Journal of Microbiology

Journal Article

Enzyme activity of Aspergillus section Nigri strains isolated from the Korean fermentation starter, nuruk: Eunji Jeong , Jeong-Ah Seo; J. Microbiol. 2022;60(10):998-1006. Published online August 19, 2022; DOI: https://doi.org/10.1007/s12275-022-2071-6

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Aspergillus section Nigri is a fungus used industrially because of its ability to produce enzymes such as cellulolytic, amylolytic and proteolytic enzymes. In this study, we obtained twentyeight strains of Aspergillus section Nigri from the traditional Korean fermentation starter, nuruk, which is known as a mixed culture of enzymatic filamentous fungi and yeasts. All strains were identified as Aspergillus section Nigri through combined phylogenetic analysis using partial β-tubulin and calmodulin gene sequences. The cellulase, amylase and protease activities of Korean strains were measured and compared with ten reference strains of Aspergillus niger. Most Korean strains showed higher cellulolytic activity than reference strains, and Aspergillus neoniger KCN5 showed the highest β-glucosidase activity. Two-thirds of the Korean strains showed similar levels of α- and glucoamylase activity as the reference strains. The protease activity of Aspergillus section Nigri strains was the highest at pH 3.0, and A. niger KSJ2 showed the highest acidic protease activity. By comparing ten reference strains and twenty-eight Korean strains, our results suggested useful Aspergillus section Nigri strains from nuruk with high enzyme activity, such as KCN5 and KSJ2, and their potential for industrial applications as enzyme producers.

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Effect of Aspergillus niger Fermentation on the Metabolites in Corn Stalks
Zhen Fan, Tianming Chen, Guolin Cai, Xiaoyu Huang, Suchuan Zhong, Xiaoming Li, Enping Zhang
Fermentation.2023; 9(1): 50. CrossRef

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

A Functional and Phylogenetic Comparison of Quorum Sensing Related Genes in Brucella melitensis 16M: Aniel Jessica Leticia Brambila-Tapia , Ernesto Pérez-Rueda; J. Microbiol. 2014;52(8):709-715. Published online July 4, 2014; DOI: https://doi.org/10.1007/s12275-014-3570-x

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Abstract

A quorum-sensing (QS) system is involved in Brucella melitensis survival inside the host cell. Two transcriptional regulators identified in B. melitensis, BlxR and VjbR, regulate the expression of virB, an operon required for bacterial intracellular persistence. In this work, 628 genes affected by VjbR and 124 by BlxR were analyzed to gain insights into their functional and taxonomical distributions among the Bacteria and Archaea cellular domains. In this regard, the Cluster of Orthologous Groups (COG) genes and orthologous genes in 789 nonredundant bacterial and archaeal genomes were obtained and compared against a group of randomly selected genes. From these analyses, we found 71 coaffected genes between VjbR and BlxR. In the COG comparison, VjbR activated genes associated with intracellular trafficking, secretion and vesicular transport and defense mechanisms, while BlxR affected genes related to energy production and conversion (with an equal effect) and translation, ribosomal structure and biogenesis, posttranslational modifications and carbohydrate and amino acid metabolism (with a negative effect). When the taxonomical distribution of orthologous genes was evaluated, the VjbR- and BlxRrelated genes presented more orthologous genes in Crenarchaeota (Archaea), Firmicutes, and Tenericutes and fewer genes in Proteobacteria than expected by chance. These findings suggest that QS system exert a fine-tuning modulation of gene expression, by which VjbR activates genes related to infection persistence and defense, while BlxR represses general bacterial metabolism for intracellular adaptations. Finally, these affected genes present a degree of presence among Bacteria and Archaea genomes that is different from that expected by chance.

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Brucella mediates autophagy, inflammation, and apoptosis to escape host killing
Yaqiong Qin, Gengxu Zhou, Fengyuan Jiao, Chuan Cheng, Chi Meng, Lingjie Wang, Shengping Wu, Cailiang Fan, Jixiang Li, Bo Zhou, Yuefeng Chu, Hanwei Jiao
Frontiers in Cellular and Infection Microbiology.2024;[Epub] CrossRef
The VirB System Plays a Crucial Role in Brucella Intracellular Infection
Xue Xiong, Bowen Li, Zhixiong Zhou, Guojing Gu, Mengjuan Li, Jun Liu, Hanwei Jiao
International Journal of Molecular Sciences.2021; 22(24): 13637. CrossRef
Uncovering the Hidden Credentials ofBrucellaVirulence
R. Martin Roop, Ian S. Barton, Dariel Hopersberger, Daniel W. Martin
Microbiology and Molecular Biology Reviews.2021;[Epub] CrossRef
Rich Repertoire of Quorum Sensing Protein Coding Sequences in CPR and DPANN Associated with Interspecies and Interkingdom Communication
Charles Bernard, Romain Lannes, Yanyan Li, Éric Bapteste, Philippe Lopez, Robert G. Beiko
mSystems.2020;[Epub] CrossRef
BASI74, a Virulence-Related sRNA in Brucella abortus
Hao Dong, Xiaowei Peng, Yufu Liu, Tonglei Wu, Xiaolei Wang, Yanyan De, Tao Han, Lin Yuan, Jiabo Ding, Chuanbin Wang, Qingmin Wu
Frontiers in Microbiology.2018;[Epub] CrossRef

Simultaneous Detection of Major Enteric Viruses Using a Combimatrix Microarray: Ju-Mi Kim , Sung Yeon Kim , Young Bin Park , Hye Jin Kim , Byung Sup Min , Jae-Chang Cho , Jai Myung Yang , You-Hee Cho , GwangPyo Ko; J. Microbiol. 2012;50(6):970-977. Published online October 27, 2012; DOI: https://doi.org/10.1007/s12275-012-2228-9

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Abstract: Various enteric viruses including norovirus, rotavirus, adenovirus, and astrovirus are the major etiological agents of food-borne and water-borne disease outbreaks and frequently cause non-bacterial gastroenteritis worldwide. Sensitive and high-throughput detection methods for these viral pathogens are compulsory for diagnosing viral pathogens and subsequently improving public health. Hence, we developed a sensitive, specific, and high-throughput analytical assay to detect most major enteric viral pathogens using “Combimatrix” platform oligonucleotide probes. In order to detect four different enteric viral pathogens in a sensitive and simultaneous manner, we first developed a multiplex RT-PCR assay targeting partial gene sequences of these viruses with fluorescent labeling for the subsequent microarray. Then, five olignonucleotides specific to each of the four major enteric viruses were selected for the microarray from the oligonulceotide pools targeting the specific genes obtained by multiplex PCR of these viruses. The oligonucleotide microarray was evaluated against stool specimens containing single or mixed viral species. As a result, we demonstrated that the multiplex RT-PCR assay specifically amplified partial sequences of four enteric viruses and the subsequent microarray assay was capable of sensitive and simultaneous detection of those viruses. The developed method could be useful for diagnosing enteric viruses in both clinical and environmental specimens.

Parallel Gene Loss and Acquisition Among Strains of Different Brucella Species and Biovars: Zhijun Zhong , Yufei Wang , Jie Xu , Yanfen Chen , Yuehua Ke , Xiaoyan Zhou , Xitong Yuan , Dongsheng Zhou , Yi Yang , Ruifu Yang , Guangneng Peng , Hai Jiang , Jing Yuan , Hongbin Song , Buyun Cui , Liuyu Huang , Zeliang Chen; J. Microbiol. 2012;50(4):567-574. Published online August 25, 2012; DOI: https://doi.org/10.1007/s12275-012-2022-8

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Abstract: The genus Brucella is divided into six species; of these, B. melitensis and B. abortus are pathogenic to humans, and B. ovis and B. neotomae are nonpathogenic to humans. The definition of gene loss and acquisition is essential for understanding Brucella’s ecology, evolutionary history, and host relationships. A DNA microarray containing unique genes of B. melitensis Type strain 16MT and B. abortus 9-941 was constructed and used to determine the gene contents of the representative strains of Brucella. Phylogenetic relationships were inferred from sequences of housekeeping genes. Gene loss and acquisition of different Brucella species were inferred. A total of 214 genes were found to be differentially distributed, and 173 of them were clustered into 15 genomic islands (GIs). Evidence of horizontal gene transfer was observed for 10 GIs. Phylogenetic analysis indicated that the 19 strains formed five clades, and some of the GIs had been lost or acquired independently among the different lineages. The derivation of Brucella lineages is concomitant with the parallel loss or acquisition of GIs, indicating a complex interaction between various Brucella species and hosts.

NOTE] Evaluation of a Fosmid-Clone-Based Microarray for Comparative Analysis of Swine Fecal Metagenomes: Soo-Je Park , Dong-Hwan Kim , Man-Young Jung , So-Jeong Kim , Hongik Kim , Yang-Hoon Kim , Jong-Chan Chae , Sung-Keun Rhee; J. Microbiol. 2012;50(4):684-688. Published online July 21, 2012; DOI: https://doi.org/10.1007/s12275-012-2115-4

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Abstract: Glass slide arrayed with fosmid clone DNAs generated from swine feces as probes were fabricated and used as a metagenome microarray (MGA). MGA appeared to be specific to their corresponding target genomic fragments. The detection limit was 10 ng of genomic DNA (ca. 106 bacterial cells) in the presence of 1000 ng of background DNA. Linear relationships between the signal intensity and the target DNA (20–100 ng) were observed (r2=0.98). Application of MGA to the comparison of swine fecal metagenomes suggested that the microbial community composition of swine intestine could be dependent on the health state of swine.

Detection of Representative Enteropathogenic Bacteria, Vibrio spp., Pathogenic Escherichia coli, Salmonella spp., Shigella spp., and Yersinia enterocolitica, Using a Virulence Factor Gene-Based Oligonucleotide Microarray§: Dong-Hun Kim , Bok-Kwon Lee , Yong-Dae Kim , Sung-Keun Rhee , Young-Chang Kim; J. Microbiol. 2010;48(5):682-688. Published online November 3, 2010; DOI: https://doi.org/10.1007/s12275-010-0119-5

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Abstract: Rapid identification of enteropathogenic bacteria in stool samples is critical for clinical diagnosis and antimicrobial therapy. In this study, we describe the development of an approach that couples multiplex PCR with hybridization to a DNA microarray, to allow the simultaneous detection of the 10 pathogens. The microarray was synthesized with 20-mer oligonucleotide probes that were designed to be specific for virulencefactor genes of each strain. The detection limit for genomic DNA from a single strain was approximately 10 fg. In the presence of heterogeneous non-target DNA, the detection sensitivity of the array decreased to approximately 100 fg. We did not observe any non-specific hybridization. In addition, we successfully used this oligonucleotide-based DNA microarray to identify the causative agents in clinical stool samples from patients with food-borne enteritis.

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

Phenotypic Diversity of Escherichia coli O157:H7 Strains Associated with the Plasmid O157: Ji Youn Lim , Joon Bae Hong , Haiqing Sheng , Smriti Shringi , Rajinder Kaul , Thomas E. Besser , Carolyn J. Hovde; J. Microbiol. 2010;48(3):347-357. Published online June 23, 2010; DOI: https://doi.org/10.1007/s12275-010-9228-4

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Abstract: Escherichia coli O157:H7, a food-borne pathogen, causes hemorrhagic colitis and the hemolytic-uremic syndrome. A putative virulence factor of E. coli O157:H7 is a 60-MDa plasmid (pO157) found in 99% of all clinical isolates and many bovine-derived strains. The well characterized E. coli O157:H7 Sakai strain (Sakai) and its pO157-cured derivative (Sakai-Cu) were compared for phenotypic differences. Sakai-Cu had enhanced survival in synthetic gastric fluid, did not colonize cattle as well as wild-type Sakai, and had unchanged growth rates and tolerance to salt and heat. These results are consistent with our previous findings with another E. coli O157:H7 disease outbreak isolate ATCC 43894 and its pO157-cured (43894-Cu). However, despite the essentially sequence identical pO157 in these strains, Sakai-Cu had changes in antibiotic susceptibility and motility that did not occur in the 43894-Cu strain. This unexpected result was systematically analyzed using phenotypic microarrays testing 1,920 conditions with Sakai, 43894, and the plasmid-cured mutants. The influence of the pO157 differed between strains on a wide number of growth/survival conditions. Relative expression of genes related to acid resistance (gadA, gadX, and rpoS) and flagella production (fliC and flhD) were tested using quantitative real-time PCR and gadA and rpoS expression differed between Sakai-Cu and 43894-Cu. The strain-specific differences in phenotype that resulted from the loss of essentially DNA-sequence identical pO157 were likely due to the chromosomal genetic diversity between strains. The O157:H7 serotype diversity was further highlighted by phenotypic microarray comparisons of the two outbreak strains with a genotype 6 bovine E. coli O157:H7 isolate, rarely associated with human disease.

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

ppGpp-Mediated Stationary Phase Induction of the Genes Encoded by Horizontally Acquired Pathogenicity Islands and cob/pdu Locus in Salmonella enterica serovar Typhimurium: Miryoung Song , Hyun-Ju Kim , Sangryeol Ryu , Hyunjin Yoon , Jiae Yun , Hyon E. Choy; J. Microbiol. 2010;48(1):89-95. Published online March 11, 2010; DOI: https://doi.org/10.1007/s12275-009-0179-6

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Abstract: Salmonella enterica is highly diverse in terms of genome structure, which is at least partly due to the horizontal transfer of genetic elements from various sources. In this study, we examined the expression profiles of such genes in Salmonella Pathogenicity Islands (SPIs) and the cob/pdu locus, horizontally acquired large DNA segments, during growth under standard growth conditions. Transcripts from exponentially growing and early stationary phase Salmonellae were compared using various methods including cDNA microarray analysis. Nearly all genes encoded by SPIs and the cob/pdu locus were induced at the onset of the stationary phase in a stringent molecule ppGpp-dependent but stationary phase σ, σ38-independent manner. Although, it has been suggested that ppGpp acts in concert with DksA, we found the stationary phase induction of those SPI genes was not DksA dependent. It is suggested that ppGpp stimulates the expression of these stress-inducible genes encoded by horizontally acquired DNA, by itself or in concert with DksA.

Journal Article

Gene Expression Profile of Helicobacter pylori in Response to Growth Temperature Variation: Yue-hua Han , Wen-zhong Liu , Yao-zhou Shi , Li-qiong Lu , Shu-dong Xiao , Qing-hua Zhang; J. Microbiol. 2009;47(4):455-465. Published online September 9, 2009; DOI: https://doi.org/10.1007/s12275-009-0003-3

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Abstract: A Helicobacter pylori whole-genome DNA microarray was constructed to study expression profiles of H. pylori in response to a sudden temperature transfer from 37°C to 20°C. The expression level of the genome at each of four time points (15, 30, 60, and 120 min) after temperature downshift was compared with that just before cold treatment. Globally, 10.2% (n=167) of the total predicted H. pylori genes (n=1636) represented on the microarray were significantly differentially expressed (p<0.05) over a 120 min period after shift to low temperature. The expression profiles of the differentially expressed genes were grouped, and their expression patterns were validated by quantitative real-time PCR. Up-regulated genes mainly included genes involved in energy metabolism and substance metabolism, cellular processes, protein fate, ribosomal protein genes, and hypothetical protein genes, which indicate the compensational responses of H. pylori to temperature downshift. Those genes play important roles in adaption to temperature downshift of H. pylori. Down-regulation of DNA metabolism genes and cell envelope genes and cellular processes genes may reflect damaged functions under low temperature, which is unfavorable to bacterial infection and propagation. Overall, this time-course study provides new insights into the primary response of H. pylori to a sudden temperature downshift, which allow the bacteria to survive and adapt to the new host environment.

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

Gene Expression Analysis of Phanerochaete chrysosporium During the Transition Time from Primary Growth to Secondary Metabolism: Mingfeng Jiang , Xiao Li , Liang Zhang , Hong Feng , Yizheng Zhang; J. Microbiol. 2009;47(3):308-318. Published online June 26, 2009; DOI: https://doi.org/10.1007/s12275-008-0275-z

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Abstract: In order to identify the secondary metabolism-related genes of Phanerochaete chrysosporium growing under pure O2 and nitrogen-limited conditions, 2322 ESTs fragments originated from two suppression-subtractive libraries were analyzed using the cDNA microarray technique. Ten significantly upregulated and 22 significantly downregulated genes were identified in the 72 h cultured mycelia RNA samples (secondary metabolism). According to qPCR, 16 out of the 32 genes were expressed differently in secondary metabolism. Transcripts of secondary metabolism up-regulation genes exhibited homologies to aryl-alcohol dehydrogenase (SSh1554), ABC transporter gene (SSH624), chitinase (SSH963), heat shock protein (SSH1193), catalase (SSH317), cytochrome P450 (SSH331), glucosamine-6-phosphate isomerase (SSH611), and alkyl hydroperoxide reductase (SSH362) genes. Ninety-three genes could be classified by Eukaryotic Orthologous Groups (KOG). Among the genes assigned a function, gene expression patterns were different in both secondary metabolism and primary metabolism. In the group of “Cellular Processes and Signaling,” most of the genes were from the primary metabolism library. On the other hand, genes from the secondary metabolism library were found mainly in the “Information Storage” and “Processing and Poorly Characterized” groups. Based on the KOG functional assignments, six genes belong to the ubiquitin system, and all of them were from primary metabolism phase. The presence of the H2O2-relevant genes suggested that parts of the genes expressed in 72 h might be involved in the ligninolytic process during secondary metabolism of P. chrysosporium.

DNA Microarray-Based Global Transcriptional Profiling of Yersinia pestis in Multicellularity: Jingfu Qiu , Zhaobiao Guo , Haihong Liu , Dongsheng Zhou , Yanping Han , Ruifu Yang; J. Microbiol. 2008;46(5):557-563. Published online October 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0140-0

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Abstract: Yersinia pestis, the causative agent of plague, has a feature of forming multicellular aggregates at liquid-air interface around the wall of glass tube. In this study, we employed the whole-genome DNA microarray of Y. pestis to investigate the global transcriptional profile in multicellularity compared with that in its planktonic growth. A total of 177 genes were differentially expressed in Y. pestis during early stage of multicellular formation; Seventy genes of them were up-regulated while 107 down-regulated. In addition to a large number of genes encoding unknown functions, most of the induced genes encode cell envelope and transport/binding proteins. The up-regulation of amino acid biosynthesis, the differentially altered genes that are involved in virulence, and the cold shock protein genes were for the first time reported to be associated with the multicellular formation. Our results revealed the global gene expression of Y. pestis were changed in the formation of multicellularity, providing insights into the molecular mechanism of multicellular behaviour, which need investigating further.

Genome-Wide Transcriptional Responses to Sulfite in Saccharomyces cerevisiae: Hoon Park , Yoon-Sun Hwan; J. Microbiol. 2008;46(5):542-548. Published online October 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0053-y

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Abstract: Sulfite is a commonly used preservative in foods, beverages, and pharmaceuticals because it is toxic to many microorganisms. In order to understand the global response of Saccharomyces cerevisiae to sulfite, genome-wide transcript profiling following sulfite exposure was obtained. The transcription levels of 21 genes were increased more than 2-fold, while those of 37 genes decreased to a similar extent. Genes involved in carbohydrate metabolism represented the highest proportion of induced genes, which may account for the easily acquired resistance to sulfite. Most of down-regulated genes are involved in transcription, protein biosynthesis, and cell growth. The down-regulation of these genes is thought to reflect growth arrest which occurs during sulfite treatment, allowing cells to save energy. Cells treated with sulfite generated more than 70% of acetaldehyde than untreated cells, suggesting that the increased acetaldehyde production is correlated with the induction of PDC1 gene encoding pyruvate decarboxylase.

Comparative Genomics Profiling of Clinical Isolates of Helicobacter pylori in Chinese Populations Using DNA Microarray: Yue-Hua Han , Wen-Zhong Liu , Yao-Zhou Shi , Li-Qiong Lu , Shudong Xiao , Qing-Hua Zhang , Guo-Ping Zhao; J. Microbiol. 2007;45(1):21-28.; DOI: https://doi.org/2496 [pii]

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Abstract: In order to search for specific genotypes related to this unique phenotype, we used whole genomic DNA microarray to characterize the genomic diversity of Helicobacter pylori (H. pylori) strains isolated from clinical patients in China. The open reading frame (ORF) fragments on our microarray were generated by PCR using gene-specific primers. Genomic DNA of H. pylori 26695 and J99 were used as templates. <br>Thirty-four H. pylori isolates were obtained from patients in Shanghai. Results were judged based on ln(x) transformed and normalized Cy3/Cy5 ratios. Our microarray included 1882 DNA fragments corresponding to 1636 ORFs of both sequenced H. pylori strains. Cluster analysis, revealed two diverse regions in the H. pylori genome that were not present in other isolates. Among the 1636 genes, 1091 (66.7%) were common to all H. pylori strains, representing the functional core of the genome. Most of the genes found in the H. pylori functional core were responsible for metabolism, cellular processes, transcription and biosynthesis of amino acids, functions that are essential to H. pylori’s growth and colonization in its host. In contrast, 522 (31.9%) genes were strain-specific genes that were missing from at least one strain of H. pylori. Strainspecific genes primarily included restriction modification system components, transposase genes, hypothetical proteins and outer membrane proteins. These strain-specific genes may aid the bacteria under specific circumstances during their long-term infection in genetically diverse hosts. Our results suggest 34 H. pylori clinical strains have extensive genomic diversity. Core genes and strain-specific genes both play essential roles in H. pylori propagation and pathogenesis. Our microarray experiment may help select relatively significant genes for further research on the pathogenicity of H. pylori and development of a <br>vaccine for H. pylori.

Microarray-Mediated Transcriptome Analysis of the Tributyltin (TBT)-Resistant Bacterium Pseudomonas aeruginosa 25W in the Presence of TBT: Santosh K. Dubey , Tsutomu Tokashiki , Satoru Suzuki; J. Microbiol. 2006;44(2):200-205.; DOI: https://doi.org/2364 [pii]

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Abstract: The tributyltin (TBT)-resistant bacterium, Pseudomonas aeruginosa 25W, which was isolated in seawater from the Arabian Sea, was subjected to transcriptome analysis in the presence of high concentrations of TBT. Only slight effects were observed at TBT concentration of 50 μM, but exposure to 500 μM resulted in the upregulation of 6 genes and the downregulation of 75. Among the 75 downregulated genes, 53% (40 out of 75) were of hypothetical function, followed by 14 transcriptional regulation- and translationassociated genes. The results of this study indicated that although the 25W strain was highly resistant to TBT, high concentrations of TBT result in toxic effect on the transcriptional and translational levels. The target genes likely belong to a specific category of transcription- and translation-associated genes rather than to other gene categories.

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