plantarum TDM41 and P. pentosaceus TAA01 prove to be potential candidates for Tella industrial starter cultures and similar cereal products owing to their robust technological properties.

Journal Article

The Salmonella enterica EnvE is an Outer Membrane Lipoprotein and Its Gene Expression Leads to Transcriptional Repression of the Virulence Gene msgA: Sinyeon Kim, Yong Heon Lee; J. Microbiol. 2024;62(11):1013-1022. Published online November 15, 2024; DOI: https://doi.org/10.1007/s12275-024-00183-4

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Abstract: The envE gene of Salmonella enterica serovar Typhimurium is encoded within Salmonella Pathogenicity Island-11 (SPI-11) and is located immediately upstream of the virulence gene msgA (macrophage survival gene A) in the same transcriptional orientation. To date, the characteristics and roles of envE remain largely unexplored. In this study, we show that EnvE, a predicted lipoprotein, is localized on the outer membrane using sucrose gradient ultracentrifugation. Under oxidative stress conditions, envE transcription is suppressed, while msgA transcription is induced, indicating an inverse correlation between the mRNA levels of the two neighboring genes. Importantly, inactivation of envE leads to constitutive transcription of msgA regardless of the presence of oxidative stress. Moreover, trans-complementation of the envE mutant with a plasmid-borne envE fails to prevent the induction of msgA transcription, suggesting that envE functions as a cis-regulatory element rather than a trans-acting factor. We further show that both inactivation and complementation of envE confer wild-type levels of resistance to oxidative stress by ensuring the expression of msgA. Our data suggest that the S. enterica envE gene encodes an outer membrane lipoprotein, and its transcription represses msgA expression in a cis-acting manner, probably by transcriptional interference, although the exact molecular details are yet unclear.

Reviews

Extensive Genomic Rearrangement of Catalase-Less Cyanobloom-Forming Microcystis aeruginosa in Freshwater Ecosystems: Minkyung Kim, Jaejoon Jung, Wonjae Kim, Yerim Park, Che Ok Jeon, Woojun Park; J. Microbiol. 2024;62(11):933-950. Published online October 8, 2024; DOI: https://doi.org/10.1007/s12275-024-00172-7

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Abstract: Many of the world's freshwater ecosystems suffer from cyanobacteria-mediated blooms and their toxins. However, a mechanistic understanding of why and how Microcystis aeruginosa dominates over other freshwater cyanobacteria during warmer summers is lacking. This paper utilizes comparative genomics with other cyanobacteria and literature reviews to predict the gene functions and genomic architectures of M. aeruginosa based on complete genomes. The primary aim is to understand this species' survival and competitive strategies in warmer freshwater environments. M. aeruginosa strains exhibiting a high proportion of insertion sequences (~ 11%) possess genomic structures with low synteny across different strains. This indicates the occurrence of extensive genomic rearrangements and the presence of many possible diverse genotypes that result in greater population heterogeneities than those in other cyanobacteria in order to increase survivability during rapidly changing and threatening environmental challenges. Catalase-less M. aeruginosa strains are even vulnerable to low light intensity in freshwater environments with strong ultraviolet radiation. However, they can continuously grow with the help of various defense genes (e.g., egtBD, cruA, and mysABCD) and associated bacteria. The strong defense strategies against biological threats (e.g., antagonistic bacteria, protozoa, and cyanophages) are attributed to dense exopolysaccharide (EPS)-mediated aggregate formation with efficient buoyancy and the secondary metabolites of M. aeruginosa cells. Our review with extensive genome analysis suggests that the ecological vulnerability of M. aeruginosa cells can be overcome by diverse genotypes, secondary defense metabolites, reinforced EPS, and associated bacteria.

Reverse Zoonotic Transmission of SARS-CoV-2 and Monkeypox Virus: A Comprehensive Review: Chiranjib Chakraborty, Manojit Bhattacharya, Md Aminul Islam, Hatem Zayed, Elijah Ige Ohimain, Sang-Soo Lee, Prosun Bhattacharya, Kuldeep Dhama; J. Microbiol. 2024;62(5):337-354. Published online May 23, 2024; DOI: https://doi.org/10.1007/s12275-024-00138-9

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Abstract

Reverse zoonosis reveals the process of transmission of a pathogen through the human-animal interface and the spillback of the zoonotic pathogen. In this article, we methodically demonstrate various aspects of reverse zoonosis, with a comprehensive discussion of SARS-CoV-2 and MPXV reverse zoonosis. First, different components of reverse zoonosis, such as humans, different pathogens, and numerous animals (poultry, livestock, pets, wild animals, and zoo animals), have been demonstrated. Second, it explains the present status of reverse zoonosis with different pathogens during previous occurrences of various outbreaks, epidemics, and pandemics. Here, we present 25 examples from literature. Third, using several examples, we comprehensively illustrate the present status of the reverse zoonosis of SARS-CoV-2 and MPXV. Here, we have provided 17 examples of SARS-CoV-2 reverse zoonosis and two examples of MPXV reverse zoonosis. Fourth, we have described two significant aspects of reverse zoonosis: understanding the fundamental aspects of spillback and awareness. These two aspects are required to prevent reverse zoonosis from the current infection with two significant viruses. Finally, the One Health approach was discussed vividly, where we urge scientists from different areas to work collaboratively to solve the issue of reverse zoonosis.

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Development of a multiplex real-time PCR for the simultaneous detection of monkeypox virus clades I, II, and goatpox virus
Yongqiang Lin, Zijing Guo, Jinsong Chen, Xianwen Zhang, Long Zhou, Yanmin Li, Zhidong Zhang
Frontiers in Veterinary Science.2024;[Epub] CrossRef

Journal Articles

Comparative Transcriptomic Analysis of Flagellar‑Associated Genes in Salmonella Typhimurium and Its rnc Mutant: Seungmok Han , Ji-Won Byun , Minho Lee; J. Microbiol. 2024;62(1):33-48. Published online January 5, 2024; DOI: https://doi.org/10.1007/s12275-023-00099-5

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Abstract

Salmonella enterica serovar Typhimurium (S. Typhimurium) is a globally recognized foodborne pathogen that affects both animals and humans. Endoribonucleases mediate RNA processing and degradation in the adaptation of bacteria to environmental changes and have been linked to the pathogenicity of S. Typhimurium. Not much is known about the specific regulatory mechanisms of these enzymes in S. Typhimurium, particularly in the context of environmental adaptation. Thus, this study carried out a comparative transcriptomic analysis of wild-type S. Typhimurium SL1344 and its mutant (Δrnc), which lacks the rnc gene encoding RNase III, thereby elucidating the detailed regulatory characteristics that can be attributed to the rnc gene. Global gene expression analysis revealed that the Δrnc strain exhibited 410 upregulated and 301 downregulated genes (fold-change > 1.5 and p < 0.05), as compared to the wild-type strain. Subsequent bioinformatics analysis indicated that these differentially expressed genes are involved in various physiological functions, in both the wild-type and Δrnc strains. This study provides evidence for the critical role of RNase III as a general positive regulator of flagellar-associated genes and its involvement in the pathogenicity of S. Typhimurium.

Citations

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CspA regulates stress resistance, flagellar motility and biofilm formation in Salmonella Enteritidis
Xiang Li, Yan Cui, Xiaohui Sun, Chunlei Shi, Shoukui He, Xianming Shi
Food Bioscience.2025; 66: 106237. CrossRef
Influence of Flagella on Salmonella Enteritidis Sedimentation, Biofilm Formation, Disinfectant Resistance, and Interspecies Interactions
Huixue Hu, Jingguo Xu, Jingyu Chen, Chao Tang, Tianhao Zhou, Jun Wang, Zhuangli Kang
Foodborne Pathogens and Disease.2024;[Epub] CrossRef

Effects of Phosphorus‑dissolving Dark Septate Endophytes on the Growth of Blueberry: Qixin Luo , Rui Hou , Xiaojing Shang , Si Li; J. Microbiol. 2023;61(9):837-851. Published online October 5, 2023; DOI: https://doi.org/10.1007/s12275-023-00080-2

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Abstract

Dark septate endophytes (DSEs) are widely distributed and improve plant growth. DSEs secrete large amounts of enzymes to mineralize insoluble phosphorus in soil and convert it into soluble phosphorus, promoting plant uptake of phosphorus. However, the effects of DSEs with phosphate-solubilizing ability on host plants need further study. In this study, phosphorusdissolving DSEs were screened for growth-promoting effects. We isolated, identified and characterized three DSE species (Thozetella neonivea, Pezicula ericae and Hyaloscyphaceae sp.) showing phosphate-solubilizing ability. The impact of single, dual or triple inoculation of DSEs on blueberry plant characteristics was studied. Their effects on colonization intensity, seedling biomass, nutrients in plants and soil, and activities of plant resistance enzymes and soil enzymes were markedly upregulated relative to the control (P < 0.05). The available phosphorus and acid phosphatase levels in different combinations were significantly increased. These findings indicate that the application of the three DSEs may be valuable in facilitating the cultivation of blueberry with a higher biomass and improved plant quality.

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Diversity and Functional Roles of Root-Associated Endophytic Fungi in Two Dominant Pioneer Trees Reclaimed from a Metal Mine Slag Heap in Southwest China
Bo Bi, Yuqing Xiao, Xiaonan Xu, Qianqian Chen, Haiyan Li, Zhiwei Zhao, Tao Li
Microorganisms.2024; 12(10): 2067. CrossRef
Short-term organic fertilizer substitution increases sorghum yield by improving soil physicochemical characteristics and regulating microbial community structure
Mengen Nie, Guangqian Yue, Lei Wang, Yizhong Zhang
Frontiers in Plant Science.2024;[Epub] CrossRef

Lactobacillus rhamnosus KBL2290 Ameliorates Gut Inflammation in a Mouse Model of Dextran Sulfate Sodium‑Induced Colitis: Woon-ki Kim , Sung-gyu Min , Heeun Kwon , SungJun Park , Min Jung Jo , GwangPyo Ko; J. Microbiol. 2023;61(7):673-682. Published online June 14, 2023; DOI: https://doi.org/10.1007/s12275-023-00061-5

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Abstract

Ulcerative colitis, a major form of inflammatory bowel disease (IBD) associated with chronic colonic inflammation, may be induced via overreactive innate and adaptive immune responses. Restoration of gut microbiota abundance and diversity is important to control the pathogenesis. Lactobacillus spp., well-known probiotics, ameliorate IBD symptoms via various mechanisms, including modulation of cytokine production, restoration of gut tight junction activity and normal mucosal thickness, and alterations in the gut microbiota. Here, we studied the effects of oral administration of Lactobacillus rhamnosus (L. rhamnosus) KBL2290 from the feces of a healthy Korean individual to mice with DSS-induced colitis. Compared to the dextran sulfate sodium (DSS) + phosphate-buffered saline control group, the DSS + L. rhamnosus KBL2290 group evidenced significant improvements in colitis symptoms, including restoration of body weight and colon length, and decreases in the disease activity and histological scores, particularly reduced levels of pro-inflammatory cytokines and an elevated level of anti-inflammatory interleukin-10. Lactobacillus rhamnosus KBL2290 modulated the levels of mRNAs encoding chemokines and markers of inflammation; increased regulatory T cell numbers; and restored tight junction activity in the mouse colon. The relative abundances of genera Akkermansia, Lactococcus, Bilophila, and Prevotella increased significantly, as did the levels of butyrate and propionate (the major short-chain fatty acids). Therefore, oral L. rhamnosus KBL2290 may be a useful novel probiotic.

Citations

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Dietary supplementation with proanthocyanidins and rutin alleviates the symptoms of type 2 diabetes mice and regulates gut microbiota
Yue Gao, Binbin Huang, Yunyi Qin, Bing Qiao, Mengfei Ren, Liqing Cao, Yan Zhang, Maozhen Han
Frontiers in Microbiology.2025;[Epub] CrossRef
Probiotics: Shaping the gut immunological responses
Eirini Filidou, Leonidas Kandilogiannakis, Anne Shrewsbury, George Kolios, Katerina Kotzampassi
World Journal of Gastroenterology.2024; 30(15): 2096. CrossRef
Synergistic effects of probiotics with soy protein alleviate ulcerative colitis by repairing the intestinal barrier and regulating intestinal flora
Rentang Zhao, Bingqing Shang, Luyan Sun, Suyuan Lv, Guolong Liu, Qiu Wu, Yue Geng
Journal of Functional Foods.2024; 122: 106514. CrossRef
Lactobacillus gasseri BNR17 and Limosilactobacillus fermentum ABF21069 Ameliorate High Sucrose-Induced Obesity and Fatty Liver via Exopolysaccharide Production and β-oxidation
Yu Mi Jo, Yoon Ji Son, Seul-Ah Kim, Gyu Min Lee, Chang Won Ahn, Han-Oh Park, Ji-Hyun Yun
Journal of Microbiology.2024; 62(10): 907. CrossRef
Immune-Stimulating Potential of Lacticaseibacillus rhamnosus LM1019 in RAW 264.7 Cells and Immunosuppressed Mice Induced by Cyclophosphamide
Yeji You, Sung-Hwan Kim, Chul-Hong Kim, In-Hwan Kim, YoungSup Shin, Tae-Rahk Kim, Minn Sohn, Jeseong Park
Microorganisms.2023; 11(9): 2312. CrossRef

Review

Membrane Proteins as a Regulator for Antibiotic Persistence in Gram‑Negative Bacteria: Jia Xin Yee , Juhyun Kim , Jinki Yeom; J. Microbiol. 2023;61(3):331-341. Published online February 17, 2023; DOI: https://doi.org/10.1007/s12275-023-00024-w

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Abstract

Antibiotic treatment failure threatens our ability to control bacterial infections that can cause chronic diseases. Persister bacteria are a subpopulation of physiological variants that becomes highly tolerant to antibiotics. Membrane proteins play crucial roles in all living organisms to regulate cellular physiology. Although a diverse membrane component involved in persistence can result in antibiotic treatment failure, the regulations of antibiotic persistence by membrane proteins has not been fully understood. In this review, we summarize the recent advances in our understanding with regards to membrane proteins in Gram-negative bacteria as a regulator for antibiotic persistence, highlighting various physiological mechanisms in bacteria.

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Amino Acid and Au(III) Self-Assembled Supramolecular Nanozymes for Antimicrobial Applications
Yunzhu Xu, Dahai Hou, Min Zhao, Tong Zhao, Yong Ma, Yafeng Zhang, Yang Guo, Weiwei Tao, Hui Wang
ACS Applied Nano Materials.2024; 7(19): 22505. CrossRef
PhoPQ-mediated lipopolysaccharide modification governs intrinsic resistance to tetracycline and glycylcycline antibiotics in Escherichia coli
Byoung Jun Choi, Umji Choi, Dae-Beom Ryu, Chang-Ro Lee, Mehrad Hamidian, You-Hee Cho
mSystems.2024;[Epub] CrossRef
Bacterial Regulatory Mechanisms for the Control of Cellular Processes: Simple Organisms’ Complex Regulation
Jin-Won Lee
Journal of Microbiology.2023; 61(3): 273. CrossRef

Journal Articles

Alpha‑Hemolysin from Staphylococcus aureus Obstructs Yeast‑Hyphae Switching and Diminishes Pathogenicity in Candida albicans: Xiaoyu Yu , Yinhe Mao , Guangbo Li , Xianwei Wu , Qiankun Xuan , Simin Yang , Xiaoqing Chen , Qi Cao , Jian Guo , Jinhu Guo , Wenjuan Wu; J. Microbiol. 2023;61(2):233-243. Published online February 9, 2023; DOI: https://doi.org/10.1007/s12275-022-00006-4

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Abstract

The use of antibiotics can disrupt the body’s natural balance and increase the susteptibility of patients towards fungal infections. Candida albicans is a dimorphic opportunistic fungal pathogen with niches similar to those of bacteria. Our aim was to study the interaction between this pathogen and bacteria to facilitate the control of C. albicans infection. Alpha-hemolysin (Hla), a protein secreted from Staphylococcus aureus, causes cell wall damage and impedes the yeast–hyphae transition in C. albicans. Mechanistically, Hla stimulation triggered the formation of reactive oxygen species that damaged the cell wall and mitochondria of C. albicans. The cell cycle was arrested in the G0/G1 phase, CDC42 was downregulated, and Ywp1 was upregulated, disrupting yeast hyphae switching. Subsequently, hyphae development was inhibited. In mouse models, C. albicans pretreated with Hla reduced the C. albicans burden in skin and vaginal mucosal infections, suggesting that S. aureus Hla can inhibit hyphal development and reduce the pathogenicity of candidiasis in vivo.

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Candida albicans and Candida glabrata : global priority pathogens
Myrto Katsipoulaki, Mark H. T. Stappers, Dhara Malavia-Jones, Sascha Brunke, Bernhard Hube, Neil A. R. Gow, Joseph Heitman
Microbiology and Molecular Biology Reviews.2024;[Epub] CrossRef

Brachybacterium kimchii sp. nov. and Brachybacterium halotolerans subsp. kimchii subsp. nov., isolated from the Korean fermented vegetables, kimchi, and description of Brachybacterium halotolerans subsp. halotolerans subsp. nov.: Yujin Kim , Yeon Bee Kim , Juseok Kim , Joon Yong Kim , Tae Woong Whon , Won-Hyong Chung , Eun-Ji Song , Young-Do Nam , Se Hee Lee , Seong Woon Roh; J. Microbiol. 2022;60(7):678-688. Published online July 4, 2022; DOI: https://doi.org/10.1007/s12275-022-1581-6

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Abstract

Two Gram-stain-positive, oxidase-negative, catalase-positive, and coccus-shaped bacterial strains, designated CBA3104T and CBA3105T, were isolated from kimchi. Strain CBA3104T and CBA3105T grew at 10–35°C (optimum, 25°C and 30°C, respectively), at pH 6.0–8.5 (optimum, pH 6.5), and in the presence of 0–15% (w/v) NaCl (optimum, 5%). A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CBA3104T formed a distinct phylogenetic lineage within the genus Brachybacterium whereas strain CBA3105T was closely positioned with Brachybacterium halotolerans MASK1Z-5T. The 16S rRNA gene sequence similarity between strains CBA3104T and CBA3105T was 99.9%, but ANI and dDDH values between strains CBA3104T and CBA3105T were 93.61% and 51.5%, respectively. Strain CBA3104T showed lower ANI and dDDH values than species delineation against three closely related strains and type species of the genus Brachybacterium, however, strain CBA3105T showed 96.63% ANI value and 69.6% dDDH value with Brachybacterium halotolerans MASK1Z-5T. Among biochemical analysis results, strain CBA3104T could uniquely utilize bromo-succinic acid whereas only strain CBA3105T was positive for alkaline phosphatase and α-fucosidase among two novel strains, closely related strains, and type species of the genus Brachybacterium. Compared with strain CBA3105T and Brachybacterium halotolerans JCM 34339T, strain CBA3105T was differentially positive for acid production of D-arabinose, D-adonitol, and potassium 5-ketogluconate and enzyme activity of β-glucuronidase. Both strains contained menaquinone-7 as the dominant quinone. The cell-wall peptidoglycan of two novel strains contained meso-diaminopimelic acid. The major fatty acids of strains CBA3104T and CBA3105T were anteiso-C15:0, anteiso-C17:0, and iso-C16:0. The major polar lipids of both strains were phosphatidylglycerol and diphosphatidylglycerol. Strain CBA3104T possessed a uniquely higher abundance of tRNA (97 tRNAs) than four Brachybacterium strains used for comparative taxonomic analysis (54–62 tRNAs). Both the CBA3104T and CBA3105T strain harbored various oxidoreductase, transferase, hydrolase, and lyase as strain-specific functional genes compared to closely related strains and Brachybacterium type species. The results of biochemical/physiological, chemotaxonomic, and genomic analyses demonstrated that strains CBA3104T and CBA3105T represent a novel species of the genus Brachybacterium and a novel subspecies of B. halotolerans, respectively, for which the names Brachybacterium kimchii sp. nov. and B. halotolerans subsp. kimchii subsp. nov. are proposed. The type strains of the novel species and the novel subspecies are CBA3104T (= KCCM 43417T = JCM 34759T) and CBA3105T (= KCCM 43418T = JCM 34760T), respectively.

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Metagenomic Insights into the Taxonomic and Functional Features of Traditional Fermented Milk Products from Russia
Alexander G. Elcheninov, Kseniya S. Zayulina, Alexandra A. Klyukina, Mariia K. Kremneva, Ilya V. Kublanov, Tatiana V. Kochetkova
Microorganisms.2023; 12(1): 16. CrossRef
Validation List no. 208. 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 .2022;[Epub] CrossRef
Complete Genome Sequence of Brachybacterium sp. Strain NBEC-018, Isolated from Nematode-Infected Potatoes
Ling Chen, Yueying Wang, Nanxi Liu, Lei Zhu, Yong Min, Yimin Qiu, Yuxi Tian, Xiaoyan Liu, David Rasko
Microbiology Resource Announcements.2022;[Epub] CrossRef

Availability of polyamines affects virulence and survival of Neisseria meningitidis: Poonam Kanojiya , Riya Joshi , Sunil D. Saroj; J. Microbiol. 2022;60(6):640-648. Published online April 18, 2022; DOI: https://doi.org/10.1007/s12275-022-1589-y

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Abstract

Neisseria meningitidis is a Gram-negative human-restricted pathogen that asymptomatically resides in the human respiratory tract. Meningococcal meningitis and sepsis both are caused by N. meningitidis. The bacterium must adhere to host epithelial cells in order to colonize effectively. The factors that determine the initial attachment to the host and dispersal, are not well understood. Metabolites released by the host may aid in meningococcal colonization and dissemination. Polyamines are aliphatic polycations that assist in cell survival and proliferation. The virulence properties of N. meningitidis after exposure to polyamines were investigated. Adhesion to nasopharyngeal epithelial cells increased in the presence of spermine. Also, the relative expression of adhesin, pilE increased in the presence of spermine. Further, relative expression of ctrA, ctrB and lipB was upregulated in the presence of spermidine, indicating increased capsule formation. Upregulated capsule synthesis of N. meningitidis in the presence of spermidine allows it to survive in murine macrophages. The study suggests the importance of the extracellular pool of polyamines in promoting virulence in N. meningitidis.

Citations

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Epsilon-poly-l-lysine inhibits biofilm formation and aids dispersion in Acinetobacter baumannii
Ujjayni Saha, Sakshi Shinde, Savita Jadhav, Sunil D. Saroj
Medicine in Microecology.2024; 21: 100110. CrossRef
Effect of respiratory tract co-colonizers on initial attachment of Neisseria meningitidis
Poonam Kanojiya, Sunil D. Saroj
Archives of Microbiology.2023;[Epub] CrossRef
Antibiotics modulates the virulence of Neisseria meningitidis by regulating capsule synthesis
Tiyasa Haldar, Riya Joshi, Sunil D. Saroj
Microbial Pathogenesis.2023; 179: 106117. CrossRef

The human symbiont Bacteroides thetaiotaomicron promotes diet-induced obesity by regulating host lipid metabolism: Sang-Hyun Cho , Yong-Joon Cho , Joo-Hong Park; J. Microbiol. 2022;60(1):118-127. Published online December 29, 2021; DOI: https://doi.org/10.1007/s12275-022-1614-1

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Abstract

The gut microbiome plays an important role in lipid metabolism. Consumption of a high-fat diet (HFD) alters the bacterial communities in the gut, leading to metabolic disorders. Several bacterial species have been associated with diet-induced obesity, nonalcoholic fatty liver disease, and metabolic syndrome. However, the mechanisms underlying the control of lipid metabolism by symbiotic bacteria remain elusive. Here, we show that the human symbiont Bacteroides thetaiotaomicron aggravates metabolic disorders by promoting lipid digestion and absorption. Administration of B. thetaiotaomicron to HFD-fed mice promoted weight gain, elevated fasting glucose levels, and impaired glucose tolerance. Furthermore, B. thetaiotaomicron treatment upregulated the gene expression of the fatty acid transporter and increased fatty acid accumulation in the liver. B. thetaiotaomicron inhibits expression of the gene encoding a lipoprotein lipase inhibitor, angiopoietin-like protein 4 (ANGPTL4), thereby increasing lipase activity in the small intestine. In particular, we found that B. thetaiotaomicron induced the expression of hepcidin, the master regulator of iron metabolism and an antimicrobial peptide, in the liver. Hepcidin treatment resulted in a decrease in ANGPTL4 expression in Caco-2 cells, whereas treatment with an iron chelator restored ANGPTL4 expression in hepcidin- treated cells. These results indicate that B. thetaiotaomicron- mediated regulation of iron storage in intestinal epithelial cells may contribute to increased fat deposition and impaired glucose tolerance in HFD-fed mice.

Citations

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Integrating transcriptomics and Microbiomics to unravel the regulatory effects of Anji white tea on lipid metabolism in HFD-induced obese mice
Zhenyu Wang, Yifang Zhang, Xiaolei Shi, Xiaojun Li, Shangxiong Qi, Chunli Hu, Jin Zhao
Food Research International.2025; 206: 116101. CrossRef
Effects of dietary lipid and protein levels on metamorphosis, growth, metabolism and gut microbiota of tadpole (Lithobates catesbeianus)
Bo Zhu, Lei Zhong, Chuang Shao, Wenjie Xu, Shuhui Xiang, Shuiquan Fu, Yi Hu
Aquaculture.2024; 587: 740900. CrossRef
Beneficial metabolic effects of PAHSAs depend on the gut microbiota in diet-induced obese mice but not in chow-fed mice
Jennifer Lee, Kerry Wellenstein, Ali Rahnavard, Andrew T. Nelson, Marlena M. Holter, Bethany P. Cummings, Vladimir Yeliseyev, Angela Castoldi, Clary B. Clish, Lynn Bry, Dionicio Siegel, Barbara B. Kahn
Proceedings of the National Academy of Sciences.2024;[Epub] CrossRef
Anti-obesity activity of human gut microbiota Bacteroides stercoris KGMB02265
Seoung Woo Ryu, Jeong Chan Moon, Byeong Seob Oh, Seung Yeob Yu, Jeong Eun Bak, Eun Seo Heo, Jae-Ho Jeong, Ju Huck Lee
Archives of Microbiology.2024;[Epub] CrossRef
Bacteroides thetaiotaomicron ameliorates mouse hepatic steatosis through regulating gut microbial composition, gut-liver folate and unsaturated fatty acids metabolism
Hu Li, Xue-Kai Wang, Mei Tang, Lei Lei, Jian-Rui Li, Han Sun, Jing Jiang, Biao Dong, Hong-Ying Li, Jian-Dong Jiang, Zong-Gen Peng
Gut Microbes.2024;[Epub] CrossRef
Gut microbiota and metabolic modulation by supplementation of polysaccharide-producing Bacillus licheniformis from Tibetan Yaks: A comprehensive multi-omics analysis
Zhibo Zeng, Chuxian Quan, Shimeng Zhou, Saisai Gong, Mudassar Iqbal, Muhammad Fakhar-e-Alam Kulyar, Shah Nawaz, Kewei Li, Jiakui Li
International Journal of Biological Macromolecules.2024; 254: 127808. CrossRef
Insights from metagenomics into gut microbiome associated with acute coronary syndrome therapy
Yuee Guan, Shuru Zhao, Jing Li, Wenqian Zhang, Zhonghao Guo, Yi Luo, Xiaofei Jiang, Jun Li, Jianxiong Liu, Xi Chen, Zicheng Zhao, Zhe Zhang
Frontiers in Microbiology.2024;[Epub] CrossRef
Whole genome sequencing of mouse lines divergently selected for fatness (FLI) and leanness (FHI) revealed several genetic variants as candidates for novel obesity genes
Martin Šimon, Špela Mikec, Santosh S. Atanur, Janez Konc, Nicholas M. Morton, Simon Horvat, Tanja Kunej
Genes & Genomics.2024; 46(5): 557. CrossRef
Extract of Gardenia jasminoides Ellis Attenuates High-Fat Diet-Induced Glycolipid Metabolism Disorder in Rats by Targeting Gut Microbiota and TLR4/Myd88/NF-κB Pathway
Chenghao Lv, Xin Liu, Shiyun Chen, Yuhang Yi, Xinnian Wen, Tao Li, Si Qin
Antioxidants.2024; 13(3): 293. CrossRef
A microbial causal mediation analytic tool for health disparity and applications in body mass index
Chan Wang, Jiyoung Ahn, Thaddeus Tarpey, Stella S. Yi, Richard B. Hayes, Huilin Li
Microbiome.2023;[Epub] CrossRef
Differences in dietary patterns related to metabolic health by gut microbial enterotypes of Korean adults
Hwan-Hee Jang, Hwayoung Noh, Gichang Kim, Su-Yeon Cho, Hyeon-Jeong Kim, Jeong-Sook Choe, Jeongseon Kim, Augustin Scalbert, Marc J. Gunter, Oran Kwon, Hyesook Kim
Frontiers in Nutrition.2023;[Epub] CrossRef
Impact of diet and host genetics on the murine intestinal mycobiome
Yask Gupta, Anna Lara Ernst, Artem Vorobyev, Foteini Beltsiou, Detlef Zillikens, Katja Bieber, Simone Sanna-Cherchi, Angela M. Christiano, Christian D. Sadik, Ralf J. Ludwig, Tanya Sezin
Nature Communications.2023;[Epub] CrossRef
Effects of OsomeFood Clean Label plant-based meals on the gut microbiome
Dwiyanto Jacky, Chia Bibi, Look Melvin Chee Meng, Fong Jason, Tan Gwendoline, Lim Jeremy, Chong Chun Wie
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Antibacterial pathway of cefquinome against Staphylococcus aureus based on label-free quantitative proteomics analysis: Linglin Gao , Hao Zhu , Yun Chen , Yuhui Yang; J. Microbiol. 2021;59(12):1112-1124. Published online November 9, 2021; DOI: https://doi.org/10.1007/s12275-021-1201-x

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Abstract

Cefquinome (CEQ) is a novel β-lactam antibiotic that exhibits excellent antibacterial activity against Staphylococcus aureus. However, the bacterial protein targets of CEQ are unclear. To evaluate the relationship between the pharmacokinetic/ pharmacodynamic (PK/PD) parameters of CEQ and strains with varying degrees of resistance and to elucidate bacterial protein responses to CEQ treatment, label-free quantitative proteomics analysis was conducted. The sensitive S. aureus ATCC6538 and the resistant 2MIC and 8MIC were tested for differentially expressed proteins. An in vitro model was treated with different concentrations of CEQ (3, 5, or 10 μg/ml) with different terminal half-lives (2.5 or 5 h) at different intervals (12 or 24 h). Differentially expressed proteins were evaluated using Gene Ontology analysis followed by KEGG pathway enrichment analysis and STRING network analysis. RT-qPCR was performed to validate the differentially expressed proteins at the molecular level. The results showed that the degree of resistance increased in a cumulative manner and increased gradually with the extension of administration time. The resistant strain would not have appeared in the model only if %T > mutant prevention concentration ≥ 50%. The expression of 45 proteins significantly changed following CEQ treatment, among which 42 proteins were obviously upregulated and 3 were downregulated. GO analysis revealed that the differentially expressed proteins were mainly present on cells and the cell membrane, participated in metabolic and intracellular processes, and had catalytic and binding activities. The RPSO, SDHB, CITZ, ADK, and SAOUHSC 00113 genes in S. aureus may play important roles in the development of resistance to CEQ. These results provided important reference candidate proteins as targets for overcoming S. aureus resistance to CEQ.

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Detection of Antibiotic Resistance in Feline-Origin ESBL Escherichia coli from Different Areas of China and the Resistance Elimination of Garlic Oil to Cefquinome on ESBL E. coli
Yin-Chao Tong, Peng-Cheng Li, Yang Yang, Qing-Yi Lin, Jin-Tong Liu, Yi-Nuo Gao, Yi-Ning Zhang, Shuo Jin, Su-Zhu Qing, Fu-Shan Xing, Yun-Peng Fan, Ying-Qiu Liu, Wei-Ling Wang, Wei-Min Zhang, Wu-Ren Ma
International Journal of Molecular Sciences.2023; 24(11): 9627. CrossRef

Review

Overview of bioinformatic methods for analysis of antibiotic resistome from genome and metagenome data: Kihyun Lee , Dae-Wi Kim , Chang-Jun Cha; J. Microbiol. 2021;59(3):270-280. Published online February 23, 2021; DOI: https://doi.org/10.1007/s12275-021-0652-4

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Abstract

Whole genome and metagenome sequencing are powerful approaches that enable comprehensive cataloging and profiling of antibiotic resistance genes at scales ranging from a single clinical isolate to ecosystems. Recent studies deal with genomic and metagenomic data sets at larger scales; therefore, designing computational workflows that provide high efficiency and accuracy is becoming more important. In this review, we summarize the computational workflows used in the research field of antibiotic resistome based on genome or metagenome sequencing. We introduce workflows, software tools, and data resources that have been successfully employed in this rapidly developing field. The workflow described in this review can be used to list the known antibiotic resistance genes from genomes and metagenomes, quantitatively profile them, and investigate the epidemiological and evolutionary contexts behind their emergence and transmission. We also discuss how novel antibiotic resistance genes can be discovered and how the association between the resistome and mobilome can be explored.

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Journal Article

iTRAQ-facilitated proteomic analysis of Bacillus cereus via degradation of malachite green: Bobo Wang , Jing Lu , Junfang Zheng , Zhisheng Yu; J. Microbiol. 2021;59(2):142-150. Published online February 1, 2021; DOI: https://doi.org/10.1007/s12275-021-0441-0

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Abstract

The wide use of malachite green (MG) as a dye has caused substantial concern owing to its toxicity. Bacillus cereus can against the toxic effect of MG and efficiently decolourise it. However, detailed information regarding its underlying adaptation and degradation mechanisms based on proteomic data is scarce. In this study, the isobaric tags for relative and absolute quantitation (iTRAQ)-facilitated quantitative method was applied to analyse the molecular mechanisms by which B. cereus degrades MG. Based on this analysis, 209 upregulated proteins and 198 downregulated proteins were identified with a false discovery rate of 1% or less during MG biodegradation. Gene ontology and KEGG analysis determined that the differentially expressed proteins were enriched in metabolic processes, catalytic activity, antioxidant activity, and responses to stimuli. Furthermore, real-time qPCR was utilised to further confirm the regulated proteins involved in benzoate degradation. The proteins BCE_4076 (Acetyl-CoA acetyltransferase), BCE_5143 (Acetyl-CoA acetyltransferase), BCE_5144 (3-hydroxyacyl-CoA dehydrogenase), BCE_4651 (Enoyl-CoA hydratase), and BCE_5474 (3-hydroxyacyl-CoA dehydrogenase) involved in the benzoate degradation pathway may play an important role in the biodegradation of MG by B. cereus. The results of this study not only provide a comprehensive view of proteomic changes in B. cereus upon MG loading but also shed light on the mechanism underlying MG biodegradation by B. cereus.

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Engineering globins for efficient biodegradation of malachite green: two case studies of myoglobin and neuroglobin
Jiao Liu, Jia-Kun Xu, Hong Yuan, Xiao-Juan Wang, Shu-Qin Gao, Ge-Bo Wen, Xiang-Shi Tan, Ying-Wu Lin
RSC Advances.2022; 12(29): 18654. CrossRef

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