Journal of Microbiology

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Multi-omics to evaluate the protective mechanisms during Akkermansia muciniphila treatment of Candida albicans colonization and subsequent infection: Qiulin Luo, Huan Zhang, Youming Pu, Yingpu Wei, Jiangkun Yu, Xiaoshen Wang, Qin Cai, Ying Hu, Wenli Yuan; J. Microbiol. 2025;63(8):e2502007. Published online August 31, 2025; DOI: https://doi.org/10.71150/jm.2502007

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Abstract PDF Supplementary Material: Akkermansia muciniphila (AKK, A. muciniphila) fortifies the intestinal barrier, inhibits the colonization of pathogenic bacteria, and protects the host’s health. Nevertheless, the existing literature offers inadequate evidence to ascertain whether A. muciniphila can effectively treat Candida albicans (C. albicans) infections in vitro, and the underlying mechanisms remain ambiguous. This study, animal models were established through gavage with clinical isolates of C. albicans to induce gastrointestinal tract colonization and subsequent translocation infection. The models were subsequently administered A. muciniphila. We examined the analysis of 16S rRNA gene sequencing, metabolomics of colonic contents, and transcriptomics of colonic tissue. The intestinal barrier, inflammatory responses, and immune cell infiltration are analyzed. This study revealed that A. muciniphila markedly mitigated C. albicans translocation infection and modified the intestinal microbial community structure and metabolic attributes in model mice. After administering A. muciniphila to the translocation infection group, there was a notable increase in the prevalence of bacteria that produce short-chain fatty acids, including Eubacterium_F. Moreover, there was a significant increase in the levels of specific pathogens, including Faecalibaculum, Turicibacter, and Turicimonas. The study demonstrated that A. muciniphila treatment can improve the composition of intestinal microbiota and metabolites, augment the tight junctions of colonic tissue and diminish systemic inflammatory response. This presents an innovative therapeutic approach for the potential treatment of intestinal C. albicans infection using A. muciniphila.

Journal Article

Effect of exopolysaccharides of Paenibacillus polymyxa rhizobacteria on physiological and morphological variables of wheat seedlings: Irina V. Yegorenkova , Kristina V. Tregubova , Alexander I. Krasov , Nina V. Evseeva , Larisa Yu. Matora; J. Microbiol. 2021;59(8):729-735. Published online July 24, 2021; DOI: https://doi.org/10.1007/s12275-021-0623-9

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Paenibacillus polymyxa is a promising plant-growth-promoting rhizobacterium that associates with a wide range of host plants, including agronomically important ones. Inoculation of wheat seedlings with P. polymyxa strains CCM 1465 and 92 was found to increase the mitotic index of the root cells 1.2- and 1.6-fold, respectively. Treatment of seedlings with the exopolysaccharides (EPSs) of these strains increased the mitotic index 1.9-fold (P. polymyxa CCM 1465) and 2.8-fold (P. polymyxa 92). These increases indicate activation of cell division in the root meristems. Analysis of the morphometric variables of the seedlings showed that P. polymyxa CCM 1465, P. polymyxa 92, and their EPSs promoted wheat growth, increasing root and shoot length up to 22% and root and shoot dry weight up to 28%, as compared with the control. In addition, both strains were found to intensely colonize the seedling root surface. Thus, P. polymyxa EPSs are active metabolites that, along with whole cells, are responsible for the contact interactions of the bacteria with wheat roots and are implicated in the induction of plant responses to these interactions. The strains used in this work are of interest for further study to broaden the existing understanding of the mechanisms of plant–bacterial interactions and to develop effective biofertilizers for agricultural purposes.

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Review

Omics in gut microbiome analysis: Tae Woong Whon , Na-Ri Shin , Joon Yong Kim , Seong Woon Roh; J. Microbiol. 2021;59(3):292-297. Published online February 23, 2021; DOI: https://doi.org/10.1007/s12275-021-1004-0

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Abstract PDF

Our understanding of the interactions between microbial communities and their niche in the host gut has improved owing to recent advances in environmental microbial genomics. Integration of metagenomic and metataxonomic sequencing data with other omics data to study the gut microbiome has become increasingly common, but downstream analysis after data integration and interpretation of complex omics data remain challenging. Here, we review studies that have explored the gut microbiome signature using omics approaches, including metagenomics, metataxonomics, metatranscriptomics, and metabolomics. We further discuss recent analytics programs to analyze and integrate multi-omics datasets and further utilization of omics data with other advanced techniques, such as adaptive immune receptor repertoire sequencing, microbial culturomics, and machine learning, to evaluate important microbiome characteristics in the gut.

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Journal Articles

Poly-γ-glutamic acid productivity of Bacillus subtilis BsE1 has positive function in motility and biocontrol against Fusarium graminearum: Luyao Wang , Ning Wang , Dandan Mi , Yuming Luo , Jianhua Guo; J. Microbiol. 2017;55(7):554-560. Published online June 30, 2017; DOI: https://doi.org/10.1007/s12275-017-6589-y

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Abstract PDF

In this study, we investigate the relationship between γ-PGA productivity and biocontrol capacity of Bacillus subtilis BsE1; one bacterial isolate displayed 62.14% biocontrol efficacy against Fusarium root rot. The γ-PGA yield assay, motility assay, wheat root colonization assay, and biological control assay were analysed in different γ-PGA yield mutants of BsE1. The pgsB (PGA-synthase-CapB gene) deleted mutant of BsE1 reduced γ-PGA yield and exhibited apparent decline of in vitro motile ability. Deletion of pgsB impaired colonizing capacity of BsE1 on wheat root in 30 days, also lowered biocontrol efficacies from 62.08% (wild type BsE1) to 14.22% in greenhouse experiment against Fusarium root rot. The knockout of pgdS and ggt (genes relate to two γ-PGA degrading enzymes) on BsE1, leads to a considerable improvement in polymer yield and biocontrol efficacy, which attains higher level compared with wild type BsE1. Compared with ΔpgsB mutant, defense genes related to reactive oxygen species (ROS) and phytoalexin expressed changes by notable levels on wheat roots treated with BsE1, demonstrating the functional role γ-PGA plays in biocontrol against Fusarium root rot. γ-PGA is not only important to the motile and plant root colonization ability of BsE1, but also essential to the biological control performed by BsE1 against Fusarium root rot. Our goal in this study is to reveals a new perspective of BCAs screening on bacterial isolates, without good performance during pre-assays of antagonism ability.

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Colonization study of gfp-tagged Achromobacter marplatensis strain in sugar beet: YingWu Shi , Chun Li Li , HongMei Yang , Tao Zhang , Yan Gao , Min Chu , Jun Zeng , Qing Lin , OuTiKu Er , YuGuo Li , Xiangdong Huo , Kai Lou; J. Microbiol. 2017;55(4):267-272. Published online January 26, 2017; DOI: https://doi.org/10.1007/s12275-017-6371-1

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Abstract PDF

This study details the introduction of a gfp marker into an endophytic bacterial strain (Achromobacter marplatensis strain 17, isolated from sugar beet) to monitor its coloniza-tion of sugar beet (Beta. vulgaris L.). Stability of the plasmid encoding the gfp was confirmed in vitro for at least 72 h of bacterial growth and after the colonization of tissues, under nonselective conditions. The colonization was observed us-ing fluorescence microscopy and enumeration of culturable endophytes in inoculated sugar beet plants that grew for 10 or 20 days. gfp-Expressing strains were re-isolated from the inner tissues of surface-sterilized roots and stems of inocu-lated plants, and the survival of the Achromobacter marpla-tensis 17:gfp strain in plants 20 days after inoculation, even in the absence of selective pressure, suggests that it is good colonizer. These results also suggest that this strain could be a useful tool for the delivery of enzymes or other proteins into plants. In addition, the study highlights that sugar beet plants can be used effectively for detailed in vitro studies on the interactions between A. marplatensis strain 17 and its host, particularly if a gfp-tagged strain of the pathogen is used.

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Research Support, Non-U.S. Gov't

Pneumococcal wall teichoic acid is required for the pathogenesis of Streptococcus pneumoniae in murine models: Hongmei Xu , Libin Wang , Jian Huang , Yanqing Zhang , Feng Ma , Jianmin Wang , Wenchun Xu , Xuemei Zhang , Yibing Yin , Kaifeng Wu; J. Microbiol. 2015;53(2):147-154. Published online January 28, 2015; DOI: https://doi.org/10.1007/s12275-015-4616-4

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Abstract

Pneumococcal asymptomatic colonization of the respiratory tracts is a major risk for invasive pneumococcal disease. We have previously shown that pneumococcal wall teichoic acid (WTA) was involved in pneumococcal infection of sepsis and adherence to epithelial and endothelial cells. In this study, we investigated the contribution of pneumococcal WTA to bacterial colonization and dissemination in murine models. The result showed that nasopharynx colonizing D39 bacterial cells have a distinct phenotype showing an increased exposure of teichoic acids relative to medium-grown bacteria. The WTA-deficient mutants were impaired in their colonization to the nasopharynx and lungs, and led to a mild inflammation in the lungs at 36 h post-inoculation. Pretreatment of the murine nares with WTA reduced the ability of wild type D39 bacteria to colonize the nasopharynx. In addition, the WTA-deficient strain was impaired in its ability to invade the blood and brain following intranasal administration. WTA-deficient D39 strain was reduced in C3 deposition but was more susceptible to the killing by the neutrophils as compared with its parent strain. Our results also demonstrated that the WTA enhanced pneumococcal colonization and dissemination independently of the host strains. These results indicate that WTA plays an important role in pneumococcal pathogenesis, both in colonization and dissemination processes.

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spd1672, a novel in vivo-induced gene, affects inflammatory response in a murine model of Streptococcus pneumoniae infection
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Canadian Journal of Microbiology.2018; 64(6): 401. CrossRef
Lipoteichoic acid deficiency permits normal growth but impairs virulence of Streptococcus pneumoniae
Nathalie Heß, Franziska Waldow, Thomas P. Kohler, Manfred Rohde, Bernd Kreikemeyer, Alejandro Gómez-Mejia, Torsten Hain, Dominik Schwudke, Waldemar Vollmer, Sven Hammerschmidt, Nicolas Gisch
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Review

Minireivew] Protective Role of Gut Commensal Microbes against Intestinal Infections: My Young Yoon , Keehoon Lee , Sang Sun Yoon; J. Microbiol. 2014;52(12):983-989. Published online November 29, 2014; DOI: https://doi.org/10.1007/s12275-014-4655-2

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The human gastrointestinal tract is colonized by multitudes of microorganisms that exert beneficial effects on human health. Mounting evidence suggests that intestinal microbiota contributes to host resistance against enteropathogenic bacterial infection. However, molecular details that account for such an important role has just begun to be understood. The commensal microbes in the intestine regulate gut homeostasis through activating the development of host innate immunity and producing molecules with antimicrobial activities that directly inhibit propagation of pathogenic bacteria. Understanding the protective roles of gut microbiota will provide a better insight into the molecular basis that underlies complicated interaction among host-pathogen-symbiont. In this review, we highlighted recent findings that help us broaden our knowledge of the intestinal ecosystem and thereby come up with a better strategy for combating enteropathogenic infection.

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Research Support, Non-U.S. Gov't

Live/Dead State Is Not the Factor Influencing Adhesion Ability of Bifidobacterium animalis KLDS2.0603: Li-Qun Wang , Feng Zhao , Fei Liu , Xiang-Chen Meng; J. Microbiol. 2013;51(5):584-589. Published online September 14, 2013; DOI: https://doi.org/10.1007/s12275-013-2632-9

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Two essential requirements for probiotic bifidobacteria are that they be “live” and have “colonization” ability, following FAO/WHO guideline recommendations. The amount of research on the adhesion ability of bifidobacteria compares poorly with that of other probiotic bacteria, such as lactobacilli. The aim of the present study was to determine how gastrointestinal conditions affect the adhesion ability of bifidobacteria, and to investigate the relationship between the adhesion ability and the live/dead state of bifidobacteria. The adhesion ability of Bifidobacterium animalis KLDS2.0603 that had been subjected to the digestive enzymes, pepsin, trypsin, and proteinase K, was decreased significantly, but these treatments did not significantly change the strain’s survival rates, which were 98.78%, 97.60%, and 97.63% respectively. B. animalis KLDS2.0603 subjected to LiCl retained its adhesion ability but had a lower survival rate (59.28%) than the control group (P<0.01). B. animalis KLDS 2.0603 subjected to sodium metaperiodate exhibited higher adhesion ability than the control group (P<0.01), but the bacterial cells were killed totally. The results of transmission electron microscopy and laser scanning confocal microscopy showed that live/dead state of bifidobacteria was not one of the main factors that affected the adhesion ability of bifidobacteira, and that the substances affecting the adhesion ability of bifidobacteria were on the outer surface layer of the bifidobacterial cells. Our results also indicated that the substances related to the adhesion ability of bifidobacteria are proteinaceous. The above results will help us to understand the adhesion and colonization processes of bifidobacteria in the human gastrointestinal tract.

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Journal Article

Interrelationship of Bradyrhizobium sp. and Plant Growth-Promoting Bacteria in Cowpea: Survival and Symbiotic Performance: Artenisa Cerqueira Rodrigues , Jadson Emanuel Lopes Antunes , Antônio Félix da Costa , José de Paula Oliveira , Marcia do Vale Barreto Figueiredo; J. Microbiol. 2013;51(1):49-55. Published online March 2, 2013; DOI: https://doi.org/10.1007/s12275-013-2335-2

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The objective of this study was to evaluate the survival of cowpea during bacterial colonization and evaluate the interrelationship of the Bradyrhizobium sp. and plant growthpromoting bacteria (PGPB) as a potential method for optimizing symbiotic performance and cowpea development. Two experiments using the model legume cowpea cv. “IPA 206” were conducted. In the first experiment, cowpea seeds were disinfected, germinated and transferred to sterilized Gibson tubes containing a nitrogen-free nutritive solution. The experimental design was randomized blocks with 24 treatments [Bradyrhizobium sp. (BR 3267); 22 PGPB; absolute control (AC)] with three replicates. In the second experiment, seeds were disinfected, inoculated according to their specific treatment and grown in Leonard jars containing washed and autoclaved sand. The experimental design was randomized blocks with 24 treatments [BR 3267; 22 BR 3267 + PGPB; AC] with three replicates. Scanning electron microscopy demonstrated satisfactory colonization of the roots of inoculated plants. Additionally, synergism between BR 3267 and PGPB in cowpeas was observed, particularly in the BR 3267 + Paenibacillus graminis (MC 04.21) and BR 3267 + P. durus (C 04.50), which showed greater symbiotic performance and promotion of cowpea development.

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SP0454, A Putative Threonine Dehydratase, Is Required For Pneumococcal Virulence In Mice: WenJuan Yan , Hong Wang , WenChun Xu , KaiFeng Wu , Run Yao , XiuYu Xu , Jie Dong , YanQing Zhang , Wen Zhong , XueMei Zhang; J. Microbiol. 2012;50(3):511-517. Published online June 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2014-8

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Increasing pressure in antibiotic resistance and the requirement for the design of new vaccines are the objectives of clarifying the putative virulence factors in pneumococcal infection. In this study, the putative threonine dehydratase sp0454 was inactivated by erythromycin-resistance cassette replacement in Streptococcus pneumoniae CMCC 31203 strain. The sp0454 mutant was tested for cell growth, adherence, colonization, and virulence in a murine model. The Δsp0454 mutant showed decreased ability for colonization and impaired ability to adhere to A549 cells. However, the SP0454 polypeptide or its antiserum did not affect pneumococcal CMCC 31203 adhesion to A549 cells. The sp0454 deletion mutant was less virulent in a murine intranasal infection model. Real-time RT-PCR analysis revealed significant decrease of the pneumococcal surface antigen A expression in the sp0454 mutant. These results suggest that SP0454 contributes to virulence and colonization, which could be explained in part by modulating the expression of other virulence factors, such as psaA in pneumococcal infection.

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Many seeds carry endophytes, which ensure good chances of seedling colonization. In this work, we have studied the seed-borne bacterial flora of rice varieties cultivated in the northeast of Argentina. Surface-sterilized husked seeds of the rice cultivars CT6919, El Paso 144, CAMBA, and IRGA 417 contained an average of 5×106 CFU/g of mesophilic and copiotrophic bacteria. Microbiological, physiological, and molecular characterization of a set of 39 fast-growing isolates from the CT6919 seeds revealed an important diversity of seed-borne mesophiles and potential plant probiotic activities, including diazotrophy and antagonism of fungal pathogens. In fact, the seed-borne bacterial flora protected the rice seedlings against Curvularia sp. infection. The root colonization pattern of 2 Pantoea isolates from the seeds was studied by fluorescence microscopy of the inoculated axenic rice seedlings. Both isolates strongly colonized the site of emergence of the lateral roots and lenticels, which may represent the entry sites for endophytic spreading. These findings suggest that rice plants allow grain colonization by bacterial species that may act as natural biofertilizers and bioprotectives early from seed germination.

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Gibberellins-Producing Rhizobacteria Increase Endogenous Gibberellins Content and Promote Growth of Red Peppers: Gil-Jae Joo , Young-Mog Kim , Jung-Tae Kim , In-Koo Rhee , Jin-Ho Kim , In-Jung Lee; J. Microbiol. 2005;43(6):510-515.; DOI: https://doi.org/2297 [pii]

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Abstract PDF: The growth of red pepper plants was enhanced by treatment with the rhizobacterium, Bacillus cereus MJ-1. Red pepper shoots showed a 1.38-fold increase in fresh weight (fw) and roots showed a 1.28-fold fw gain. This plant growth-promoting rhizobacterium (PGPR) has been reported to produce gibberellins (GAs). Other GAs-producing rhizobacteria, Bacillus macroides CJ-29 and Bacillus pumilus CJ-69, also enhanced the fw of the plants. They were less effective than B. cereus MJ-1, though. The endogenous GAs content of pepper shoots inoculated with MJ-1 was also higher than in shoots inoculated with CJ-29 or CJ-69. When inoculated with MJ-1, bacterial colonization rate of the roots was higher than that of roots inoculated with CJ-29 or CJ-69. These results support the idea that the plant growth-promoting effect of the bacteria also positively related with the efficiency of root colonization by the bacteria. In addition, we identified the major endogenous GAs of the red pepper as originating from both the early C-13 hydroxylation and the early non C-13 hydroxylation pathways, with the latter being the predominant pathway of GA biosynthesis in red pepper shoots.

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