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Microbial genetics, genomics and proteomics

This section aims to publish studies relating to all aspects of microbial genomics, transcriptomics, proteomics, metabolomics and microbial genome editing.

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  1. Bacterial plasmids often carry antibiotic resistance genes and are a significant factor in the spread of antibiotic resistance. The ability to completely assemble plasmid sequences would facilitate the localiz...

    Authors: Astrid P. Heikema, Rick Jansen, Saskia D. Hiltemann, John P. Hays and Andrew P. Stubbs

    Citation: BMC Microbiology 2021 21:171

    Content type: Software

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  2. Significant progress has been made in advancing and standardizing tools for human genomic and biomedical research. Yet, the field of next-generation sequencing (NGS) analysis for microorganisms (including mult...

    Authors: Delphine Larivière, Laura Wickham, Kenneth Keiler and Anton Nekrutenko

    Citation: BMC Microbiology 2021 21:168

    Content type: Methodology article

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  3. Computational approaches are often used to predict regulatory RNAs in bacteria, but their success is limited to RNAs that are highly conserved across phyla, in sequence and structure. The ANTAR regulatory syst...

    Authors: Dolly Mehta and Arati Ramesh

    Citation: BMC Microbiology 2021 21:159

    Content type: Research article

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  4. Antimicrobial resistance (AMR) poses a complex threat to global health security and universal health coverage. Recently, nosocomial infections with carbapenemase-producing Gram-negative bacilli (GNB) is increa...

    Authors: Hana S. Elbadawi, Kamal M. Elhag, Elsheikh Mahgoub, Hisham N. Altayb, Francine Ntoumi, Linzy Elton, Timothy D. McHugh, John Tembo, Giuseppe Ippolito, Abdinasir Yusuf Osman, Alimuddin Zumla and Muzamil M. Abdel Hamid

    Citation: BMC Microbiology 2021 21:136

    Content type: Research article

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  5. Klebsiella pneumoniae is the most frequent KPC-producing bacteria. The blaKPC gene is frequently embedded in Tn4401 transposon, and less frequently in non-Tn4401 elements (NTEKPC) variants I-III. The first case o...

    Authors: Aniela Wozniak, Cristian Figueroa, Francisco Moya-Flores, Piero Guggiana, Claudia Castillo, Lina Rivas, José M. Munita and Patricia C. García

    Citation: BMC Microbiology 2021 21:107

    Content type: Research article

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  6. Microbial organisms encounter a variety of environmental conditions, including changes to metal ion availability. Metal ions play an important role in many biological processes for growth and survival. As such...

    Authors: A. Sukumaran, S. Pladwig and J. Geddes-McAlister

    Citation: BMC Microbiology 2021 21:43

    Content type: Research article

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  7. Melatonin (MT), ubiquitous in almost all organisms, functions as a free radical scavenger. Despite several reports on its role as an antioxidant in animals, plants, and some microorganisms, extensive studies i...

    Authors: Yang Yu, Zhaowei Teng, Zongmin Mou, Yan Lv, Tao Li, Suiyun Chen, Dake Zhao and Zhiwei Zhao

    Citation: BMC Microbiology 2021 21:40

    Content type: Research article

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  8. Species-level genetic characterization of complex bacterial communities has important clinical applications in both diagnosis and treatment. Amplicon sequencing of the 16S ribosomal RNA (rRNA) gene has proven ...

    Authors: Yoshiyuki Matsuo, Shinnosuke Komiya, Yoshiaki Yasumizu, Yuki Yasuoka, Katsura Mizushima, Tomohisa Takagi, Kirill Kryukov, Aisaku Fukuda, Yoshiharu Morimoto, Yuji Naito, Hidetaka Okada, Hidemasa Bono, So Nakagawa and Kiichi Hirota

    Citation: BMC Microbiology 2021 21:35

    Content type: Methodology article

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  9. Studies on the rhizosphere microbiome of various plants proved that rhizosphere microbiota carries out various vital functions and can regulate the growth and improve the yield of plants. However, the rhizosph...

    Authors: Yan Zhang, Wei Wang, Zhangjun Shen, Jingjing Wang, Yajun Chen, Dong Wang, Gang Liu and Maozhen Han

    Citation: BMC Microbiology 2021 21:30

    Content type: Research article

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  10. Salmonella enterica remains a leading cause of food-borne diseases worldwide. Serotype information is important in food safety and public health activities to reduce the burden of salmonellosis. In the current st...

    Authors: Assèta Kagambèga, Lari M. Hiott, David S. Boyle, Elizabeth A. McMillan, Poonam Sharma, Sushim K. Gupta, Hazem Ramadan, Sohyun Cho, Shaheen B. Humayoun, Tiffanie A. Woodley, Nicolas Barro, Charlene R. Jackson and Jonathan G. Frye

    Citation: BMC Microbiology 2021 21:29

    Content type: Research article

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  11. Pseudomonas putida KT2440 is a metabolically versatile, HV1-certified, genetically accessible, and thus interesting microbial chassis for biotechnological applications. However, its obligate aerobic nature hamper...

    Authors: Linde F. C. Kampers, Jasper J. Koehorst, Ruben J. A. van Heck, Maria Suarez-Diez, Alfons J. M. Stams and Peter J. Schaap

    Citation: BMC Microbiology 2021 21:9

    Content type: Research article

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  12. Ruminants burp massive amounts of methane into the atmosphere and significantly contribute to the deposition of greenhouse gases and the consequent global warming. It is therefore urgent to devise strategies t...

    Authors: Sandra Bibiana Aguilar-Marin, Claudia Lorena Betancur-Murillo, Gustavo A. Isaza, Henry Mesa and Juan Jovel

    Citation: BMC Microbiology 2020 20:364

    Content type: Research article

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  13. Infections caused by Shewanella spp. have been increasingly reported worldwide. The advances in genomic sciences have enabled better understanding about the taxonomy and epidemiology of this agent. However, the s...

    Authors: Vinicius Buiatte de Andrade Alves, Eneas Carvalho, Paloma Alonso Madureira, Elizangela Domenis Marino, Andreia Cristina Nakashima Vaz, Ana Maria Centola Vidal and Vera Letticie de Azevedo Ruiz

    Citation: BMC Microbiology 2020 20:360

    Content type: Research article

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  14. Providencia rettgeri is a nosocomial pathogen associated with urinary tract infections and related to Healthcare-Associated Infection (HAI). In recent years isolates producing New Delhi Metallo-β-lactamase (NDM) ...

    Authors: Adriana Piza-Buitrago, Verónica Rincón, John Donato, Sandra Yamile Saavedra, Carolina Duarte, Jaime Morero, Laurent Falquet, María Teresa Reguero and Emiliano Barreto-Hernández

    Citation: BMC Microbiology 2020 20:345

    Content type: Research article

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  16. Vibrio scophthalmi is an opportunistic bacterial pathogen, which is widely distributed in the marine environment. Earlier studies have suggested that it is a normal microorganism in the turbot gut. However, recen...

    Authors: Zheng Zhang, Yong-xiang Yu, Yin-geng Wang, Xiao Liu, Li-fang Wang, Hao Zhang, Mei-jie Liao and Bin Li

    Citation: BMC Microbiology 2020 20:341

    Content type: Research article

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    The Correction to this article has been published in BMC Microbiology 2020 20:375

  17. Staphylococcus lugdunensis is a coagulase-negative Staphylococcus part of the commensal skin flora but emerge as an important opportunistic pathogen. Because iron limitation is a crucial stress during infectious ...

    Authors: Marion Aubourg, Anne Dhalluin, François Gravey, Marine Pottier, Nicolas Thomy, Benoit Bernay, Didier Goux, Matthieu Martineau and Jean-Christophe Giard

    Citation: BMC Microbiology 2020 20:328

    Content type: Research article

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  19. Whole-genome sequencing using high throughput technologies has revolutionized and speeded up the scientific investigation of bacterial genetics, biochemistry, and molecular biology. Lactic acid bacteria (LABs)...

    Authors: Rim El Jeni, Kais Ghedira, Monia El Bour, Sonia Abdelhak, Alia Benkahla and Balkiss Bouhaouala-Zahar

    Citation: BMC Microbiology 2020 20:322

    Content type: Research article

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  20. Methicillin-resistant Staphylococcus aureus (MRSA) belong to diverse genetic backgrounds that differ in antibiotic resistance. Knowledge of the local clonal composition of MRSA strains is important for patients’ ...

    Authors: Samar S. Boswihi, Edet E. Udo and Wadha AlFouzan

    Citation: BMC Microbiology 2020 20:314

    Content type: Research article

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  22. Tolerance to antibiotics and persistence are associated with antibiotic treatment failures, chronic-relapsing infections, and emerging antibiotic resistance in various bacteria, including Staphylococcus aureus. M...

    Authors: Michal Meir, Anna Rozenblit, Simona Fliger, Yuval Geffen and Daniel Barkan

    Citation: BMC Microbiology 2020 20:288

    Content type: Research article

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  23. Acinetobacter baumannii has traditionally been considered an opportunistic pathogen with low virulence. In this study, we characterized the carbapenem-resistant hypervirulent A. baumannii (CR-hvAB) stains isolate...

    Authors: Jun Li, Ting Yu, Yi Luo, Jing-Yi Peng, Yu-Jia Li, Xiao-Yan Tao, Yong-Mei Hu, Hai-Chen Wang and Ming-Xiang Zou

    Citation: BMC Microbiology 2020 20:281

    Content type: Research article

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  24. To respond and adapt to environmental challenges, prokaryotes regulate cellular processes rapidly and reversibly through protein phosphorylation and dephosphorylation. This study investigates the intracellular...

    Authors: Carolina Robertsson, Gunnel Svensäter, Zoltan Blum and Claes Wickström

    Citation: BMC Microbiology 2020 20:280

    Content type: Research article

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  25. Pectobacterium carotovorum subsp. carotovorum belongs to the Enterobacteriaceae family, which causes soft-rot disease in numerous plants worldwide resulting in significant economic losses. Results from our previo...

    Authors: Jyun-Wei Wang, Reymund C. Derilo, Ruchi Briam James S. Lagitnay, Huang-Pin Wu, Kai-In Chen and Duen-Yau Chuang

    Citation: BMC Microbiology 2020 20:273

    Content type: Research article

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  26. Continuous monocropping can affect the physicochemical and biological characteristics of cultivated soil. Sophora flavescens is a valuable herbal medicine and sensitive to continuous monocropping. Currently, dive...

    Authors: Haiying Lei, Ake Liu, Qinwen Hou, Qingsong Zhao, Jia Guo and Zhijun Wang

    Citation: BMC Microbiology 2020 20:272

    Content type: Research article

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  27. Mannheimia haemolytica strains isolated from North American cattle have been classified into two genotypes (1 and 2). Although members of both genotypes have been isolated from the upper and lower respiratory tra...

    Authors: Michael L. Clawson, Gennie Schuller, Aaron M. Dickey, James L. Bono, Robert W. Murray, Michael T. Sweeney, Michael D. Apley, Keith D. DeDonder, Sarah F. Capik, Robert L. Larson, Brian V. Lubbers, Brad J. White, Jochen Blom, Carol G. Chitko-McKown, Dayna M. Brichta-Harhay and Timothy P. L. Smith

    Citation: BMC Microbiology 2020 20:250

    Content type: Research article

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  28. Surface layers (S-layers) are two-dimensional crystalline arrays of repeating proteinaceous subunits that form the outermost layer of many bacterial cell envelopes. Within the Lactobacillus genus, S-layer presenc...

    Authors: Courtney Klotz, Yong Jun Goh, Sarah O’Flaherty and Rodolphe Barrangou

    Citation: BMC Microbiology 2020 20:248

    Content type: Research article

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  29. At present, azithromycin has become an effective treatment for severe diarrhea caused by Enterotoxigenic Escherichia coli (ETEC) infection. However, enterobacteria have begun to develop resistance to azithromycin...

    Authors: Ying Xiang, Feng Wu, Yinghui Chai, Xuebin Xu, Lang Yang, Sai Tian, Haoran Zhang, Yinxia Li, Chaojie Yang, Hongbo Liu, Shaofu Qiu, Hongbin Song and Yansong Sun

    Citation: BMC Microbiology 2020 20:247

    Content type: Research article

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  30. Himalaya is an ecologically pristine environment. The geo-tectonic activities have shaped various environmental niches with diverse microbial populations throughout the Himalayan biosphere region. Albeit, limi...

    Authors: Nitish Sharma, Jitesh Kumar, Md. Minhajul Abedin, Dinabandhu Sahoo, Ashok Pandey, Amit K. Rai and Sudhir P. Singh

    Citation: BMC Microbiology 2020 20:246

    Content type: Research article

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  32. Anthrax, a zoonotic disease is caused by the Gram positive bacterium Bacillus anthracis. During January 2013, an anthrax outbreak among cattle was reported in Gundlupet Taluk, neighboring Bandipur National Park a...

    Authors: Akanxa Roonie, Saugata Majumder, Joseph J. Kingston and Manmohan Parida

    Citation: BMC Microbiology 2020 20:232

    Content type: Research article

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  33. The resistance of Streptococcus pneumoniae to macrolides is becoming an increasingly important issue and thus it is important to understand the genetics related to adaptation of this species to the widespread use...

    Authors: Petra Spanelova, Vladislav Jakubu, Lucia Malisova, Martin Musilek, Jana Kozakova, Costas C. Papagiannitsis, Ibrahim Bitar, Jaroslav Hrabak, Annalisa Pantosti, Maria del Grosso and Helena Zemlickova

    Citation: BMC Microbiology 2020 20:224

    Content type: Research article

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  34. Genome sequencing and genetic polymorphism analysis of clinical isolates of M. tuberculosis is carried out to gain further insight into molecular pathogenesis and host-pathogen interaction. Therefore the function...

    Authors: Kausik Bhattacharyya, Vishal Nemaysh, Monika Joon, Ramendra Pratap, Mandira Varma-Basil, Mridula Bose and Vani Brahmachari

    Citation: BMC Microbiology 2020 20:223

    Content type: Research article

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  35. Rickettsialpox is a febrile illness caused by the mite-borne pathogen Rickettsia akari. Several cases of this disease are reported worldwide annually. Nevertheless, the relationship between the immunogenicity of

    Authors: František Csicsay, Gabriela Flores-Ramirez, Fernando Zuñiga-Navarrete, Mária Bartošová, Alena Fučíková, Petr Pajer, Jiří Dresler, Ľudovít Škultéty and Marco Quevedo-Diaz

    Citation: BMC Microbiology 2020 20:200

    Content type: Research article

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  36. Corynespora cassiicola, as a necrotrophic phytopathogenic ascomycetous fungus, can infect hundreds of species of plants and rarely causes human diseases. This pathogen infects cucumber species and causes cucumber...

    Authors: Shigang Gao, Rong Zeng, Lihui Xu, Zhiwei Song, Ping Gao and Fuming Dai

    Citation: BMC Microbiology 2020 20:199

    Content type: Research article

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  38. Cow manure is not only an agricultural waste, but also an organic fertilizer resource. The application of organic fertilizer is a feasible practice to mitigate the soil degradation caused by overuse of chemica...

    Authors: Shuning Zhang, Litao Sun, Yu Wang, Kai Fan, Qingshan Xu, Yusheng Li, Qingping Ma, Jiguo Wang, Wanming Ren and Zhaotang Ding

    Citation: BMC Microbiology 2020 20:190

    Content type: Research article

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  39. The data on the prevalence of resistance to mupirocin (MUP), fusidic acid (FA) and retapamulin (RET) in methicillin-resistant Staphylococcus aureus (MRSA) from China are still limited. This study aimed to examine...

    Authors: Wenjing Chen, Chunyan He, Han Yang, Wen Shu, Zelin Cui, Rong Tang, Chuanling Zhang and Qingzhong Liu

    Citation: BMC Microbiology 2020 20:183

    Content type: Research article

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  40. Psychological co-morbidities in irritable bowel syndrome (IBS) have been widely recognized, whereas less is known regarding the role of gut microbial and host metabolic changes in clinical and psychological sy...

    Authors: Tong Liu, Xiang Gu, Li-Xiang Li, Ming Li, Bing Li, Xiao Cui and Xiu-li Zuo

    Citation: BMC Microbiology 2020 20:168

    Content type: Research article

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  41. Cercospora sojina is a fungal pathogen that causes frogeye leaf spot in soybean-producing regions, leading to severe yield losses worldwide. It exhibits variations in virulence due to race differentiation between...

    Authors: Xin Gu, Shuai Yang, Xiaohe Yang, Liangliang Yao, Xuedong Gao, Maoming Zhang, Wei Liu, Haihong Zhao, Qingsheng Wang, Zengjie Li, Zhimin Li and Junjie Ding

    Citation: BMC Microbiology 2020 20:166

    Content type: Research article

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  42. Members of the genus Proteus are mostly opportunistic pathogens that cause a variety of infections in humans. The molecular evolutionary characteristics and genetic relationships among Proteus species have not be...

    Authors: Hang Dai, Binghuai Lu, Zhenpeng Li, Zhenzhou Huang, Hongyan Cai, Keyi Yu and Duochun Wang

    Citation: BMC Microbiology 2020 20:152

    Content type: Research article

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  43. Whole genome sequencing promises to revolutionize our ability to link genotypic and phenotypic variation in a wide range of model and non-model species.

    Authors: Bhavani S. Gudlavalleti, Trong Phung, Charles L. Barton, Allysson Becker, Brittany L. Graul, Jarod T. Griffin, Connor J. Hays, Bailey Horn, David R. Liang, Lauren M. Rutledge, Alexandria M. Szalanczy, Bobby L. Gaffney, Rodney A. King, Claire A. Rinehart, Amanda K. Staples, Alexander A. Stewart…

    Citation: BMC Microbiology 2020 20:148

    Content type: Research article

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  44. In animals, many factors affect the small intestinal function and cecal microorganisms, including body weight and genetic background. However, whether paternal weight impacts the small intestinal function and ...

    Authors: Mingxia Ran, Bo Hu, Lumin Cheng, Shenqiang Hu, Hehe Liu, Liang Li, Jiwei Hu and Jiwen Wang

    Citation: BMC Microbiology 2020 20:145

    Content type: Research article

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  45. Lactococcus members belonging to lactic acid bacteria are widely used as starter bacteria in the production of fermented dairy products. From kimchi, a Korean food made of fermented vegetables, Lactococcus raffin...

    Authors: Min Young Jung, Changsu Lee, Myung-Ji Seo, Seong Woon Roh and Se Hee Lee

    Citation: BMC Microbiology 2020 20:136

    Content type: Research article

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  46. Conjugation plays a major role in the transmission of plasmids encoding antibiotic resistance genes in both clinical and general settings. The conjugation efficiency is influenced by many biotic and abiotic fa...

    Authors: Jesse B. Alderliesten, Sarah J. N. Duxbury, Mark P. Zwart, J. Arjan G. M. de Visser, Arjan Stegeman and Egil A. J. Fischer

    Citation: BMC Microbiology 2020 20:135

    Content type: Research article

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  47. Environmental surveillance of antibiotic resistance can contribute towards better understanding and management of human and environmental health. This study applied a combination of long-read Oxford Nanopore M...

    Authors: Didrik H. Grevskott, Francisco Salvà-Serra, Edward R. B. Moore and Nachiket P. Marathe

    Citation: BMC Microbiology 2020 20:134

    Content type: Research article

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  48. Mortality due to tuberculosis (TB) has increased due to the development of drug resistance, the mechanisms of which have not been fully elucidated. Our research group identified a low expression of lipF gene in M...

    Authors: Ana Leticia Arriaga-Guerrero, Carlos E. Hernández-Luna, Joyce Rigal-Leal, Rene J. Robles-González, Laura Adiene González-Escalante, Beatriz Silva-Ramírez, Roberto Mercado-Hernández, Javier Vargas-Villarreal, Mario Bermúdez de León and Katia Peñuelas-Urquides

    Citation: BMC Microbiology 2020 20:132

    Content type: Research article

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  50. Gene editing is key for elucidating gene function. Traditional methods, such as consecutive single-crossovers, have been widely used to modify bacterial genomes. However, cumbersome cloning and limited efficie...

    Authors: Francesca Romana Cianfanelli, Olivier Cunrath and Dirk Bumann

    Citation: BMC Microbiology 2020 20:129

    Content type: Methodology article

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