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Microbial genetics, genomics and proteomics

Section edited by Hirotada Mori

This section aims to publish studies relating to all aspects of microbial genomics, proteomics, metabolomics and systems biology.

Page 1 of 7

  1. Content type: Research article

    The opportunistic pathogen, Pseudomonas aeruginosa is well known for its environmental and metabolic versatility, yet many of the functions of its gene-products remain to be fully elucidated. This study’s objecti...

    Authors: Bradley W. Wright, Karthik S. Kamath, Christoph Krisp and Mark P. Molloy

    Citation: BMC Microbiology 2019 19:69

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  2. Content type: Research article

    Structured noncoding RNAs (ncRNAs) play essential roles in many biological processes such as gene regulation, signaling, RNA processing, and protein synthesis. Among the most common groups of ncRNAs in bacteri...

    Authors: Shira Stav, Ruben M. Atilho, Gayan Mirihana Arachchilage, Giahoa Nguyen, Gadareth Higgs and Ronald R. Breaker

    Citation: BMC Microbiology 2019 19:66

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  3. Content type: Research article

    Porphyromonas gingivalis, a microorganism residing in the oral cavity within complex multispecies biofilms, is one of the keystone pathogens in the onset and progression of periodontitis. In this in vitro study, ...

    Authors: María C. Sánchez, Patricia Romero-Lastra, Honorato Ribeiro-Vidal, Arancha Llama-Palacios, Elena Figuero, David Herrera and Mariano Sanz

    Citation: BMC Microbiology 2019 19:58

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  4. Content type: Research article

    With the current rise of antibiotic resistance in bacteria, it is important to monitor the efficacy of antimicrobials in clinical use. Paeniclostridium sordellii (previously Clostridium sordellii) is a bacterial ...

    Authors: Callum J. Vidor, Dieter Bulach, Milena Awad and Dena Lyras

    Citation: BMC Microbiology 2019 19:53

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  5. Content type: Methodology article

    Ornithobacterium (O.) rhinotracheale is an emerging bacterial pathogen in poultry and not fully understood to date. Because of its importance particularly for the global turkey meat industry, reliable diagnostic ...

    Authors: Inês M. B. Veiga, Dörte Lüschow, Stefanie Gutzer, Hafez M. Hafez and Kristin Mühldorfer

    Citation: BMC Microbiology 2019 19:31

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  6. Content type: Research article

    Metarhizium robertsii, a widely distributed insect pathogen, is presently used as a natural alternative to chemical insecticides. Unfortunately, its worldwide commercial use has been restricted by a short shelf l...

    Authors: Tian Xie, Yulong Wang, Deshui Yu, Qilin Zhang, Tingting Zhang, Zhangxun Wang and Bo Huang

    Citation: BMC Microbiology 2019 19:25

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  7. Content type: Research article

    Group A Streptococcus (GAS) is a major human pathogen, which is associated with a wide spectrum of invasive diseases, such as pharyngitis, scarlet fever, rheumatic fever, and streptococcal toxic shock syndrome (S...

    Authors: Shunsuke Yamada, Masaki Shibasaki, Kazunori Murase, Takayasu Watanabe, Chihiro Aikawa, Takashi Nozawa and Ichiro Nakagawa

    Citation: BMC Microbiology 2019 19:24

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  8. Content type: Research article

    To describe the temporal dynamics, molecular characterization, clinical and ex vivo virulence of emerging O1:K1 neonatal meningitis Escherichia coli (NMEC) strains of Sequence Type complex (STc) 95 in France.

    Authors: Guillaume Geslain, André Birgy, Sandrine Adiba, Mélanie Magnan, Céline Courroux, Corinne Levy, Robert Cohen, Philippe Bidet and Stéphane Bonacorsi

    Citation: BMC Microbiology 2019 19:17

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  9. Content type: Research article

    Lactobacillus plantarum, a versatile lactic acid-fermenting bacterium, isolated from the traditional pickles in Ningbo of China, was chosen for grass carp fermentation, which could also improve the flavor of gras...

    Authors: Tinghong Ming, Jiaojiao Han, Yanyan Li, Chenyang Lu, Dihong Qiu, Ye Li, Jun Zhou and Xiurong Su

    Citation: BMC Microbiology 2018 18:216

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  10. Content type: Research article

    Q fever, caused by Coxiella burnetii, is a zoonosis that presents a worldwide distribution and affects both humans and animals. The route of dispersal of the pathogen by ruminants into the environment usually inv...

    Authors: Dimosthenis Chochlakis, Ana Sofia Santos, Nektarios D. Giadinis, Dimitrios Papadopoulos, Leonidas Boubaris, Emmanouil Kalaitzakis, Anna Psaroulaki, Spyridon K. Kritas and Evanthia I. Petridou

    Citation: BMC Microbiology 2018 18:204

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  11. Content type: Research article

    Hepatitis B virus (HBV) infection is one of the most serious public health issues. Recent HBV genetic research has revealed novel genetic rearrangements termed complex structural variations (SVs), which are co...

    Authors: Kei Fujiwara, Kentaro Matsuura, Kayoko Matsunami, Etsuko Iio and Shunsuke Nojiri

    Citation: BMC Microbiology 2018 18:202

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  12. Content type: Research article

    Klebsiella oxytoca DSM 29614 - isolated from acid mine drainages - grows anaerobically using Fe(III)-citrate as sole carbon and energy source, unlike other enterobacteria and K. oxytoca clinical isolates. The DSM...

    Authors: Giuseppe Gallo, Luana Presta, Elena Perrin, Michele Gallo, Davide Marchetto, Anna Maria Puglia, Renato Fani and Franco Baldi

    Citation: BMC Microbiology 2018 18:198

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  13. Content type: Research article

    Staphylococcus aureus is an important foodborne pathogen. Lactococcus garvieae is a lactic acid bacterium found in dairy products; some of its strains are able to inhibit S. aureus growth by producing H2O2. Three...

    Authors: Clothilde Queiroux, Muriel Bonnet, Taous Saraoui, Pierre Delpech, Philippe Veisseire, Etienne Rifa, Cécile Moussard, Geneviève Gagne, Céline Delbès and Stéphanie Bornes

    Citation: BMC Microbiology 2018 18:193

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  14. Content type: Research article

    Gray leaf spot is a devastating disease caused by Stemphylium lycopersici that threatens tomato-growing areas worldwide. Typically, many pathogenesis-related and unrelated secreted proteins can be predicted in ge...

    Authors: Rong Zeng, Shigang Gao, Lihui Xu, Xin Liu and Fuming Dai

    Citation: BMC Microbiology 2018 18:191

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    The Correction to this article has been published in BMC Microbiology 2019 19:19

  15. Content type: Research article

    The ProPrems trial, a multi-center, double-blind, placebo-controlled randomized trial, previously reported a 54% reduction in necrotizing enterocolitis (NEC) of Bell stage 2 or more from 4.4 to 2.0% in 1099 infan...

    Authors: Erica L. Plummer, Dieter M. Bulach, Gerald L. Murray, Susan E. Jacobs, Sepehr N. Tabrizi and Suzanne M. Garland

    Citation: BMC Microbiology 2018 18:184

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  16. Content type: Research article

    Streptococcus pluranimalium is a new member of the Streptococcus genus isolated from multiple different animal hosts. It has been identified as a pathogen associated with subclinical mastitis, valvular endocardit...

    Authors: Yushan Pan, Haoran An, Tong Fu, Shiyu Zhao, Chengwang Zhang, Genhui Xiao, Jingren Zhang, Xinfang Zhao and Gongzheng Hu

    Citation: BMC Microbiology 2018 18:182

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  17. Content type: Research article

    Alternaria solani is a known air-born deuteromycete fungus with a polycyclic life cycle and is the causal agent of early blight that causes significant yield losses of potato worldwide. However, the molecular mec...

    Authors: Dai Zhang, Jia-Yu He, Parham Haddadi, Jie-Hua Zhu, Zhi-Hui Yang and Lisong Ma

    Citation: BMC Microbiology 2018 18:176

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  18. Content type: Methodology article

    Transposon mutagenesis is highly valuable for bacterial genetic and genomic studies. The transposons are usually delivered into host cells through conjugation or electroporation of a suicide plasmid. However, ...

    Authors: Santa S. Naorem, Jin Han, Stephanie Y. Zhang, Junyi Zhang, Lindsey B. Graham, Angelou Song, Cameron V. Smith, Fariha Rashid and Huatao Guo

    Citation: BMC Microbiology 2018 18:158

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  19. Content type: Research article

    The pteropine orthoreovirus (PRV) was isolated from monkey (Macaca fascicularis) faecal samples collected from human-inhabited areas in Lopburi Province, Thailand. These samples were initially obtained to survey ...

    Authors: Nathamon Kosoltanapiwat, Onrapak Reamtong, Tamaki Okabayashi, Sumate Ampawong, Amporn Rungruengkitkun, Tipparat Thiangtrongjit, Narin Thippornchai, Pornsawan Leaungwutiwong, Aongart Mahittikorn, Hirotake Mori, Thanada Yoohanngoa and Prechaya Yamwong

    Citation: BMC Microbiology 2018 18:135

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  20. Content type: Research article

    Rhodobacter sphaeroides has two sets of flagellar genes, fla1 and fla2, that are responsible for the synthesis of two different flagellar structures. The expression of the fla2 genes is under control of CtrA. In ...

    Authors: Anet Rivera-Osorio, Aurora Osorio, Sebastian Poggio, Georges Dreyfus and Laura Camarena

    Citation: BMC Microbiology 2018 18:129

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  21. Content type: Research article

    Pathogenic Gram-negative bacteria interact with their eukaryotic hosts by deploying the type III translocon to inject effector proteins into the cytosol of eukaryotic cells. The translocon compositions, the nu...

    Authors: Xuan Wang, Liyuan Zhang, Hongtao Ji, Xuyan Mo, Ping Li, Junzhi Wang and Hansong Dong

    Citation: BMC Microbiology 2018 18:105

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  22. Content type: Research article

    Anthrax, the zoonotic disease caused by the gram-positive bacterium Bacillus anthracis, is nowadays rare in northern parts of Europe including Finland and Scandinavia. Only two minor outbreaks of anthrax in 1988 ...

    Authors: Taru Lienemann, Wolfgang Beyer, Kirsti Pelkola, Heidi Rossow, Alexandra Rehn, Markus Antwerpen and Gregor Grass

    Citation: BMC Microbiology 2018 18:102

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  23. Content type: Research article

    Bacillus endophyticus is a soil plant-endophytic bacterium, while B. anthracis is the causative agent of anthrax. The virulence factors of B. anthracis are the plasmid encoded tripartite toxins (pXO1) and poly-γ-...

    Authors: Kgaugelo Edward Lekota, Oliver Keoagile Ignatius Bezuidt, Joseph Mafofo, Jasper Rees, Farai Catherine Muchadeyi, Evelyn Madoroba and Henriette van Heerden

    Citation: BMC Microbiology 2018 18:67

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  24. Content type: Research article

    Bacillus strains producing highly resistant spores have been isolated from cleanrooms and space craft assembly facilities. Organisms that can survive such conditions merit planetary protection concern and if that...

    Authors: Madhan R. Tirumalai, Victor G. Stepanov, Andrea Wünsche, Saied Montazari, Racquel O. Gonzalez, Kasturi Venkateswaran and George E. Fox

    Citation: BMC Microbiology 2018 18:57

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  25. Content type: Research article

    Iron plays important roles in the growth, reproduction and pathogenicity of Aeromonas hydrophila. In this study, we detected and compared the mRNA and protein expression profiles of A. hydrophila under normal and...

    Authors: Tao Teng, Bingwen Xi, Kai Chen, Liangkun Pan, Jun Xie and Pao Xu

    Citation: BMC Microbiology 2018 18:52

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  26. Content type: Research article

    Pathogen avirulence (Avr) genes can evolve rapidly when challenged by the widespread deployment of host genes for resistance. They can be effectively isolated by positional cloning provided a robust and well-popu...

    Authors: Tonghui Li, Jianqiang Wen, Yaling Zhang, James Correll, Ling Wang and Qinghua Pan

    Citation: BMC Microbiology 2018 18:47

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  27. Content type: Research article

    Yersinia pseudotuberculosis is a zoonotic pathogen, causing mild gastrointestinal infection in humans. From this comparatively benign pathogenic species emerged the highly virulent plague bacillus, Yersinia pesti...

    Authors: Samuel J. Willcocks, Richard A. Stabler, Helen S. Atkins, Petra F. Oyston and Brendan W. Wren

    Citation: BMC Microbiology 2018 18:46

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  28. Content type: Research article

    The aim of this study was to identify mutations of rpoB, katG, inhA and ahp-genes associated Mycobacterium tuberculosis resistance to rifampicin (RIF) and isoniazid (INH) in Kyrgyz Republic. We studied 633 smear ...

    Authors: Jainagul Isakova, Nurmira Sovkhozova, Denis Vinnikov, Zoy Goncharova, Elnura Talaibekova, Nazira Aldasheva and Almaz Aldashev

    Citation: BMC Microbiology 2018 18:22

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  29. Content type: Research article

    A remarkable exception to the large genetic diversity often observed for bacteriophages infecting a specific bacterial host was found for the Cutibacterium acnes (formerly Propionibacterium acnes) phages, which a...

    Authors: Lucy Cheng, Laura J. Marinelli, Noël Grosset, Sorel T. Fitz-Gibbon, Charles A. Bowman, Brian Q. Dang, Daniel A. Russell, Deborah Jacobs-Sera, Baochen Shi, Matteo Pellegrini, Jeff F. Miller, Michel Gautier, Graham F. Hatfull and Robert L. Modlin

    Citation: BMC Microbiology 2018 18:19

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  30. Content type: Research article

    Rhodotorula toruloides is an outstanding producer of lipids and carotenoids. Currently, information on the key metabolic pathways and their molecular basis of regulation remains scarce, severely limiting efforts ...

    Authors: Yanbin Liu, Chong Mei John Koh, Sihui Amy Yap, Minge Du, Mya Myintzu Hlaing and Lianghui Ji

    Citation: BMC Microbiology 2018 18:14

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  31. Content type: Research article

    Recurrent acute otitis media (rAOM, recurrent ear infection) is a common childhood disease caused by bacteria termed otopathogens, for which current treatments have limited effectiveness. Generic probiotic therap...

    Authors: Rachael Lappan, Kara Imbrogno, Chisha Sikazwe, Denise Anderson, Danny Mok, Harvey Coates, Shyan Vijayasekaran, Paul Bumbak, Christopher C. Blyth, Sarra E. Jamieson and Christopher S. Peacock

    Citation: BMC Microbiology 2018 18:13

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  32. Content type: Research article

    The gene expression profile and metabolic pathways of Aspergillus oryzae underlying the anatomical and morphological differentiation across different growth stages have not been fully characterized. The rapid dev...

    Authors: Bin He, Zhihong Hu, Long Ma, Haoran Li, Mingqiang Ai, Jizhong Han and Bin Zeng

    Citation: BMC Microbiology 2018 18:12

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  33. Content type: Methodology Article

    Microbial arrays, with a large number of different strains on a single plate printed with robotic precision, underpin an increasing number of genetic and genomic approaches. These include Synthetic Genetic Arr...

    Authors: David B. H. Barton, Danae Georghiou, Neelam Dave, Majed Alghamdi, Thomas A. Walsh, Edward J. Louis and Steven S. Foster

    Citation: BMC Microbiology 2018 18:9

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  34. Content type: Research article

    Phosphate is an essential compound for life. Escherichia coli employs a signal transduction pathway that controls the expression of genes that are required for the high-affinity acquisition of phosphate and the u...

    Authors: Ramesh K. Vuppada, Colby R. Hansen, Kirsta A. P. Strickland, Keilen M. Kelly and William R. McCleary

    Citation: BMC Microbiology 2018 18:8

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  35. Content type: Research article

    Plague is a flea-borne zoonotic and invasive disease caused by a gram negative coccobacillus bacterium called Yersinia pestis. Plague has caused three devastating pandemics globally namely: the Justinian, Black D...

    Authors: Stanley S. Nyirenda, Bernard M. Hang′ombe, Edgar Simulundu, Evans Mulenga, Ladslav Moonga, Robert S. Machang′u, Gerald Misinzo and Bukheti S. Kilonzo

    Citation: BMC Microbiology 2018 18:2

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  36. Content type: Research article

    Mycobacteriophages are viruses that infect Mycobacterium hosts. A large collection of phages known to infect the same bacterial host strain – Mycobacterium smegmatis mc2155 – exhibit substantial diversity and cha...

    Authors: Rebekah M. Dedrick, Travis N. Mavrich, Wei L. Ng and Graham F. Hatfull

    Citation: BMC Microbiology 2017 17:225

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  37. Content type: Research article

    Crotalaria aegyptiaca, a low shrub is commonly observed in the sandy soils of wadis desert and is found throughout all regions in Oman. A survey for phytoplasma diseases was conducted....

    Authors: Ali Al-Subhi, Saskia A. Hogenhout, Rashid A. Al-Yahyai and Abdullah M. Al-Sadi

    Citation: BMC Microbiology 2017 17:221

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  38. Content type: Research article

    The bacterial spirochete Borrelia burgdorferi is the causative agent of the most commonly reported arthropod-borne illness in the United States, Lyme disease. A family of proteins containing von Willebrand Factor...

    Authors: Christina M. Brock, Manuel Bañó-Polo, Maria J. Garcia-Murria, Ismael Mingarro and Maria Esteve-Gasent

    Citation: BMC Microbiology 2017 17:219

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  39. Content type: Research article

    The genomic diversity of different species within the genus Lactococcus and the relationships between genomic differentiation and environmental factors remain unclear. In this study, type isolates of ten Lactococ...

    Authors: Jie Yu, Yuqin Song, Yan Ren, Yanting Qing, Wenjun Liu and Zhihong Sun

    Citation: BMC Microbiology 2017 17:213

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  40. Content type: Research article

    Bacterial nucleoid consists of genome DNA, RNA, and hundreds of nucleoid-associated proteins (NAPs). Escherichia coli nucleoid is compacted towards the stationary phase, replacing most log-phase NAPs with the maj...

    Authors: Yuri Ushijima, Ryosuke L. Ohniwa and Kazuya Morikawa

    Citation: BMC Microbiology 2017 17:207

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  41. Content type: Research article

    Caseous lymphadenitis (CLA) is a disease that affects sheep, goats and occasionally humans. The etiologic agent is the Corynebacterium pseudotuberculosis bacillus. The objective of this study was to build a gene ...

    Authors: Cleber Eduardo Galvão, Stenio Perdigão Fragoso, Carina Elisei de Oliveira, Odinéia Forner, Renata Ribeiro Bastos Pereira, Cleber Oliveira Soares and Grácia Maria Soares Rosinha

    Citation: BMC Microbiology 2017 17:202

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