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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. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. Rhodococci are industrially important soil-dwelling Gram-positive bacteria that are well known for both nitrile hydrolysis and oxidative metabolism of aromatics. Rhodococcus rhodochrous ATCC BAA-870 is capable of...

    Authors: Joni Frederick, Fritha Hennessy, Uli Horn, Pilar de la Torre Cortés, Marcel van den Broek, Ulrich Strych, Richard Willson, Charles A. Hefer, Jean-Marc G. Daran, Trevor Sewell, Linda G. Otten and Dean Brady

    Citation: BMC Genomics 2020 21:3

    Content type: Research article

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  9. Mycobacterium pinnipedii, a member of the Mycobacterium tuberculosis Complex (MTBC), is capable of infecting several host species, including humans. Recently, ancient DNA from this organism was recovered from pre...

    Authors: Taiana T. Silva-Pereira, Cássia Y. Ikuta, Cristina K. Zimpel, Naila C. S. Camargo, Antônio F. de Souza Filho, José S. Ferreira Neto, Marcos B. Heinemann and Ana M. S. Guimarães

    Citation: BMC Genomics 2019 20:1030

    Content type: Research article

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  10. Bacteria within the genus Streptomyces remain a major source of new natural product discovery and as soil inoculants in agriculture where they promote plant growth and protect from disease. Recently, Streptomyces

    Authors: Stephen C. Heinsch, Szu-Yi Hsu, Lindsey Otto-Hanson, Linda Kinkel and Michael J. Smanski

    Citation: BMC Genomics 2019 20:994

    Content type: Research article

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  11. Reverse vaccinology accelerates the discovery of potential vaccine candidates (PVCs) prior to experimental validation. Current programs typically use one bacterial proteome to identify PVCs through a filtering...

    Authors: Adonis D’Mello, Christian P. Ahearn, Timothy F. Murphy and Hervé Tettelin

    Citation: BMC Genomics 2019 20:981

    Content type: Methodology article

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  12. Metagenomes can be analysed using different approaches and tools. One of the most important distinctions is the way to perform taxonomic and functional assignment, choosing between the use of assembly algorith...

    Authors: Javier Tamames, Marta Cobo-Simón and Fernando Puente-Sánchez

    Citation: BMC Genomics 2019 20:960

    Content type: Research article

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  13. Mycobacterium smegmatis is a saprophytic bacterium frequently used as a genetic surrogate to study pathogenic Mycobacterium tuberculosis. The PrrAB two-component genetic regulatory system is essential in M. tuber...

    Authors: Jason D. Maarsingh, Shanshan Yang, Jin G. Park and Shelley E. Haydel

    Citation: BMC Genomics 2019 20:942

    Content type: Research article

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    The Correction to this article has been published in BMC Genomics 2019 21:1

  14. Xanthomonads are an important clade of Gram-negative bacteria infecting a plethora of economically important host plants, including citrus. Knowledge about the pathogen’s diversity and population structure are...

    Authors: Kwanho Jeong, Alejandra Muñoz-Bodnar, Nathalia Arias Rojas, Lucie Poulin, Luis Miguel Rodriguez-R, Lionel Gagnevin, Christian Vernière, Olivier Pruvost and Ralf Koebnik

    Citation: BMC Genomics 2019 20:917

    Content type: Research article

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  15. Lactobacillus buchneri is a lactic acid bacterium frequently associated with food bioprocessing and fermentation and has been found to be either beneficial or detrimental to industrial food processes depending on...

    Authors: Matthew A. Nethery, Emily DeCrescenzo Henriksen, Katheryne V. Daughtry, Suzanne D. Johanningsmeier and Rodolphe Barrangou

    Citation: BMC Genomics 2019 20:902

    Content type: Research article

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  16. Latent tuberculosis infection is attributed in part to the existence of Mycobacterium tuberculosis in a persistent non-replicating dormant state that is associated with tolerance to host defence mechanisms and an...

    Authors: Malobi Nandi, Kriti Sikri, Neha Chaudhary, Shekhar Chintamani Mande, Ravi Datta Sharma and Jaya Sivaswami Tyagi

    Citation: BMC Genomics 2019 20:887

    Content type: Research article

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  17. Microbial communities recurrently establish metabolic associations resulting in increased fitness and ability to perform complex tasks, such as xenobiotic degradation. In a previous study, we have described a ...

    Authors: Ana C. Reis, Boris A. Kolvenbach, Mohamed Chami, Luís Gales, Conceição Egas, Philippe F.-X. Corvini and Olga C. Nunes

    Citation: BMC Genomics 2019 20:885

    Content type: Research article

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  18. The enhancing incidence of carbapenem-resistant Klebsiella pneumoniae (CRKP)-mediated infections in Mengchao Hepatobiliary Hospital of Fujian Medical University in 2017 is the motivation behind this investigation...

    Authors: Xiaoling Yu, Wen Zhang, Zhiping Zhao, Chengsong Ye, Shuyan Zhou, Shaogui Wu, Lifen Han, Zhaofang Han and Hanhui Ye

    Citation: BMC Genomics 2019 20:822

    Content type: Research article

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  19. Clade 5 Clostridioides difficile diverges significantly from the other clades and is therefore, attracting increasing attention due its great heterogeneity. In this study, we used third-generation sequencing tech...

    Authors: Yuan Wu, Lin Yang, Wen-Ge Li, Wen Zhu Zhang, Zheng Jie Liu and Jin-Xing Lu

    Citation: BMC Genomics 2019 20:796

    Content type: Research article

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  20. Nontuberculous mycobacteria (NTM) are a major cause of pulmonary and systemic disease in at-risk populations. Gaps in knowledge about transmission patterns, evolution, and pathogenicity during infection have p...

    Authors: Jennifer M. Bouso and Paul J. Planet

    Citation: BMC Genomics 2019 20:793

    Content type: Methodology article

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  21. Host genotype plays a crucial role in microbial composition of laying hens, which may lead to dissimilar odor gas production. The objective of this study was to investigate the relationship among layer breed, ...

    Authors: Chun-Bo Huang, Lei Xiao, Si-Cheng Xing, Jing-Yuan Chen, Yi-Wen Yang, Yang Zhou, Wei Chen, Juan-Boo Liang, Jian-Dui Mi, Yan Wang, Yin-Bao Wu and Xin-Di Liao

    Citation: BMC Genomics 2019 20:770

    Content type: Research article

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  22. Escherichia coli C forms more robust biofilms than other laboratory strains. Biofilm formation and cell aggregation under a high shear force depend on temperature and salt concentrations. It is the last of five E...

    Authors: Jarosław E. Król, Donald C. Hall Jr, Sergey Balashov, Steven Pastor, Justin Sibert, Jennifer McCaffrey, Steven Lang, Rachel L. Ehrlich, Joshua Earl, Joshua C. Mell, Ming Xiao and Garth D. Ehrlich

    Citation: BMC Genomics 2019 20:767

    Content type: Research article

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  23. Horizontal gene transfer (HGT), which is affected by environmental pollution and climate change, promotes genetic communication, changing bacterial pathogenicity and drug resistance. However, few studies have ...

    Authors: Yiqin Deng, Haidong Xu, Youlu Su, Songlin Liu, Liwen Xu, Zhixun Guo, Jinjun Wu, Changhong Cheng and Juan Feng

    Citation: BMC Genomics 2019 20:761

    Content type: Research article

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  24. Genomic composition has been found to be species specific and is used to differentiate bacterial species. To date, almost no published composition-based approaches are able to distinguish between most closely ...

    Authors: Yizhuang Zhou, Wenting Zhang, Huixian Wu, Kai Huang and Junfei Jin

    Citation: BMC Genomics 2019 20:754

    Content type: Methodology article

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  25. The rapid identification of lineage remains a challenge in the genotyping of clinical isolates of recombinogenic pathogens. The chromosome of Mycobacterium avium subsp. hominissuis (MAH), an agent of Mycobacteriu...

    Authors: Hirokazu Yano, Haruo Suzuki, Fumito Maruyama and Tomotada Iwamoto

    Citation: BMC Genomics 2019 20:752

    Content type: Research article

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  26. Haemophilus influenzae (Hi) can cause invasive diseases such as meningitis, pneumonia, or sepsis. Typeable Hi includes six serotypes (a through f), each expressing a unique capsular polysaccharide. The capsule, e...

    Authors: Caelin C. Potts, Nadav Topaz, Lorraine D. Rodriguez-Rivera, Fang Hu, How-Yi Chang, Melissa J. Whaley, Susanna Schmink, Adam C. Retchless, Alexander Chen, Edward Ramos, Gregory H. Doho and Xin Wang

    Citation: BMC Genomics 2019 20:733

    Content type: Research article

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  27. TetR-family transcriptional regulators (TFTRs) are DNA binding factors that regulate gene expression in bacteria. Well-studied TFTRs, such as AcrR, which regulates efflux pump expression, are usually encoded a...

    Authors: A. L. Colclough, J. Scadden and J. M. A. Blair

    Citation: BMC Genomics 2019 20:731

    Content type: Research article

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  28. 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

    Content type: Research article

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  29. 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

    Content type: Research article

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  30. 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

    Content type: Research article

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  31. 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

    Content type: Research article

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  32. 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

    Content type: Research article

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  33. 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

    Content type: Research article

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  34. 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

    Content type: Research article

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  35. 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

    Content type: Research article

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  36. 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

    Content type: Research article

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  37. 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

    Content type: Research article

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  38. 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

    Content type: Research article

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  39. 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

    Content type: Research article

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  40. 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

    Content type: Research article

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  41. 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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  42. 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

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