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Prokaryote microbial genomics

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

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  1. BCG is the most widely used vaccine of all time and remains the only licensed vaccine for use against tuberculosis in humans. BCG also protects other species such as cattle against tuberculosis, but due to its...

    Authors: Tom A. Mendum, Aneesh Chandran, Kerstin Williams, H. Martin Vordermeier, Bernardo Villarreal-Ramos, H. Wu, Albel Singh, Alex A. Smith, Rachel E. Butler, Aravind Prasad, Neeraj Bharti, Ruma Banerjee, Sunitha M. Kasibhatla, Apoorva Bhatt, Graham R. Stewart and Johnjoe McFadden

    Citation: BMC Genomics 2019 20:431

    Content type: Research article

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  2. Repeated culture reduces within-sample Mycobacterium tuberculosis genetic diversity due to selection of clones suited to growth in culture and/or random loss of lineages, but it is not known to what extent omitti...

    Authors: Camus Nimmo, Liam P. Shaw, Ronan Doyle, Rachel Williams, Kayleen Brien, Carrie Burgess, Judith Breuer, Francois Balloux and Alexander S. Pym

    Citation: BMC Genomics 2019 20:389

    Content type: Research article

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    The Correction to this article has been published in BMC Genomics 2019 20:433

  3. Several lines of evidence suggest that recombination plays a central role in replication and evolution of herpes simplex virus-1 (HSV-1). G-quadruplex (G4)-motifs have been linked to recombination events in hu...

    Authors: Nandhini Saranathan, Banhi Biswas, Anupam Patra and Perumal Vivekanandan

    Citation: BMC Genomics 2019 20:382

    Content type: Research article

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  4. Toxigenic Vibrio cholerae serogroup O1 is the causative pathogen in the sixth and seventh cholera pandemics. Cholera toxin is the major virulent factor but other virulence and virulence-related factors play certa...

    Authors: Zhenpeng Li, Bo Pang, Duochun Wang, Jie Li, Jialiang Xu, Yujie Fang, Xin Lu and Biao Kan

    Citation: BMC Genomics 2019 20:360

    Content type: Research article

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  5. In natural environments, bacteria must frequently cope with extremely scarce nutrients. Most studies focus on bacterial growth in nutrient replete conditions, while less is known about the stationary phase. He...

    Authors: Jochen Bathke, Anne Konzer, Bernhard Remes, Matthew McIntosh and Gabriele Klug

    Citation: BMC Genomics 2019 20:358

    Content type: Research article

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  6. Obligate sulfur oxidizing chemolithoauthotrophic strains of Hydrogenovibrio crunogenus have been isolated from multiple hydrothermal vent associated habitats. However, a hydrogenase gene cluster (encoding the hyd...

    Authors: Giorgio Gonnella, Nicole Adam and Mirjam Perner

    Citation: BMC Genomics 2019 20:339

    Content type: Research article

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  7. Bacteria carry a wide array of genes, some of which have multiple alleles. These different alleles are often responsible for distinct types of virulence and can determine the classification at the subspecies l...

    Authors: Lusine Khachatryan, Margriet E. M. Kraakman, Alexandra T. Bernards and Jeroen F. J. Laros

    Citation: BMC Genomics 2019 20:338

    Content type: Methodology article

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  8. Rhodococcus ruber strain Chol-4, a strain isolated from a sewage sludge sample, is able to grow in minimal medium supplemented with several compounds, showing a broad catabolic capacity. We have previously determ...

    Authors: Govinda Guevara, Maria Castillo Lopez, Sergio Alonso, Julián Perera and Juana María Navarro-Llorens

    Citation: BMC Genomics 2019 20:332

    Content type: Research article

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  9. Bacillus pumilus is a Gram-positive and endospore-forming bacterium broadly existing in a variety of environmental niches. Because it produces and secrets many industrially useful enzymes, a lot of studies have b...

    Authors: Lin-Li Han, Yong-Cheng Liu, Cui-Cui Miao and Hong Feng

    Citation: BMC Genomics 2019 20:327

    Content type: Research article

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  10. Gene duplication underlies a significant proportion of gene functional diversity and genome complexity in both eukaryotes and prokaryotes. Although several reports in the literature described the duplication o...

    Authors: Manuel Bernabeu, José Francisco Sánchez-Herrero, Pol Huedo, Alejandro Prieto, Mário Hüttener, Julio Rozas and Antonio Juárez

    Citation: BMC Genomics 2019 20:313

    Content type: Research article

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  11. The genetic diversity in Australian populations of Xanthomonas species associated with bacterial leaf spot in tomato, capsicum and chilli were compared to worldwide bacterial populations. The aim of this study wa...

    Authors: R. Roach, R. Mann, C. G. Gambley, T. Chapman, R. G. Shivas and B. Rodoni

    Citation: BMC Genomics 2019 20:310

    Content type: Research article

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  12. Temperate bacteriophages are capable of lysogenic conversion of new bacterial hosts. This phenomenon is often ascribed to “moron” elements that are acquired horizontally and transcribed independently from the ...

    Authors: Danielle L. Peters, Jaclyn G. McCutcheon, Paul Stothard and Jonathan J. Dennis

    Citation: BMC Genomics 2019 20:300

    Content type: Research article

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  13. The effect of mutations conferring antibiotic resistance can depend on the genetic background. To determine if a previously de novo acquired antibiotic resistance influences the adaptation to a second antibiot...

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

    Citation: BMC Genomics 2019 20:284

    Content type: Research article

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  14. Wild birds, in particular pigeons are considered a natural reservoir for stx2f-carrying E. coli. An extensive comparison of isolates from pigeons and humans from the same region is lacking, which hampers justifia...

    Authors: Angela H. A. M. van Hoek, Janieke N. J. van Veldhuizen, Ingrid Friesema, Claudia Coipan, John W. A. Rossen, Indra L. Bergval and Eelco Franz

    Citation: BMC Genomics 2019 20:271

    Content type: Research article

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  15. Although high-throughput marker gene studies provide valuable insight into the diversity and relative abundance of taxa in microbial communities, they do not provide direct measures of their functional capacit...

    Authors: Joseph L. Sevigny, Derek Rothenheber, Krystalle Sharlyn Diaz, Ying Zhang, Kristin Agustsson, R. Daniel Bergeron and W. Kelley Thomas

    Citation: BMC Genomics 2019 20:268

    Content type: Research article

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  16. Continuing evolution of the Mycobacterium tuberculosis (Mtb) complex genomes associated with resistance to anti-tuberculosis drugs is threatening tuberculosis disease control efforts. Both multi- and extensively ...

    Authors: Yaa E. A. Oppong, Jody Phelan, João Perdigão, Diana Machado, Anabela Miranda, Isabel Portugal, Miguel Viveiros, Taane G. Clark and Martin L. Hibberd

    Citation: BMC Genomics 2019 20:252

    Content type: Research article

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  17. Of the hundreds of Vibrio cholerae serogroups, O1 and O139 are the main epidemic-causing ones. Although non-O1/non-O139 serogroups rarely cause epidemics, the possibility exists for strains within them to have pa...

    Authors: Zhenpeng Li, Xin Lu, Duochun Wang, Wei Li Liang, Jingyun Zhang, Jie Li, Jialiang Xu, Bo Pang and Biao Kan

    Citation: BMC Genomics 2019 20:241

    Content type: Research article

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  18. The phytopathogenic bacterium Xylella fastidiosa was thought to be restricted to the Americas where it infects and kills numerous hosts. Its detection worldwide has been blooming since 2013 in Europe and Asia. Ge...

    Authors: Nicolas Denancé, Martial Briand, Romain Gaborieau, Sylvain Gaillard and Marie-Agnès Jacques

    Citation: BMC Genomics 2019 20:239

    Content type: Research article

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  19. The human pathogen Streptococcus pyogenes, or group A Streptococcus, is responsible for mild infections to life-threatening diseases. To facilitate the characterization of regulatory networks involved in the adap...

    Authors: Isabelle Rosinski-Chupin, Elisabeth Sauvage, Agnès Fouet, Claire Poyart and Philippe Glaser

    Citation: BMC Genomics 2019 20:236

    Content type: Research article

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  20. The coordination of group behaviors in bacteria is achieved by a cell-cell signaling process called quorum sensing (QS). QS is an intercellular communication system, which synchronously controls expression of ...

    Authors: Miriam Khider, Erik Hjerde, Hilde Hansen and Nils Peder Willassen

    Citation: BMC Genomics 2019 20:220

    Content type: Research article

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  21. Halomicronema hongdechloris was the first cyanobacterium to be identified that produces chlorophyll (Chl) f. It contains Chl a and uses phycobiliproteins as its major light-harvesting components under white light...

    Authors: Min Chen, Miguel A. Hernandez-Prieto, Patrick C. Loughlin, Yaqiong Li and Robert D. Willows

    Citation: BMC Genomics 2019 20:207

    Content type: Research article

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  22. Escherichia coli O157:H7 (O157) has been linked to numerous foodborne disease outbreaks. The ability to rapidly sequence and analyze genomes is important for understanding epidemiology, virulence, survival, and e...

    Authors: Vijay K. Sharma, Suryatej Akavaram, Robert G. Schaut and Darrell O. Bayles

    Citation: BMC Genomics 2019 20:196

    Content type: Research article

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  23. Diseases on Prunus spp. have been associated with a large number of phylogenetically different pathovars and species within the P. syringae species complex. Despite their economic significance, there is a severe ...

    Authors: Michela Ruinelli, Jochen Blom, Theo H. M. Smits and Joël F. Pothier

    Citation: BMC Genomics 2019 20:172

    Content type: Research article

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  24. Recent adva1nces in whole genome sequencing (WGS) based technologies have facilitated multi-step applications for predicting antimicrobial resistance (AMR) and investigating the molecular epidemiology of Neisseri...

    Authors: Reema Singh, Jo-Anne R. Dillon, Walter Demczuk and Anthony Kusalik

    Citation: BMC Genomics 2019 20:165

    Content type: Software Article

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  25. Prostate cancer (PCa) is the most common malignant neoplasm among men in many countries. Since most precancerous and cancerous tissues show signs of inflammation, chronic bacterial prostatitis has been hypothe...

    Authors: Ye Feng, Varune Rohan Ramnarine, Robert Bell, Stanislav Volik, Elai Davicioni, Vanessa M. Hayes, Shancheng Ren and Colin C. Collins

    Citation: BMC Genomics 2019 20:146

    Content type: Research article

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  26. A previous laboratory study involving wild type, mutant and devR/dosR complemented strains of Mycobacterium tuberculosis reported the attenuation phenotype of complemented strain, Comp1. This phenotype was intrig...

    Authors: Shyamasree De Majumdar, Kriti Sikri, Payel Ghosh, Neetika Jaisinghani, Malobi Nandi, Sheetal Gandotra, Shekhar Mande and Jaya Sivaswami Tyagi

    Citation: BMC Genomics 2019 20:129

    Content type: Research article

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  27. We describe the virulence factors of a methicillin-sensitive Staphylococcus aureus sequence type (ST) 45 strain, MCRF184, (spa type t917), that caused severe necrotizing fasciitis in a 72-year-old diabetic male. ...

    Authors: Vijay Aswani, Fares Najar, Madhulatha Pantrangi, Bob Mau, William R. Schwan and Sanjay K. Shukla

    Citation: BMC Genomics 2019 20:123

    Content type: Research article

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  28. Salmonella enterica subsp. diarizonae (IIIb) is frequently isolated from the environment, cold-blooded reptiles, sheep and humans; however only a few studies describe the isolation of this subspecies from invasiv...

    Authors: Joaquín Giner-Lamia, Pablo Vinuesa, Laura Betancor, Claudia Silva, Julieta Bisio, Lorena Soleto, José A. Chabalgoity, José Luis Puente and Francisco García-del Portillo

    Citation: BMC Genomics 2019 20:99

    Content type: Research article

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    The Correction to this article has been published in BMC Genomics 2020 21:373

  29. 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

    Content type: Research article

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  30. 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

    Content type: Research article

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  31. 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

    Content type: Research article

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  32. 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

    Content type: Research article

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  33. 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

    Content type: Research article

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  34. 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

    Content type: Research article

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  35. 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

    Content type: Research article

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  36. 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

    Content type: Research article

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  37. 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

    Content type: Research article

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  38. 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

    Content type: Research article

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    The Correspondence to this article has been published in BMC Genomics 2020 21:335

  39. 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

    Content type: Research article

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  40. 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

    Content type: Research article

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  41. 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

    Content type: Research article

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  42. 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

    Content type: Research article

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    The Data Descriptor to this article has been published in Scientific Data 2021 8:51

  43. 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

    Content type: Research article

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  44. 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

    Content type: Research article

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  45. 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

    Content type: Research article

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