Skip to main content


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.

Page 1 of 5

  1. Content type: Research article

    The decomposition of Microcystis can dramatically change the physicochemical properties of freshwater ecosystems. Bacteria play an important role in decomposing organic matters and accelerating the cycling of mat...

    Authors: Shuren Wang, Dayong Zhao, Jin Zeng, Huimin Xu, Rui Huang, Congcong Jiao and Lin Guo

    Citation: BMC Microbiology 2019 19:207

    Published on:

  2. Content type: Research article

    Cross-resistance, a phenomenon that a pathogen resists to one antimicrobial compound also resists to one or several other compounds, is one of major threats to human health and sustainable food production. It ...

    Authors: Li-Na Yang, Meng-Han He, Hai-Bing Ouyang, Wen Zhu, Zhe-Chao Pan, Qi-Jun Sui, Li-Ping Shang and Jiasui Zhan

    Citation: BMC Microbiology 2019 19:205

    Published on:

  3. Content type: Research article

    Microbial community and its management are crucial to the stabilization of culture environment for recirculating aquaculture system (RAS). Although several studies have been carried out for the microbial commu...

    Authors: Zhao Chen, Zhiqiang Chang, Long Zhang, Yuli Jiang, Hongxing Ge, Xiefa Song, Shibo Chen, Fazhen Zhao and Jian Li

    Citation: BMC Microbiology 2019 19:192

    Published on:

  4. Content type: Research article

    Holobionts comprising nitrogen-fixing diazotrophs and phytoplankton or zooplankton are ubiquitous in the pelagic sea. However, neither the community structure of plankton-associated diazotrophs (PADs) nor thei...

    Authors: Qing-Song Yang, Jun-De Dong, Manzoor Ahmad, Juan Ling, Wei-Guo Zhou, Ye-Hui Tan, Yuan-Zhou Zhang, Dan-Dan Shen and Yan-Ying Zhang

    Citation: BMC Microbiology 2019 19:188

    Published on:

  5. Content type: Research article

    Helicobacter pylori recurrence after successful eradication is an important problem. Children are particularly vulnerable to reinfection, by intrafamilial transmission which facilitates the acquisition or recombi...

    Authors: Sandra Mendoza-Elizalde, Ana Caren Cortés-Márquez, Gerardo Zuñiga, René Cerritos, Pedro Valencia-Mayoral, Alejandra Consuelo Sánchez, Hector Olivares-Clavijo and Norma Velázquez-Guadarrama

    Citation: BMC Microbiology 2019 19:184

    Published on:

  6. Content type: Research article

    Endophytic Fungi (EF) are an underexplored group of microorganisms as only a few plants have been studied with regards to their community. Diversity of EF found in young and old leaves of Enset plant has not b...

    Authors: Nitin M. Chauhan, Abdissa D. Gutama and Afras Aysa

    Citation: BMC Microbiology 2019 19:172

    Published on:

  7. Content type: Research article

    Anthrax is a zoonotic disease caused by the Gram-positive bacterium Bacillus anthracis. In Russia, there are more than 35 thousand anthrax stationary unfavourable sites. At the same time, there is very little pub...

    Authors: Sergey V. Pisarenko, Eugene I. Eremenko, Alla G. Ryazanova, Dmitry A. Kovalev, Nina P. Buravtseva, Lyudmila Yu. Aksenova, Anna Yu. Evchenko, Olga V. Semenova, Olga V. Bobrisheva, Irina V. Kuznetsova, Tatyana M. Golovinskaya, Dmitriy K. Tchmerenko, Alexander N. Kulichenko and Vitaliy Yu. Morozov

    Citation: BMC Microbiology 2019 19:165

    Published on:

  8. Content type: Research article

    Gastrodia elata is a widely distributed achlorophyllous orchid and is highly valued as both medicine and food. Gastrodia elata produces dust-like seeds and relies on mycorrhizal fungi for its germination and grow...

    Authors: Lin Chen, Yu-Chuan Wang, Li-Yuan Qin, Hai-Yan He, Xian-Lun Yu, Ming-Zhi Yang and Han-Bo Zhang

    Citation: BMC Microbiology 2019 19:158

    Published on:

  9. Content type: Research article

    We used genetic Multi-Locus VNTR Analysis (MLVA) data gathered from surveillance efforts to better understand the ongoing bovine tuberculosis (bTB) epidemic in Northern Irish cattle herds. We modelled the fact...

    Authors: M. G. Milne, J. Graham, A. Allen, C. McCormick, E. Presho, R. Skuce and A. W. Byrne

    Citation: BMC Microbiology 2019 19:154

    Published on:

  10. Content type: Research article

    Due to the cave oligotrophic environment, this habitat presents a challenge for microorganisms to colonize and thrive. However, it has been well documented that microorganisms play important roles in cave deve...

    Authors: Apirak Wiseschart, Wuttichai Mhuantong, Sithichoke Tangphatsornruang, Duriya Chantasingh and Kusol Pootanakit

    Citation: BMC Microbiology 2019 19:144

    Published on:

  11. Content type: Research article

    In nature, microorganisms have to adapt to long-term stressful conditions often with growth limitations. However, little is known about the evolution of the adaptability of new bacteria to such environments. Pseu...

    Authors: Hamouda Elabed, Enrique González-Tortuero, Claudia Ibacache-Quiroga, Amina Bakhrouf, Paul Johnston, Kamel Gaddour, Jesús Blázquez and Alexandro Rodríguez-Rojas

    Citation: BMC Microbiology 2019 19:142

    Published on:

  12. Content type: Research article

    Actinobacteria are famous for the production of unique secondary metabolites that help in controlling the continuously emerging drug resistance all over the globe. This study aimed at the investigation of an e...

    Authors: Adeela Fatima, Usman Aftab, Khaled A. Shaaban, Jon S. Thorson and Imran Sajid

    Citation: BMC Microbiology 2019 19:49

    Published on:

  13. Content type: Research article

    The importance of the gut microbiota at the early stage of life and their longitudinal effect on host health have recently been well investigated. In particular, Bifidobacterium longum subsp. longum, a common com...

    Authors: Kaihei Oki, Takuya Akiyama, Kazunori Matsuda, Agata Gawad, Hiroshi Makino, Eiji Ishikawa, Kenji Oishi, Akira Kushiro and Junji Fujimoto

    Citation: BMC Microbiology 2018 18:209

    Published on:

  14. Content type: Research article

    Understanding the recovery of bacterial communities after extreme environmental disturbances offers key opportunities to investigate ecosystem resilience. However, it is not yet clear whether bacterial communi...

    Authors: Yang Hu, Chengrong Bai, Jian Cai, Keqiang Shao, Xiangming Tang and Guang Gao

    Citation: BMC Microbiology 2018 18:195

    Published on:

  15. Content type: Research article

    Pectin is one of the major and most complex plant cell wall components that needs to be overcome by microorganisms as part of their strategies for plant invasion or nutrition. Microbial pectinolytic enzymes th...

    Authors: Lea Atanasova, Mukesh Dubey, Marica Grujić, Mikael Gudmundsson, Cindy Lorenz, Mats Sandgren, Christian P. Kubicek, Dan Funck Jensen and Magnus Karlsson

    Citation: BMC Microbiology 2018 18:178

    Published on:

  16. Content type: Research article

    The airways of the majority of adolescent cystic fibrosis (CF) patients are persistently colonized or infected by Staphylococcus aureus. Using whole genome sequencing, we studied the evolutionary traits within a

    Authors: Lars Langhanki, Petya Berger, Janina Treffon, Francesco Catania, Barbara C. Kahl and Alexander Mellmann

    Citation: BMC Microbiology 2018 18:152

    Published on:

  17. Content type: Research article

    Free-living amoeba (FLA) are wide-spread protozoa that are found in different environmental sources including water, soil, dust, hospital units and ventilation areas. These amoebas can act as opportunistic or ...

    Authors: Shiva Ghaderifar, Ali Asghar Najafpoor, Hossein Zarrinfar, Habibollah Esmaily and Elham Hajialilo

    Citation: BMC Microbiology 2018 18:139

    Published on:

  18. Content type: Research article

    Ganzi Prefecture in Western China is situated geographically at the transition regions between Tibetan Plateau and Sichuan Basin in a highly tectonically active boundary area between the India and Eurasia plat...

    Authors: Jie Tang, Yuanmei Liang, Dong Jiang, Liheng Li, Yifan Luo, Md. Mahfuzur R. Shah and Maurycy Daroch

    Citation: BMC Microbiology 2018 18:134

    Published on:

  19. Content type: Research article

    The presence of microrganisms in pharmaceutical production plant environments is typically monitored by cultural methods, however these cannot detect the unculturable fraction of the microbial community. To ge...

    Authors: Filippo Pacchioni, Alfonso Esposito, Elisabetta Giacobazzi, Clotilde Bettua, Paolo Struffi and Olivier Jousson

    Citation: BMC Microbiology 2018 18:124

    Published on:

  20. Content type: Research article

    Basalt is the most common igneous rock on the Earth’s surface covering. Basalt-associated microorganisms drive the cycling and sequestration of different elements such as nitrogen, carbon and other nutrients, ...

    Authors: Bo Byloos, Pieter Monsieurs, Mohamed Mysara, Natalie Leys, Nico Boon and Rob Van Houdt

    Citation: BMC Microbiology 2018 18:122

    Published on:

  21. 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

    Published on:

  22. 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

    Published on:

  23. 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

    Published on:

  24. 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

    Published on:

  25. 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

    Published on:

  26. 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

    Published on:

  27. 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

    Published on:

  28. 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

    Published on:

  29. 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

    Published on:

  30. 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

    Published on:

  31. 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

    Published on:

  32. 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

    Published on:

  33. 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

    Published on:

  34. 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

    Published on:

  35. 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

    Published on:

  36. 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

    Published on:

  37. 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

    Published on:

  38. 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

    Published on:

  39. 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

    Published on:

  40. 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

    Published on:

  41. 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

    Published on:

  42. 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

    Published on:

  43. 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

    Published on:

  44. 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

    Published on:

  45. 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

    Published on:

  46. 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

    Published on:

  47. 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

    Published on:

  48. 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

    Published on: