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Ecological and evolutionary microbiology

Section edited by Jizhong Zhou

This section aims to publish studies looking at all aspects of ecological and evolutionary microbiology, including microbial ecology, ecosystems, biodiversity, evolution, population genetics, phylogenetics, microbial communities and biofilms, marine and freshwater microbiology.

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  1. Content type: Database

    As microbiome research becomes increasingly prevalent in the fields of human health, agriculture and biotechnology, there exists a need for a resource to better link organisms and environmental chemistries. Ex...

    Authors: Suzanne M. Kosina, Annette M. Greiner, Rebecca K. Lau, Stefan Jenkins, Richard Baran, Benjamin P. Bowen and Trent R. Northen

    Citation: BMC Microbiology 2018 18:115

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  2. Content type: Research article

    The blunt snout bream (Megalobrama amblycephala) is one of the most important commercial herbivorous fish in China, and dietary transition is an important event in blunt snout bream development. Gut microbiota ha...

    Authors: Jin Wei, Xianwu Guo, Han Liu, Yuanyuan Chen and Weimin Wang

    Citation: BMC Microbiology 2018 18:99

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  3. Content type: Research article

    In many Asian countries including Bangladesh E. coli O157 are prevalent in animal reservoirs and in the food chain, but the incidence of human infection due to E. coli O157 is rare. One of the reasons could be in...

    Authors: Mahdia Rahman, Ashikun Nabi, Md Asadulghani, Shah M. Faruque and Mohammad Aminul Islam

    Citation: BMC Microbiology 2018 18:98

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  4. Content type: Research article

    The rumen bacterial community plays a critical role in feeds degradation and productivity. The effects of different forage to concentrate ratios on the ruminal microbial population structure have been studied ...

    Authors: Yanliang Bi, Shuqin Zeng, Rong Zhang, Qiyu Diao and Yan Tu

    Citation: BMC Microbiology 2018 18:69

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  5. Content type: Research article

    Actinobacteria are often known to be great producers of antibiotics. The rapid increase in the global burden of antibiotic-resistance with the concurrent decline in the discovery of new antimicrobial molecules...

    Authors: Ranjita Das, Wahengbam Romi, Rictika Das, Hridip Kumar Sharma and Debajit Thakur

    Citation: BMC Microbiology 2018 18:71

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  6. Content type: Research article

    Exploiting soil microorganisms in the rhizosphere of plants can significantly improve agricultural productivity; however, the mechanism by which microorganisms specifically affect agricultural productivity is ...

    Authors: Zhaohui Wu, Qingshu Liu, Zhenyu Li, Wei Cheng, Jimin Sun, Zhaohui Guo, Yongmei Li, Jianqun Zhou, Delong Meng, Hongbo Li, Ping Lei and Huaqun Yin

    Citation: BMC Microbiology 2018 18:51

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  7. Content type: Research article

    Alleviating arsenic (As) contamination is a high-priority environmental issue. Hyperaccumulator plants may harbor endophytic bacteria able to detoxify As. Therefore, we investigated the distribution, diversity...

    Authors: Yunfu Gu, Yingyan Wang, Yihao Sun, Ke Zhao, Quanju Xiang, Xiumei Yu, Xiaoping Zhang and Qiang Chen

    Citation: BMC Microbiology 2018 18:42

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  8. Content type: Research article

    The expansion of offshore oil exploration increases the risk of marine species being exposed to oil pollution in currently pristine areas. The adverse effects of oil exposure through toxic properties of polycy...

    Authors: Andrea Bagi, Even Sannes Riiser, Hilde Steine Molland, Bastiaan Star, Thomas H. A. Haverkamp, Magne Olav Sydnes and Daniela Maria Pampanin

    Citation: BMC Microbiology 2018 18:25

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  9. Content type: Research article

    The spreading of antibiotic resistant bacteria is becoming nowadays an alarming threat to human and animal health. There is increasing evidence showing that wild birds could significantly contribute to the tra...

    Authors: Houssem Ben Yahia, Rym Ben Sallem, Ghassan Tayh, Naouel Klibi, Insaf Ben Amor, Haythem Gharsa, Abdellatif Boudabbous and Karim Ben Slama

    Citation: BMC Microbiology 2018 18:26

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  10. Content type: Research article

    This study was conducted to examine effects of nitrate on ruminal methane production, methanogen abundance, and composition. Six rumen-fistulated Limousin×Jinnan steers were fed diets supplemented with either ...

    Authors: Liping Zhao, Qingxiang Meng, Yan Li, Hao Wu, Yunlong Huo, Xinzhuang Zhang and Zhenming Zhou

    Citation: BMC Microbiology 2018 18:21

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  11. Content type: Research article

    The cyclic-di-GMP (c-di-GMP) second messenger exemplifies a signaling system that regulates many bacterial behaviors of key importance; among them, c-di-GMP controls the transition between motile and sessile l...

    Authors: Alberto Ramírez Mata, César Millán Pacheco, José F. Cruz Pérez, Martha Minjárez Sáenz and Beatriz E. Baca

    Citation: BMC Microbiology 2018 18:20

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  12. Content type: Research article

    Soil contaminated with the heavy metal Cadmium (Cd) is a widespread problem in many parts of the world. Based on metagenomic analysis, we investigated the functional potential and structural diversity of the m...

    Authors: Gang Feng, Tian Xie, Xin Wang, Jiuyuan Bai, Lin Tang, Hai Zhao, Wei Wei, Maolin Wang and Yun Zhao

    Citation: BMC Microbiology 2018 18:11

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  13. Content type: Research article

    Brucellosis incidence in China is divided into three stages: high incidence (1950s–1960s), decline (1970s–1980s), and re-emergence (1990s–2010s). At the re-emergence stage, Brucellosis incidence grew exponentiall...

    Authors: Dong-ri Piao, Xi Liu, Dong-dong Di, Pei Xiao, Zhong-zhi Zhao, Li-qing Xu, Guo-zhong Tian, Hong-yan Zhao, Wei-xing Fan, Bu-yun Cui and Hai Jiang

    Citation: BMC Microbiology 2018 18:7

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  14. Content type: Methodology Article

    Many of the bacterial genomic studies exploring evolution processes of the host adaptation focus on the accessory genome describing how the gains and losses of genes can explain the colonization of new habitat...

    Authors: Arnaud Felten, Meryl Vila Nova, Kevin Durimel, Laurent Guillier, Michel-Yves Mistou and Nicolas Radomski

    Citation: BMC Microbiology 2017 17:222

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  15. Content type: Research article

    Anthrax is a globally distributed disease affecting primarily herbivorous mammals. It is caused by the soil-dwelling and spore-forming bacterium Bacillus anthracis. The dormant B. anthracis spores become vegetati...

    Authors: Karoline Valseth, Camilla L. Nesbø, W. Ryan Easterday, Wendy C. Turner, Jaran S. Olsen, Nils Chr. Stenseth and Thomas H. A. Haverkamp

    Citation: BMC Microbiology 2017 17:206

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  16. Content type: Research article

    Total community rDNA was used to determine the diversity of bacteria and archaea from water, wet sediment and microbial mats samples of hot springs in the Eastern lowlands of Eritrea. The temperatures of the s...

    Authors: Amanuel M. Ghilamicael, Nancy L. M. Budambula, Sylvester E. Anami, Tadesse Mehari and Hamadi I. Boga

    Citation: BMC Microbiology 2017 17:203

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  17. Content type: Research article

    Benthic ciliates and the environmental factors shaping their distribution are far from being completely understood. Likewise, deep-sea systems are amongst the least understood ecosystems on Earth. In this stud...

    Authors: Feng Zhao, Sabine Filker, Thorsten Stoeck and Kuidong Xu

    Citation: BMC Microbiology 2017 17:192

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  18. Content type: Research article

    Enterohemorrhagic Escherichia coli (EHEC) O145 are among the top non-O157 serogroups associated with severe human disease worldwide. Two serotypes, O145:H25 and O145:H28 have been isolated from human patients but...

    Authors: Sandra C. Lorenz, Narjol Gonzalez-Escalona, Michael L. Kotewicz, Markus Fischer and Julie A. Kase

    Citation: BMC Microbiology 2017 17:183

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  19. Content type: Research article

    G-protein coupled receptors (GPCRs) are the largest family of transmembrane receptors in fungi, where they play important roles in signal transduction. Among them, the Pth11-related GPCRs form a large and dive...

    Authors: Xihui Xu, Guopeng Li, Lu Li, Zhenzhu Su and Chen Chen

    Citation: BMC Microbiology 2017 17:166

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  20. Content type: Research article

    Intramuscular fat (IMF) that deposits among muscle fibers or within muscle cells is an important meat quality trait in pigs. Previous studies observed the effects of dietary nutrients and additives on improvin...

    Authors: Shaoming Fang, Xingwei Xiong, Ying Su, Lusheng Huang and Congying Chen

    Citation: BMC Microbiology 2017 17:162

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  21. Content type: Research article

    Gut microbiota plays an important role in the harvesting, storage, and expenditure of energy obtained from one’s diet. Our cross-sectional study aimed to identify differences in gut microbiota according to bod...

    Authors: Yeojun Yun, Han-Na Kim, Song E. Kim, Seong Gu Heo, Yoosoo Chang, Seungho Ryu, Hocheol Shin and Hyung-Lae Kim

    Citation: BMC Microbiology 2017 17:151

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  22. Content type: Research article

    The importance of upper airway structure in the susceptibility of the lower respiratory tract to colonization with potential pathogens is well established. With the advent of rapid, high throughput, next gener...

    Authors: Mohamed M. Zeineldin, James F. Lowe, Elsbeth D. Grimmer, Maria R. C. de Godoy, Mohamed M. Ghanem, Yassein M. Abd El-Raof and Brian M. Aldridge

    Citation: BMC Microbiology 2017 17:138

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  23. Content type: Research article

    With the growing demand for fossil fuels and the severe energy crisis, lignocellulose is widely regarded as a promising cost-effective renewable resource for ethanol production, and the use of lignocellulose r...

    Authors: Bailin Cong, Nengfei Wang, Shenghao Liu, Feng Liu, Xiaofei Yin and Jihong Shen

    Citation: BMC Microbiology 2017 17:129

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  24. Content type: Research article

    In drug-drug interactions, there are surprising cases in which the growth inhibition of bacteria by a single antibiotic decreases when a second antibiotic is added. These interactions are termed suppressive an...

    Authors: Casey Beppler, Elif Tekin, Cynthia White, Zhiyuan Mao, Jeffrey H. Miller, Robert Damoiseaux, Van M. Savage and Pamela J. Yeh

    Citation: BMC Microbiology 2017 17:107

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  25. Content type: Research article

    Here, we aimed to investigate the effects of ensiled mulberry leaves (EML) and sun-dried mulberry fruit pomace (SMFP) on fecal bacterial communities in Simmental crossbred finishing steers. To this end, the st...

    Authors: Yan Li, Qingxiang Meng, Bo Zhou and Zhenming Zhou

    Citation: BMC Microbiology 2017 17:97

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  26. Content type: Research article

    The nitrogen (N) cycle consists of complex microbe-mediated transformations driven by a variety of factors, including diversity and concentrations of N compounds. In this study, we examined taxonomic diversity...

    Authors: Suchismita Ghosh, Paul A. Ayayee, Oscar J. Valverde-Barrantes, Christopher B. Blackwood, Todd V. Royer and Laura G. Leff

    Citation: BMC Microbiology 2017 17:87

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  27. Content type: Research article

    Establishing an optimal proportion of nitrifying microbial populations, including ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB), complete nitrite oxidizers (comammox) and ammonia-oxidizing...

    Authors: Giantommaso Scarascia, Hong Cheng, Moustapha Harb and Pei-Ying Hong

    Citation: BMC Microbiology 2017 17:85

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  28. Content type: Research article

    Staphylococcus aureus more than any other human pathogen is a better model for the study of the adaptive evolution of bacterial resistance to antibiotics, as it has demonstrated a rema...

    Authors: Asinamai Athliamai Bitrus, Zakaria Zunita, Siti Khairani Bejo, Sarah Othman and Nur Adilah Ahmad Nadzir

    Citation: BMC Microbiology 2017 17:83

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  29. Content type: Research article

    The nasopharyngeal (NP) microbiota plays an important role in bovine health, comprising a rich and diverse microbial community. The nasopharynx is also the niche for potentially pathogenic agents which are ass...

    Authors: Devin B. Holman, Edouard Timsit, Samat Amat, D. Wade Abbott, Andre G. Buret and Trevor W. Alexander

    Citation: BMC Microbiology 2017 17:70

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    The Erratum to this article has been published in BMC Microbiology 2017 17:95

  30. Content type: Research article

    Present study focuses on diversity and distribution analysis of endophytic fungi associated with different tissues of the Monarda citriodora Cerv. ex Lag. (Lamiaceae/Labiatae). Anticancer and antimicrobial potent...

    Authors: Meenu Katoch, Shipra Phull, Shagun Vaid and Shashank Singh

    Citation: BMC Microbiology 2017 17:44

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  31. Content type: Research article

    Natural transformation enables acquisition of adaptive traits and drives genome evolution in prokaryotes. Yet, the selective forces responsible for the evolution and maintenance of natural transformation remai...

    Authors: Nils Hülter, Vidar Sørum, Kristina Borch-Pedersen, Mikkel M. Liljegren, Ane L. G. Utnes, Raul Primicerio, Klaus Harms and Pål J. Johnsen

    Citation: BMC Microbiology 2017 17:34

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  32. Content type: Researc article

    Unconventional natural gas (UNG) extraction (fracking) is ongoing in 29 North American shale basins (20 states), with ~6000 wells found within the Fayetteville shale (north-central Arkansas). If the chemical s...

    Authors: Wilson H. Johnson, Marlis R. Douglas, Jeffrey A. Lewis, Tara N. Stuecker, Franck G. Carbonero, Bradley J. Austin, Michelle A. Evans-White, Sally A. Entrekin and Michael E. Douglas

    Citation: BMC Microbiology 2017 17:29

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  33. Content type: Research article

    While recent advances in next generation sequencing technologies have enabled researchers to readily identify countless microbial species in soil, rhizosphere, and phyllosphere microbiomes, the biological func...

    Authors: Maja Hilber-Bodmer, Michael Schmid, Christian H. Ahrens and Florian M. Freimoser

    Citation: BMC Microbiology 2017 17:4

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  34. Content type: Research article

    During chronic lung infections of cystic fibrosis patients Pseudomonas aeruginosa populations undergo extensive evolutionary diversification. However, the selective drivers of this evolutionary process are poorly...

    Authors: Emily V. Davies, Chloe E. James, Michael A. Brockhurst and Craig Winstanley

    Citation: BMC Microbiology 2017 17:3

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  35. Content type: Research article

    Previous studies on the bacteria associated with the bryophytes showed that there were abundant bacteria inhabited in/on these hosts. However, the type of bacteria and whether these discriminate between differ...

    Authors: Jing Yan Tang, Jing Ma, Xue Dong Li and Yan Hong Li

    Citation: BMC Microbiology 2016 16:276

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  36. Content type: Methodology article

    Currently, bacterial 16S rRNA gene analyses are based on sequencing of individual variable regions of the 16S rRNA gene (Kozich, et al Appl Environ Microbiol 79:5112–5120, 2013).This short read approach can intro...

    Authors: Josef Wagner, Paul Coupland, Hilary P. Browne, Trevor D. Lawley, Suzanna C. Francis and Julian Parkhill

    Citation: BMC Microbiology 2016 16:274

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  37. Content type: Research article

    Heterogeneity and niche adaptation in bacterial biofilm involve changes to the genetic makeup of the bacteria and gene expression control. We hypothesized that i) spontaneous mutations in the flhD operon can eith...

    Authors: Shelley M. Horne, Joseph Sayler, Nicholas Scarberry, Meredith Schroeder, Ty Lynnes and Birgit M. Prüß

    Citation: BMC Microbiology 2016 16:262

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  38. Content type: Research article

    Soil populations of bacteria rapidly degrading atrazine are critical to the environmental fate of the herbicide. An enrichment bias from the routine isolation procedure prevents studying the diversity of atraz...

    Authors: Dmitry P. Bazhanov, Chengyun Li, Hongmei Li, Jishun Li, Xinjian Zhang, Xiangfeng Chen and Hetong Yang

    Citation: BMC Microbiology 2016 16:265

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  39. Content type: Research article

    Antimicrobial resistance (AMR) is a growing and significant threat to public health on a global scale. Escherichia coli comprises Gram-negative, fecal-borne pathogenic and commensal bacteria that are frequently a...

    Authors: Beatus Lyimo, Joram Buza, Murugan Subbiah, Woutrina Smith and Douglas R. Call

    Citation: BMC Microbiology 2016 16:254

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  40. Content type: Research article

    The microbiota plays an essential role in host health, particularly through competition with opportunistic pathogens. Changes in total bacterial load and microbiota structure can indicate early stages of disea...

    Authors: Andrea M. Tarnecki, William F. Patterson III and Covadonga R. Arias

    Citation: BMC Microbiology 2016 16:245

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  41. Content type: Research article

    The interaction mechanism between crop and soil microbial communities is a key issue in both agriculture and soil ecology. However, how soil microbial communities respond to crop planting and ultimately affect...

    Authors: Jiaojiao Niu, Zhongwen Rang, Chao Zhang, Wu Chen, Feng Tian, Huaqun Yin and Linjian Dai

    Citation: BMC Microbiology 2016 16:233

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  42. Content type: Research article

    Filamentous tropical marine cyanobacteria such as Moorea producens strain JHB possess a rich community of heterotrophic bacteria on their polysaccharide sheaths; however, these bacterial communities have not y...

    Authors: Susie L. Cummings, Debby Barbé, Tiago Ferreira Leao, Anton Korobeynikov, Niclas Engene, Evgenia Glukhov, William H. Gerwick and Lena Gerwick

    Citation: BMC Microbiology 2016 16:198

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  43. Content type: Research article

    Ophiocordyceps sinensis (DongChong XiaCao (DCXC) in Chinese), a fungal parasite of caterpillars, is a traditional Chinese medicine. Bioactive components isolated from natural DCXC poss...

    Authors: Fei Xia, Yan Liu, Meng-Yuan Guo, Guang-Rong Shen, Juan Lin and Xuan-Wei Zhou

    Citation: BMC Microbiology 2016 16:196

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  44. Content type: Research article

    Although semi-selective growth media have been developed for the isolation of Burkholderia cepacia complex bacteria from the environment, thus far Burkholderia multivorans has rarely been isolated from such sampl...

    Authors: Charlotte Peeters, Stijn Daenekindt and Peter Vandamme

    Citation: BMC Microbiology 2016 16:184

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  45. Content type: Research article

    Xiangjiang River (Hunan, China) has been contaminated with heavy metal for several decades by surrounding factories. However, little is known about the influence of a gradient of heavy metal contamination on t...

    Authors: Shiqi Jie, Mingming Li, Min Gan, Jianyu Zhu, Huaqun Yin and Xueduan Liu

    Citation: BMC Microbiology 2016 16:179

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  46. Content type: Research article

    Mycobacterium tuberculosis, the tuberculosis (TB) pathogen, despite a low level of genetic diversity, has revealed a high variety of biological and epidemiological characteristics link...

    Authors: Van Anh Thi Nguyen, Anne-Laure Bañuls, Thanh Hoa Thi Tran, Kim Lien Thi Pham, Thai Son Nguyen, Hung Van Nguyen, Ngoc Lan Thi Nguyen, Nam Lien Thi Nguyen, Duc Anh Dang, Guy B. Marks and Marc Choisy

    Citation: BMC Microbiology 2016 16:167

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  47. Content type: Research article

    Biogenic sulfuric acid (BSA) corrosion damages sewerage and wastewater treatment facilities but is not well investigated in sludge digesters. Sulfur/sulfide oxidizing bacteria (SOB) oxidize sulfur compounds to...

    Authors: Bettina Huber, Bastian Herzog, Jörg E. Drewes, Konrad Koch and Elisabeth Müller

    Citation: BMC Microbiology 2016 16:153

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  48. Content type: Research article

    Multiple types of solid waste in developing countries is disposed of together in dumpsites where there is interaction between humans, animals and the bacteria in the waste. To study the bacteria at the dumpsit...

    Authors: Kilaza Samson Mwaikono, Solomon Maina, Aswathy Sebastian, Megan Schilling, Vivek Kapur and Paul Gwakisa

    Citation: BMC Microbiology 2016 16:145

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