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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 15

  1. Viruses are the most abundant biological entities on earth and play import roles in marine biogeochemical cycles. Here, viral communities in the surface water of the East China Sea (ECS) were collected from th...

    Authors: Shuang Wu, Liang Zhou, Yifan Zhou, Hongming Wang, Jinzhou Xiao, Shuling Yan and Yongjie Wang

    Citation: BMC Genomics 2020 21:441

    Content type: Research article

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  2. In bacteria, pan-genomes are the result of an evolutionary “tug of war” between selection and horizontal gene transfer (HGT). High rates of HGT increase the genetic pool and the effective population size (Ne), re...

    Authors: Mirna Vázquez-Rosas-Landa, Gabriel Yaxal Ponce-Soto, Jonás A. Aguirre-Liguori, Shalabh Thakur, Enrique Scheinvar, Josué Barrera-Redondo, Enrique Ibarra-Laclette, David S. Guttman, Luis E. Eguiarte and Valeria Souza

    Citation: BMC Genomics 2020 21:418

    Content type: Research article

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  3. The Escherichia coli ER2566 strain (NC_CP014268.2) was developed as a BL21 (DE3) derivative strain and had been widely used in recombinant protein expression. However, like many other current RefSeq annotations, ...

    Authors: Lizhi Zhou, Hai Yu, Kaihang Wang, Tingting Chen, Yue Ma, Yang Huang, Jiajia Li, Liqin Liu, Yuqian Li, Zhibo Kong, Qingbing Zheng, Yingbin Wang, Ying Gu, Ningshao Xia and Shaowei Li

    Citation: BMC Genomics 2020 21:407

    Content type: Research article

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  4. Mycoplasma anserisalpingitidis is a waterfowl pathogen that mainly infects geese, can cause significant economic losses and is present worldwide. With the advance of whole genome sequencing technologies, new meth...

    Authors: Áron B. Kovács, Zsuzsa Kreizinger, Barbara Forró, Dénes Grózner, Alexa Mitter, Szilvia Marton, Krisztina Bali, Anna Sawicka, Grzegorz Tomczyk, Krisztián Bányai and Miklós Gyuranecz

    Citation: BMC Genomics 2020 21:403

    Content type: Research article

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  5. Lytic bacteriophages that infect Campylobacter spp. have been utilized to develop therapeutic/decontamination techniques. However, the association of Campylobacter spp. and bacteriophages has been the focus of se...

    Authors: Steven Hooton, Daniela D’Angelantonio, Yang Hu, Phillippa L. Connerton, Giuseppe Aprea and Ian F. Connerton

    Citation: BMC Genomics 2020 21:400

    Content type: Research article

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  6. Lanthipeptides belong to the ribosomally synthesized and post-translationally modified peptide group of natural products and have a variety of biological activities ranging from antibiotics to antinociceptives...

    Authors: Mark C. Walker, Sara M. Eslami, Kenton J. Hetrick, Sarah E. Ackenhusen, Douglas A. Mitchell and Wilfred A. van der Donk

    Citation: BMC Genomics 2020 21:387

    Content type: Research article

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  7. Salmonella enterica is a leading cause of foodborne illness worldwide resulting in considerable public health and economic costs. Testing for the presence of this pathogen in food is often hampered by the presenc...

    Authors: Ana Victoria C. Pilar, Nicholas Petronella, Forest M. Dussault, Adrian J. Verster, Sadjia Bekal, Roger C. Levesque, Lawrence Goodridge and Sandeep Tamber

    Citation: BMC Genomics 2020 21:377

    Content type: Research article

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  8. Bacteriophages are bacterial parasites and are considered the most abundant and diverse biological entities on the planet. Previously we identified 154 prophages from 151 serovars of Salmonella enterica subsp. en...

    Authors: Ruimin Gao, Sohail Naushad, Sylvain Moineau, Roger Levesque, Lawrence Goodridge and Dele Ogunremi

    Citation: BMC Genomics 2020 21:374

    Content type: Research article

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  9. Pathogens with a global distribution face diverse biotic and abiotic conditions across populations. Moreover, the ecological and evolutionary history of each population is unique. Xylella fastidiosa is a xylem-dw...

    Authors: Andreina I. Castillo, Carlos Chacón-Díaz, Neysa Rodríguez-Murillo, Helvecio D. Coletta-Filho and Rodrigo P. P. Almeida

    Citation: BMC Genomics 2020 21:369

    Content type: Research article

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  10. A virus community is the spectrum of viral strains populating an infected host, which plays a key role in pathogenesis and therapy response in viral infectious diseases. However automatic and dedicated pipelin...

    Authors: Mingjie Wang, Jianfeng Li, Xiaonan Zhang, Yue Han, Demin Yu, Donghua Zhang, Zhenghong Yuan, Zhitao Yang, Jinyan Huang and Xinxin Zhang

    Citation: BMC Genomics 2020 21:363

    Content type: Software

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  11. Species of the genus Vibrio, one of the most diverse bacteria genera, have undergone niche adaptation followed by clonal expansion. Niche adaptation and ultimately the formation of ecotypes and speciation in this...

    Authors: Cynthia Maria Chibani, Olivia Roth, Heiko Liesegang and Carolin Charlotte Wendling

    Citation: BMC Genomics 2020 21:354

    Content type: Research article

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  12. Compromised intestinal barrier (CIB) has been associated with many enteropathies, including colorectal cancer (CRC) and inflammatory bowel disease (IBD). We hypothesized that CIB could lead to increased host-d...

    Authors: Puzi Jiang, Senying Lai, Sicheng Wu, Xing-Ming Zhao and Wei-Hua Chen

    Citation: BMC Genomics 2020 21:348

    Content type: Research article

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  13. Monochamus alternatus Hope is one of the insect vectors of pinewood nematode (Bursaphelenchus xylophilus), which causes the destructive pine wilt disease. The microorganisms within the ecosystem, comprising plant...

    Authors: Yajie Guo, Qiannan Lin, Lyuyi Chen, Rebeca Carballar-Lejarazú, Aishan Zhang, Ensi Shao, Guanghong Liang, Xia Hu, Rong Wang, Lei Xu, Feiping Zhang and Songqing Wu

    Citation: BMC Genomics 2020 21:337

    Content type: Research article

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  14. In their paper entitled “Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa” (BMC Genomics (2018) 19:931), Fit...

    Authors: Aharon Oren and George M. Garrity

    Citation: BMC Genomics 2020 21:335

    Content type: Correspondence

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    The original article was published in BMC Genomics 2018 19:931

  15. Lactobacillus fermentum, a member of the lactic acid bacteria complex, has recently garnered increased attention due to documented antagonistic properties and interest in assessing the probiotic potential of sele...

    Authors: Katelyn Brandt, Matthew A. Nethery, Sarah O’Flaherty and Rodolphe Barrangou

    Citation: BMC Genomics 2020 21:328

    Content type: Research article

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  16. Nontuberculous mycobacterium (NTM) species are ubiquitous microorganisms. NTM pulmonary disease (NTM-PD) is thought to be caused not by human-to-human transmission but by independent environmental acquisition....

    Authors: Jung-Ki Yoon, Taek Soo Kim, Jong-Il Kim and Jae-Joon Yim

    Citation: BMC Genomics 2020 21:322

    Content type: Research article

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  17. Campylobacter jejuni and Campylobacter coli are major global causes of bacterial gastroenteritis. Whilst several individual colonisation and virulence factors have been identified, our understanding of their role...

    Authors: Jai W. Mehat, Roberto M. La Ragione and Arnoud H. M. van Vliet

    Citation: BMC Genomics 2020 21:314

    Content type: Research article

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  18. Interest in studying the spatial distribution of gene expression in tissues is rapidly increasing. Spatial Transcriptomics is a novel sequencing-based technology that generates high-throughput information on t...

    Authors: Emelie Berglund, Sami Saarenpää, Anders Jemt, Joel Gruselius, Ludvig Larsson, Ludvig Bergenstråhle, Joakim Lundeberg and Stefania Giacomello

    Citation: BMC Genomics 2020 21:298

    Content type: Methodology article

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  19. Pseudomonas syringae is an important plant pathogen, which could adapt many different environmental conditions. Under the nutrient-limited and other stress conditions, P. syringae produces nucleotide signal molec...

    Authors: Jun Liu, Menghao Yu, Tiyakhon Chatnaparat, Jae Hoon Lee, Yanli Tian, Baishi Hu and Youfu Zhao

    Citation: BMC Genomics 2020 21:296

    Content type: Research article

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  20. Recent studies have suggested that the gut microbiota is altered in children with juvenile idiopathic arthritis (JIA). However, age, sex, and body mass index (BMI) were not matched in the previous studies, and...

    Authors: Xubo Qian, Yong-Xin Liu, Xiaohong Ye, Wenjie Zheng, Shaoxia Lv, Miaojun Mo, Jinjing Lin, Wenqin Wang, Weihan Wang, Xianning Zhang and Meiping Lu

    Citation: BMC Genomics 2020 21:286

    Content type: Research article

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  21. Shigella is a Gram-negative facultative intracellular bacterium that causes bacillary dysentery in humans. Shigella invades cells of the colonic mucosa owing to its virulence plasmid-encoded Type 3 Secretion Syst...

    Authors: Ramón Cervantes-Rivera, Sophie Tronnet and Andrea Puhar

    Citation: BMC Genomics 2020 21:285

    Content type: Research article

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  22. Emergence of antibiotic resistance is a global public health concern. The relationships between antibiotic use, the gut community composition, normal physiology and metabolism, and individual and public health...

    Authors: Lei Xu, Anil Surathu, Isaac Raplee, Ashok Chockalingam, Sharron Stewart, Lacey Walker, Leonard Sacks, Vikram Patel, Zhihua Li and Rodney Rouse

    Citation: BMC Genomics 2020 21:263

    Content type: Research article

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  23. The nucleotide second messengers, i.e., guanosine tetraphosphate and pentaphosphate [collectively referred to as (p) ppGpp], trigger the stringent response under nutrient starvation conditions and play an esse...

    Authors: Ho-wen Yang, Menghao Yu, Jae Hoon Lee, Tiyakhon Chatnaparat and Youfu Zhao

    Citation: BMC Genomics 2020 21:261

    Content type: Research article

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  24. The Brazilian endemic clone Pseudomonas aeruginosa ST277 carries important antibiotic resistance determinants, highlighting the gene coding for SPM-1 carbapenemase. However, the resistance and persistence of this...

    Authors: Melise Chaves Silveira, Cláudio Marcos Rocha-de-Souza, Rodolpho Mattos Albano, Ivson Cassiano de Oliveira Santos and Ana Paula D’Alincourt Carvalho-Assef

    Citation: BMC Genomics 2020 21:255

    Content type: Research article

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  25. In recent years, interest in Bacillus velezensis has increased significantly due to its role in many industrial water bioremediation processes. In this study, we isolated and assessed the transcriptome of Bacillu...

    Authors: Guangxin Liu, Sarath Babu Vijayaraman, Yanjun Dong, Xinfeng Li, Binda Tembeng Andongmaa, Lijuan Zhao, Jiagang Tu, Jin He and Li Lin

    Citation: BMC Genomics 2020 21:215

    Content type: Research article

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  26. Cupriavidus strain STM 6070 was isolated from nickel-rich soil collected near Koniambo massif, New Caledonia, using the invasive legume trap host Mimosa pudica. STM 6070 is a heavy metal-tolerant strain that is h...

    Authors: Agnieszka Klonowska, Lionel Moulin, Julie Kaye Ardley, Florence Braun, Margaret Mary Gollagher, Jaco Daniel Zandberg, Dora Vasileva Marinova, Marcel Huntemann, T. B. K. Reddy, Neha Jacob Varghese, Tanja Woyke, Natalia Ivanova, Rekha Seshadri, Nikos Kyrpides and Wayne Gerald Reeve

    Citation: BMC Genomics 2020 21:214

    Content type: Research article

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  27. Salmonella enterica subsp. enterica serovar Napoli (S. Napoli) is among the top serovars causing human infections in Italy, although it is relatively uncommon in other European countries; it is mainly isolated fr...

    Authors: Eleonora Mastrorilli, Sara Petrin, Massimiliano Orsini, Alessandra Longo, Debora Cozza, Ida Luzzi, Antonia Ricci, Lisa Barco and Carmen Losasso

    Citation: BMC Genomics 2020 21:202

    Content type: Research article

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  28. Whole-genome approaches are widely preferred for species delineation in prokaryotes. However, these methods require pairwise alignments and calculations at the whole-genome level and thus are computationally i...

    Authors: Yizhuang Zhou, Jifang Zheng, Yepeng Wu, Wenting Zhang and Junfei Jin

    Citation: BMC Genomics 2020 21:183

    Content type: Methodology article

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  29. Tuberculosis (TB), particularly multi- and or extensive drug resistant TB, is still a global medical emergency. Whole genome sequencing (WGS) is a current alternative to the WHO-approved probe-based methods fo...

    Authors: Bugwesa Z. Katale, Peter M. Mbelele, Nsiande A. Lema, Susana Campino, Stephen E. Mshana, Mark M. Rweyemamu, Jody E. Phelan, Julius D. Keyyu, Mtebe Majigo, Erasto V. Mbugi, Hazel M. Dockrell, Taane G. Clark, Mecky I. Matee and Stellah Mpagama

    Citation: BMC Genomics 2020 21:174

    Content type: Research article

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  30. The state-of-the-art in nucleic acid based biodetection continues to be polymerase chain reaction (PCR), and many real-time PCR assays targeting biodefense pathogens for biosurveillance are in widespread use. ...

    Authors: Robert Player, Kathleen Verratti, Andrea Staab, Christopher Bradburne, Sarah Grady, Bruce Goodwin and Shanmuga Sozhamannan

    Citation: BMC Genomics 2020 21:166

    Content type: Methodology article

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  31. Plant growth-promoting rhizobacteria (PGPR) are good alternatives for chemical fertilizers and pesticides, which cause severe environmental problems worldwide. Even though many studies focus on PGPR, most of t...

    Authors: Zhibo Li, Chunxu Song, Yanglei Yi and Oscar P. Kuipers

    Citation: BMC Genomics 2020 21:157

    Content type: Research article

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  32. Tannerella forsythia is a bacterial pathogen implicated in periodontal disease. Numerous virulence-associated T. forsythia genes have been described, however, it is necessary to expand the knowledge on T. forsyth...

    Authors: Nikolaus F. Zwickl, Nancy Stralis-Pavese, Christina Schäffer, Juliane C. Dohm and Heinz Himmelbauer

    Citation: BMC Genomics 2020 21:150

    Content type: Research article

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  33. We investigated the association of symptoms and disease severity of shigellosis patients with genetic determinants of infecting Shigella and entero-invasive Escherichia coli (EIEC), because determinants that pred...

    Authors: Amber C. A. Hendriks, Frans A. G. Reubsaet, A. M. D. ( Mirjam) Kooistra-Smid, John W. A. Rossen, Bas E. Dutilh, Aldert L. Zomer and Maaike J. C. van den Beld

    Citation: BMC Genomics 2020 21:138

    Content type: Research article

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  34. Herbaspirillum seropedicae is a diazotrophic bacterium from the β-proteobacteria class that colonizes endophytically important gramineous species, promotes their growth through phytohormone-dependent stimulation ...

    Authors: Tatiane Dobrzanski, Vânia Pobre, Leandro Ferreira Moreno, Helba Cirino de Souza Barbosa, Rose Adele Monteiro, Fábio de Oliveira Pedrosa, Emanuel Maltempi de Souza, Cecília Maria Arraiano and Maria Berenice Reynaud Steffens

    Citation: BMC Genomics 2020 21:134

    Content type: Research article

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  35. Bacteriophages encode genes that modify bacterial functions during infection. The acquisition of phage-encoded virulence genes is a major mechanism for the rise of bacterial pathogens. In coral reefs, high bac...

    Authors: Cynthia B. Silveira, Felipe H. Coutinho, Giselle S. Cavalcanti, Sean Benler, Michael P. Doane, Elizabeth A. Dinsdale, Robert A. Edwards, Ronaldo B. Francini-Filho, Cristiane C. Thompson, Antoni Luque, Forest L. Rohwer and Fabiano Thompson

    Citation: BMC Genomics 2020 21:126

    Content type: Research article

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  36. Acidophilic members of the genus Streptomyces can be a good source for novel secondary metabolites and degradative enzymes of biopolymers. In this study, a genome-based approach on Streptomyces yeochonensis CN732...

    Authors: Adeel Malik, Yu Ri Kim, In Hee Jang, Sunghoon Hwang, Dong-Chan Oh and Seung Bum Kim

    Citation: BMC Genomics 2020 21:118

    Content type: Research article

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  37. Multidrug-resistant Neisseria gonorrhoeae strains are prevalent, threatening gonorrhoea treatment globally, and understanding of emergence, evolution, and spread of antimicrobial resistance (AMR) in gonococci rem...

    Authors: Daniel Golparian, Simon R. Harris, Leonor Sánchez-Busó, Steen Hoffmann, William M. Shafer, Stephen D. Bentley, Jörgen S. Jensen and Magnus Unemo

    Citation: BMC Genomics 2020 21:116

    Content type: Research article

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  38. Next generation sequencing (NGS) has become a universal practice in modern molecular biology. As the throughput of sequencing experiments increases, the preparation of conventional multiplexed libraries become...

    Authors: Jennifer Chiniquy, Megan E. Garber, Aindrila Mukhopadhyay and Nathan J. Hillson

    Citation: BMC Genomics 2020 21:85

    Content type: Methodology article

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  39. Mixed infections of Mycobacterium tuberculosis and antibiotic heteroresistance continue to complicate tuberculosis (TB) diagnosis and treatment. Detection of mixed infections has been limited to molecular genotyp...

    Authors: Christine Anyansi, Arlin Keo, Bruce J. Walker, Timothy J. Straub, Abigail L. Manson, Ashlee M. Earl and Thomas Abeel

    Citation: BMC Genomics 2020 21:80

    Content type: Research article

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  40. Mycoplasma bovis is an important etiologic agent of bovine mycoplasmosis affecting cattle production and animal welfare. In the past in Israel, M. bovis has been most frequently associated with bovine respiratory...

    Authors: Yael Yair, Ilya Borovok, Inna Mikula, Rama Falk, Larry K. Fox, Uri Gophna and Inna Lysnyansky

    Citation: BMC Genomics 2020 21:70

    Content type: Research article

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  41. Shotgun metagenomic sequencing reveals the potential in microbial communities. However, lower-cost 16S ribosomal RNA (rRNA) gene sequencing provides taxonomic, not functional, observations. To remedy this, we ...

    Authors: Nicole R. Narayan, Thomas Weinmaier, Emilio J. Laserna-Mendieta, Marcus J. Claesson, Fergus Shanahan, Karim Dabbagh, Shoko Iwai and Todd Z. DeSantis

    Citation: BMC Genomics 2020 21:56

    Content type: Research article

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    The Correction to this article has been published in BMC Genomics 2020 21:105

  42. Clostridium perfringens is a Gram-positive anaerobic pathogen that causes multiple diseases in humans and animals. C. perfringens lack flagella but have type IV pili (TFP) and can glide on agar surfaces. When C. ...

    Authors: Samantha R. Soncini, Andrea H. Hartman, Tara M. Gallagher, Gary J. Camper, Roderick V. Jensen and Stephen B. Melville

    Citation: BMC Genomics 2020 21:45

    Content type: Research article

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  43. The genus Trichococcus currently contains nine species: T. flocculiformis, T. pasteurii, T. palustris, T. collinsii, T. patagoniensis, T. ilyis, T. paludicola, T. alkaliphilus, and T. shcherbakoviae. In general,

    Authors: Nikolaos Strepis, Henry D. Naranjo, Jan Meier-Kolthoff, Markus Göker, Nicole Shapiro, Nikos Kyrpides, Hans-Peter Klenk, Peter J. Schaap, Alfons J. M. Stams and Diana Z. Sousa

    Citation: BMC Genomics 2020 21:24

    Content type: Research article

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  44. The genus Borrelia comprises spirochaetal bacteria maintained in natural transmission cycles by tick vectors and vertebrate reservoir hosts. The main groups are represented by a species complex including the caus...

    Authors: Konstantin V. Kuleshov, Gabriele Margos, Volker Fingerle, Joris Koetsveld, Irina A. Goptar, Mikhail L. Markelov, Nadezhda M. Kolyasnikova, Denis S. Sarksyan, Nina P. Kirdyashkina, German A. Shipulin, Joppe W. Hovius and Alexander E. Platonov

    Citation: BMC Genomics 2020 21:16

    Content type: Research article

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  45. Pseudomonas aeruginosa is a cause of nosocomial infections, especially in patients with cystic fibrosis and burn wounds. PAO1 strain and its derivatives are widely used to study the biology of this bacterium, how...

    Authors: Adam Kawalek, Karolina Kotecka, Magdalena Modrzejewska, Jan Gawor, Grazyna Jagura-Burdzy and Aneta Agnieszka Bartosik

    Citation: BMC Genomics 2020 21:14

    Content type: Research article

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  46. Human metapneumovirus (HMPV) is an important cause of acute respiratory illness in young children. Whole genome sequencing enables better identification of transmission events and outbreaks, which is not alway...

    Authors: Everlyn Kamau, John W. Oketch, Zaydah R. de Laurent, My V. T. Phan, Charles N. Agoti, D. James Nokes and Matthew Cotten

    Citation: BMC Genomics 2020 21:5

    Content type: Methodology article

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    The Correction to this article has been published in BMC Genomics 2020 21:83

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