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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. 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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  2. 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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  3. 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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  4. 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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  5. 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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  7. 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

  8. 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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  10. 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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  11. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  41. 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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  42. Bacillus cereus is a bacterial species which grows efficiently on a wide range of carbon sources and accumulates biopolymer poly-hydroxybutyrate (PHB) up to 80% cell dry weight. PHB is an aliphatic polymer produc...

    Authors: Hui Li, Joshua O’Hair, Santosh Thapa, Sarabjit Bhatti, Suping Zhou, Yong Yang, Tara Fish and Theodore W. Thannhauser

    Citation: BMC Microbiology 2020 20:122

    Content type: Research article

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  43. Careful consideration of experimental artefacts is required in order to successfully apply high-throughput 16S ribosomal ribonucleic acid (rRNA) gene sequencing technology. Here we introduce experimental desig...

    Authors: Shantelle Claassen-Weitz, Sugnet Gardner-Lubbe, Kilaza S. Mwaikono, Elloise du Toit, Heather J. Zar and Mark P. Nicol

    Citation: BMC Microbiology 2020 20:113

    Content type: Methodology article

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  44. Antimonite [Sb(III)]-oxidizing bacterium has great potential in the environmental bioremediation of Sb-polluted sites. Bacillus sp. S3 that was previously isolated from antimony-contaminated soil displayed high S...

    Authors: Jiaokun Li, Tianyuan Gu, Liangzhi Li, Xueling Wu, Li Shen, Runlan Yu, Yuandong Liu, Guanzhou Qiu and Weimin Zeng

    Citation: BMC Microbiology 2020 20:106

    Content type: Research article

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  45. Different mulches have variable effects on soil physicochemical characteristics, bacterial and fungal communities and ecosystem functions. However, the information about soil microbial diversity, community str...

    Authors: Shuning Zhang, Yu Wang, Litao Sun, Chen Qiu, Yiqian Ding, Honglian Gu, Linjun Wang, Zhaoshun Wang and Zhaotang Ding

    Citation: BMC Microbiology 2020 20:103

    Content type: Research article

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  46. Murine kobuviruses (MuKV) are newly recognized picornaviruses first detected in murine rodents in the USA in 2011. Little information on MuKV epidemiology in murine rodents is available. Therefore, we conducte...

    Authors: Fang-Fei You, Min-Yi Zhang, Huan He, Wen-Qiao He, Yong-Zhi Li and Qing Chen

    Citation: BMC Microbiology 2020 20:94

    Content type: Research article

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  47. Mycobacterium tuberculosis resides inside host macrophages during infection and adapts to resilient stresses generated by the host immune system. As a response, M. tuberculosis codes for short-chain dehydrogenase...

    Authors: Gunapati Bhargavi, Sameer Hassan, Subramanyam Balaji, Srikanth Prasad Tripathy and Kannan Palaniyandi

    Citation: BMC Microbiology 2020 20:93

    Content type: Research article

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  48. The performance of multiplex PCR (mPCR) for detection of antimicrobial resistance from clinical isolates is unknown. We assessed the ability of mPCR to analyse resistance genes directly from clinical samples.

    Authors: Irene Katharina Sigmund, Nora Renz, Susanne Feihl, Christian Morgenstern, Sabrina Cabric and Andrej Trampuz

    Citation: BMC Microbiology 2020 20:88

    Content type: Research article

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  49. There is a need for better tools to evaluate new or repurposed TB drugs. The whole blood bactericidal activity (WBA) assay has been advocated for this purpose. We investigated whether transcriptional responses...

    Authors: Philip Kam Weng Kwan, Wenwei Lin, Ahmad Nazri Mohamed Naim, Balamurugan Periaswamy, Paola Florez De Sessions, Martin L. Hibberd and Nicholas I. Paton

    Citation: BMC Microbiology 2020 20:81

    Content type: Research article

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  50. Circular bacteriocins are antimicrobial peptides produced by bacteria with a N and C termini ligation. They have desirable properties such as activity at low concentrations along with thermal, pH and proteolyt...

    Authors: Ben Vezina, Bernd H. A. Rehm and Andrew T. Smith

    Citation: BMC Microbiology 2020 20:77

    Content type: Research article

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