Journal of Microbiology

Journal Article

miR-135b Aggravates Fusobacterium nucleatum-Induced Cisplatin Resistance in Colorectal Cancer by Targeting KLF13: Wei Zeng , Jia Pan , Guannan Ye; J. Microbiol. 2024;62(2):63-73. Published online February 24, 2024; DOI: https://doi.org/10.1007/s12275-023-00100-1

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Abstract: Cisplatin resistance is the main cause of colorectal cancer (CRC) treatment failure, and the cause has been reported to be related to Fusobacterium nucleatum (Fn) infection. In this study, we explored the role of Fn in regulating cisplatin resistance of CRC cells and its underlying mechanism involved. The mRNA and protein expressions were examined by qRT-PCR and western blot. Cell proliferation and cell apoptosis were assessed using CCK8 and flow cytometry assays, respectively. Dual-luciferase reporter gene assay was adopted to analyze the molecular interactions. Herein, our results revealed that Fn abundance and miR-135b expression were markedly elevated in CRC tissues, with a favorable association between the two. Moreover, Fn infection could increase miR-135b expression via a concentration-dependent manner, and it also enhanced cell proliferation but reduced apoptosis and cisplatin sensitivity by upregulating miR-135b. Moreover, KLF13 was proved as a downstream target of miR-135b, of which overexpression greatly diminished the promoting effect of miR-135b or Fn-mediated cisplatin resistance in CRC cells. In addition, it was observed that upstream 2.5 kb fragment of miR-135b promoter could be interacted by β-catenin/TCF4 complex, which was proved as an effector signaling of Fn. LF3, a blocker of β-catenin/TCF4 complex, was confirmed to diminish the promoting role of Fn on miR-135b expression. Thus, it could be concluded that Fn activated miR-135b expression through TCF4/β-catenin complex, thereby inhibiting KLF13 expression and promoting cisplatin resistance in CRC.

Review

Influence of Microbiota on Vaccine Effectiveness: “Is the Microbiota the Key to Vaccine‑induced Responses?”: So-Hee Hong; J. Microbiol. 2023;61(5):483-494. Published online April 13, 2023; DOI: https://doi.org/10.1007/s12275-023-00044-6

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Abstract: Vaccines are one of the most powerful tools for preventing infectious diseases. To effectively fight pathogens, vaccines should induce potent and long-lasting immune responses that are specific to the pathogens. However, not all vaccines can induce effective immune responses, and the responses vary greatly among individuals and populations. Although several factors, such as age, host genetics, nutritional status, and region, affect the effectiveness of vaccines, increasing data have suggested that the gut microbiota is critically associated with vaccine-induced immune responses. In this review, I discuss how gut microbiota affects vaccine effectiveness based on the clinical and preclinical data, and summarize possible underlying mechanisms related to the adjuvant effects of microbiota. A better understanding of the link between vaccine-induced immune responses and the gut microbiota using high-throughput technology and sophisticated system vaccinology approaches could provide crucial insights for designing effective personalized preventive and therapeutic vaccination strategies.

Journal Articles

Flavobacterium zhairuonensis sp. nov., a gliding bacterium isolated from marine sediment of the East China Sea: Sanjit Chandra Debnath , Ahmed Mohammed Abdo Miyah , Can Chen , Huan Sheng , Xue-Wei Xu , Yue-Hong Wu , Dao-Qiong Zheng , Jin-Zhong Xu , Ya-Nan Di , Pin-Mei Wang , Li Shen; J. Microbiol. 2019;57(12):1065-1072. Published online September 27, 2019; DOI: https://doi.org/10.1007/s12275-019-9194-4

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Abstract: A yellow pigmented, Gram-stain-negative, aerobic bacterium designated A5.7T was studied to evaluate the taxonomic position following the modern polyphasic approach. The strain was isolated from sediments near Zhairuo Island, which is situated in the East China Sea. Cells were non-spore forming rods without flagella but showed motility by gliding. Growth was observed at 15–35°C (optimum 28°C), pH 6.0–9.0 (optimum pH 6.5) and 0–2% (w/v) NaCl (optimum 0–0.5%) in LB broth. The major respiratory quinone of A5.7T was menaquinone 6. The major polar lipid of A5.7T was phosphatidylethanolamine and the predominant fatty acids (> 5%) were iso-C15:0, iso-C17:0 3-OH, C15:1 ω6c, iso-C15:0 3-OH, iso-C15:1 G, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c) and summed feature 9 (iso-C17:1 ω9c and/or C16:0 10-methyl). Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belongs to the genus Flavobacterium and shares the highest sequence similarities with Flavobacterium sharifuzzamanii A7.6T (98.5%), Flavobacterium tistrianum GB 56.1T (98.3%), Flavobacterium nitrogenifigens NXU-44T (97.8%), Flavobacterium anhuiense D3T (97.6%), Flavobacterium ginsenosidimutans THG 01T (97.6%), and Flavobacterium foetidum CJ42T (97.6%). Digital DNA-DNA hybridization and average nucleotide identity values between the strain and its closest phylogenetic neighbors showed the ranges from 19.6 to 34.1% and 73.7 to 87.9%, respectively. Therefore, based on polyphasic characteristics, strain A5.7T represents a novel species of the genus Flavobacterium for which the name Flavobacterium zhairuonensis sp. nov. is proposed. The type strain is A5.7T (= KCTC 62406T = MCCC 1K03494T).

Whole genome analysis of Aspergillus sojae SMF 134 supports its merits as a starter for soybean fermentation: Kang Uk Kim , Kyung Min Kim , Yong-Ho Choi , Byung-Serk Hurh , Inhyung Lee; J. Microbiol. 2019;57(10):874-883. Published online June 27, 2019; DOI: https://doi.org/10.1007/s12275-019-9152-1

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Abstract: Aspergillus sojae is a koji (starter) mold that has been applied for food fermentation in Asia. The whole genome of A. sojae SMF 134, which was isolated from meju (Korean soybean fermented brick), was analyzed at the genomic level to evaluate its potential as a starter for soybean fermentation. The genome size was 40.1 Mbp, which was expected to be composed of eight chromosomes with 13,748 ORFs. Strain SMF 134 had a total of 151 protease genes, among which two more leucine aminopeptidase (lap) genes were found in addition to the previously known lap1, and three γ-glutamyltranspeptidase (ggt) genes were newly identified. Such genomic characteristics of SMF 134 with many protease and flavor-related (lap and ggt) genes support its merits as a starter for soybean fermentation. In addition, this first complete genome of A. sojae will allow for further genetic studies to better understand the production of various enzymes, including proteases, LAPs, and GGTs, as well as other characteristics as a starter mold for soybean fermentation.

Acinetobacter chinensis, a novel Acinetobacter species, carrying blaNDM-1, recovered from hospital sewage: Yiyi Hu , Yu Feng , Jiayuan Qin , Xiaoxia Zhang , Zhiyong Zong; J. Microbiol. 2019;57(5):350-355. Published online February 26, 2019; DOI: https://doi.org/10.1007/s12275-019-8485-0

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Abstract: Two strains of the genus Acinetobacter, named WCHAc- 010005 and WCHAc010052, were isolated from hospital sewage at West China Hospital in Chengdu, China. The two strains were found to be resistant to carbapenems due to the presence of carbapenemase gene blaNDM-1. Based on the comparative analysis of the rpoB sequence, the two strains formed a strongly supported and internally coherent cluster (intracluster identity of 98.7%), which was clearly separated from all known Acinetobacter species (≤ 83.4%). The two strains also formed a tight and distinct cluster based on the genuswide comparison of whole-cell mass fingerprints generated by MALDI-TOF mass spectrometry. In addition, the combination of their ability to assimilate malonate but not benzoate, and the inability to grow at 37°C could distinguish the two strains from all known Acinetobacter species. The two strains were subjected to whole genome sequencing using both short-read Illumina HiSeq2500 platform and the longread MinION sequencer. The average nucleotide identity and in silico DNA-DNA hybridization value between the genomes of WCHAc010005 and WCHAc010052 was 96.69% and 74.3% respectively, whereas those between the two genomes and the known Acinetobacter species were < 80% and < 30%, respectively. Therefore, the two strains represent a novel species of the genus Acinetobacter, for which the name Acinetobacter chinensis sp. nov. is proposed, and the type strain is WCHAc- 010005T (= GDMCC 1.1232T = KCTC 62813T).

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

Full Sequence Analysis and Characterization of a Human Astrovirus Type 1 Isolate from South Korea: Sung-Geun Lee , Lae-Hyung Kang , Weon-Hwa Jheong , Mi-Hwa Oh , Gyu-Cheol Lee , Sujeong Park , Soon-Young Paik; J. Microbiol. 2013;51(1):123-129. Published online March 2, 2013; DOI: https://doi.org/10.1007/s12275-013-2505-2

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Abstract: Human astroviruses are recognized as an important cause of infantile gastroenteritis around the world. In South Korea, sporadic cases of HAstV infection have been reported since 2002. However, hitherto, there have been no studies reporting the whole genome sequence of an HAstV isolate from South Korea. Hence, we sequenced and analyzed the entire genome of an HAstV-1 strain (lhar) that was isolated in Seoul, South Korea. The whole-genome sequence analysis revealed 3 open reading frames comprising the whole genome: ORF1a (2,763 bp), ORF1b (1,548 bp), and ORF2 (2,364 bp). The lhar strain showed amino acid identities with 8 other reference strains of 87.6–98.7%, 94.2–98.8%, and 62.6–99.0% in the ORF1a, ORF1b, and ORF2 regions, respectively. The amino acid sequence of the capsid region encoded by ORF2 was compared with a total of 19 HAstV-1 strains and 8 HAstVs reference strains isolated in various countries. This revealed 1 amino acid substitution, at aa412 (Pro → Arg) in ORF2. This study, the first to report the fulllength sequence of an HAstV isolated in South Korea, is meaningful in that it can be used as a full-length HAstV sequence standard for future comparison studies. It may also prove useful to the field of public health field by facilitating the diagnosis and the prediction of new emerging variants.

Comparative Analysis of the Genomes of Bombyx mandarina and Bombyx mori Nucleopolyhedroviruses: Yi-Peng Xu , Zheng-Pei Ye , Chang-Ying Niu , Yan-Yuan Bao , Wen-Bing Wang , Wei-De Shen , Chuan-Xi Zhang; J. Microbiol. 2010;48(1):102-110. Published online March 11, 2010; DOI: https://doi.org/10.1007/s12275-009-0197-4

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Abstract: The Bombyx mandarina nucleopolyhedrovirus (BomaNPV) S1 strain can infect the silkworm, Bombyx mori, but is significantly less virulent than B. mori nucleopolyhedrovirus (BmNPV) T3 strain. The complete nucleotide sequence of the S1 strain of BomaNPV was determined and compared with the BmNPV T3 strain. The circular, double stranded DNA genome of the S1 strain was 126,770 nucleotides long (GenBank accession no. FJ882854), with a G+C content of 40.23%. The genome contained 133 potential ORFs. Most of the putative proteins were more than 96% identical to homologs in the BmNPV T3 strain, except for bro-a, lef-12, bro-c, and bro-d. Compared with the BmNPV T3 strain, however, this genome did not encode the bro-b and bro-e genes. In addition, hr1 lacked two repeat units, while hr2L, hr2R, hr3, hr4L, hr4R, and hr5 were similar to the corresponding hrs in the T3 strain. The sequence strongly suggested that BomaNPV and BmNPV are variants with each other, and supported the idea that baculovirus strain heterogeneity may often be caused by variation in the hrs and bro genes.

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