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Prokaryote microbial genomics

This section covers the structure and function of the genomes of prokaryotic and archaea microorganisms.

Page 5 of 16

  1. Staphylococcus caprae is an animal-associated bacterium regarded as part of goats’ microflora. Recently, S. caprae has been reported to cause human nosocomial infections such as bacteremia and bone and joint infe...

    Authors: Shinya Watanabe, Yoshifumi Aiba, Xin-Ee Tan, Feng-Yu Li, Tanit Boonsiri, Kanate Thitiananpakorn, Bintao Cui, Yusuke Sato’o, Kotaro Kiga, Teppei Sasahara and Longzhu Cui

    Citation: BMC Genomics 2018 19:810

    Content type: Research article

    Published on:

  2. Animal studies show that high fat (HF) diet-induced gut microbiota contributes to the development of obesity. Oil composition of high-fat diet affects metabolic inflammation differently with deleterious effect...

    Authors: Vania Patrone, Andrea Minuti, Michela Lizier, Francesco Miragoli, Franco Lucchini, Erminio Trevisi, Filippo Rossi and Maria Luisa Callegari

    Citation: BMC Genomics 2018 19:808

    Content type: Research article

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  3. Salmonella enterica is a significant foodborne pathogen, which can be transmitted via several distinct routes, and reports on acquisition of antimicrobial resistance (AMR) are increasing. To better understand the...

    Authors: Suchawan Pornsukarom, Arnoud H M van Vliet and Siddhartha Thakur

    Citation: BMC Genomics 2018 19:801

    Content type: Research article

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  4. Dickeya sp. strain PA1 is the causal agent of bacterial soft rot in Phalaenopsis, an important indoor orchid in China. PA1 and a few other strains were grouped into a novel species, Dickeya fangzhongdai, and only...

    Authors: Jingxin Zhang, John Hu, Huifang Shen, Yucheng Zhang, Dayuan Sun, Xiaoming Pu, Qiyun Yang, Qiurong Fan and Birun Lin

    Citation: BMC Genomics 2018 19:782

    Content type: Research article

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  5. Bacterial filamentation occurs when rod-shaped bacteria grow without dividing. To identify genetically encoded inhibitors of division that promote filamentation, we used cell sorting flow cytometry to enrich f...

    Authors: Daniel G. Mediati, Catherine M. Burke, Shirin Ansari, Elizabeth J. Harry and Iain G. Duggin

    Citation: BMC Genomics 2018 19:781

    Content type: Research article

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  6. Small RNAs (sRNAs) are noncoding molecules that regulate different cellular activities in several bacteria. The role of sRNAs in gene expression regulation is poorly characterized in the etiological agent of p...

    Authors: Tiago Ebert Fritsch, Franciele Maboni Siqueira and Irene Silveira Schrank

    Citation: BMC Genomics 2018 19:767

    Content type: Research article

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  7. The cattle gastrointestinal tract (GIT) is the main enterohemorrhagic Escherichia coli (EHEC) reservoir. In order to identify nutrients required for the survival or multiplication of EHEC in the bovine GIT, we co...

    Authors: Audrey Segura, Marine Bertoni, Pauline Auffret, Christophe Klopp, Olivier Bouchez, Clémence Genthon, Alexandra Durand, Yolande Bertin and Evelyne Forano

    Citation: BMC Genomics 2018 19:766

    Content type: Research article

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  8. Gluconobacter oxydans is a strictly aerobic Gram-negative acetic acid bacterium used industrially for oxidative biotransformations due to its exceptional type of catabolism. It incompletely oxidizes a wide variet...

    Authors: Angela Kranz, Andrea Steinmann, Ursula Degner, Aliye Mengus-Kaya, Susana Matamouros, Michael Bott and Tino Polen

    Citation: BMC Genomics 2018 19:753

    Content type: Research article

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  9. Plant-bacteria associations have been extensively studied for their potential in increasing crop productivity in a sustainable manner. Serratia marcescens is a species of Enterobacteriaceae found in a wide range ...

    Authors: Filipe P Matteoli, Hemanoel Passarelli-Araujo, Régis Josué A Reis, Letícia O da Rocha, Emanuel M de Souza, L Aravind, Fabio L Olivares and Thiago M Venancio

    Citation: BMC Genomics 2018 19:750

    Content type: Research article

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  10. Biocontrol of bacterial pathogens by bacteriophages (phages) represents a promising strategy. Vibrio alginolyticus, a gram-negative bacterium, is a notorious pathogen responsible for the loss of economically impo...

    Authors: Peng Luo, Long Yun, Yingying Li, Yushun Tian, Qiuting Liu, Wen Huang and Chaoqun Hu

    Citation: BMC Genomics 2018 19:741

    Content type: Research article

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  11. Streptococcus agalactiae (Group B Streptococcus, GBS) is a common bacteria species infecting both human and bovine. Previous studies have shown that the GBS isolated from human and bovine are mostly unrelated and...

    Authors: Rui Wang, Liping Li, Ting Huang, Yan Huang, Weiyi Huang, Xiuying Yang, Aiying Lei and Ming Chen

    Citation: BMC Genomics 2018 19:716

    Content type: Research article

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  12. Prosthetic joint infections are clinically difficult to diagnose and treat. Previously, we demonstrated metagenomic sequencing on an Illumina MiSeq replicates the findings of current gold standard microbiologi...

    Authors: Nicholas D Sanderson, Teresa L Street, Dona Foster, Jeremy Swann, Bridget L Atkins, Andrew J Brent, Martin A McNally, Sarah Oakley, Adrian Taylor, Tim E A Peto, Derrick W Crook and David W Eyre

    Citation: BMC Genomics 2018 19:714

    Content type: Methodology article

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  13. Aeromonas hydrophila is a potential zoonotic pathogen and primary fish pathogen. With overlapping characteristics, multiple isolates are often mislabelled and misclassified. Moreover, the potential pathogenic fac...

    Authors: Furqan Awan, Yuhao Dong, Jin Liu, Nannan Wang, Muhammad Hassan Mushtaq, Chengping Lu and Yongjie Liu

    Citation: BMC Genomics 2018 19:712

    Content type: Research article

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  14. Listeria monocytogenes is a widespread foodborne pathogen that can cause listeriosis, a potentially fatal infection. L. monocytogenes is subdivided into four phylogenetic lineages, with the highest incidence of l...

    Authors: Cary Pirone-Davies, Yi Chen, Arthur Pightling, Gina Ryan, Yu Wang, Kuan Yao, Maria Hoffmann and Marc W. Allard

    Citation: BMC Genomics 2018 19:708

    Content type: Research article

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  15. JWB phytoplasma is a kind of insect-transmitted and uncultivable bacterial plant pathogen causeing a destructive Jujube disease. To date, no genome information about JWB phytoplasma has been published, which h...

    Authors: Jie Wang, Laiqing Song, Qiqing Jiao, Shuke Yang, Rui Gao, Xingbo Lu and Guangfang Zhou

    Citation: BMC Genomics 2018 19:689

    Content type: Research article

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  16. Enterohemorrhagic Escherichia coli (EHEC) O26:H11/H, the most common non-O157 serotype causing hemolytic uremic syndrome worldwide, are evolutionarily highly dynamic with new pathogenic clones emerging rapidly. ...

    Authors: Lucia Karnisova, Monika Marejkova, Hana Hrbackova, Alexander Mellmann, Helge Karch, Angelika Fruth, Pavel Drevinek, Kveta Blahova, Martina Bielaszewska and Jaroslav Nunvar

    Citation: BMC Genomics 2018 19:647

    Content type: Research article

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  17. Rhizobia are alpha-proteobacteria commonly found in soil and root nodules of legumes. It was recently reported that nitrogen-fixing rhizobia also inhabit legume seeds. In this study, we examined whole-genome s...

    Authors: Alejandro Aguilar, Yolanda Mora, Araceli Dávalos, Lourdes Girard, Jaime Mora and Humberto Peralta

    Citation: BMC Genomics 2018 19:645

    Content type: Research article

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  18. Chronic lung infections caused by Pseudomonas aeruginosa are a significant cause of morbidity and mortality in people with cystic fibrosis (CF). Shared P. aeruginosa strains, that can be transmitted between patie...

    Authors: Bryan A. Wee, Anna S. Tai, Laura J. Sherrard, Nouri L. Ben Zakour, Kirt R. Hanks, Timothy J. Kidd, Kay A. Ramsay, Iain Lamont, David M. Whiley, Scott C. Bell and Scott A. Beatson

    Citation: BMC Genomics 2018 19:644

    Content type: Research article

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  19. Pontimonas salivibrio strain CL-TW6T (=KCCM 90105 = JCM18206) was characterized as the type strain of a new genus within the Actinobacterial family Microbacteriaceae. It was isolated from a coastal marine environ...

    Authors: Byung Cheol Cho, Stephen C. Hardies, Gwang Il Jang and Chung Yeon Hwang

    Citation: BMC Genomics 2018 19:625

    Content type: Research article

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  20. Mixed, polyclonal Mycobacterium tuberculosis infection occurs in natural populations. Developing an effective method for detecting such cases is important in measuring the success of treatment and reconstruction ...

    Authors: Benjamin Sobkowiak, Judith R. Glynn, Rein M. G. J. Houben, Kim Mallard, Jody E. Phelan, José Afonso Guerra-Assunção, Louis Banda, Themba Mzembe, Miguel Viveiros, Ruth McNerney, Julian Parkhill, Amelia C. Crampin and Taane G. Clark

    Citation: BMC Genomics 2018 19:613

    Content type: Research article

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  21. The molecular mechanisms underlying bacterial cell death due to stresses or bactericidal antibiotics are complex and remain puzzling. Due to the current crisis of antibiotic resistance, development of effectiv...

    Authors: Sardar Karash and Young Min Kwon

    Citation: BMC Genomics 2018 19:610

    Content type: Research article

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  22. Host specialization is a hallmark of numerous plant pathogens including bacteria, fungi, oomycetes and viruses. Yet, the molecular and evolutionary bases of host specificity are poorly understood. In some case...

    Authors: Nicolas W. G. Chen, Laurana Serres-Giardi, Mylène Ruh, Martial Briand, Sophie Bonneau, Armelle Darrasse, Valérie Barbe, Lionel Gagnevin, Ralf Koebnik and Marie-Agnès Jacques

    Citation: BMC Genomics 2018 19:606

    Content type: Research article

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  23. Resistance to 3rd-generation cephalosporins in Escherichia coli is mostly mediated by extended-spectrum beta-lactamases (ESBLs) or AmpC beta-lactamases. Besides overexpression of the species-specific chromosomal

    Authors: Michael Pietsch, Alexandra Irrgang, Nicole Roschanski, Geovana Brenner Michael, Axel Hamprecht, Heime Rieber, Annemarie Käsbohrer, Stefan Schwarz, Uwe Rösler, Lothar Kreienbrock, Yvonne Pfeifer, Stephan Fuchs and Guido Werner

    Citation: BMC Genomics 2018 19:601

    Content type: Research article

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  24. Bacteria belonging to the Rhodococcus genus play an important role in the degradation of many contaminants, including methylbenzenes. These bacteria, widely distributed in the environment, are known to be a power...

    Authors: Alessandra Di Canito, Jessica Zampolli, Alessandro Orro, Pasqualina D’Ursi, Luciano Milanesi, Guido Sello, Alexander Steinbüchel and Patrizia Di Gennaro

    Citation: BMC Genomics 2018 19:587

    Content type: Research article

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  25. In order to start to understand the function of individual members of gut microbiota, we cultured, sequenced and analysed bacterial anaerobes from chicken caecum.

    Authors: Matej Medvecky, Darina Cejkova, Ondrej Polansky, Daniela Karasova, Tereza Kubasova, Alois Cizek and Ivan Rychlik

    Citation: BMC Genomics 2018 19:561

    Content type: Research article

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  26. Streptococcus agalactiae, also known as Group B Streptococcus (GBS), is a Gram-positive bacterium that colonizes the gastrointestinal and genitourinary tract of humans. This bacterium has also been isolated from ...

    Authors: Ivan Rodrigo Wolf, Alexandre Rossi Paschoal, Cecilia Quiroga, Douglas Silva Domingues, Rogério Fernandes de Souza, Lucienne Garcia Pretto-Giordano and Laurival Antonio Vilas-Boas

    Citation: BMC Genomics 2018 19:556

    Content type: Research article

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  27. Mycobacterium tuberculosis infection in humans is often associated with extended period of latency. To adapt to the hostile hypoxic environment inside a macrophage, M. tuberculosis cells undergo several physiolog...

    Authors: Tungadri Bose, Chandrani Das, Anirban Dutta, Vishnuvardhan Mahamkali, Sudipta Sadhu and Sharmila S. Mande

    Citation: BMC Genomics 2018 19:555

    Content type: Research article

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  28. Bacterial genomes have characteristic compositional skews, which are differences in nucleotide frequency between the leading and lagging DNA strands across a segment of a genome. It is thought that these stran...

    Authors: Lena M. Joesch-Cohen, Max Robinson, Neda Jabbari, Christopher G. Lausted and Gustavo Glusman

    Citation: BMC Genomics 2018 19:528

    Content type: Methodology article

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  29. Mycoplasma hominis is a human urogenital pathogen involved in gynaecological, neonatal and extra-genital infections. However, no versatile genetic tools are currently available to study the pathogenicity of this ...

    Authors: S. Pereyre, C. Bénard, C. Brès, C. Le Roy, J. P. Mauxion, F. Rideau, P. Sirand-Pugnet, B. Henrich and C. Bébéar

    Citation: BMC Genomics 2018 19:525

    Content type: Methodology article

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  30. Streptomyces species produce a vast diversity of secondary metabolites of clinical and biotechnological importance, in particular antibiotics. Recent developments in metabolic engineering, synthetic and systems b...

    Authors: Adam Amara, Eriko Takano and Rainer Breitling

    Citation: BMC Genomics 2018 19:519

    Content type: Research article

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  31. Cronobacter species are associated with severe foodborne infections in neonates and infants, with particular pathovars associated with specific clinical presentations. However, before 2008 the genus was regarded ...

    Authors: Qingyan Guo, Jielin Yang, S. J. Forsythe, Yuan Jiang, Wei Han, Yuping He and Bing Niu

    Citation: BMC Genomics 2018 19:506

    Content type: Methodology article

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  32. In streptococci of the mitis group, competence for natural transformation is a transient physiological state triggered by competence stimulating peptides (CSPs). Although low transformation yields and the abse...

    Authors: G. Salvadori, R. Junges, H. A. Åmdal, T. Chen, D. A. Morrison and F. C. Petersen

    Citation: BMC Genomics 2018 19:453

    Content type: Research article

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  33. Cyanobacteria of the genus Nostoc are capable of forming symbioses with a wide range of organism, including a diverse assemblage of cyanolichens. Only certain lineages of Nostoc appear to be able to form a close,...

    Authors: Andrey N. Gagunashvili and Ólafur S. Andrésson

    Citation: BMC Genomics 2018 19:434

    Content type: Research article

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  34. Thinning supplies of natural resources increase attention to sustainable microbial production of bio-based fuels. The strain Clostridium beijerinckii NRRL B-598 is a relatively well-described butanol producer reg...

    Authors: Karel Sedlar, Pavlina Koscova, Maryna Vasylkivska, Barbora Branska, Jan Kolek, Kristyna Kupkova, Petra Patakova and Ivo Provaznik

    Citation: BMC Genomics 2018 19:415

    Content type: Research article

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  35. Streptococcus salivarius is an abundant isolate of the human oral microbiota. Since both pH and glucose availability fluctuate frequently in the oral cavity, the goal of this study was to investigate regulation b...

    Authors: Jianing Geng, Szu-Chuan Huang, Yueh-Ying Chen, Cheng-Hsun Chiu, Songnian Hu and Yi-Ywan M. Chen

    Citation: BMC Genomics 2018 19:386

    Content type: Research article

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  36. Type strains of the genus Porphyrobacter belonging to the family Erythrobacteraceae and the class Alphaproteobacteria have been isolated from various environments, such as swimming pools, lake water and hot sprin...

    Authors: Lin Xu, Yue-Hong Wu, Peng Zhou, Hong Cheng, Qian Liu and Xue-Wei Xu

    Citation: BMC Genomics 2018 19:385

    Content type: Research article

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  37. The increasing spectrum of multidrug-resistant bacteria is a major global public health concern, necessitating discovery of novel antimicrobial agents. Here, members of the genus Bacillus are investigated as a po...

    Authors: Ghofran Othoum, Salim Bougouffa, Rozaimi Razali, Ameerah Bokhari, Soha Alamoudi, André Antunes, Xin Gao, Robert Hoehndorf, Stefan T. Arold, Takashi Gojobori, Heribert Hirt, Ivan Mijakovic, Vladimir B. Bajic, Feras F. Lafi and Magbubah Essack

    Citation: BMC Genomics 2018 19:382

    Content type: Research article

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  38. Drug resistance in Mycobacterium tuberculosis (MTB) is one of the major challenges in tuberculosis (TB) treatment. However, known mutations cannot explain all of the cases of resistance and little research has fo...

    Authors: Xi Zeng, Jamie Sui-Lam Kwok, Kevin Yi Yang, Kenneth Siu-Sing Leung, Mai Shi, Zhiyuan Yang, Wing-Cheong Yam and Stephen Kwok-Wing Tsui

    Citation: BMC Genomics 2018 19:365

    Content type: Research article

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  39. Recent experimental evidence showed that lactobacilli could be used as potential therapeutic agents for hyperammonemia. However, lack of understanding on how lactobacilli reduce blood ammonia levels limits app...

    Authors: Parul Singh, Hea-Jong Chung, In-Ah Lee, Roshan D’Souza, Hyeon-Jin Kim and Seong-Tshool Hong

    Citation: BMC Genomics 2018 19:292

    Content type: Research article

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  40. Bacterial taxonomy aims to classify bacteria based on true evolutionary events and relies on a polyphasic approach that includes phenotypic, genotypic and chemotaxonomic analyses. Until now, complete genomes a...

    Authors: Raffael C. Inglin, Leo Meile and Marc J. A. Stevens

    Citation: BMC Genomics 2018 19:284

    Content type: Research article

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  41. In shotgun metagenomics, microbial communities are studied through direct sequencing of DNA without any prior cultivation. By comparing gene abundances estimated from the generated sequencing reads, functional...

    Authors: Mariana Buongermino Pereira, Mikael Wallroth, Viktor Jonsson and Erik Kristiansson

    Citation: BMC Genomics 2018 19:274

    Content type: Research article

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  42. Species of the genus Halomonas are salt-tolerant organisms that have a versatile metabolism and can degrade a variety of xenobiotic compounds, utilizing them as their sole carbon source. In this study, we examine...

    Authors: Ana Florencia Gasperotti, María Victoria Revuelta, Claudia Alicia Studdert and María Karina Herrera Seitz

    Citation: BMC Genomics 2018 19:266

    Content type: Research article

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    The Correction to this article has been published in BMC Genomics 2018 19:442

  43. Many cyanobacteria are capable of fixing atmospheric nitrogen, playing a crucial role in biogeochemical cycling. Little is known about freshwater unicellular cyanobacteria Synechococcus spp. at the genomic level,...

    Authors: Andrea Di Cesare, Pedro J. Cabello-Yeves, Nathan A. M. Chrismas, Patricia Sánchez-Baracaldo, Michaela M. Salcher and Cristiana Callieri

    Citation: BMC Genomics 2018 19:259

    Content type: Research article

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  44. Coxiella burnetii is a Gram-negative gammaproteobacterium and zoonotic agent of Q fever. C. burnetii’s genome contains an abundance of pseudogenes and numerous selfish genetic elements. MITEs (miniature inverted-...

    Authors: Shaun Wachter, Rahul Raghavan, Jenny Wachter and Michael F. Minnick

    Citation: BMC Genomics 2018 19:247

    Content type: Research article

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  45. There is a worldwide interest for sustainable and environmentally-friendly ways to produce fuels and chemicals from renewable resources. Among them, the production of acetone, butanol and ethanol (ABE) or Isop...

    Authors: Hadrien Máté de Gérando, François Wasels, Angélique Bisson, Benjamin Clement, Frédérique Bidard, Etienne Jourdier, Ana María López-Contreras and Nicolas Lopes Ferreira

    Citation: BMC Genomics 2018 19:242

    Content type: Research article

    Published on:

    The Correction to this article has been published in BMC Genomics 2018 19:423

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