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Prokaryote microbial genomics

This section covers the structure and function of the genomes of prokaryotic and archaea microorganisms.

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  1. Infectious bronchitis virus (IBV) is one of the most relevant viruses affecting the poultry industry, and several studies have investigated the factors involved in its biological cycle and evolution. However, ...

    Authors: Giovanni Franzo, Claudia Maria Tucciarone, Matteo Legnardi and Mattia Cecchinato

    Citation: BMC Genomics 2021 22:244

    Content type: Research article

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  2. Spiroplasma is a widely distributed endosymbiont of insects, arthropods, and plants. In insects, Spiroplasma colonizes the gut, hemolymph, and reproductive organs of the host. Previous metagenomic surveys of the ...

    Authors: Arturo Vera-Ponce León, Marian Dominguez-Mirazo, Rafael Bustamante-Brito, Víctor Higareda-Alvear, Mónica Rosenblueth and Esperanza Martínez-Romero

    Citation: BMC Genomics 2021 22:240

    Content type: Research article

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  3. There is a dearth of sequenced and closed microbial genomes from environments that exceed > 500 m below level terrestrial surface. Coupled with even fewer cultured isolates, study and understanding of how life...

    Authors: Trevor R. Murphy, Rui Xiao and Scott D. Hamilton-Brehm

    Citation: BMC Genomics 2021 22:209

    Content type: Research article

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  4. Genetic resources are important natural assets. Discovery of new enzyme gene sequences has been an ongoing effort in biotechnology industry. In the genomic age, genomes of microorganisms from various environme...

    Authors: Jun Lin, Wenqian Jiang, Lin Chen, Huilian Zhang, Yang Shi, Xin Liu and Weiwen Cai

    Citation: BMC Genomics 2021 22:173

    Content type: Research article

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  5. Ralstonia solanacearum is the causal agent of bacterial wilt, a devastating plant disease responsible for serious economic losses especially on potato, tomato, and other solanaceous plant species in temperate cou...

    Authors: R. de Pedro-Jové, M. Puigvert, P. Sebastià, A. P. Macho, J. S. Monteiro, N. S. Coll, J. C. Setúbal and M. Valls

    Citation: BMC Genomics 2021 22:170

    Content type: Research article

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  6. High-pressure processing (HPP) is a commonly used technique in the food industry to inactivate pathogens, including L. monocytogenes. It has been shown that L. monocytogenes is able to recover from HPP injuries a...

    Authors: Ilhan Cem Duru, Florentina Ionela Bucur, Margarita Andreevskaya, Bahareh Nikparvar, Anne Ylinen, Leontina Grigore-Gurgu, Tone Mari Rode, Peter Crauwels, Pia Laine, Lars Paulin, Trond Løvdal, Christian U. Riedel, Nadav Bar, Daniela Borda, Anca Ioana Nicolau and Petri Auvinen

    Citation: BMC Genomics 2021 22:117

    Content type: Research article

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  7. Processing and analyzing whole genome sequencing (WGS) is computationally intense: a single Illumina MiSeq WGS run produces ~ 1 million 250-base-pair reads for each of 24 samples. This poses significant obstac...

    Authors: Jayanthi Gangiredla, Hugh Rand, Daniel Benisatto, Justin Payne, Charles Strittmatter, Jimmy Sanders, William J. Wolfgang, Kevin Libuit, James B. Herrick, Melanie Prarat, Magaly Toro, Thomas Farrell and Errol Strain

    Citation: BMC Genomics 2021 22:114

    Content type: Software

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  8. The polynucleotide phosphorylase (PNPase) is conserved among both Gram-positive and Gram-negative bacteria. As a core part of the Escherichia coli degradosome, PNPase is involved in maintaining proper RNA levels ...

    Authors: Daniel-Timon Spanka, Carina Maria Reuscher and Gabriele Klug

    Citation: BMC Genomics 2021 22:106

    Content type: Research article

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  9. Most studies investigating human gut microbiome dynamics are conducted on humans living in an urban setting. However, few studies have researched the gut microbiome of the populations living traditional lifest...

    Authors: Xue Zhu, Jiyue Qin, Chongyang Tan and Kang Ning

    Citation: BMC Genomics 2021 22:83

    Content type: Research article

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  10. Toxin-antitoxin (TA) systems, abundant in prokaryotes, are composed of a toxin gene and its cognate antitoxin. Several toxins are implied to affect the physiological state and stress tolerance of bacteria in a...

    Authors: Jingyu Peng, Lindsay R. Triplett and George W. Sundin

    Citation: BMC Genomics 2021 22:74

    Content type: Research article

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  11. Efficient regulation of bacterial genes in response to the environmental stimulus results in unique gene clusters known as operons. Lack of complete operonic reference and functional information makes the pred...

    Authors: Syed Shujaat Ali Zaidi, Masood Ur Rehman Kayani, Xuegong Zhang, Younan Ouyang and Imran Haider Shamsi

    Citation: BMC Genomics 2021 22:60

    Content type: Software

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  12. Chicken skeletal muscle is an important economic product. The late stages of chicken development constitute the main period that affects meat production. LncRNAs play important roles in controlling the epigene...

    Authors: Yuanfang Li, Wenjiao Jin, Bin Zhai, Yi Chen, Guoxi Li, Yanhua Zhang, Yujie Guo, Guirong Sun, Ruili Han, Zhuanjian Li, Hong Li, Yadong Tian, Xiaojun Liu and Xiangtao Kang

    Citation: BMC Genomics 2021 22:44

    Content type: Research article

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  13. Tomato plant growth is frequently hampered by a high susceptibility to pests and diseases. Traditional chemical control causes a serious impact on both the environment and human health. Therefore, seeking envi...

    Authors: Lu Zhou, Chunxu Song, Zhibo Li and Oscar P. Kuipers

    Citation: BMC Genomics 2021 22:29

    Content type: Research article

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  14. Psychrotrophic lactic acid bacteria (LAB) species are the dominant species in the microbiota of cold-stored modified-atmosphere-packaged food products and are the main cause of food spoilage. Despite the impor...

    Authors: Ilhan Cem Duru, Anne Ylinen, Sergei Belanov, Alan Avila Pulido, Lars Paulin and Petri Auvinen

    Citation: BMC Genomics 2021 22:28

    Content type: Research article

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  15. The genus Ehrlichia consists of tick-borne obligatory intracellular bacteria that can cause deadly diseases of medical and agricultural importance. Ehrlichia sp. HF, isolated from Ixodes ovatus ticks in Japan [al...

    Authors: Mingqun Lin, Qingming Xiong, Matthew Chung, Sean C. Daugherty, Sushma Nagaraj, Naomi Sengamalay, Sandra Ott, Al Godinez, Luke J. Tallon, Lisa Sadzewicz, Claire Fraser, Julie C. Dunning Hotopp and Yasuko Rikihisa

    Citation: BMC Genomics 2021 22:11

    Content type: Research article

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  16. Studies on the airway microbiome have been performed using a wide range of laboratory protocols for high-throughput sequencing of the bacterial 16S ribosomal RNA (16S rRNA) gene. We sought to determine the imp...

    Authors: Christine Drengenes, Tomas M. L. Eagan, Ingvild Haaland, Harald G. Wiker and Rune Nielsen

    Citation: BMC Genomics 2021 22:3

    Content type: Research article

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  17. Listeria (L.) monocytogenes strains show a high diversity regarding stress tolerance and virulence potential. Genome studies have mainly focused on specific sequence types (STs) predominantly associated with eith...

    Authors: Eva Wagner, Andreas Zaiser, Rebekka Leitner, Narciso M. Quijada, Nadja Pracser, Ariane Pietzka, Werner Ruppitsch, Stephan Schmitz-Esser, Martin Wagner and Kathrin Rychli

    Citation: BMC Genomics 2020 21:847

    Content type: Research article

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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  41. 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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  42. 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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  43. 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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  44. 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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  45. 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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  46. 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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