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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 14

  1. Content type: Research article

    Biosynthetic gene clusters produce a wide range of metabolites with activities that are of interest to the pharmaceutical industry. Specific interest is shown towards those metabolites that exhibit antimicrobi...

    Authors: Ghofran Othoum, Salim Bougouffa, Ameerah Bokhari, Feras F. Lafi, Takashi Gojobori, Heribert Hirt, Ivan Mijakovic, Vladimir B. Bajic and Magbubah Essack

    Citation: BMC Genomics 2019 20:696

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  2. Content type: Research article

    Ensifer alkalisoli YIC4027, a recently characterized nitrogen-fixing bacterium of the genus Ensifer, has been isolated from root nodules of the host plant Sesbania cannabina. This plant is widely used as green ma...

    Authors: Xiaoxiao Dang, Zhihong Xie, Wei Liu, Yu Sun, Xiaolin Liu, Yongqiang Zhu and Christian Staehelin

    Citation: BMC Genomics 2019 20:643

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  3. Content type: Research article

    The candidate genus “Methylacidiphilum” comprises thermoacidophilic aerobic methane oxidizers belonging to the Verrucomicrobia phylum. These are the first described non-proteobacterial aerobic methane oxidizer...

    Authors: Thomas Kruse, Chandini Murarilal Ratnadevi, Helge-André Erikstad and Nils-Kåre Birkeland

    Citation: BMC Genomics 2019 20:642

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  4. Content type: Research article

    Herbaspirillum seropedicae is an environmental β-proteobacterium that is capable of promoting the growth of economically relevant plants through biological nitrogen fixation and phytohormone production. However, ...

    Authors: Helisson Faoro, Willian K. Oliveira, Vinicius A. Weiss, Michelle Z. Tadra-Sfeir, Rodrigo L. Cardoso, Eduardo Balsanelli, Liziane C. C. Brusamarello-Santos, Doumit Camilios-Neto, Leonardo M. Cruz, Roberto T. Raittz, Ana C. Q. Marques, John LiPuma, Cyntia M. T. Fadel-Picheth, Emanuel M. Souza and Fabio O. Pedrosa

    Citation: BMC Genomics 2019 20:630

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  5. Content type: Research article

    Mycobacterium bovis bacillus Calmette-Guérin (M. bovis BCG) is the only vaccine available against tuberculosis (TB). In an effort to standardize the vaccine production, three substrains, i.e. BCG Danish 1331, Tok...

    Authors: Katlyn Borgers, Jheng-Yang Ou, Po-Xing Zheng, Petra Tiels, Annelies Van Hecke, Evelyn Plets, Gitte Michielsen, Nele Festjens, Nico Callewaert and Yao-Cheng Lin

    Citation: BMC Genomics 2019 20:561

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  6. Content type: Research article

    Typhoid fever, caused by Salmonella Typhi, follows a fecal-oral transmission route and is a major global public health concern, especially in developing countries like Bangladesh. Increasing emergence of antimicr...

    Authors: Nicholas Costa Barroso Lima, Arif M. Tanmoy, Emilie Westeel, Luiz Gonzaga Paula de Almeida, Alain Rajoharison, Maksuda Islam, Hubert P. Endtz, Samir K. Saha, Ana Tereza Ribeiro de Vasconcelos and Florence Komurian-Pradel

    Citation: BMC Genomics 2019 20:530

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  7. Content type: Research article

    Enterohemorrhagic Escherichia coli (E. coli) are intestinal pathogenic bacteria that cause life-threatening disease in humans. Their cardinal virulence factor is Shiga toxin (Stx), which is encoded on lambdoid ph...

    Authors: Petya Berger, Ivan U. Kouzel, Michael Berger, Nadja Haarmann, Ulrich Dobrindt, Gerald B. Koudelka and Alexander Mellmann

    Citation: BMC Genomics 2019 20:504

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  8. Content type: Research article

    Salmonella enterica possess several iron acquisition systems, encoded on the chromosome and plasmids. Recently, we demonstrated that incompatibility group (Inc) FIB plasmid-encoded iron acquisition systems (Sit a...

    Authors: Bijay K. Khajanchi, Joshua Xu, Christopher J. Grim, Andrea R. Ottesen, Padmini Ramachandran and Steven L. Foley

    Citation: BMC Genomics 2019 20:490

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  9. Content type: Research article

    Pectobacterium carotovorum subsp. brasiliense is a broad host range bacterial pathogen, which causes blackleg of potatoes and bacterial soft rot of vegetables worldwide. Production of plant cell wall degrading en...

    Authors: Lei Li, Lifang Yuan, Yanxia Shi, Xuewen Xie, Ali Chai, Qi Wang and Baoju Li

    Citation: BMC Genomics 2019 20:486

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  10. Content type: Research article

    Salt pond restoration aims to recover the environmental damages that accumulated over the long history of salt production. Of the restoration strategies, phytoremediation that utilizes salt-tolerant plants and...

    Authors: Huyen-Trang Tran, Hao-Chu Wang, Tsai-Wen Hsu, Rakesh Sarkar, Chao-Li Huang and Tzen-Yuh Chiang

    Citation: BMC Genomics 2019 20:478

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  11. Content type: Research article

    A critical goal in biology is to relate the phenotype to the genotype, that is, to find the genetic determinants of various traits. However, while simple monofactorial determinants are relatively easy to ident...

    Authors: George S. Long, Mohammed Hussen, Jonathan Dench and Stéphane Aris-Brosou

    Citation: BMC Genomics 2019 20:470

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  12. Content type: Research article

    Coxiella burnetii is a zoonotic pathogen that resides in wild and domesticated animals across the globe and causes a febrile illness, Q fever, in humans. An improved understanding of the genetic diversity of C. b...

    Authors: Claudia M. Hemsley, Paul A. O’Neill, Angela Essex-Lopresti, Isobel H. Norville, Tim P. Atkins and Richard W. Titball

    Citation: BMC Genomics 2019 20:441

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  13. Content type: Research article

    Bacillus cereus sensu lato s.l.) is a group of bacteria displaying close phylogenetic relationships but a high ecological diversity. The three most studied species are Bacillus anthracis, Bacillus cereus sensu st...

    Authors: Nancy Fayad, Mireille Kallassy Awad and Jacques Mahillon

    Citation: BMC Genomics 2019 20:436

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  14. Content type: Research article

    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

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  15. Content type: Research article

    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

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

  16. Content type: Research article

    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

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  17. Content type: Research article

    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

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  18. Content type: Research article

    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

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  19. Content type: Research article

    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

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  20. Content type: Methodology article

    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

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  21. Content type: Research article

    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

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  22. Content type: Research article

    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

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  23. Content type: Research article

    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

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  24. Content type: Research article

    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

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  25. Content type: Research article

    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

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  26. Content type: Research article

    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

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  27. Content type: Research article

    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

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  28. Content type: Research article

    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

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  29. Content type: Research article

    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

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  30. Content type: Research article

    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

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  31. Content type: Research article

    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

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  32. Content type: Research article

    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

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  33. Content type: Research article

    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

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  34. Content type: Research article

    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

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  35. Content type: Research article

    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

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  36. Content type: Research article

    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

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  37. Content type: Software Article

    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

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  38. Content type: Research article

    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

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  39. Content type: Research article

    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

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  40. Content type: Research article

    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

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  41. Content type: Research article

    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

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