Journal of Microbiology

Journal Articles

Evaluation of Cyc1 protein stability in Acidithiobacillus ferrooxidans bacterium after E121D mutation by molecular dynamics simulation to improve electron transfer: Mahnaz Shojapour , Somayeh Farahmand , Faezeh Fatemi , Marzieh Dehghan Shasaltaneh; J. Microbiol. 2022;60(5):526-532. Published online March 14, 2022; DOI: https://doi.org/10.1007/s12275-022-1645-7

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Cyc1 (Cytochrome c552) is a protein in the electron transport chain of the Acidithiobacillus ferrooxidans (Af) bacteria which obtain their energy from oxidation Fe2+ to Fe3+. The electrons are directed through Cyc2, RCY (rusticyanin), Cyc1, and Cox aa3 proteins to O2. Cyc1 protein consists of two chains, A and B. In the present study, a novel mutation (E121D) in the A chain of Cyc1 protein was selected due to electron receiving from Histidine 143 of RCY. Then, the changes performed in the E121D mutant were evaluated by MD simulations analyzes. Cyc1 and RCY proteins were docked by a Patchdock server. By E121D mutation, the connection between Zn 1388 of chain B and aspartate 121 of chain A weaken. Asp 121 gets farther from Zn 1388. Therefore, the aspartate gets closer to Cu 1156 of the RCY leading to the higher stability of the RCY/ Cyc1 complex. Further, an acidic residue (Glu121) becomes a more acidic residue (Asp121) and improves the electron transfer to Cyc1 protein. The results of RMSF analysis showed further ligand flexibility in mutation. This leads to fluctuation of the active site and increases redox potential at the mutation point and the speed of electron transfer. This study also predicts that in all respiratory chain proteins, electrons probably enter the first active site via glutamate and exit histidine in the second active site of each respiratory chain protein.

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Point mutation consideration in CcO protein of the electron transfer chain by MD simulation
Mahnaz Shojapour, Somayeh Farahmand
Journal of Molecular Graphics and Modelling.2022; 117: 108309. CrossRef

The discovery of potent immunostimulatory CpG-ODNs widely distributed in bacterial genomes: Juan Liu , Yan Wei , Yongling Lu , Yangyuling Li , Qian Chen , Yan Li; J. Microbiol. 2020;58(2):153-162. Published online December 23, 2019; DOI: https://doi.org/10.1007/s12275-020-9289-y

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Abstract

Oligodeoxynucleotides containing unmethylated CpG dinucleotides (CpG-ODN) can be specifically recognized by Toll-like receptor 9 (TLR9), provoking innate immune responses. Designed according to this structural feature, many synthetic phosphorothioate CpG-ODNs successfully activate macrophages. However, it is difficult to find potent stimulatory CpG-DNA fragments in microbial genomes. Therefore, whether microbial CpG-DNA substantially contributes to infectious and immune diseases remains controversial. In this study, high-throughput scanning was carried out for thousands of bacterial genomes with bioinformatics tools to comprehensively evaluate the distribution of CpG-DNA fragments. A random sampling test was then performed to verify their immunostimulatory properties by experiments in vitro and in vivo. Natural TLR9-dependent and potent stimulatory CpG-DNA fragments were found in microbial genomes. Interestingly, highly conserved stimulatory CpG-DNA fragments were found in 16S and 23S rDNA sequences with multiple copies, while others were species-specific. Additionally, we found that the reported active motifs were mostly nonstimulatory in natural CpG fragments. This evidence indicates that the previous structural descriptions of functional CpG-ODNs are incomplete. Our study has assessed the distribution of microbial CpG-DNA fragments, and identified natural stimulatory CpG-DNA fragments. These findings provide a deeper understanding of CpG-ODN structures and new evidence for microbial DNA inflammatory function and pathogenicity.

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Advances in protein subunit vaccines against H1N1/09 influenza
Yu Zhang, Jingyao Gao, Wenqi Xu, Xingyu Huo, Jingyan Wang, Yirui Xu, Wenting Ding, Zeliang Guo, Rongzeng Liu
Frontiers in Immunology.2024;[Epub] CrossRef
Cell-free DNA beyond a biomarker for rejection: Biological trigger of tissue injury and potential therapeutics
Naoko Tsuji, Sean Agbor-Enoh
The Journal of Heart and Lung Transplantation.2021; 40(6): 405. CrossRef

Reviews

Microbial ecology in Hydra: Why viruses matter: Thomas C.G. Bosch , Juris A. Grasis , Tim Lachnit; J. Microbiol. 2015;53(3):193-200. Published online March 3, 2015; DOI: https://doi.org/10.1007/s12275-015-4695-2

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Abstract

While largely studied because of their harmful effects on human health, there is growing appreciation that viruses are also important members of the animal holobiont. This review highlights recent findings on viruses associated with Hydra and related Cnidaria. These early evolutionary diverging animals not only select their bacterial communities but also select for viral communities in a species-specific manner. The majority of the viruses associating with these animals are bacteriophages. We demonstrate that the animal host and its virome have evolved into a homeostatic, symbiotic relationship and propose that viruses are an important part of the Hydra holobiont by controlling the species-specific microbiome. We conclude that beneficial virus-bacterial-host interactions should be considered as an integral part of animal development and evolution.

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Hydra for 21st Century—A Fine Model in Freshwater Research
Goran Kovačević, Petra Korać, Davor Želježić, Mirela Sertić Perić, Petra Peharec Štefanić, Damir Sirovina, Maja Novosel, Sanja Gottstein
Water.2024; 16(15): 2114. CrossRef
Four Novel Caudoviricetes Bacteriophages Isolated from Baltic Sea Water Infect Colonizers of Aurelia aurita
Melissa Stante, Nancy Weiland-Bräuer, Urska Repnik, Almut Werner, Marc Bramkamp, Cynthia M. Chibani, Ruth A. Schmitz
Viruses.2023; 15(7): 1525. CrossRef
Dysbiosis of intestinal homeostasis contribute to Whitmania pigra edema disease
Caijiao Dai, Xin Chen, Shiyu Qian, Yihui Fan, Lijuan Li, Junfa Yuan
Microbial Biotechnology.2023; 16(10): 1940. CrossRef
First evidence of virus-like particles in the bacterial symbionts of Bryozoa
A. E. Vishnyakov, N. P. Karagodina, G. Lim-Fong, P. A. Ivanov, T. F. Schwaha, A. V. Letarov, A. N. Ostrovsky
Scientific Reports.2021;[Epub] CrossRef
Interactions of host‐associated multispecies bacterial communities
Heidi Goodrich‐Blair
Periodontology 2000.2021; 86(1): 14. CrossRef
Oyster hemolymph is a complex and dynamic ecosystem hosting bacteria, protists and viruses
S. Dupont, A. Lokmer, E. Corre, J.-C. Auguet, B. Petton, E. Toulza, C. Montagnani, G. Tanguy, D. Pecqueur, C. Salmeron, L. Guillou, C. Desnues, B. La Scola, J. Bou Khalil, J. de Lorgeril, G. Mitta, Y. Gueguen, J.-M. Escoubas
Animal Microbiome.2020;[Epub] CrossRef
Upside-Down but Headed in the Right Direction: Review of the Highly Versatile Cassiopea xamachana System
Aki H. Ohdera, Michael J. Abrams, Cheryl L. Ames, David M. Baker, Luis P. Suescún-Bolívar, Allen G. Collins, Christopher J. Freeman, Edgar Gamero-Mora, Tamar L. Goulet, Dietrich K. Hofmann, Adrian Jaimes-Becerra, Paul F. Long, Antonio C. Marques, Laura A.
Frontiers in Ecology and Evolution.2018;[Epub] CrossRef
Temperate phages as self-replicating weapons in bacterial competition
Xiang-Yi Li, Tim Lachnit, Sebastian Fraune, Thomas C. G. Bosch, Arne Traulsen, Michael Sieber
Journal of The Royal Society Interface.2017; 14(137): 20170563. CrossRef
Grazing of Nuclearia thermophila and Nuclearia delicatula (Nucleariidae, Opisthokonta) on the toxic cyanobacterium Planktothrix rubescens
Sebastian Dirren, Gianna Pitsch, Marisa O.D. Silva, Thomas Posch
European Journal of Protistology.2017; 60: 87. CrossRef
The Intra-Dependence of Viruses and the Holobiont
Juris A. Grasis
Frontiers in Immunology.2017;[Epub] CrossRef
Transitioning from Microbiome Composition to Microbial Community Interactions: The Potential of the Metaorganism Hydra as an Experimental Model
Peter Deines, Thomas C. G. Bosch
Frontiers in Microbiology.2016;[Epub] CrossRef
Bacterial associations with the hydromedusaNemopsis bacheiand scyphomedusaAurelia auritafrom the North Atlantic Ocean
Meaghan C. Daley, Juanita Urban-Rich, Pia H. Moisander
Marine Biology Research.2016; 12(10): 1088. CrossRef
Promiscuous and specific bacterial symbiont acquisition in the amoeboid genusNuclearia(Opisthokonta)
Sebastian Dirren, Thomas Posch, Julie Olson
FEMS Microbiology Ecology.2016; 92(8): fiw105. CrossRef

REVIEW] Enterococcus Infection Biology: Lessons from Invertebrate Host Models: Grace J. Yuen , Frederick M. Ausubel; J. Microbiol. 2014;52(3):200-210. Published online March 1, 2014; DOI: https://doi.org/10.1007/s12275-014-4011-6

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Abstract

The enterococci are commensals of the gastrointestinal tract of many metazoans, from insects to humans. While they normally do not cause disease in the intestine, they can become pathogenic when they infect sites outside of the gut. Recently, the enterococci have become important nosocomial pathogens, with the majority of human enterococcal infections caused by two species, Enterococcus faecalis and Enterococcus faecium. Studies using invertebrate infection models have revealed insights into the biology of enterococcal infections, as well as general principles underlying host innate immune defense. This review highlights recent findings on Enterococcus infection biology from two invertebrate infection models, the greater wax moth Galleria mellonella and the free-living bacteriovorous nematode Caenorhabditis elegans.

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Microbiological profiles and clinical outcomes of critically ill surgical patients with lower gastrointestinal perforation in Japan: a single-center retrospective observational study
Takashi Nishikawa, Jiro Ito, Ryutaro Seo, Koichi Ariyoshi, Hiroyuki Mima
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Navigating ESKAPE Pathogens: Considerations and Caveats for Animal Infection Models Development
Haojie Yu, Yongchang Xu, Saber Imani, Zhuo Zhao, Saif Ullah, Qingjing Wang
ACS Infectious Diseases.2024; 10(7): 2336. CrossRef
Unveiling MurM inhibitors in Enterococcus faecalis V583: a promising approach to tackle antibiotic resistance
Km.Rakhi, Rittik Bhati, Monika Jain, Amit Kumar Singh, Jayaraman Muthukumaran
Journal of Biomolecular Structure and Dynamics.2024; : 1. CrossRef
Multi-omics reveals the ecological and biological functions of Enterococcus mundtii in the intestine of lepidopteran insects
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Comparative Biochemistry and Physiology Part D: Genomics and Proteomics.2024; 52: 101309. CrossRef
Caenorhabditis elegansfor research on cancer hallmarks
Julián Cerón
Disease Models & Mechanisms.2023;[Epub] CrossRef
Enterococcus casseliflavus Infection: A Review of Clinical Features and Treatment
Yusuke Yoshino
Infection and Drug Resistance.2023; Volume 16: 363. CrossRef
It's all relative: analyzing microbiome compositions, its significance, pathogenesis and microbiota derived biofilms: Challenges and opportunities for disease intervention
Sahar Zaidi, Khursheed Ali, Asad U. Khan
Archives of Microbiology.2023;[Epub] CrossRef
Antimicrobial Activity of Ceragenins against Vancomycin-Susceptible and -Resistant Enterococcus spp.
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Pharmaceuticals.2023; 16(12): 1643. CrossRef
Assessing Clinical Outcomes of Vancomycin Treatment in Adult Patients with Vancomycin-Susceptible Enterococcus faecium Bacteremia
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Antibiotics.2023; 12(11): 1577. CrossRef
The transmittable through stinging microbiota differs between honeybees and wasps: a potentially greater microbial risk of the wasp sting for humans
Ioanna Gkitsaki, Alexandros Papachristoforou, Sofia Michailidou, Nikolaos Karamvalis, Ioannis Iliadis, Dimitra Graikini, Christina Sakarikou, Evangelos Tsoukis, Anagnostis Argyriou, Efstathios Giaouris
International Microbiology.2023; 26(3): 663. CrossRef
Analysis of Virulence Genes, Drug Resistance Detection, and Pathogenicity in Enterococcus from Diverse Animal Populations
Kang Xinyun, Yanqin Wei, Xiaofei Fan, Shuangyan Luo, Xiaofeng Luo, Sijun Zhao, Guiqin Wang
SSRN Electronic Journal .2022;[Epub] CrossRef
Enterococcal symbionts of caterpillars facilitate the utilization of a suboptimal diet
Bosheng Chen, Charles J. Mason, Michelle Peiffer, Dayu Zhang, Yongqi Shao, Gary W. Felton
Journal of Insect Physiology.2022; 138: 104369. CrossRef
Analysis of virulence genes, drug resistance detection, and pathogenicity in Enterococcus from farm animals
Xinyun Kang, Yanqin Wei, Xiaofei Fan, Shuangyan Luo, Xiaofeng Luo, Sijun Zhao, Guiqin Wang
Microbial Pathogenesis.2022; 171: 105745. CrossRef
The Prevalence of Virulent and Multidrug-Resistant Enterococci in River Water and in Treated and Untreated Municipal and Hospital Wastewater
Anna Gotkowska-Płachta
International Journal of Environmental Research and Public Health.2021; 18(2): 563. CrossRef
First Report of the Local Spread of Vancomycin-Resistant Enterococci Ascribed to the Interspecies Transmission of a vanA Gene Cluster-Carrying Linear Plasmid
Yusuke Hashimoto, Izumi Kita, Masato Suzuki, Hidetada Hirakawa, Hirofumi Ohtaki, Haruyoshi Tomita, Paul D. Fey
mSphere.2020;[Epub] CrossRef
The red flour beetle Tribolium castaneum: A model for host-microbiome interactions
Aparna Agarwal, Deepa Agashe, Jeffrey P. Demuth
PLOS ONE.2020; 15(10): e0239051. CrossRef
RNA-Seq comparative analysis reveals the response of Enterococcus faecalis TV4 under fluoride exposure
Guannan Li, Min Shi, Shan Zhao, Dan Li, Yaohang Long, Chengfei Yang, Yong Zhu
Gene.2020; 726: 144197. CrossRef
Determination of vancomicin- resistant strains (VRE) with VanA and VanB enzymes among field isolates of Enterococcus spp., obtained from drinking water samples
T.A. Garkavenko, O.I. Gorbatiuk, T.G. Kozitska, V.O. Andriyashchuk, S.M. Dibkova
Bulletin "Veterinary biotechnology".2020; 36: 21. CrossRef
Galleria mellonella as an experimental model to study human oral pathogens
Rodnei Dennis Rossoni, Felipe de Camargo Ribeiro, Hanna Flávia Santana dos Santos, Jéssica Diane dos Santos, Nicássia de Sousa Oliveira, Marignês Theotonio dos Santos Dutra, Simone Aparecida Biazzi de Lapena, Juliana Campos Junqueira
Archives of Oral Biology.2019; 101: 13. CrossRef
Association between vancomycin pharmacokinetic/pharmacodynamic parameters, patient characteristics, and mortality in patients with bacteremia caused by vancomycin-susceptible Enterococcus faecium: a single-center retrospective study
Ichiro Nakakura, Kota Sakakura, Kaori Imanishi, Rumi Sako, Kunio Yamazaki
Journal of Pharmaceutical Health Care and Sciences.2019;[Epub] CrossRef
Interplay between mitochondria and diet mediates pathogen and stress resistance in Caenorhabditis elegans
Alexey V. Revtovich, Ryan Lee, Natalia V. Kirienko, Danielle A. Garsin
PLOS Genetics.2019; 15(3): e1008011. CrossRef
Pathogenicity of Enterococci
Elizabeth Fiore, Daria Van Tyne, Michael S. Gilmore, Vincent A. Fischetti, Richard P. Novick, Joseph J. Ferretti, Daniel A. Portnoy, Miriam Braunstein, Julian I. Rood
Microbiology Spectrum.2019;[Epub] CrossRef
Detection of transferable oxazolidinone resistance determinants in Enterococcus faecalis and Enterococcus faecium of swine origin in Sichuan Province, China
Zhuang-Zhuang Kang, Chang-Wei Lei, Ling-Han Kong, Yu-Long Wang, Xiao-Lan Ye, Bo-Heng Ma, Xue-Chun Wang, Cui Li, Yu Zhang, Hong-Ning Wang
Journal of Global Antimicrobial Resistance.2019; 19: 333. CrossRef
Sortase-Dependent Proteins Promote Gastrointestinal Colonization by Enterococci
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Infection and Immunity.2019;[Epub] CrossRef
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Research Support, Non-U.S. Gov't

Nucleotide-Binding Oligomerization Domain 2 (Nod2) Is Dispensable for the Innate Immune Responses of Macrophages against Yersinia enterocolitica: Yu-Jin Jeong , Chang-Hwan Kim , Eun-Jung Song , Min-Jung Kang , Jee-Cheon Kim , Sang-Muk Oh , Kyung-Bok Lee , Jong-Hwan Park; J. Microbiol. 2012;50(3):489-495. Published online June 30, 2012; DOI: https://doi.org/10.1007/s12275-012-1534-6

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Abstract: Nucleotide-binding oligomerization domain 2 (Nod2) is a cytosolic sensor for muramyl dipeptide, a component of bacterial peptidoglycan. In this study, we have examined whether Nod2 mediates the immune response of macrophages against Yersinia enterocolitica. Bone-marrow-derived macrophages (BMDMs) were isolated from WT and Nod2-deficient mice and were infected with various strains of Y. enterocolitica. ELISA showed that the production of IL-6 and TNF-α in BMDMs infected with Y. enterocolitica was not affected by the Nod2 deficiency. iNOS mRNA expression was induced in both WT and Nod2-deficienct BMDMs in response to Y. enterocolitica, beginning 2 h after infection. Nitric oxide (NO) production by Y. enterocolitica did not differ between WT and Nod2-deficient BMDMs. Western blot analysis revealed that Y. enterocolitica induces activation of NF-κB, p38, and ERK MAPK through a Nod2-independent pathway. Neither LDH release by Y. enterocolitica nor the phagocytic activity of the macrophages was altered by Nod2 deficiency. An in vivo experiment showed that bacterial clearance ability and production of IL-6 and KC in serum were comparable in WT and Nod2-deficient mice infected with Y. enterocolitica. These findings suggest that Nod2 may not be critical for initiating the innate immune response of macrophages against Yersinia infection.

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