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Microbial genetics, genomics and proteomics

This section aims to publish studies relating to all aspects of microbial genomics, transcriptomics, proteomics, metabolomics and microbial genome editing.

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  1. 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

    Content type: Research article

    Published on:

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

  2. 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

    Content type: Research article

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  3. 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

    Content type: Research article

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  4. 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

    Content type: Research article

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  5. 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

    Content type: Methodology article

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  6. 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

    Content type: Research article

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  7. 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

    Content type: Research article

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  8. 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

    Content type: Research article

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  9. 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

    Content type: Research article

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  10. 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

    Content type: Research article

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  11. 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

    Content type: Research article

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  12. 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

    Content type: Research article

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  13. 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

    Content type: Research article

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  14. 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

    Content type: Research article

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  15. 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

    Content type: Research article

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  16. 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

    Content type: Research article

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  17. 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

    Content type: Research article

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  18. 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

    Content type: Research article

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  19. 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

    Content type: Research article

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  20. 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

    Content type: Methodology Article

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  21. 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

    Content type: Research article

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  22. 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

    Content type: Research article

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  23. 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

    Content type: Research article

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  24. 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

    Content type: Research article

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  25. 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

    Content type: Research article

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  26. 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

    Content type: Research article

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  27. 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

    Content type: Research article

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  28. 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

    Content type: Research article

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  29. The aminoglycoside antibiotic gentamicin was supposed to induce a crosstalk between the Cpx- and the Arc-two-component systems (TCS). Here, we investigated the physical interaction of the respective TCS compon...

    Authors: Emina Ćudić, Kristin Surmann, Gianna Panasia, Elke Hammer and Sabine Hunke

    Citation: BMC Microbiology 2017 17:197

    Content type: Research article

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  30. Advancements in Next Generation Sequencing (NGS) technologies regarding throughput, read length and accuracy had a major impact on microbiome research by significantly improving 16S rRNA amplicon sequencing. A...

    Authors: Imane Allali, Jason W. Arnold, Jeffrey Roach, Maria Belen Cadenas, Natasha Butz, Hosni M. Hassan, Matthew Koci, Anne Ballou, Mary Mendoza, Rizwana Ali and M. Andrea Azcarate-Peril

    Citation: BMC Microbiology 2017 17:194

    Content type: Research article

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  31. The microbial composition of the equine respiratory tract, and differences due to mild equine asthma (also called Inflammatory Airway Disease (IAD)) have not been reported. The primary treatment for control of...

    Authors: Stephanie L. Bond, Edouard Timsit, Matthew Workentine, Trevor Alexander and Renaud Léguillette

    Citation: BMC Microbiology 2017 17:184

    Content type: Research article

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  32. Aeromonas spp. are gram-negative bacteria that can cause a variety of infections in both humans and animals and play a controversial role in diarrhea outbreaks. Our aim was to identify...

    Authors: Lívia Christina Alves da Silva, Tereza Cristina Leal-Balbino, Beatriz Souza Toscano de Melo, Carina Lucena Mendes-Marques, Antonio Mauro Rezende, Alzira Maria Paiva de Almeida and Nilma Cintra Leal

    Citation: BMC Microbiology 2017 17:179

    Content type: Research article

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  33. Porphyromonas gingivalis is a major causative pathogen of chronic periodontitis. Within the inflammatory microenvironment, there exists extreme pH values, elevated temperatures and oxi...

    Authors: Xiaoyu Xu, Tong Tong, Xue Yang, Yaping Pan, Li Lin and Chen Li

    Citation: BMC Microbiology 2017 17:178

    Content type: Research article

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  34. Moniliophthora perniciosa is a phytopathogenic fungus responsible for witches’ broom disease of cacao trees (Theobroma cacao L.). Understanding the molecular events during germination ...

    Authors: Joise Hander Mares, Karina Peres Gramacho, Everton Cruz Santos, André da Silva Santiago, Juliano Oliveira Santana, Aurizângela Oliveira de Sousa, Fátima Cerqueira Alvim and Carlos Priminho Pirovani

    Citation: BMC Microbiology 2017 17:176

    Content type: Research article

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  35. Stony corals provide the structural foundation of coral reef ecosystems and are termed holobionts given they engage in symbioses, in particular with photosynthetic dinoflagellates of the genus Symbiodinium. Besid...

    Authors: Jan D. Brüwer, Shobhit Agrawal, Yi Jin Liew, Manuel Aranda and Christian R. Voolstra

    Citation: BMC Microbiology 2017 17:174

    Content type: Research article

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  36. In bacteria, many transcription activator and repressor proteins regulate multiple transcription units that are often distally distributed on the bacterial genome. To investigate the subcellular location of DN...

    Authors: Laura E. Sellars, Jack A. Bryant, María-Antonia Sánchez-Romero, Eugenio Sánchez-Morán, Stephen J. W. Busby and David J. Lee

    Citation: BMC Microbiology 2017 17:170

    Content type: Research article

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  37. Bacterial and Archaeal communities have a complex, symbiotic role in crude oil bioremediation. Their biosurfactants and degradation enzymes have been in the spotlight, mainly due to the awareness of ecosystem ...

    Authors: Jorge S. Oliveira, Wydemberg J. Araújo, Ricardo M. Figueiredo, Rita C. B. Silva-Portela, Alaine de Brito Guerra, Sinara Carla da Silva Araújo, Carolina Minnicelli, Aline Cardoso Carlos, Ana Tereza Ribeiro de Vasconcelos, Ana Teresa Freitas and Lucymara F. Agnez-Lima

    Citation: BMC Microbiology 2017 17:168

    Content type: Research article

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  38. The eighth step of l-histidine biosynthesis is carried out by an enzyme called histidinol-phosphate phosphatase (HolPase). Three unrelated HolPase families are known so far. Two of them are well studied: HAD-type...

    Authors: Robert Kasimir Kulis-Horn, Christian Rückert, Jörn Kalinowski and Marcus Persicke

    Citation: BMC Microbiology 2017 17:161

    Content type: Research article

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  39. Bacillus pumilus can secret abundant extracellular enzymes, and may be used as a potential host for the industrial production of enzymes. It is necessary to understand the metabolic pr...

    Authors: Lin-Li Han, Huan-Huan Shao, Yong-Cheng Liu, Gang Liu, Chao-Ying Xie, Xiao-Jie Cheng, Hai-Yan Wang, Xue-Mei Tan and Hong Feng

    Citation: BMC Microbiology 2017 17:156

    Content type: Research article

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  40. Xanthomonas citri subsp. citri (Xac) is the causal agent of citrus canker. A proteomic analysis under in planta infectious and non-infectious conditions was conducted in order to incre...

    Authors: Leandro M. Moreira, Márcia R. Soares, Agda P. Facincani, Cristiano B. Ferreira, Rafael M. Ferreira, Maria I. T. Ferro, Fábio C. Gozzo, Érica B. Felestrino, Renata A. B. Assis, Camila Carrião M. Garcia, João C. Setubal, Jesus A. Ferro and Julio C.F. de Oliveira

    Citation: BMC Microbiology 2017 17:155

    Content type: Research article

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  41. The genus Geobacillus comprises bacteria that are Gram positive, thermophilic spore-formers, which are found in a variety of environments from hot-springs, cool soils, to food manufacturing plants, including dair...

    Authors: S. A. Burgess, S. H. Flint, D. Lindsay, M. P. Cox and P. J. Biggs

    Citation: BMC Microbiology 2017 17:140

    Content type: Research article

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  42. The internal transcribed spacer (ITS), RNA polymerase II second largest subunit (RPB2), and elongation factor 1-alpha (EF1α) are often used in fungal taxonomy and phylogenetic analysis. As we know, an ideal mo...

    Authors: Xiao-Lan He, Qian Li, Wei-Hong Peng, Jie Zhou, Xue-Lian Cao, Di Wang, Zhong-Qian Huang, Wei Tan, Yu Li and Bing-Cheng Gan

    Citation: BMC Microbiology 2017 17:139

    Content type: Research article

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