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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 8

  1. Content type: Research article

    TnaphA6-carrying repAci6 plasmids have been detected in Acinetobacter baumannii isolates belonging to global clones, GC1 and GC2, worldwide. Here, we examined whether RepAci6 plasmids family play a role in the di...

    Authors: Parisa Aris, Mohammad Ali Boroumand and Masoumeh Douraghi

    Citation: BMC Microbiology 2019 19:221

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  2. Content type: Research article

    Cellulose is synthesized by an array of bacterial species. Komagataeibacter xylinus is the best characterized as it produces copious amounts of the polymer extracellularly. Despite many advances in the past decad...

    Authors: Luis Salgado, Silvia Blank, Reza Alipour Moghadam Esfahani, Janice L. Strap and Dario Bonetta

    Citation: BMC Microbiology 2019 19:216

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  3. Content type: Research article

    Several serious vegetable-associated outbreaks of enterohemorrhagic Escherichia coli (EHEC) infections have occurred during the last decades. In this context, vegetables have been suggested to function as seconda...

    Authors: Thorsten Bufe, André Hennig, Jochen Klumpp, Agnes Weiss, Kay Nieselt and Herbert Schmidt

    Citation: BMC Microbiology 2019 19:212

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  4. Content type: Research article

    Efflux pump mediated antibiotic resistance is an unnoticed and undetected mechanism in clinical microbiology laboratory. RND efflux systems are known for aminoglycoside and tetracycline resistance whereas thei...

    Authors: Shiela Chetri, Deepshikha Bhowmik, Deepjyoti Paul, Piyush Pandey, Debadatta Dhar Chanda, Atanu Chakravarty, Debajyoti Bora and Amitabha Bhattacharjee

    Citation: BMC Microbiology 2019 19:210

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  5. Content type: Research article

    Plants have evolved intimate interactions with soil microbes for a range of beneficial functions including nutrient acquisition, pathogen resistance and stress tolerance. Further understanding of this system i...

    Authors: Fang Liu, Tarek Hewezi, Sarah L. Lebeis, Vince Pantalone, Parwinder S. Grewal and Margaret E. Staton

    Citation: BMC Microbiology 2019 19:201

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  6. Content type: Research article

    Enterocytozoon bieneusi is one of the commonest microsporidians contributing to human microsporidiosis, and is frequently found in animals in various countries. However, there is limited epidemiological informati...

    Authors: Yan Zhang, Anson V. Koehler, Tao Wang, David Cunliffe and Robin B. Gasser

    Citation: BMC Microbiology 2019 19:183

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  7. Content type: Research article

    Salmonella enterica is regarded as a major public health threat worldwide. Salmonella secretes the novel translocated effector protein K2 (SseK2), but it is unclear whether this protein plays a significant role i...

    Authors: Xiaojie Zhang, Lei He, Chunjie Zhang, Chuan Yu, Yadong Yang, Yanyan Jia, Xiangchao Cheng, Yinju Li, Chengshui Liao, Jing Li, Zuhua Yu and Fuyu Du

    Citation: BMC Microbiology 2019 19:182

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  8. Content type: Research article

    Most species of Shewanella harbor two ferrochelatase paralogues for the biosynthesis of c-type cytochromes, which are crucial for their respiratory versatility. In our previous study of the Shewanella loihica PV-...

    Authors: Jingcheng Dai, Yaqi Liu, Shuangyuan Liu, Shuyang Li, Na Gao, Jing Wang, Jizhong Zhou and Dongru Qiu

    Citation: BMC Microbiology 2019 19:173

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  9. Content type: Research article

    Termites are an important food resource for many human populations around the world, and are a good supply of nutrients. The fungus-farming ‘higher’ termite members of Macrotermitinae are also consumed by mode...

    Authors: Stephanie L. Schnorr, Courtney A. Hofman, Shandukani R. Netshifhefhe, Frances D. Duncan, Tanvi P. Honap, Julie Lesnik and Cecil M. Lewis

    Citation: BMC Microbiology 2019 19:164

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  10. Content type: Research article

    The role of soil microorganisms in plant growth, nutrient utilization, drought tolerance as well as biocontrol activity cannot be over-emphasized, especially in this era when food crisis is a global challenge....

    Authors: Nicholas O. Igiehon, Olubukola O. Babalola and Bukola R. Aremu

    Citation: BMC Microbiology 2019 19:159

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  11. Content type: Research article

    Staphylococcus epidermidis has emerged as an often encountered pathogen responsible for hospital-acquired infections. The aim of present study is to investigate the microbiological characteristic of S. epidermidi...

    Authors: Yinjuan Guo, Yu Ding, Li Liu, Xiaofei Shen, Zhihao Hao, Jingjing Duan, Ye Jin, Zengqiang Chen and Fangyou Yu

    Citation: BMC Microbiology 2019 19:157

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  12. Content type: Research article

    UK public health organisations perform routine antimicrobial susceptibility tests (ASTs) to characterise the potential for antimicrobial resistance in Salmonella enterica serovars. Genetic determinants of these r...

    Authors: Nana Mensah, Yue Tang, Shaun Cawthraw, Manal AbuOun, Jackie Fenner, Nicholas R. Thomson, Alison E. Mather and Liljana Petrovska-Holmes

    Citation: BMC Microbiology 2019 19:148

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  13. Content type: Research article

    The presence and activity of CRISPR-Cas defense systems is a hallmark of many prokaryotic microorganisms. Here, the distribution of sequences related to the highly iterated palindrome 1 (HIP1) element and the ...

    Authors: Ingeborg Scholz, Steffen C. Lott, Juliane Behler, Katrin Gärtner, Martin Hagemann and Wolfgang R. Hess

    Citation: BMC Microbiology 2019 19:147

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  14. Content type: Research article

    Enterococcus faecalis is a major clinically relevant nosocomial bacterial pathogen frequently isolated from polymicrobial infections. The biofilm forming ability of E. faecalis attributes a key role in its virule...

    Authors: Karthika Suryaletha, Lekshmi Narendrakumar, Joby John, Megha Periyappilly Radhakrishnan, Sanil George and Sabu Thomas

    Citation: BMC Microbiology 2019 19:146

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  15. Content type: Research article

    Complete and contiguous genome assemblies greatly improve the quality of subsequent systems-wide functional profiling studies and the ability to gain novel biological insights. While a de novo genome assembly ...

    Authors: Vincent Somerville, Stefanie Lutz, Michael Schmid, Daniel Frei, Aline Moser, Stefan Irmler, Jürg E. Frey and Christian H. Ahrens

    Citation: BMC Microbiology 2019 19:143

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  16. Content type: Research article

    Recently, in India, there has been a shift from NDM to OXA48-like carbapenemases. OXA-181 and OXA-232 are the frequently produced variants of OXA48-like carbapenemases. OXA48-like carbapenemases are also known...

    Authors: Chaitra Shankar, Purva Mathur, Manigandan Venkatesan, Agila Kumari Pragasam, Shalini Anandan, Surbhi Khurana and Balaji Veeraraghavan

    Citation: BMC Microbiology 2019 19:137

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  17. Content type: Research article

    The Latin American & Mediterranean (LAM) spoligotype family is one of the most successful genotype of Mycobacterium tuberculosis worldwide and particularly prevalent in South-America. Within this family, a sublin...

    Authors: Chyntia Carolina Díaz Acosta, Graciela Russomando, Norma Candia, Viviana Ritacco, Sidra E. G. Vasconcellos, Marcia de Berrêdo Pinho Moreira, Nilda J. de Romero, Nora Morcillo, Jacobus Henri De Waard, Harrison Magdinier Gomes and Philip Noel Suffys

    Citation: BMC Microbiology 2019 19:131

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  18. Content type: Research article

    RNA-binding proteins (RBPs) are well known as key factors in gene expression regulation in eukaryotes. These proteins associate with mRNAs and other proteins to form mRNP complexes that ultimately determine th...

    Authors: Helisa Helena Wippel, Juliane Soldi Malgarin, Alexandre Haruo Inoue, Felipe da Veiga Leprevost, Paulo Costa Carvalho, Samuel Goldenberg and Lysangela Ronalte Alves

    Citation: BMC Microbiology 2019 19:128

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  19. Content type: Research article

    Methicillin-resistant Staphylococcus aureus (MRSA) is known as a leading cause of morbidity and mortality. Investigation of the MRSA’s virulence and resistance mechanisms is a continuing concern toward controllin...

    Authors: Mohamed S. Ali, Nurulfiza M. Isa, Faisal M. Abedelrhman, Tahani B. Alyas, Sara E. Mohammed, Abdallah E. Ahmed, Zainab S. A. Ahmed, Nyok-Sean Lau, Mohamed I. Garbi, Abdullah Al-Ashraf Amirul, Almeen O. Seed, Rihab A. Omer and Sofia B. Mohamed

    Citation: BMC Microbiology 2019 19:126

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  20. Content type: Research article

    Pseudorabies virus (PRV, or suid herpesvirus, SuHV-1), a member of the herpesvirus family, has an extremely broad host range and threatens the pig industry in China. PRV can evade host innate immunity and infe...

    Authors: Yi Fan, Ling Zhu, Xiangang Sun, Wenting Lyu, Lei Xu, Yue Yin, Jun Zhao, Jianbo Huang, Yichao Den, Zhiyi Jiang, Shiyao Xu, Xiyu Mao and Zhiwen Xu

    Citation: BMC Microbiology 2019 19:125

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  21. Content type: Research article

    Clostridium cellulovorans is a mesophilic, cellulosome-producing bacterium containing 57 genomic cellulosomal enzyme-encoding genes. In addition to cellulosomal proteins, C. cellulovorans also secretes non-cellul...

    Authors: Shunsuke Aburaya, Wataru Aoki, Kouichi Kuroda, Hiroshi Minakuchi and Mitsuyoshi Ueda

    Citation: BMC Microbiology 2019 19:118

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  22. Content type: Research article

    The Escherichia coli sequence type 131 (ST131) is a well established clone causing significant extraintestinal infections worldwide. However, no studies have been reported the phenotypic and molecular traits of S...

    Authors: Zoya Hojabri, Narges Darabi, Maedeh Arab, Fereshteh Saffari and Omid Pajand

    Citation: BMC Microbiology 2019 19:117

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  23. Content type: Research article

    Methicillin-resistant Staphylococcus aureus (MRSA) biofilm producers represent an important etiological agent of many chronic human infections. Antibiotics and host immune responses are largely ineffective agains...

    Authors: Khulood Hamid Dakheel, Raha Abdul Rahim, Vasantha Kumari Neela, Jameel R. Al-Obaidi, Tan Geok Hun, Mohd Noor Mat Isa and Khatijah Yusoff

    Citation: BMC Microbiology 2019 19:114

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  24. Content type: Research article

    Hfq is a widely conserved bacterial RNA-binding protein which generally mediates the global regulatory activities involv ed in physiological process and virulence. The goal of this study was to characterize th...

    Authors: Xuelu Liu, Yuping Yan, Haodi Wu, Changyong Zhou and Xuefeng Wang

    Citation: BMC Microbiology 2019 19:103

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  25. Content type: Research article

    Burkholderia pseudomallei is a human pathogen causing severe infections in tropical and subtropical regions and is classified as a bio-threat agent. B. thailandensis strain E264 has been proposed as less pathogen...

    Authors: A. Kovacs-Simon, C. M. Hemsley, A. E. Scott, J. L. Prior and R. W. Titball

    Citation: BMC Microbiology 2019 19:97

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  26. Content type: Methodology article

    Obtaining sufficient RNA yield and quality for comprehensive transcriptomic studies is cumbersome for clinical samples in which RNA from the pathogen is present in low numbers relative to the nucleic acids fro...

    Authors: Antonio Rodríguez and Mario Vaneechoutte

    Citation: BMC Microbiology 2019 19:94

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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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

  41. 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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  42. 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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  43. 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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  44. 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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  45. 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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  46. 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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