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Prokaryote microbial genomics

Section edited by Theo Smits

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

Page 1 of 13

  1. Content type: Research article

    The genus Anaplasma is made up of organisms characterized by small genomes that are undergoing reductive evolution. Anaplasma ovis, one of the seven recognized species in this genus, is an understudied pathogen o...

    Authors: Zhijie Liu, Austin M. Peasley, Jifei Yang, Youquan Li, Guiquan Guan, Jianxun Luo, Hong Yin and Kelly A. Brayton

    Citation: BMC Genomics 2019 20:69

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  2. Content type: Research article

    Antibiotic therapy is commonly used in animal agriculture. Antibiotics excreted by the animals can contaminate farming environments, resulting in long term exposure of animals to sub-inhibitory levels of antib...

    Authors: Bart J. F. Keijser, Valeria Agamennone, Tim J. van den Broek, Martien Caspers, Adri van de Braak, Richard Bomers, Mieke Havekes, Eric Schoen, Martin van Baak, Daniël Mioch, Lonneke Bomers and Roy C. Montijn

    Citation: BMC Genomics 2019 20:65

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  3. Content type: Research article

    The gram-negative Xanthomonas genus contains a large group of economically important plant pathogens, which cause severe diseases on many crops worldwide. The diffusible signal factor (DSF) - mediated quorum sens...

    Authors: Lei Li, Jinyun Li, Yunzeng Zhang and Nian Wang

    Citation: BMC Genomics 2019 20:55

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  4. Content type: Research article

    Co-colonization by Pseudomonas aeruginosa and Staphylococcus aureus is frequent in cystic fibrosis patients. Polymicrobial infections involve both detrimental and beneficial interactions between different bacteri...

    Authors: Mikaël Tognon, Thilo Köhler, Alexandre Luscher and Christian van Delden

    Citation: BMC Genomics 2019 20:30

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  5. Content type: Research article

    Short-read sequencing technologies have made microbial genome sequencing cheap and accessible. However, closing genomes is often costly and assembling short reads from genomes that are repetitive and/or have e...

    Authors: Sarah Goldstein, Lidia Beka, Joerg Graf and Jonathan L. Klassen

    Citation: BMC Genomics 2019 20:23

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  6. Content type: Research article

    Salmonella enterica subspecies enterica is an animal and zoonotic pathogen of global importance. Cattle are a significant reservoir of human non-typhoidal salmonellosis and can suffer enteric and systemic disease...

    Authors: Prerna Vohra, Roy R. Chaudhuri, Matthew Mayho, Christina Vrettou, Cosmin Chintoan-Uta, Nicholas R. Thomson, Jayne C. Hope, John Hopkins and Mark P. Stevens

    Citation: BMC Genomics 2019 20:20

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  7. Content type: Research article

    The ability of bacteria to acquire resistance to antibiotics relies to a large extent on their capacity for genome modification. Prokaryotic genomes are highly plastic and can utilize horizontal gene transfer,...

    Authors: Marloes Hoeksema, Martijs J. Jonker, Keshia Bel, Stanley Brul and Benno H. ter Kuile

    Citation: BMC Genomics 2018 19:973

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  8. Content type: Research article

    Crohn’s disease is associated with gut dysbiosis. Independent studies have shown an increase in the abundance of certain bacterial species, particularly Escherichia coli with the adherent-invasive pathotype, in t...

    Authors: Alexander V. Tyakht, Alexander I. Manolov, Alexandra V. Kanygina, Dmitry S. Ischenko, Boris A. Kovarsky, Anna S. Popenko, Alexander V. Pavlenko, Anna V. Elizarova, Daria V. Rakitina, Julia P. Baikova, Valentina G. Ladygina, Elena S. Kostryukova, Irina Y. Karpova, Tatyana A. Semashko, Andrei K. Larin, Tatyana V. Grigoryeva…

    Citation: BMC Genomics 2018 19:968

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  9. Content type: Research article

    Genome-scale metabolic modeling is a cornerstone of systems biology analysis of microbial organisms and communities, yet these genome-scale modeling efforts are invariably based on incomplete functional annota...

    Authors: Marc Griesemer, Jeffrey A. Kimbrel, Carol E. Zhou, Ali Navid and Patrik D’haeseleer

    Citation: BMC Genomics 2018 19:948

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  10. Content type: Research article

    Faecalibacterium prausnitzii is a ubiquitous member of the human gut microbiome, constituting up to 15% of the total bacteria in the human gut. Substantial evidence connects decreased levels of F. prausnitzii wit...

    Authors: Cormac Brian Fitzgerald, Andrey N. Shkoporov, Thomas D. S. Sutton, Andrei V. Chaplin, Vimalkumar Velayudhan, R. Paul Ross and Colin Hill

    Citation: BMC Genomics 2018 19:931

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  11. Content type: Research article

    Restriction-modification (R-M) systems protect bacteria and archaea from attacks by bacteriophages and archaeal viruses. An R-M system specifically recognizes short sites in foreign DNA and cleaves it, while s...

    Authors: I. S. Rusinov, A. S. Ershova, A. S. Karyagina, S. A. Spirin and A. V. Alexeevski

    Citation: BMC Genomics 2018 19:885

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  12. Content type: Research article

    Corynebacterium diphtheriae is the main etiological agent of diphtheria, a global disease causing life-threatening infections, particularly in infants and children. Vaccination with diphtheria toxoid protects aga...

    Authors: Verlaine J. Timms, Trang Nguyen, Taryn Crighton, Marion Yuen and Vitali Sintchenko

    Citation: BMC Genomics 2018 19:869

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  13. Content type: Research article

    Photorhabdus luminescens is an enteric bacterium, which lives in mutualistic association with soil nematodes and is highly pathogenic for a broad spectrum of insects. A complete genome sequence for the type strai...

    Authors: Maria-Antonia Zamora-Lagos, Simone Eckstein, Angela Langer, Athanasios Gazanis, Friedhelm Pfeiffer, Bianca Habermann and Ralf Heermann

    Citation: BMC Genomics 2018 19:854

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  14. Content type: Research article

    Acetogenic bacteria constitute promising biocatalysts for the conversion of CO2/H2 or synthesis gas (H2/CO/CO2) into biofuels and value-added biochemicals. These microorganisms are naturally capable of autotrophi...

    Authors: Yoseb Song, Jongoh Shin, Sangrak Jin, Jung-Kul Lee, Dong Rip Kim, Sun Chang Kim, Suhyung Cho and Byung-Kwan Cho

    Citation: BMC Genomics 2018 19:837

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  15. Content type: Research article

    Helicobacter pylori is a human stomach pathogen, naturally-competent for DNA uptake, and prone to homologous recombination. Extensive homoplasy (i.e., phylogenetically-unlinked identical variations) observed in H...

    Authors: Sujay Chattopadhyay, Peter B. Chi, Vladimir N. Minin, Douglas E. Berg and Evgeni V. Sokurenko

    Citation: BMC Genomics 2018 19:835

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  16. Content type: Research article

    The genus Helicobacter are gram-negative, microaerobic, flagellated, mucus-inhabiting bacteria associated with gastrointestinal inflammation and classified as gastric or enterohepatic Helicobacter species (EHS) a...

    Authors: Anthony Mannion, Zeli Shen and James G. Fox

    Citation: BMC Genomics 2018 19:830

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  17. Content type: Research article

    Pseudomonas syringae is a widespread bacterial species complex that includes a number of significant plant pathogens. Amongst these, P. syringae pv. actinidiae (Psa) initiated a worldwide pandemic in 2008 on cult...

    Authors: Peter A. McAtee, Lara Brian, Ben Curran, Otto van der Linden, Niels J. Nieuwenhuizen, Xiuyin Chen, Rebecca A. Henry-Kirk, Erin A. Stroud, Simona Nardozza, Jay Jayaraman, Erik H. A. Rikkerink, Cris G. Print, Andrew C. Allan and Matthew D. Templeton

    Citation: BMC Genomics 2018 19:822

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  18. Content type: Research article

    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

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  19. Content type: Research article

    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

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  20. Content type: Research article

    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

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  21. Content type: Research article

    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

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  22. Content type: Research article

    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

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  23. Content type: Research article

    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

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  24. Content type: Research article

    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

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  25. Content type: Research article

    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

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  26. Content type: Research article

    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

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  27. Content type: Research article

    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

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  28. Content type: Methodology article

    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

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  29. Content type: Research article

    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

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  30. Content type: Research article

    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

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  31. Content type: Research article

    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

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  32. Content type: Research article

    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

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  33. Content type: Research article

    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

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  34. Content type: Research article

    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

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  35. Content type: Research article

    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

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  36. Content type: Research article

    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

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  37. Content type: Research article

    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

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  38. Content type: Research article

    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

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  39. Content type: Research article

    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

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  40. Content type: Research article

    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

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  41. Content type: Research article

    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

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  42. Content type: Research article

    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

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  43. Content type: Research article

    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

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  44. Content type: Research article

    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

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  45. Content type: Methodology article

    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

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  46. Content type: Methodology article

    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

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  47. Content type: Research article

    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

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