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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. Wolbachia are the most widely spread endosymbiotic bacteria, present in a wide variety of insects and two families of nematodes. As of now, however, relatively little genomic data has been available. The Wolbachi...

    Authors: Emilie Lefoulon, Travis Clark, Fanni Borveto, Marco Perriat-Sanguinet, Catherine Moulia, Barton E. Slatko and Laurent Gavotte

    Citation: BMC Microbiology 2020 20:188

    Content type: Research article

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  2. Bats are hosts for a variety of microorganisms, however, little is known about the presence of Chlamydiales and hemotropic mycoplasmas. This study investigated 475 captive and free-living bats from Switzerland, G...

    Authors: Janine Fritschi, Hanna Marti, Helena M. B. Seth-Smith, Sébastien Aeby, Gilbert Greub, Marina L. Meli, Regina Hofmann-Lehmann, Kristin Mühldorfer, Nadine Stokar-Regenscheit, Danja Wiederkehr, Paola Pilo, Peggy Rüegg- Van Den Broek and Nicole Borel

    Citation: BMC Microbiology 2020 20:182

    Content type: Research article

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  3. Chikungunya (CHIKV), yellow fever (YFV) and Zika (ZIKV) viruses circulate in sylvatic transmission cycles in southeastern Senegal, where they share common hosts and vectors. All three viruses undergo periodic amp...

    Authors: Diawo Diallo, Gamou Fall, Cheikh Tidiane Diagne, Alioune Gaye, Yamar Ba, Ibrahima Dia, Ousmane Faye and Mawlouth Diallo

    Citation: BMC Microbiology 2020 20:181

    Content type: Research article

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  4. Bacteria adapted to live within animals can protect their hosts against harmful infections. Beyond antagonism with pathogens, a ‘defensive’ bacterial symbiont could engage in additional interactions with other...

    Authors: Dylan Dahan, Gail M. Preston, Jordan Sealey and Kayla C. King

    Citation: BMC Microbiology 2020 20:159

    Content type: Research article

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  5. Earthen sites are immobile cultural relics and an important part of cultural heritage with historical, artistic and scientific values. The deterioration of features in earthen sites result in permanent loss of...

    Authors: Jing Li, Xiaoyue Zhang, Lin Xiao, Ke Liu, Yue Li, Ziwei Zhang, Qiang Chen, Xiaolin Ao, Decong Liao, Yunfu Gu, Menggen Ma, Xiumei Yu, Quanju Xiang, Ji Chen, Xiaoping Zhang, Tao Yang…

    Citation: BMC Microbiology 2020 20:147

    Content type: Research article

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  6. Most lactobacilli found in animal intestines are generally non-motile, but there are few exceptions. Our previous work showed that Lactobacillus agilis BKN88, which is a highly motile strain originating from a ch...

    Authors: Shunya Suzuki, Koki Fujita, Shintaro Maeno, Yuh Shiwa, Akihito Endo, Kenji Yokota, Shizunobu Igimi and Akinobu Kajikawa

    Citation: BMC Microbiology 2020 20:142

    Content type: Research article

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  7. Karst caves are considered as extreme environments with nutrition deficiency, darkness, and oxygen deprivation, and they are also the sources of biodiversity and metabolic pathways. Microorganisms are usually ...

    Authors: Yiyi Dong, Jie Gao, Qingshan Wu, Yilang Ai, Yu Huang, Wenzhang Wei, Shiyu Sun and Qingbei Weng

    Citation: BMC Microbiology 2020 20:137

    Content type: Research article

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  8. Biodiversity and productivity of coral-reef ecosystems depend upon reef-building corals and their associations with endosymbiotic Symbiodiniaceae, which offer diverse functional capabilities to their hosts. The n...

    Authors: Timothy D. Swain, Simon Lax, Vadim Backman and Luisa A. Marcelino

    Citation: BMC Microbiology 2020 20:124

    Content type: Research article

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  9. To date, the microbiota of the human penis has been studied mostly in connection with circumcision, HIV risk and female partner bacterial vaginosis (BV). These studies have shown that male circumcision reduces...

    Authors: Harris Onywera, Anna-Lise Williamson, Luca Cozzuto, Sarah Bonnin, Zizipho Z. A. Mbulawa, David Coetzee, Julia Ponomarenko and Tracy L. Meiring

    Citation: BMC Microbiology 2020 20:78

    Content type: Research article

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  10. Neisseria meningitidis (N.meningitidis) bacteria belonging to clonal complex 4821 (CC4821) have been mainly reported in China and have been characterized by a high resistance rate to ciprofloxacin (CIP). The aim ...

    Authors: Pan Zhao, Li Xu, Aiyu Zhang, Bingqing Zhu and Zhujun Shao

    Citation: BMC Microbiology 2020 20:71

    Content type: Research article

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  11. Daqu, the saccharification, fermentation, and aroma-producing agents for Baijiu brewing, is prepared using a complex process. Aging is important for improving the quality of Daqu, but its impact has rarely been s...

    Authors: Guangsen Fan, Zhilei Fu, Chao Teng, Pengxiao Liu, Qiuhua Wu, Md Khondakar Raziur Rahman and Xiuting Li

    Citation: BMC Microbiology 2020 20:67

    Content type: Research article

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  12. Previous phylogenetic analyses of species within the genus Golovinomyces (Ascomycota, Erysiphales), based on ITS and 28S rDNA sequence data, revealed a co-evolutionary relationship between powdery mildew species ...

    Authors: Peng-Lei Qiu, Shu-Yan Liu, Michael Bradshaw, Suzanne Rooney-Latham, Susumu Takamatsu, Timur S. Bulgakov, Shu-Rong Tang, Jing Feng, Dan-Ni Jin, Temitope Aroge, Yu Li, Li-Lan Wang and Uwe Braun

    Citation: BMC Microbiology 2020 20:51

    Content type: Research article

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  13. Quinolone resistant Escherichia coli (QREC) have been found in samples from Norwegian broiler chicken, despite quinolones not being administered to poultry in Norway. Biofilm production may be one factor contribu...

    Authors: Live L. Nesse, Ane Mohr Osland, Solveig S. Mo, Camilla Sekse, Jannice S. Slettemeås, Anna Eline E. Bruvoll, Anne Margrete Urdahl and Lene K. Vestby

    Citation: BMC Microbiology 2020 20:46

    Content type: Research article

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  14. Production of antibiotics to inhibit competitors affects soil microbial community composition and contributes to disease suppression. In this work, we characterized whether Streptomyces bacteria, prolific antibio...

    Authors: Mohamed E. Hamid, Thomas Reitz, Martin R. P. Joseph, Kerstin Hommel, Adil Mahgoub, Mogahid M. Elhassan, François Buscot and Mika Tarkka

    Citation: BMC Microbiology 2020 20:33

    Content type: Research article

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  15. Many recent studies have gravitated towards manipulating the gastrointestinal (GI) microbiome of livestock to improve host nutrition and health using dietary interventions. Few studies, however, have evaluated...

    Authors: Shaobo Yu, Guangyu Zhang, Zhibo Liu, Peng Wu, Zhongtang Yu and Jiakun Wang

    Citation: BMC Microbiology 2020 20:29

    Content type: Research article

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  16. Amplification of small subunit (SSU) rRNA genes with universal primers is a common method used to assess microbial populations in various environmental samples. However, owing to limitations in coverage of the...

    Authors: Ru-Yi Zhang, Bin Zou, Yong-Wei Yan, Che Ok Jeon, Meng Li, Mingwei Cai and Zhe-Xue Quan

    Citation: BMC Microbiology 2020 20:25

    Content type: Methodology article

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  17. Coagulase-negative staphylococci (CoNS) are a group of opportunistic pathogens, which are widely spread in the environment. Animal breeding is an important source of pathogen spreading. However, the concentrat...

    Authors: Yuanqing Lu, Qin Lu, Yiluo Cheng, Guoyuan Wen, Qingping Luo, Huabin Shao and Tengfei Zhang

    Citation: BMC Microbiology 2020 20:21

    Content type: Research article

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  18. The total bacterial community plays an important role in aquatic ecosystems. In this study, bacterial communities and diversity along the shores of the Upper Gulf of Thailand were first characterized. The asso...

    Authors: Pongrawee Nimnoi and Neelawan Pongsilp

    Citation: BMC Microbiology 2020 20:19

    Content type: Research article

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  19. Understanding the patterns of species richness across elevational gradients is a key concept for contemporary research in ecology and evolution, and critical to understanding large-scale trends in biodiversity...

    Authors: Wei Deng, Jia-Liang Wang, Matthew B. Scott, Yi-Hao Fang, Shuo-Ran Liu, Xiao-Yan Yang and Wen Xiao

    Citation: BMC Microbiology 2020 20:15

    Content type: Research article

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  20. Cronobacter sakazakii is an emerging opportunistic bacterial pathogen known to cause neonatal and pediatric infections, including meningitis, necrotizing enterocolitis, and bacteremia. Multiple disease outbreaks ...

    Authors: Isaiah Paolo A. Lee and Cheryl P. Andam

    Citation: BMC Microbiology 2019 19:306

    Content type: Research article

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  21. In modern lifestyles, people make their everyday tasks easier by using household appliances, for example dishwashers. Previous studies showed massive contamination of dishwasher rubber seals with fungi, thus b...

    Authors: Jerneja Zupančič, Martina Turk, Miha Črnigoj, Jerneja Ambrožič Avguštin and Nina Gunde-Cimerman

    Citation: BMC Microbiology 2019 19:300

    Content type: Research article

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  22. Listeria monocytogenes is the causative agent of listeriosis, a serious disease affecting both animals and humans. Here, multilocus sequence typing (MLST) was used to characterize the genetic diversity of Listeri...

    Authors: Bojan Papić, Mateja Pate, Benjamin Félix and Darja Kušar

    Citation: BMC Microbiology 2019 19:299

    Content type: Research article

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  23. The complete genome sequences of 44 Bacillus cereus group isolates collected from diverse sources in Japan were analyzed to determine their genetic backgrounds and diversity levels in Japan. Multilocus sequence t...

    Authors: Akiko Okutani, Satoshi Inoue, Akira Noguchi, Yoshihiro Kaku and Shigeru Morikawa

    Citation: BMC Microbiology 2019 19:296

    Content type: Research article

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  24. Due to its rapid lethal effect in the early development stage of shrimp, acute hepatopancreatic necrosis disease (AHPND) has been causing great economic losses, since its first outbreak in southeast China in 2...

    Authors: Shawon Ahmmed, Md. Abdullah-Al-Kamran Khan, Md. Mostavi Enan Eshik, Nusrat Jahan Punom, Abul Bashar Mir Md. Khademul Islam and Mohammad Shamsur Rahman

    Citation: BMC Microbiology 2019 19:270

    Content type: Research article

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  25. Diet is a major determinant of bacterial community structure in termite guts, but evidence of its importance in the closely related cockroaches is conflicting. Here, we investigated the ecological drivers of t...

    Authors: Niclas Lampert, Aram Mikaelyan and Andreas Brune

    Citation: BMC Microbiology 2019 19:238

    Content type: Research article

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  26. Recent studies demonstrated that warming and elevated carbon dioxide (CO2) indirectly affect the soil microbial community structure via plant root exudates. However, there is no direct evidence for how the root e...

    Authors: Jiahui Wu and Shixiao Yu

    Citation: BMC Microbiology 2019 19:224

    Content type: Research article

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  27. 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

    Content type: Research article

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  28. 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

    Content type: Research article

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  29. 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

    Content type: Research article

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  30. 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

    Content type: Research article

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  31. 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

    Content type: Research article

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  32. 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

    Content type: Research article

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  33. 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

    Content type: Research article

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  34. 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

    Content type: Research article

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  35. 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

    Content type: Research article

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  36. 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

    Content type: Research article

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  37. 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

    Content type: Research article

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  38. 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

    Content type: Research article

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  39. 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

    Content type: Research article

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  40. 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

    Content type: Research article

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  41. 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

    Content type: Research article

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  42. 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

    Content type: Research article

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  43. 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

    Content type: Research article

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  44. 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

    Content type: Research article

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  45. 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

    Content type: Research article

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  46. 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

    Content type: Research article

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  47. 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

    Content type: Database

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  48. 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

    Content type: Research article

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