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Microbial genetics, genomics and proteomics

This section aims to publish studies relating to all aspects of microbial genomics, transcriptomics, proteomics, metabolomics and microbial genome editing.

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  1. The development of diagnostic metagenomics is driven by the need for universal, culture-independent methods for detection and characterization of pathogens to substitute the time-consuming, organism-specific, ...

    Authors: Sandra Christine Andersen, Kristoffer Kiil, Christoffer Bugge Harder, Mathilde Hasseldam Josefsen, Søren Persson, Eva Møller Nielsen and Jeffrey Hoorfar

    Citation: BMC Microbiology 2017 17:133

    Content type: Research article

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  2. Phosphorylation of amino acid residues on proteins is an important and common post-translational modification in both eukaryotes and prokaryotes. Most research work has been focused on phosphorylation of serin...

    Authors: Shu-Jung Lai, I-Fan Tu, Wan-Ling Wu, Jhih-Tian Yang, Louis Y. P. Luk, Mei-Chin Lai, Yu-Hsuan Tsai and Shih-Hsiung Wu

    Citation: BMC Microbiology 2017 17:123

    Content type: Research article

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  3. Vibrio parahaemolyticus is an autochthonous marine bacterial species comprising strains able to grow in broth containing bile salts at 37 °C, a condition seldom found in the ocean. How...

    Authors: Katherine García, Cristian Yáñez, Nicolás Plaza, Francisca Peña, Pedro Sepúlveda, Diliana Pérez-Reytor and Romilio T. Espejo

    Citation: BMC Microbiology 2017 17:118

    Content type: Research article

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  4. DNA processing chain A (DprA) is a DNA binding protein which is ubiquitous in bacteria, and is required for DNA transformation to various extents among bacterial species. However, the interaction of DprA with ...

    Authors: Getachew Tesfaye Beyene, Shewit Kalayou, Tahira Riaz and Tone Tonjum

    Citation: BMC Microbiology 2017 17:96

    Content type: Research article

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  5. Successful commensal bacteria have evolved to maintain colonization in challenging environments. The oral viridans streptococci are pioneer colonizers of dental plaque biofilm. Some of these bacteria have adap...

    Authors: Elaine M. Haase, Yurong Kou, Amarpreet Sabharwal, Yu-Chieh Liao, Tianying Lan, Charlotte Lindqvist and Frank A. Scannapieco

    Citation: BMC Microbiology 2017 17:94

    Content type: Research article

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    The Erratum to this article has been published in BMC Microbiology 2017 17:149

  6. Fibronectin (Fn) plays a major role in the attachment of Staphylococcus aureus to host cells by bridging staphylococcal fibronectin-binding proteins (FnBPs) and cell-surface integrins. A previous study demonstrat...

    Authors: Hong-Yi Chen, Mei-Hui Lin, Chien-Cheng Chen and Jwu-Ching Shu

    Citation: BMC Microbiology 2017 17:92

    Content type: Research article

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  7. The nuclear envelope is considered a key classification marker that distinguishes prokaryotes from eukaryotes. However, this marker does not apply to the family Planctomycetaceae, which has intracellular space...

    Authors: Min Guo, Ruifu Yang, Chen Huang, Qiwen Liao, Guangyi Fan, Chenghang Sun and Simon Ming-Yuen Lee

    Citation: BMC Microbiology 2017 17:86

    Content type: Research article

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  8. Polynucleotide phosphorylase (PNPase, encoded by pnp) is generally thought of as an enzyme dedicated to RNA metabolism. The pleiotropic effects of PNPase deficiency is imputed to altered processing and turnover o...

    Authors: Thomas Carzaniga, Giulia Sbarufatti, Federica Briani and Gianni Dehò

    Citation: BMC Microbiology 2017 17:81

    Content type: Research article

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  9. In 2006, we found healthy subjects carrying ST131 Escherichia coli in their intestinal microbiota consisting of two populations: a subdominant population of fluoroquinolone-resistant E. coli belonging to subclone...

    Authors: Marie-Hélène Nicolas-Chanoine, Marie Petitjean, Azucena Mora, Noémie Mayer, Jean-Philippe Lavigne, Olivier Boulet, Véronique Leflon-Guibout, Jorge Blanco and Didier Hocquet

    Citation: BMC Microbiology 2017 17:71

    Content type: Research article

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  10. Corynebacterium pseudotuberculosis biovar ovis, a facultative intracellular pathogen, is the etiologic agent of caseous lymphadenitis in small ruminants. During the infection process,

    Authors: Wanderson M. Silva, Fernanda A. Dorella, Siomar C. Soares, Gustavo H. M. F. Souza, Thiago L. P. Castro, Núbia Seyffert, Henrique Figueiredo, Anderson Miyoshi, Yves Le Loir, Artur Silva and Vasco Azevedo

    Citation: BMC Microbiology 2017 17:55

    Content type: Researc article

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  11. It was previously reported in China that two recent large-scale outbreaks of Streptococcus suis serotype 2 (S. suis 2) infections in human were caused by two highly virulent S. suis 2 strains, from which a novel ...

    Authors: Jing Wang, Youjun Feng, Changjun Wang, Feng Zheng, Bachar Hassan, Liming Zhi, Wenjuan Li, Yi Yao, Elaine He, Shibo Jiang and Jiaqi Tang

    Citation: BMC Microbiology 2017 17:67

    Content type: Research article

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    The Erratum to this article has been published in BMC Microbiology 2017 17:152

  12. Multilocus sequence typing (MLST) is a highly discriminatory typing strategy; it is reproducible and scalable. There is a MLST scheme for Clostridium difficile (CD), a gram positive bacillus causing different pat...

    Authors: Marina Muñoz, Dora Inés Ríos-Chaparro, Manuel Alfonso Patarroyo and Juan David Ramírez

    Citation: BMC Microbiology 2017 17:62

    Content type: Research article

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  13. Hydrogen sulfide (H2S) is a toxic foul-smelling gas produced by subgingival biofilms in patients with periodontal disease and is suggested to be part of the pathogenesis of the disease. We studied the H2S-produci...

    Authors: Amina Basic, Madeleine Blomqvist, Gunnar Dahlén and Gunnel Svensäter

    Citation: BMC Microbiology 2017 17:61

    Content type: Research article

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  14. Cystic Fibrosis (CF) is an autosomal recessive disease that affects the function of a number of organs, principally the lungs, but also the gastrointestinal tract. The manifestations of cystic fibrosis transme...

    Authors: D.G. Burke, F. Fouhy, M. J. Harrison, M. C. Rea, P. D. Cotter, O. O’Sullivan, C. Stanton, C. Hill, F. Shanahan, B. J. Plant and R. P. Ross

    Citation: BMC Microbiology 2017 17:58

    Content type: Research article

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    The Erratum to this article has been published in BMC Microbiology 2017 17:102

  15. Escherichia coli O157:H7 (O157) strain 86–24, linked to a 1986 disease outbreak, displays curli- and biofilm-negative phenotypes that are correlated with the lack of Congo red (CR) bin...

    Authors: V. K. Sharma, D. O. Bayles, D. P. Alt, T. Looft, B. W. Brunelle and J. A. Stasko

    Citation: BMC Microbiology 2017 17:56

    Content type: Research article

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  16. Enterococcus is ubiquitous in nature and is a commensal of both the bovine and human gastrointestinal (GI) tract. It is also associated with clinical infections in humans. Subtherapeut...

    Authors: Alicia G. Beukers, Rahat Zaheer, Noriko Goji, Kingsley K. Amoako, Alexandre V. Chaves, Michael P. Ward and Tim A. McAllister

    Citation: BMC Microbiology 2017 17:52

    Content type: Research article

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  17. Next Generation Sequencing (NGS) technologies provide exciting possibilities for whole genome sequencing of a plethora of organisms including bacterial strains and phages, with many possible applications in re...

    Authors: A. Sharaf, F. Mercati, I. Elmaghraby, R. M. Elbaz and E. M. Marei

    Citation: BMC Microbiology 2017 17:51

    Content type: Research article

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  18. Salmonella enterica serovar Enteritidis (S. Enteritidis) has emerged as one of the most important food-borne pathogens for humans. Lipopolysaccharide (LPS), as a component of the outer...

    Authors: Yang Jiao, Rongxian Guo, Peipei Tang, Xilong Kang, Junlei Yin, Kaiyue Wu, Shizhong Geng, Qiuchun Li, Jun Sun, Xiulong Xu, Xiaohui Zhou, Junji Gan, Xinan Jiao, Xiufan Liu and Zhiming Pan

    Citation: BMC Microbiology 2017 17:48

    Content type: Research article

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  19. Fungi are among the most abundant and diverse organisms on Earth. However, a substantial amount of the species diversity, relationships, habitats, and life strategies of these microorganisms remain to be disco...

    Authors: Fernanda Badotti, Francislon Silva de Oliveira, Cleverson Fernando Garcia, Aline Bruna Martins Vaz, Paula Luize Camargos Fonseca, Laila Alves Nahum, Guilherme Oliveira and Aristóteles Góes-Neto

    Citation: BMC Microbiology 2017 17:42

    Content type: Research article

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  20. Wound-related infection remains a major challenge for health professionals. One disadvantage in conventional antibiotics is their inability to penetrate biofilms, the main protective strategy for bacteria to e...

    Authors: Hong-yan Wang, Li Lin, Li-si Tan, Hui-Yuan Yu, Jya-Wei Cheng and Ya-ping Pan

    Citation: BMC Microbiology 2017 17:37

    Content type: Research article

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  21. Pseudomonas aeruginosa pathogenicity island 1 (PAPI-1) is one of the largest genomic islands of this important opportunistic human pathogen. Previous studies have shown that PAPI-1 enc...

    Authors: Toan Phuoc Hong, Michelle Q. Carter, Paolo Struffi, Stefano Casonato, Youai Hao, Joseph S. Lam, Stephen Lory and Olivier Jousson

    Citation: BMC Microbiology 2017 17:31

    Content type: Research article

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  22. Brucellosis is a common and chronic disease of cattle and other bovids that often causes reproductive disorders. Natural infection in cattle is caused by Brucella abortus and transmission typically occurs during ...

    Authors: Giuliano Garofolo, Elisabetta Di Giannatale, Ilenia Platone, Katiuscia Zilli, Lorena Sacchini, Anna Abass, Massimo Ancora, Cesare Cammà, Guido Di Donato, Fabrizio De Massis, Paolo Calistri, Kevin P. Drees and Jeffrey T. Foster

    Citation: BMC Microbiology 2017 17:28

    Content type: Research article

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  23. Bacteria of the class Mollicutes underwent extreme reduction of genomes and gene expression control systems. Only a few regulators are known to date. In this work, we describe a novel group of transcriptional ...

    Authors: Gleb Y. Fisunov, Daria V. Evsyutina, Valentin A. Manuvera and Vadim M. Govorun

    Citation: BMC Microbiology 2017 17:26

    Content type: Research article

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  24. Staphylococcus aureus (Staph. aureus) is one of the major pathogens causing mastitis in dairy ruminants worldwide. The chronic nature of Staph. aureus infection enhances the contagious...

    Authors: E. Capra, P. Cremonesi, A. Pietrelli, S. Puccio, M. Luini, A. Stella and B. Castiglioni

    Citation: BMC Microbiology 2017 17:21

    Content type: Research article

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  25. Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrhea in children and travelers to endemic areas. Secretion of the heat labile AB5 toxin (LT) is induced by alkaline conditions. In this study, we de...

    Authors: Lucia Gonzales-Siles, Roger Karlsson, Diarmuid Kenny, Anders Karlsson and Åsa Sjöling

    Citation: BMC Microbiology 2017 17:11

    Content type: Research article

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  26. Ruminal digestion is carried out by large numbers of bacteria, archaea, protozoa and fungi. Understanding the microbiota is important because ruminal fermentation dictates the efficiency of feed utilisation by...

    Authors: Timothy J. Snelling and R. John Wallace

    Citation: BMC Microbiology 2017 17:9

    Content type: Research article

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  27. Despite their versatile functions in multimeric protein complexes, in the modification of enzymatic activities, intercellular communication or regulatory processes, proteins shorter than 80 amino acids (μ-prot...

    Authors: Desiree Baumgartner, Matthias Kopf, Stephan Klähn, Claudia Steglich and Wolfgang R. Hess

    Citation: BMC Microbiology 2016 16:285

    Content type: Research article

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  28. In Japan, a variety of traditional dietary habits and daily routines have developed in many regions. The effects of these behaviors, and the regional differences in the composition of the gut microbiota, are y...

    Authors: Kaihei Oki, Mutsumi Toyama, Taihei Banno, Osamu Chonan, Yoshimi Benno and Koichi Watanabe

    Citation: BMC Microbiology 2016 16:284

    Content type: Research article

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  29. Meat protein in the diet has been shown to be beneficial for the growth of Lactobacillus in the caecum of growing rats; however, it is unknown whether gut microbiota in middle-aged animals have the same responses...

    Authors: Yingying Zhu, He Li, Xinglian Xu, Chunbao Li and Guanghong Zhou

    Citation: BMC Microbiology 2016 16:281

    Content type: Research article

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  30. The basidiomycetous yeast Xanthophyllomyces dendrorhous has been described as a potential biofactory for terpenoid-derived compounds due to its ability to synthesize astaxanthin. Functional knowledge of the genes...

    Authors: Nicole Werner, Melissa Gómez, Marcelo Baeza, Víctor Cifuentes and Jennifer Alcaíno

    Citation: BMC Microbiology 2016 16:278

    Content type: Research article

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  31. The outermost layer of mycobacterial cell wall is rich in lipids and glycolipids, surface molecules which differ among species. Mycobacterium smegmatis, an attractive model for the study of both pathogenic and no...

    Authors: Anna Zanfardino, Adriana Migliardi, Daniele D’Alonzo, Angela Lombardi, Mario Varcamonti and Angela Cordone

    Citation: BMC Microbiology 2016 16:267

    Content type: Research article

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  32. The emergence and prevalence of multidrug resistant (MDR) pathogenic bacteria poses a serious threat to human and animal health globally. Nosocomial infections and common ailments such as pneumonia, wound, uri...

    Authors: Malathy Krishnamurthy, Richard T. Moore, Sathish Rajamani and Rekha G. Panchal

    Citation: BMC Microbiology 2016 16:258

    Content type: Review

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  33. The study used a set of 407 human extraintestinal pathogenic E. coli strains (ExPEC) isolated from (1) skin and soft tissue infections, (2) respiratory infections, (3) intra-abdominal infections, and (4) genital ...

    Authors: Lenka Micenková, Juraj Bosák, Martin Vrba, Alena Ševčíková and David Šmajs

    Citation: BMC Microbiology 2016 16:218

    Content type: Research article

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  34. Bacterial two-component regulatory systems (TCRS) are associated with the expression of virulence factors and antibiotic susceptibility. In Staphylococcus aureus, 16 TCRS types have been identified. The histidine...

    Authors: Jung Wook Kim, Hyun-Kyung Kim, Gi Su Kang, Il-Hwan Kim, Hwa Su Kim, Yeong Seon Lee and Jae Il Yoo

    Citation: BMC Microbiology 2016 16:206

    Content type: Research article

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  35. Gene essentiality - whether or not a gene is necessary for cell growth - is a fundamental component of gene function. It is not well established how quickly gene essentiality can change, as few studies have co...

    Authors: Nikki E. Freed, Dirk Bumann and Olin K. Silander

    Citation: BMC Microbiology 2016 16:203

    Content type: Research article

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  36. Antimicrobial peptides (AMPs) are a class of antimicrobial agents with broad-spectrum activities. Several reports indicate that cationic AMPs bind to the negatively charged bacterial membrane causing membrane ...

    Authors: Ejovwoke F. Dosunmu, Atul A. Chaudhari, Swapnil Bawage, Mona K. Bakeer, Donald R. Owen, Shree R. Singh, Vida A. Dennis and Shreekumar R. Pillai

    Citation: BMC Microbiology 2016 16:192

    Content type: Research article

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  37. Sequence variability in the hepatitis C virus (HCV) genome has led to the development and classification of six genotypes and a number of subtypes. The HCV 5′ untranslated region mainly comprises an internal r...

    Authors: Evan W. Floden, Anas Khawaja, Václav Vopálenský and Martin Pospíšek

    Citation: BMC Microbiology 2016 16:187

    Content type: Database

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  38. Streptococcus suis is divided into 29 serotypes based on a serological reaction against the capsular polysaccharide (CPS). Multiplex PCR tests targeting the cps locus are also used to ...

    Authors: Taryn B. T. Athey, Sarah Teatero, Sonia Lacouture, Daisuke Takamatsu, Marcelo Gottschalk and Nahuel Fittipaldi

    Citation: BMC Microbiology 2016 16:162

    Content type: Research article

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  39. Iron homeostasis is an essential process over the entire lives of both hosts and bacterial pathogens, and also plays roles in many other metabolic functions. Currently, knowledge is limited on the iron scaveng...

    Authors: Zujie Yao, Zhihong Wang, Lina Sun, Wanxin Li, Yan Shi, Ling Lin, Wenxiong Lin and Xiangmin Lin

    Citation: BMC Microbiology 2016 16:161

    Content type: Research article

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  40. Biofilm development, specifically the fundamentally adaptive switch from acute to chronic infection phenotypes, requires global regulators and small non-coding regulatory RNAs (sRNAs). This work utilized RNA-s...

    Authors: Christine L. Miller, Manuel Romero, S. L. Rajasekhar Karna, Tsute Chen, Stephan Heeb and Kai P. Leung

    Citation: BMC Microbiology 2016 16:155

    Content type: Research article

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  41. The bacterial chromosome may be used to stably maintain foreign DNA in the mega-base range. Integration into the chromosome circumvents issues such as plasmid replication, stability, incompatibility, and copy ...

    Authors: Rogelio Hernández-Tamayo, Gonzalo Torres-Tejerizo, Susana Brom and David Romero

    Citation: BMC Microbiology 2016 16:133

    Content type: Methodology article

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  42. Escherichia coli K-12 strains contain DNA cytosine methyltransferase (Dcm), which generates 5-methylcytosine at 5′CCWGG3′ sites. Although the role of 5-methylcytosine in eukaryotic gen...

    Authors: Kevin T. Militello, Robert D. Simon, Alexandra H. Mandarano, Anthony DiNatale, Stacy M. Hennick, Justine C. Lazatin and Sarah Cantatore

    Citation: BMC Microbiology 2016 16:130

    Content type: Research article

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  43. Shigella spp. are the primary causative agents of bacillary dysentery. Since its emergence in the late 1980s, the S. flexneri serotype 1c remains poorly understood, particularly with r...

    Authors: Swee-Seong Tang, Nils I. A. Carlin, Kaisar A. Talukder, Phung D. Cam and Naresh K. Verma

    Citation: BMC Microbiology 2016 16:127

    Content type: Research article

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  44. Witches’ broom, a disease caused by the basidiomycete Moniliophthora perniciosa, is considered to be the most important disease of the cocoa crop in Bahia, an area in the Brazilian Amazon, and also in the other c...

    Authors: Joise Hander Mares, Karina Peres Gramacho, Everton Cruz dos Santos, André da Silva Santiago, Edson Mário de Andrade Silva, Fátima Cerqueira Alvim and Carlos Priminho Pirovani

    Citation: BMC Microbiology 2016 16:120

    Content type: Research article

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  45. Corynebacterium pseudotuberculosis can be classified into two biovars or biovars based on their nitrate-reducing ability. Strains isolated from sheep and goats show negative nitrate re...

    Authors: Alberto Oliveira, Pammella Teixeira, Marcela Azevedo, Syed Babar Jamal, Sandeep Tiwari, Sintia Almeida, Artur Silva, Debmalya Barh, Elaine Maria Seles Dorneles, Dionei Joaquim Haas, Marcos Bryan Heinemann, Preetam Ghosh, Andrey Pereira Lage, Henrique Figueiredo, Rafaela Salgado Ferreira and Vasco Azevedo

    Citation: BMC Microbiology 2016 16:100

    Content type: Research article

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  46. Clostridium termitidis CT1112 is an anaerobic, Gram-positive, mesophilic, spore-forming, cellulolytic bacterium, originally isolated from the gut of a wood feeding termite Nasusitermes...

    Authors: Riffat I. Munir, Victor Spicer, Oleg V. Krokhin, Dmitry Shamshurin, XiangLi Zhang, Marcel Taillefer, Warren Blunt, Nazim Cicek, Richard Sparling and David B. Levin

    Citation: BMC Microbiology 2016 16:91

    Content type: Research article

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  47. In the genus Streptomyces, one of the most remarkable control mechanisms of physiological processes is carbon catabolite repression (CCR). This mechanism regulates the expression of genes involved in the uptake a...

    Authors: Alba Romero-Rodríguez, Diana Rocha, Beatriz Ruiz-Villafan, Víctor Tierrafría, Romina Rodríguez-Sanoja, Daniel Segura-González and Sergio Sánchez

    Citation: BMC Microbiology 2016 16:77

    Content type: Research article

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  48. Identification of unexpected taxa in 16S rRNA surveys of low-density microbiota, diluted mock communities and cultures demonstrated that a variable fraction of sequence reads originated from exogenous DNA. The...

    Authors: Vladimir Lazarevic, Nadia Gaïa, Myriam Girard and Jacques Schrenzel

    Citation: BMC Microbiology 2016 16:73

    Content type: Research article

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