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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. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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

  23. 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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  24. 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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  25. 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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  26. 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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  27. 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

  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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

  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  41. 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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  42. 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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  43. 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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  44. 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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  45. 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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  46. 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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  47. 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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