Journal of Microbiology

Journal Articles

Deletion of lacD gene affected stress tolerance and virulence of Streptococcus suis serotype 2: Xiaowu Jiang , Lexin Zhu , Dongbo Zhan; J. Microbiol. 2022;60(9):948-959. Published online August 19, 2022; DOI: https://doi.org/10.1007/s12275-022-2146-4

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Streptococcus suis type 2 (S. suis type 2, SS2), an infectious pathogen which is zoonotic and can induce severely public health concern. Our previous research identified a newly differential secreted effector of tagatose-bisphosphate aldolase (LacD) mediated by VirD4 factor within the putative type IV secretion system of SS2, whereas the functional basis and roles in virulence of LacD remain elusive. Here in this study, the LacD was found enzymatic and can be activated to express under oxidative stress. Gene mutant and its complemental strain (ΔlacD and cΔlacD) were constructed to analyze the phenotypes, virulence and transcriptomic profiles as compared with the parental strain. The lacD gene deletion showed no effect on growth capability and cells morphology of SS2. However, reduced tolerance to oxidative and heat stress conditions, increased antimicrobial susceptibility to ciprofloxacin and kanamycin were found in ΔlacD strain. Further, the LacD deficiency led to weakened invasion and attenuated virulence since an easier phagocytosed and more prone to be cleared of SS2 in macrophages were shown in ΔlacD mutant. Distinctive transcriptional profiling in ΔlacD strain and typical downregulated genes with significant mRNA changes including alcohol dehydrogenase, GTPase, integrative and conjugative elements, and iron ABC transporters which were mainly involved in cell division, stress response, antimicrobial susceptibility and virulence regulation, were examined and confirmed by RNA sequencing and real time qPCR. In summary, the
results
demonstrated for the first time that LacD was a pluripotent protein mediated the metabolic, stress and virulent effect of SS2.

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Investigation of choline-binding protein of CbpD in the pathogenesis of Streptococcus suis type 2
Lexin Zhu, Mengqing Li, Guijun Yu, Dongbo Zhan, Wenzhen Zeng, Nanyan Fu, Xiaowu Jiang
Frontiers in Veterinary Science.2024;[Epub] CrossRef

Phosphorylation of tegument protein pp28 contributes to trafficking to the assembly compartment in human cytomegalovirus infection: Jun-Young Seo , Jin Ah Heo , William J. Britt; J. Microbiol. 2020;58(7):624-631. Published online June 27, 2020; DOI: https://doi.org/10.1007/s12275-020-0263-5

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Abstract

Human cytomegalovirus (HCMV) UL99 encodes a late tegument protein pp28 that is essential for envelopment and production of infectious virus. This protein is localized to the endoplasmic reticulum-Golgi intermediate compartment (ERGIC) in transfected cells but it localizes to the cytoplasmic assembly compartment (AC) in HCMV-infected cells. Trafficking of pp28 to the AC is required for the assembly of infectious virus. The N-terminal domain (aa 1-61) of pp28 is sufficient for trafficking and function of the wild type protein during viral infection. However, residues required for authentic pp28 trafficking with the exception of the acidic cluster in the N-terminal domain of pp28 remain undefined. Monitoring protein migration on SDS-PAGE, we found that pp28 is phosphorylated in the virus-infected cells and dephosphorylated in the viral particles. By generating substitution mutants of pp28, we showed that three serine residues (aa 41–43) and a tyrosine residue (aa 34) account for its phosphorylation. The mutant forms of pp28 were localized to the plasma membrane as well as the ERGIC in transfected cells. Likewise, these mutant proteins were localized to the plasma membrane as well as the AC in virus-infected cells. These results suggested that phosphorylation of pp28 contributes to its intracellular trafficking and efficient viral assembly and incorporation.

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Exploring the genetic associations and causal relationships between antibody responses, immune cells, and various types of breast cancer
Yang Yang, Jiayi Chen, Fuhong Gong, Jingge Miao, Mengping Lin, Ruimin Liu, Chenxi Wang, Fei Ge, Wenlin Chen
Scientific Reports.2024;[Epub] CrossRef
Human cytomegalovirus induces significant structural and functional changes in terminally differentiated human cortical neurons
Jacob W. Adelman, Suzette Rosas-Rogers, Megan L. Schumacher, Rebekah L. Mokry, Scott S. Terhune, Allison D. Ebert, Thomas Shenk
mBio.2023;[Epub] CrossRef
Insights into the Transcriptome of Human Cytomegalovirus: A Comprehensive Review
Janine Zeng, Di Cao, Shaomin Yang, Dabbu Kumar Jaijyan, Xiaolian Liu, Songbin Wu, Ruth Cruz-Cosme, Qiyi Tang, Hua Zhu
Viruses.2023; 15(8): 1703. CrossRef
Features and Functions of the Conserved Herpesvirus Tegument Protein UL11 and Its Binding Partners
Linjiang Yang, Mingshu Wang, Anchun Cheng, Qiao Yang, Ying Wu, Juan Huang, Bin Tian, Renyong Jia, Mafeng Liu, Dekang Zhu, Shun Chen, Xinxin Zhao, Shaqiu Zhang, Xumin Ou, Sai Mao, Qun Gao, Di Sun
Frontiers in Microbiology.2022;[Epub] CrossRef
The human cytomegalovirus decathlon: Ten critical replication events provide opportunities for restriction
Declan L. Turner, Rommel A. Mathias
Frontiers in Cell and Developmental Biology.2022;[Epub] CrossRef

Comparative analysis of the gut microbiota in distinct statin response patients in East China: Baoqing Sun , Luming Li , Xinfu Zhou; J. Microbiol. 2018;56(12):886-892. Published online November 27, 2018; DOI: https://doi.org/10.1007/s12275-018-8152-x

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Abstract

Statin response shows great interindividual variations. Recently, emerging studies have shown that gut microbiota is linked to therapeutic responses to drugs, including statins. However, the association between the gut bacteria composition and statin response is still unclear. In this study, gut microbiota of 202 hyperlipidemic patients with statin sensitive (SS) response and statin resistant (SR) response in East China were investigated by high throughput sequencing to compare the gut bacteria composition and biodiversity in distinct statin response patients. Higher biodiversity was detected in Group SS than Group SR. Specifically, group SS showed significantly increased proportion of genera Lactobacillus (P = 0.001), Eubacterium (P = 0.004), Faecalibacterium (P = 0.005), and Bifidobacterium (P = 0.002) and decreased proportion of genus Clostridium (P = 0.001) compared to Group SR. The results indicated that higher gut biodiversity was associated with statin sensitive response. The increased genera Lactobacillus, Eubacterium, Faecalibacterium, Bifidobacterium, and decreased genus Clostridium in patient gut microbiota may predict patient's statin response, and hence may guide statin dosage adjustments.

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Lara Pires, Ana M. González-Paramás, Sandrina A. Heleno, Ricardo C. Calhelha
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Angela Horvath, Kristina Zukauskaite, Olha Hazia, Irina Balazs, Vanessa Stadlbauer
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Gangani Dharmarathne, Samia Kazi, Shalinie King, Thilini N. Jayasinghe
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COPD Pathogenesis and Alterations in the Oral, Lung, and Gut Microbiomes
Nobuhiro Asai, Yoshihiro Ohkuni, Hideo Kato, Mao Hagihara, Hiroshige Mikamo, Norihiro Kaneko
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Shiqin Zhang, Xiaoling Ren, Bingzheng Zhang, Tian Lan, Bing Liu
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Role of Gut Microbiome in Atherosclerosis: Molecular and Therapeutic Aspects
Juan Salazar, Valery Morillo, María K Suárez, Ana Castro, Paola Ramírez, Milagros Rojas, Roberto Añez, Luis D'Marco, Maricarmen Chacín-González, Valmore Bermúdez
Current Cardiology Reviews.2023;[Epub] CrossRef
Reduced gut microbial diversity in familial hypercholesterolemia with no effect of omega-3 polyunsaturated fatty acids intervention – a pilot trial
Christopher Storm-Larsen, Liv Nesse Hande, Martin Kummen, Hilde Thunhaug, Beate Vestad, Simen Hyll Hansen, Anders Hovland, Marius Trøseid, Knut Tore Lappegård, Johannes R. Hov
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ChangXin Sun, ZePing Wang, LanQing Hu, XiaoNan Zhang, JiYe Chen, ZongLiang Yu, LongTao Liu, Min Wu
Frontiers in Cardiovascular Medicine.2022;[Epub] CrossRef
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Inmaculada Ramírez-Macías, Esteban Orenes-Piñero, Anny Camelo-Castillo, José Miguel Rivera-Caravaca, Cecilia López-García, Francisco Marín
Critical Reviews in Food Science and Nutrition.2022; 62(14): 3738. CrossRef
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Yunpeng Liu, Jing Dong, Ziqing Zhang, Yiqi Liu, Yang Wang
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Daniel A. Schupack, Ruben A. T. Mars, Dayne H. Voelker, Jithma P. Abeykoon, Purna C. Kashyap
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Honghong Liu, Ye Jin, Ran Tian, Siqin Feng, Shuyang Zhang, Chenhong Zhang
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Research Support, Non-U.S. Gov'ts

Deodorization of Pig Slurry and Characterization of Bacterial Diversity Using 16S rDNA Sequence Analysis: Ok-Hwa Hwang , Sebastian Raveendar , Young-Ju Kim , Ji-Hun Kim , Tae-Hun Kim , Dong-Yoon Choi , Che Ok Jeon , Sung-Back Cho , Kyung-Tai Lee; J. Microbiol. 2014;52(11):918-929. Published online October 31, 2014; DOI: https://doi.org/10.1007/s12275-014-4251-5

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Abstract

The concentration of major odor-causing compounds including phenols, indoles, short-chain fatty acids (SCFAs) and branched chain fatty acids (BCFAs) in response to the addition of powdered horse radish (PHR) and spent mushroom compost (SMC) was compared with control nontreated slurry (CNS) samples. A total of 97,465 rDNAs sequence reads were generated from three different samples (CNS, n = 2; PHR, n = 3; SMC, n = 3) using bar-coded pyrosequencing. The number of operational taxonomic units (OTUs) was lower in the PHR slurry compared with the other samples. A total of 11 phyla were observed in the slurry samples, while the phylogenetic analysis revealed that the slurry microbiome predominantly comprised members of the Bacteroidetes, Firmicutes, and Proteobacteria phyla. The rarefaction analysis showed the bacterial species richness varied among the treated samples. Overall, at the OTU level, 2,558 individual genera were classified, 276 genera were found among the three samples, and 1,832 additional genera were identified in the individual samples. A principal component analysis revealed the differences in microbial communities among the CNS, PHR, and SMC pig slurries. Correlation of the bacterial community structure with the Kyoto Encyclopedia of Genes and Genomes (KEGG) predicted pathways showed that the treatments altered the metabolic capabilities of the slurry microbiota. Overall, these results demonstrated that the PHR and SMC treatments significantly reduced the malodor compounds in pig slurry (P < 0.05).

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Impact of Bacillus subtilis on manure solids, odor, and microbiome
Okhwa Hwang, Yeo-Myeong Yun, Steven Trabue
Journal of Environmental Management.2023; 333: 117390. CrossRef
Isolation and identification of proteolytic bacteria from pig sludge and protease activity determination
S Hamdani, N Asstiyani, D Astriany, M Singgih, S Ibrahim
IOP Conference Series: Earth and Environmental Science.2019; 230: 012095. CrossRef
The gut bacteria across life stages in the synanthropic fly Chrysomya megacephala
Xiaoyun Wang, Qiao Gao, Wanqiang Wang, Xiaoping Wang, Chaoliang Lei, Fen Zhu
BMC Microbiology.2018;[Epub] CrossRef
Bacterial community composition and diversity uncovered in experimental sludge treatment reed bed systems with different swine slurry hydraulic loadings
Paula Arroyo, Luis E. Sáenz de Miera, Jorge Falagán, Gemma Ansola
Ecological Engineering.2018; 123: 175. CrossRef
Effect of pH on soil bacterial diversity
Sun-Ja Cho, Mi-Hee Kim, Young-Ok Lee
Journal of Ecology and Environment.2016;[Epub] CrossRef
Indole: a signaling molecule or a mere metabolic byproduct that alters bacterial physiology at a high concentration?
Jisun Kim, Woojun Park
Journal of Microbiology.2015; 53(7): 421. CrossRef
Application of Next Generation Sequencing to Investigate Microbiome in the Livestock Sector
Minseok Kim, Youlchang Baek, Young Kyoon Oh
Journal of Animal Environmental Science.2015; 21(3): 93. CrossRef
Survival of free-living Acholeplasma in aerated pig manure slurry revealed by 13C-labeled bacterial biomass probing
Dai Hanajima, Tomo Aoyagi, Tomoyuki Hori
Frontiers in Microbiology.2015;[Epub] CrossRef

Molecular Analysis of Prokaryotic Diversity in the Deep Subsurface of the Former Homestake Gold Mine, South Dakota, USA: Gurdeep Rastogi , Larry D. Stetler , Brent M. Peyton , Rajesh K. Sani; J. Microbiol. 2009;47(4):371-384. Published online September 9, 2009; DOI: https://doi.org/10.1007/s12275-008-0249-1

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Abstract: A culture-independent molecular phylogenetic analysis was carried out to study the prokaryotic diversity in two soil samples collected from the subsurface (1.34 km depth) of the former Homestake gold mine, Lead, South Dakota, USA at two sites, the Ross shaft and number 6 Winze. Microbial community analyses were performed by cloning and sequencing of 16S rRNA genes retrieved directly from soil samples. Geochemical characterization of soils revealed high amount of toxic metals such as As, Cd, Co, Cr, Cu, Ni, Pb, Zn, and U at both the sites. Phylogenetic analyses showed that soil samples were predominantly composed of phylotypes related to phylum Proteobacteria. Other phyla detected in libraries were Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Chlorobi, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, Verrucomicrobia, and candidate divisions OP10 and TM7. The majority (>95%) of the phylotypes retrieved in the libraries were most closely related to environmental sequences from yet-uncultured bacteria representing a hitherto unidentified diversity. The archaeal communities at both the sites exhibited lower diversity and were most closely affiliated to uncultivated species within the Crenarchaeota. Results showed the existence of diverse microbial populations in deep subsurface environment of the Homestake gold mine. Statistical analyses demonstrated that each site harbored phylogenetically distinct microbial populations that were more diverse at Ross site compare to winze site.

Microbial Diversity of a Sulfide Black Smoker in Main Endeavour Hydrothermal Vent Field, Juan de Fuca Ridge: Huaiyang Zhou , Jiangtao Li , Xiaotong Peng , Jun Meng , Fengping Wang , Yuncan Ai; J. Microbiol. 2009;47(3):235-247. Published online June 26, 2009; DOI: https://doi.org/10.1007/s12275-008-0311-z

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Abstract: Submarine hydrothermal vents are among the least-understood habitats on Earth but have been the intense focus of research in the past 30 years. An active hydrothermal sulfide chimney collected from the Dudley site in the Main Endeavour vent Field (MEF) of Juan de Fuca Ridge was investigated using mineralogical and molecular approaches. Mineral analysis indicated that the chimney was composed mainly of Fe-, Zn- and Cu-rich sulfides. According to phylogenetic analysis, within the Crenarchaeota, clones of the order Desulfurococcales predominated, comprising nearly 50% of archaeal clones. Euryarchaeota were composed mainly of clones belonging to Thermococcales and deep-sea hydrothermal vent Euryarchaeota (DHVE), each of which accounted for about 20% of all clones. Thermophilic or hyperthermophilic physiologies were common to the predominant archaeal groups. More than half of bacterial clones belonged to ε-Proteobacteria, which confirmed their prevalence in hydrothermal vent environments. Clones of Proteobacteria (γ-, δ-, β-), Cytophaga-Flavobacterium-Bacteroides (CFB) and Deinococcus-Thermus occurred as well. It was remarkable that methanogens and methanotrophs were not detected in our 16S rRNA gene library. Our results indicated that sulfur-related metabolism, which included sulfur-reducing activity carried out by thermophilic archaea and sulfur-oxidizing by mesophilic bacteria, was common and crucial to the vent ecosystem in Dudley hydrothermal site.

Characterization of the Depth-Related Changes in the Microbial Communities in Lake Hovsgol Sediment by 16S rRNA Gene-Based Approaches: Young-Do Nam , Youlboong Sung , Ho-Won Chang , Seong Woon Roh , Kyoung-Ho Kim , Sung-Keun Rhee , Jung-Chan Kim , Joo-Yong Kim , Jung-Hoon Yoon , Jin-Woo Bae; J. Microbiol. 2008;46(2):125-136. Published online June 11, 2008; DOI: https://doi.org/10.1007/s12275-007-0189-1

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Abstract: The undisturbed sediment of Lake Hovsgol (Mongolia) is scientifically important because it represents a record of the environmental changes that took place between the Holocene (the present age) and Pleistocene (the last ice age; 12,000 14C years before present day). Here, we investigated how the current microbial <br>communities change as the depth increases by PCR-denaturing gradient gel electrophoresis (DGGE) analysis of the 16S rRNA genes of the microbial communities. The microbial diversity, as estimated by the Shannon index, decreased as the depth increased. In particular, significant changes in archaeal diversity were observed in the middle depth (at 39~42 cm depth of total 60 cm depth) that marks the border between the Holocene and Pleistocene. Phylotype belonging to Beta- and Gamma-Proteobacteria were the predominant bacteria and most of these persisted throughout the depth examined. However, as the depth increased, some bacteria <br>(some genera belonging to Beta-Proteobacteria, Nitrospira, and OP8-9) were not detectable while others (some genera belonging to Alpha-, Beta-, Gamma-Proteobacteria) newly deteced by DGGE. Crenarchaea were the predominant archaea and only one phylotype belonging to Euryarchaea was found. Both the <br>archaeal and bacterial profiles revealed by the DGGE band patterns could be grouped into four and three subsets, respectively, subsets that were largely divided by the border between the Holocene and Pleistocene. Thus, the diversity of the current microbial communities in Lake Hovsgol sediments decreases with increasing <br>depth. These changes probably relate to the environmental conditions in the sediments, which were shaped by the paleoclimatic events taking place between the Holocene and Pleistocene.

Diversity of Microorganisms in Decaying Maize Stalks Revealed by a Molecular Method: Ming-Xia Yang , Han-Bo Zhang; J. Microbiol. 2007;45(4):367-370.; DOI: https://doi.org/2558 [pii]

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Abstract: Microbial diversity in decaying maize stalk was characterized by constructing and analyzing rRNA gene clone library. Total 47 OTUs were obtained from 82 bacterial clones, including Proteobacteria (64.6%), Actinobacteria (30.5%), Bacteroidetes (2.4%) and Firmicutes (2.4%). Most proteobacterial clones were members of Rhizobium, Pseudomonas and Stenotrophomonas. Eighty-four percent of Actinobacteria was related to Microbacterium. Only 14 OTUs were identified from 124 fungal clones, including Ascomycota (88%) and Basidiomycota (12%). Sixty percent of Ascomycota were members of Eupenicillium and Paecilomyces but all Basidiomycota were close to Kurtzmanomyces nectairei.

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