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BMC Genomics

Prokaryote microbial genomics

Section edited by Theo Smits

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

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  1. Content type: Research article

    Without knowledge of their genomic sequences, it is impossible to make functional models of the bacteria that make up human and animal microbiota. Unfortunately, the vast majority of publicly available genomes...

    Authors: Luis Acuña-Amador, Aline Primot, Edouard Cadieu, Alain Roulet and Frédérique Barloy-Hubler

    Citation: BMC Genomics 2018 19:54

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  2. Content type: Research article

    Among naturally occurring small molecules, tRNA-derived cyclodipeptides are a class that have attracted attention for their diverse and desirable biological activities. However, no tools are available to link ...

    Authors: Michael A. Skinnider, Chad W. Johnston, Nishanth J. Merwin, Chris A. Dejong and Nathan A. Magarvey

    Citation: BMC Genomics 2018 19:45

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  3. Content type: Software

    Expression screening of environmental DNA (eDNA) libraries is a popular approach for the identification and characterization of novel microbial enzymes with promising biotechnological properties. In such “func...

    Authors: Matteo Chiara, Antonio Placido, Ernesto Picardi, Luigi Ruggiero Ceci, David Stephen Horner and Graziano Pesole

    Citation: BMC Genomics 2018 19:44

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  4. Content type: Research article

    Bifidobacterium longum is a common member of the human gut microbiota and is frequently present at high numbers in the gut microbiota of humans throughout life, thus indicative of a close symbiotic host-microbe r...

    Authors: Silvia Arboleya, Francesca Bottacini, Mary O’Connell-Motherway, C. Anthony Ryan, R. Paul Ross, Douwe van Sinderen and Catherine Stanton

    Citation: BMC Genomics 2018 19:33

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  5. Content type: Research article

    The acetic acid bacterium Gluconobacter oxydans 621H is characterized by its exceptional ability to incompletely oxidize a great variety of carbohydrates in the periplasm. The metabolism of this α-proteobacterium...

    Authors: Angela Kranz, Tobias Busche, Alexander Vogel, Björn Usadel, Jörn Kalinowski, Michael Bott and Tino Polen

    Citation: BMC Genomics 2018 19:24

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  6. Content type: Research article

    Due to the predominant usage of short-read sequencing to date, most bacterial genome sequences reported in the last years remain at the draft level. This precludes certain types of analyses, such as the in-dep...

    Authors: Friedhelm Pfeiffer, Maria-Antonia Zamora-Lagos, Martin Blettinger, Assa Yeroslaviz, Andreas Dahl, Stephan Gruber and Bianca H. Habermann

    Citation: BMC Genomics 2018 19:20

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  7. Content type: Research article

    Xanthomonas citri, a causal agent of citrus canker, has been a well-studied model system due to recent availability of whole genome sequences of multiple strains from different geographical regions. Major limitat...

    Authors: Alberto M. Gochez, Jose C. Huguet-Tapia, Gerald V. Minsavage, Deepak Shantaraj, Neha Jalan, Annett Strauß, Thomas Lahaye, Nian Wang, Blanca I. Canteros, Jeffrey B. Jones and Neha Potnis

    Citation: BMC Genomics 2018 19:16

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  8. Content type: Research article

    In recent years, the idea of a highly immunogenic protein-based vaccine to combat Streptococcus pneumoniae and its severe invasive infectious diseases has gained considerable interest. However, the target protein...

    Authors: Gustavo Gámez, Andrés Castro, Alejandro Gómez-Mejia, Mauricio Gallego, Alejandro Bedoya, Mauricio Camargo and Sven Hammerschmidt

    Citation: BMC Genomics 2018 19:10

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  9. Content type: Research article

    Bovine tuberculosis (bTB) poses serious risks to animal welfare and economy, as well as to public health as a zoonosis. Its etiological agent, Mycobacterium bovis, belongs to the Mycobacterium tuberculosis comple...

    Authors: Moira Lasserre, Pablo Fresia, Gonzalo Greif, Gregorio Iraola, Miguel Castro-Ramos, Arturo Juambeltz, Álvaro Nuñez, Hugo Naya, Carlos Robello and Luisa Berná

    Citation: BMC Genomics 2018 19:2

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  10. Content type: Research article

    Bifidobacterium breve represents a common member of the infant gut microbiota and its presence in the gut has been associated with host well being. For this reason it is relevant to in...

    Authors: Francesca Bottacini, Aldert Zomer, Christian Milani, Chiara Ferrario, Gabriele Andrea Lugli, Muireann Egan, Marco Ventura and Douwe van Sinderen

    Citation: BMC Genomics 2017 18:991

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  11. Content type: Research article

    Brevibacterium strains are widely used for the manufacturing of surface-ripened cheeses, contributing to the breakdown of lipids and proteins and producing volatile sulfur compounds an...

    Authors: Nguyen-Phuong Pham, Séverine Layec, Eric Dugat-Bony, Marie Vidal, Françoise Irlinger and Christophe Monnet

    Citation: BMC Genomics 2017 18:955

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  12. Content type: Research article

    Xenorhabdus innexi is a bacterial symbiont of Steinernema scapterisci nematodes, which is a cricket-specialist parasite and together the nematode and bacteria infect and kill crickets....

    Authors: Il-Hwan Kim, Sudarshan K. Aryal, Dariush T. Aghai, Ángel M. Casanova-Torres, Kai Hillman, Michael P. Kozuch, Erin J. Mans, Terra J. Mauer, Jean-Claude Ogier, Jerald C. Ensign, Sophie Gaudriault, Walter G. Goodman, Heidi Goodrich-Blair and Adler R. Dillman

    Citation: BMC Genomics 2017 18:927

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  13. Content type: Methodology article

    Microbiome/host interactions describe characteristics that affect the host's health. Shotgun metagenomics includes sequencing a random subset of the microbiome to analyze its taxonomic and metabolic potential....

    Authors: Bhavya Papudeshi, J. Matthew Haggerty, Michael Doane, Megan M. Morris, Kevin Walsh, Douglas T. Beattie, Dnyanada Pande, Parisa Zaeri, Genivaldo G. Z. Silva, Fabiano Thompson, Robert A. Edwards and Elizabeth A. Dinsdale

    Citation: BMC Genomics 2017 18:915

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  14. Content type: Research article

    Streptomyces clavuligerus ATCC 27064, the industrial producer of the β-lactamase inhibitor clavulanic acid, carries 49 putative secondary metabolite gene clusters. These secondary meta...

    Authors: Rubén Álvarez-Álvarez, Yolanda Martínez-Burgo, Antonio Rodríguez-García and Paloma Liras

    Citation: BMC Genomics 2017 18:907

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  15. Content type: Research article

    Household contacts of cholera patients have a 100 times higher risk of developing a cholera infection than the general population. To compare the genetic relatedness of clinical and water source Vibrio cholerae i...

    Authors: Christine Marie George, Mahamud Rashid, Mathieu Almeida, K. M. Saif-Ur-Rahman, Shirajum Monira, Md. Sazzadul Islam Bhuyian, Khaled Hasan, Toslim T. Mahmud, Shan Li, Jessica Brubaker, Jamie Perin, Zillur Rahman, Munshi Mustafiz, David A. Sack, R. Bradley Sack, Munirul Alam…

    Citation: BMC Genomics 2017 18:903

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  16. Content type: Research article

    The Gram-positive bacterium Enterococcus faecium is a commensal of the human gastrointestinal tract and a frequent cause of bloodstream infections in hospitalized patients. The mechanisms by which E. faecium can ...

    Authors: Xinglin Zhang, Vincent de Maat, Ana M. Guzmán Prieto, Tomasz K. Prajsnar, Jumamurat R. Bayjanov, Mark de Been, Malbert R. C. Rogers, Marc J. M. Bonten, Stéphane Mesnage, Rob J. L. Willems and Willem van Schaik

    Citation: BMC Genomics 2017 18:893

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  17. Content type: Research article

    The varicelloviruses comprise a genus within the alphaherpesvirus subfamily, and infect both humans and other mammals. Recently, next-generation sequencing has been used to generate genomic sequences of severa...

    Authors: Aaron W. Kolb, Andrew C. Lewin, Ralph Moeller Trane, Gillian J. McLellan and Curtis R. Brandt

    Citation: BMC Genomics 2017 18:887

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  18. Content type: Research article

    Small regulatory RNAs (sRNAs) are widely found in bacteria and play key roles in many important physiological and adaptation processes. Studying their evolution and screening for events of coevolution with oth...

    Authors: Franck Cerutti, Ludovic Mallet, Anaïs Painset, Claire Hoede, Annick Moisan, Christophe Bécavin, Mélodie Duval, Olivier Dussurget, Pascale Cossart, Christine Gaspin and Hélène Chiapello

    Citation: BMC Genomics 2017 18:882

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  19. Content type: Research article

    Diphtheria remains a major public health concern with multiple recent outbreaks around the world. Moreover, invasive non-toxigenic strains have emerged globally causing severe infections. A diphtheria epidemic...

    Authors: Steffen Grosse-Kock, Valentina Kolodkina, Edward C. Schwalbe, Jochen Blom, Andreas Burkovski, Paul A. Hoskisson, Sylvain Brisse, Darren Smith, Iain C. Sutcliffe, Leonid Titov and Vartul Sangal

    Citation: BMC Genomics 2017 18:873

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