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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 16

  1. Core genome phylogenies are widely used to build the evolutionary history of individual prokaryote species. By using hundreds or thousands of shared genes, these approaches are the gold standard to reconstruct...

    Authors: Caroline M. Stott and Louis-Marie Bobay

    Citation: BMC Genomics 2020 21:829

    Content type: Research article

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  2. Small RNAs (sRNAs) are non-coding RNAs known to regulate various biological functions such as stress adaptation, metabolism, virulence as well as pathogenicity across a wide range of bacteria, mainly by contro...

    Authors: Vatsala Koul, Divya Srivastava, Pushplata Prasad Singh and Mandira Kochar

    Citation: BMC Genomics 2020 21:821

    Content type: Research article

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  3. Actinoplanes sp. SE50/110 is the natural producer of the diabetes mellitus drug acarbose, which is highly produced during the growth phase and ceases during the stationary phase. In previous works, the growth-dep...

    Authors: Julian Droste, Vera Ortseifen, Lena Schaffert, Marcus Persicke, Susanne Schneiker-Bekel, Alfred Pühler and Jörn Kalinowski

    Citation: BMC Genomics 2020 21:818

    Content type: Research article

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  4. The archaeal exosome is an exoribonucleolytic multiprotein complex, which degrades single-stranded RNA in 3′ to 5′ direction phosphorolytically. In a reverse reaction, it can add A-rich tails to the 3′-end of ...

    Authors: Jochen Bathke, A. Susann Gauernack, Oliver Rupp, Lennart Weber, Christian Preusser, Marcus Lechner, Oliver Rossbach, Alexander Goesmann, Elena Evguenieva-Hackenberg and Gabriele Klug

    Citation: BMC Genomics 2020 21:797

    Content type: Research article

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  5. Bacillus subtilis strain NCD-2 is an excellent biocontrol agent against plant soil-borne diseases and shows broad-spectrum antifungal activities. This study aimed to explore some secondary metabolite biosynthetic...

    Authors: Zhenhe Su, Xiuye Chen, Xiaomeng Liu, Qinggang Guo, Shezeng Li, Xiuyun Lu, Xiaoyun Zhang, Peipei Wang, Lihong Dong, Weisong Zhao and Ping Ma

    Citation: BMC Genomics 2020 21:767

    Content type: Research article

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  6. Microorganisms are not only indispensable to ecosystem functioning, they are also keystones for emerging technologies. In the last 15 years, the number of studies on environmental microbial communities has inc...

    Authors: Lisa Joos, Stien Beirinckx, Annelies Haegeman, Jane Debode, Bart Vandecasteele, Steve Baeyen, Sofie Goormachtig, Lieven Clement and Caroline De Tender

    Citation: BMC Genomics 2020 21:733

    Content type: Research article

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  7. RNA sequencing is a powerful approach to quantify the genome-wide distribution of mRNA molecules in a population to gain deeper understanding of cellular functions and phenotypes. However, unlike eukaryotic ce...

    Authors: Chatarin Wangsanuwat, Kellie A. Heom, Estella Liu, Michelle A. O’Malley and Siddharth S. Dey

    Citation: BMC Genomics 2020 21:717

    Content type: Methodology article

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  8. Borrelia bavariensis is one of the agents of Lyme Borreliosis (or Lyme disease) in Eurasia. The genome of the Borrelia burgdorferi sensu lato species complex, that includes B. bavariensis, is known to be very com...

    Authors: Noémie S. Becker, Robert E. Rollins, Kateryna Nosenko, Alexander Paulus, Samantha Martin, Stefan Krebs, Ai Takano, Kozue Sato, Sergey Y. Kovalev, Hiroki Kawabata, Volker Fingerle and Gabriele Margos

    Citation: BMC Genomics 2020 21:702

    Content type: Research article

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  9. The genome of Vibrionaceae bacteria, which consists of two circular chromosomes, is replicated in a highly ordered fashion. In fast-growing bacteria, multifork replication results in higher gene copy numbers and ...

    Authors: Cecilie Bækkedal Sonnenberg, Tim Kahlke and Peik Haugen

    Citation: BMC Genomics 2020 21:695

    Content type: Research article

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  10. The deep ocean is characterized by low temperatures, high hydrostatic pressures, and low concentrations of organic matter. While these conditions likely select for distinct genomic characteristics within proka...

    Authors: Logan M. Peoples, Than S. Kyaw, Juan A. Ugalde, Kelli K. Mullane, Roger A. Chastain, A. Aristides Yayanos, Masataka Kusube, Barbara A. Methé and Douglas H. Bartlett

    Citation: BMC Genomics 2020 21:692

    Content type: Research article

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  11. Advances in bioinformatics recently allowed for the recovery of ‘metagenomes assembled genomes’ from human microbiome studies carried on with shotgun sequencing techniques. Such approach is used as a mean to d...

    Authors: Matteo Soverini, Simone Rampelli, Silvia Turroni, Patrizia Brigidi, Elena Biagi and Marco Candela

    Citation: BMC Genomics 2020 21:678

    Content type: Research article

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  12. Flagellar motility is an efficient means of movement that allows bacteria to successfully colonize and compete with other microorganisms within their respective environments. The production and functioning of ...

    Authors: Pieter De Maayer, Talia Pillay and Teresa A. Coutinho

    Citation: BMC Genomics 2020 21:670

    Content type: Research article

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  13. Pathogenic Rickettsia species belonging to the spotted fever group are arthropod-borne, obligate intracellular bacteria which exhibit preferential tropism for host microvascular endothelium in the mammalian hosts...

    Authors: Hema P. Narra, Abha Sahni, Jessica Alsing, Casey L. C. Schroeder, George Golovko, Anna M. Nia, Yuriy Fofanov, Kamil Khanipov and Sanjeev K. Sahni

    Citation: BMC Genomics 2020 21:665

    Content type: Research article

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  14. Cyanobacteria maintain extensive repertoires of regulatory genes that are vital for adaptation to environmental stress. Some cyanobacterial genomes have been noted to encode diversity-generating retroelements ...

    Authors: Alec Vallota-Eastman, Eleanor C. Arrington, Siobhan Meeken, Simon Roux, Krishna Dasari, Sydney Rosen, Jeff F. Miller, David L. Valentine and Blair G. Paul

    Citation: BMC Genomics 2020 21:664

    Content type: Research article

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  15. The origin of most of the Lactobacillus rhamnosus genome sequences lodged in NCBI can be traced to food and faecal isolates followed by blood and tissue sites but with minimal representation from oral and vaginal...

    Authors: Mangala A. Nadkarni, Nandan P. Deshpande, Marc R. Wilkins and Neil Hunter

    Citation: BMC Genomics 2020 21:661

    Content type: Research article

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  16. Horizontal gene transfer contributes to bacterial evolution through mobilising genes across various taxonomical boundaries. It is frequently mediated by mobile genetic elements (MGEs), which may capture, maint...

    Authors: Yu Wan, Ryan R. Wick, Justin Zobel, Danielle J. Ingle, Michael Inouye and Kathryn E. Holt

    Citation: BMC Genomics 2020 21:658

    Content type: Software

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  17. Transcriptome sequencing has opened the field of genomics to a wide variety of researchers, owing to its efficiency, applicability across species and ability to quantify gene expression. The resulting datasets...

    Authors: Cameron J. Hyde, Quinn P. Fitzgibbon, Abigail Elizur, Gregory G. Smith and Tomer Ventura

    Citation: BMC Genomics 2020 21:637

    Content type: Database

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  18. We benchmarked the hybrid assembly approaches of MaSuRCA, SPAdes, and Unicycler for bacterial pathogens using Illumina and Oxford Nanopore sequencing by determining genome completeness and accuracy, antimicrob...

    Authors: Zhao Chen, David L. Erickson and Jianghong Meng

    Citation: BMC Genomics 2020 21:631

    Content type: Research article

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  19. DNA N4-methylcytosine (4mC) is a critical epigenetic modification and has various roles in the restriction-modification system. Due to the high cost of experimental laboratory detection, computational methods ...

    Authors: Zhixun Zhao, Xiaocai Zhang, Fang Chen, Liang Fang and Jinyan Li

    Citation: BMC Genomics 2020 21:627

    Content type: Research article

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  20. Vibriosis has been implicated in major losses of larvae at shellfish hatcheries. However, the species of Vibrio responsible for disease in aquaculture settings and their associated virulence genes are often varia...

    Authors: Hanna Kehlet-Delgado, Claudia C. Häse and Ryan S. Mueller

    Citation: BMC Genomics 2020 21:599

    Content type: Research article

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  21. M. morganii is a bacterium frequently associated with urinary infections in humans. While many human strains are sequenced, only the genomes of few poultry strains are available. Here, we performed a detailed cha...

    Authors: Nicola Palmieri, Claudia Hess, Michael Hess and Merima Alispahic

    Citation: BMC Genomics 2020 21:579

    Content type: Research article

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  22. Members of the bacterial family Flavobacteriaceae are widely distributed in the marine environment and often found associated with algae, fish, detritus or marine invertebrates. Yet, little is known about the cha...

    Authors: Asimenia Gavriilidou, Johanna Gutleben, Dennis Versluis, Francesca Forgiarini, Mark W. J. van Passel, Colin J. Ingham, Hauke Smidt and Detmer Sipkema

    Citation: BMC Genomics 2020 21:569

    Content type: Research article

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  23. The nosocomial pathogen Enterococcus faecium can survive for prolonged periods of time on surfaces in the absence of nutrients. This trait is thought to contribute to the ability of E. faecium to spread among pat...

    Authors: Vincent de Maat, Sergio Arredondo-Alonso, Rob J. L. Willems and Willem van Schaik

    Citation: BMC Genomics 2020 21:568

    Content type: Research article

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  24. Shiga toxin-producing E. coli (STECs) are foodborne pathogens associated with bloody diarrhea and hemolytic uremic syndrome (HUS). Although the STEC O157 serogroup accounts for the highest number of infections, H...

    Authors: Julio A. Guerra, Chengxian Zhang, Jonathan E. Bard, Donald Yergeau, Natasha Halasa and Oscar G. Gómez-Duarte

    Citation: BMC Genomics 2020 21:564

    Content type: Research article

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  25. Enterohemorrhagic Escherichia coli O157:H7 (EHEC) is a significant foodborne pathogen that resides asymptomatically within cattle and other ruminants. The EHEC genome harbors an extensive collection of mobile gen...

    Authors: Eliot Stanton, Taylor A. Wahlig, Dongjin Park and Charles W. Kaspar

    Citation: BMC Genomics 2020 21:562

    Content type: Research article

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  26. Illumina technology currently dominates bacterial genomics due to its high read accuracy and low sequencing cost. However, the incompleteness of draft genomes generated by Illumina reads limits their applicati...

    Authors: Hooman Derakhshani, Steve P. Bernier, Victoria A. Marko and Michael G. Surette

    Citation: BMC Genomics 2020 21:519

    Content type: Methodology article

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  27. Adaptive Laboratory Evolution (ALE) has emerged as an experimental approach to discover mutations that confer phenotypic functions of interest. However, the task of finding and understanding all beneficial mut...

    Authors: Patrick V. Phaneuf, James T. Yurkovich, David Heckmann, Muyao Wu, Troy E. Sandberg, Zachary A. King, Justin Tan, Bernhard O. Palsson and Adam M. Feist

    Citation: BMC Genomics 2020 21:514

    Content type: Methodology article

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  28. Bacterial blotch is a group of economically important diseases affecting the cultivation of common button mushroom, Agaricus bisporus. Despite being studied for more than a century, the identity and nomenclature ...

    Authors: Tanvi Taparia, Marjon Krijger, Edward Haynes, John G. Elphinstone, Ralph Noble and Jan van der Wolf

    Citation: BMC Genomics 2020 21:505

    Content type: Research article

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  29. Integrons are genomic elements that mediate horizontal gene transfer by inserting and removing genetic material using site-specific recombination. Integrons are commonly found in bacterial genomes, where they ...

    Authors: Mariana Buongermino Pereira, Tobias Österlund, K Martin Eriksson, Thomas Backhaus, Marina Axelson-Fisk and Erik Kristiansson

    Citation: BMC Genomics 2020 21:495

    Content type: Research article

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  30. High pressure processing (HPP; i.e. 100–600 MPa pressure depending on product) is a non-thermal preservation technique adopted by the food industry to decrease significantly foodborne pathogens, including Listeri...

    Authors: Ilhan Cem Duru, Margarita Andreevskaya, Pia Laine, Tone Mari Rode, Anne Ylinen, Trond Løvdal, Nadav Bar, Peter Crauwels, Christian U. Riedel, Florentina Ionela Bucur, Anca Ioana Nicolau and Petri Auvinen

    Citation: BMC Genomics 2020 21:455

    Content type: Research article

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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  41. 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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  42. 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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  43. 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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  44. 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

  45. 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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  46. 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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  47. 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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  48. 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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