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Microbial genetics, genomics and proteomics

Section edited by Hirotada Mori

This section aims to publish studies relating to all aspects of microbial genomics, proteomics, metabolomics and systems biology.

Page 1 of 8

  1. 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

    Published on:

  2. 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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  3. 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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  4. 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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  5. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. Infection, even outbreak, caused by Cryptococcus gattii (C. gattii) has been reported in Canada and the United States, but there were sparsely-reported cases of C. gattii in China. Our interest in occurrence, cli...

    Authors: Liang Jin, Jing-Rong Cao, Xin-Ying Xue, Hua Wu, Li-Feng Wang, Ling Guo and Ding-Xia Shen

    Citation: BMC Microbiology 2020 20:73

    Content type: Research article

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  30. Acinetobacter baylyi ADP1 is an ideal bacterial strain for high-throughput genetic analysis as the bacterium is naturally transformable. Thus, ADP1 can be used to investigate DNA mismatch repair, a mechanism for ...

    Authors: Hua Zhou, Linyue Zhang, Qingye Xu, Linghong Zhang, Yunsong Yu and Xiaoting Hua

    Citation: BMC Microbiology 2020 20:40

    Content type: Research article

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  31. The polyketide antibiotic 2,4-diacetylphloroglucinol (2,4-DAPG), produced by Pseudomonas fluorescens 2P24, is positively regulated by the GacS-GacA two-component system.

    Authors: Bo Zhang, Hui Zhao, Xiaogang Wu and Li-Qun Zhang

    Citation: BMC Microbiology 2020 20:39

    Content type: Research article

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  32. Dolichospermum circinale is a filamentous bloom-forming cyanobacterium responsible for biosynthesis of the paralytic shellfish toxins (PST), including saxitoxin. PSTs are neurotoxins and in their purified form ar...

    Authors: Paul M. D’Agostino, Bakir Al-Sinawi, Rabia Mazmouz, Julia Muenchhoff, Brett A. Neilan and Michelle C. Moffitt

    Citation: BMC Microbiology 2020 20:35

    Content type: Research article

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  33. Sodium dodecyl sulfate (SDS) is one of the most widely used anionic alkyl sulfate surfactants. Toxicological information on SDS is accumulating, however, mechanisms of SDS toxicity regulation remain poorly und...

    Authors: Chunlei Cao, Zhengfeng Cao, Peibin Yu and Yunying Zhao

    Citation: BMC Microbiology 2020 20:34

    Content type: Research article

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  34. Acinetobacter baumannii is a multidrug-resistant (MDR) hazardous bacterium with very high antimicrobial resistance profiles. Outer membrane vesicles (OMVs) help directly and/or indirectly towards antibiotic resis...

    Authors: DineshKumar Kesavan, Aparna Vasudevan, Liang Wu, Jianguo Chen, Zhaoliang Su, Shengjun Wang and Huaxi Xu

    Citation: BMC Microbiology 2020 20:31

    Content type: Research article

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  35. Wastewater treatment plants (WWTPs) are considered hotspots for the environmental dissemination of antimicrobial resistance (AMR) determinants. Vancomycin-Resistant Enterococcus (VRE) are candidates for gauging t...

    Authors: Haley Sanderson, Rodrigo Ortega-Polo, Rahat Zaheer, Noriko Goji, Kingsley K. Amoako, R. Stephen Brown, Anna Majury, Steven N. Liss and Tim A. McAllister

    Citation: BMC Microbiology 2020 20:20

    Content type: Research article

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  36. Cadmium (Cd) is a severely toxic heavy metal to most microorganisms. Many bacteria have developed Cd2+ resistance.

    Authors: Xiaoxia Yu, Zundan Ding, Yangyang Ji, Jintong Zhao, Xiaoqing Liu, Jian Tian, Ningfeng Wu and Yunliu Fan

    Citation: BMC Microbiology 2020 20:18

    Content type: Research article

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  37. Thaumarchaeota are abundant in the Amazon River, where they are the only ammonia-oxidizing archaea. Despite the importance of Thaumarchaeota, little is known about their physiology, mainly because few isolates...

    Authors: Otávio H. B. Pinto, Thais F. Silva, Carla S. Vizzotto, Renata H. Santana, Fabyano A. C. Lopes, Bruno S. Silva, Fabiano L. Thompson and Ricardo H. Kruger

    Citation: BMC Microbiology 2020 20:13

    Content type: Research article

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  38. The comparisons of molecular characterization and antibiotic resistance of Klebsiella pneumoniae (KP) isolates from humans and other animal hosts are not well studied. Our goal was to compare the molecular epidem...

    Authors: Xue-shan Zhong, Yong-zhi Li, Jing Ge, Gang Xiao, Yun Mo, Yu-qi Wen, Jing-ping Liu, Yi-quan Xiong, Min Qiu, Shu-ting Huo, Ming-ji Cheng and Qing Chen

    Citation: BMC Microbiology 2020 20:12

    Content type: Research article

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  39. Intestinal pathogen infections are widespread among impoverished populations. Enterocytozoon bieneusi is the most common pathogen of intestinal microsporidian species in humans worldwide. However, no epidemiologi...

    Authors: Yujuan Shen, Baiyan Gong, Xiaohua Liu, Yanchen Wu, Fengkun Yang, Jie Xu, Xiaofan Zhang, Jianping Cao and Aiqin Liu

    Citation: BMC Microbiology 2020 20:10

    Content type: Research article

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  40. Interactions between transcription factors and DNA lie at the centre of many biological processes including DNA recombination, replication, repair and transcription. Most bacteria encode diverse proteins that ...

    Authors: Shi-qi An, Miguel A. Valvano, Yan-hua Yu, Jeremy S. Webb and Guillermo Lopez Campos

    Citation: BMC Microbiology 2020 20:1

    Content type: Methodology article

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  41. Some of the spore-forming strains of Bacillus probiotics are marketed commercially as they survive harsh gastrointestinal conditions and bestow health benefits to the host.

    Authors: Indu Khatri, Gaurav Sharma and Srikrishna Subramanian

    Citation: BMC Microbiology 2019 19:307

    Content type: Research article

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  42. Grey mould is an important plant disease worldwide, caused by Botrytis cinerea, resulting in serious economic loss. Wuyiencin, a low toxicity, high efficiency, and broad-spectrum agricultural antibiotic, has been...

    Authors: Liming Shi, Beibei Ge, Jinzi Wang, Binghua Liu, Jinjin Ma, Qiuhe Wei and Kecheng Zhang

    Citation: BMC Microbiology 2019 19:280

    Content type: Research article

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  43. HSV-1 is a common pathogen that infects 50–90% of the human population worldwide. HSV-1 causes numerous infection-related diseases, some of which are severely life-threatening. There are antiviral medications ...

    Authors: Qiang Huang, Jue Hou, Peng Yang, Jun Yan, Xiaoliang Yu, Ying Zhuo, Sudan He and Feng Xu

    Citation: BMC Microbiology 2019 19:274

    Content type: Research article

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  44. Cannas are popular ornamental plants and widely planted for the beautiful foliage and flower. Viral disease is a major threaten to canna horticulture industry. In the city of Beijing, mosaic disease in canna w...

    Authors: Yongqiang Li, Fei Xia, Yixuan Wang, Chenge Yan, Anning Jia and Yongjiang Zhang

    Citation: BMC Microbiology 2019 19:260

    Content type: Research article

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  45. Gene overlapping is a frequent phenomenon in microbial genomes. Excluding so-called “trivial overlapping”, there are significant implications of such genetic arrangements, including regulation of gene expressi...

    Authors: Paweł Wawrzyniak, Agnieszka Sobolewska-Ruta, Piotr Zaleski, Natalia Łukasiewicz, Paulina Kabaj, Piotr Kierył, Agata Gościk, Anna Bierczyńska-Krzysik, Piotr Baran, Anna Mazurkiewicz-Pisarek, Andrzej Płucienniczak and Dariusz Bartosik

    Citation: BMC Microbiology 2019 19:254

    Content type: Research article

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  46. The human small intestine plays a central role in the processes of digestion and nutrient absorption. However, characterizations of the human gut microbiome have largely relied on stool samples, and the associ...

    Authors: Gabriela Guimaraes Sousa Leite, Walter Morales, Stacy Weitsman, Shreya Celly, Gonzalo Parodi, Ruchi Mathur, Rashin Sedighi, Gillian M. Barlow, Ali Rezaie and Mark Pimentel

    Citation: BMC Microbiology 2019 19:239

    Content type: Methodology article

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  47. Co-translational processes in bacteria are attractive drug targets, but while some processes are essential, others are not. The essentiality of Peptide Deformylase (PDF, def) for vitality of mycobacteria was spec...

    Authors: Noga Naor, Omer Gadot, Michal Meir and Daniel Barkan

    Citation: BMC Microbiology 2019 19:232

    Content type: Research article

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  48. TnaphA6-carrying repAci6 plasmids have been detected in Acinetobacter baumannii isolates belonging to global clones, GC1 and GC2, worldwide. Here, we examined whether RepAci6 plasmids family play a role in the di...

    Authors: Parisa Aris, Mohammad Ali Boroumand and Masoumeh Douraghi

    Citation: BMC Microbiology 2019 19:221

    Content type: Research article

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  49. Cellulose is synthesized by an array of bacterial species. Komagataeibacter xylinus is the best characterized as it produces copious amounts of the polymer extracellularly. Despite many advances in the past decad...

    Authors: Luis Salgado, Silvia Blank, Reza Alipour Moghadam Esfahani, Janice L. Strap and Dario Bonetta

    Citation: BMC Microbiology 2019 19:216

    Content type: Research article

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  50. Efflux pump mediated antibiotic resistance is an unnoticed and undetected mechanism in clinical microbiology laboratory. RND efflux systems are known for aminoglycoside and tetracycline resistance whereas thei...

    Authors: Shiela Chetri, Deepshikha Bhowmik, Deepjyoti Paul, Piyush Pandey, Debadatta Dhar Chanda, Atanu Chakravarty, Debajyoti Bora and Amitabha Bhattacharjee

    Citation: BMC Microbiology 2019 19:210

    Content type: Research article

    Published on:

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