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Ecological and evolutionary microbiology

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. The skin microbiome serves as a first line defense against pathogens in vertebrates. In amphibians, it has the potential to protect against the chytrid fungus Batrachochytrium dendrobatis (Bd), a likely agent of ...

    Authors: Randall R. Jiménez, Gilbert Alvarado, José Sandoval and Simone Sommer

    Citation: BMC Microbiology 2020 20:292

    Content type: Research article

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  2. Understanding the structure and drivers of gut microbiota remains a major ecological endeavour. Recent studies have shown that several factors including diet, lifestyle and geography may substantially shape th...

    Authors: Mubanga Hellen Kabwe, Surendra Vikram, Khodani Mulaudzi, Janet K. Jansson and Thulani P. Makhalanyane

    Citation: BMC Microbiology 2020 20:257

    Content type: Research article

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  3. Microbe-mediated redox transformation of arsenic (As) leading to its mobilization has become a serious environmental concern in various subsurface ecosystems especially within the alluvial aquifers. However, d...

    Authors: Soma Ghosh, Balaram Mohapatra, Tulasi Satyanarayana and Pinaki Sar

    Citation: BMC Microbiology 2020 20:256

    Content type: Research article

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  4. The contamination of the aquatic environment of urban rivers with industrial wastewater has affected the abiotic conditions and biological activities of the trophic levels of the ecosystem, particularly sedime...

    Authors: Lei Zhang, Demei Tu, Xingchen Li, Wenxuan Lu and Jing Li

    Citation: BMC Microbiology 2020 20:254

    Content type: Research article

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  5. Groundnut pre- and post-harvest contamination is commonly caused by fungi from the Genus Aspergillus. Aspergillus flavus is the most important of these fungi. It belongs to section Flavi; a group consisting of af...

    Authors: Amos Acur, Renée S. Arias, Steven Odongo, Samuel Tuhaise, Joseph Ssekandi, John Adriko, Dennis Muhanguzi, Stephen Buah and Andrew Kiggundu

    Citation: BMC Microbiology 2020 20:252

    Content type: Research article

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  6. Achlorophyllous orchids are mycoheterotrophic plants, which lack photosynthetic ability and associate with fungi to acquire carbon from different environmental sources. In tropical latitudes, achlorophyllous f...

    Authors: Lorenzo Pecoraro, Xiao Wang, Giuseppe Venturella, Wenyuan Gao, Tingchi Wen, Yusufjon Gafforov and Vijai Kumar Gupta

    Citation: BMC Microbiology 2020 20:236

    Content type: Research article

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  7. Staphylococci species are the major constituents of infectious bioaerosols, particularly methicillin-resistant Staphylococci (MRS) have serious health impacts. Here, the bacterial burden was quantified, especi...

    Authors: Himani Kumari, Trina Chakraborti, Madhuri Singh, Maneet Kumar Chakrawarti and Kasturi Mukhopadhyay

    Citation: BMC Microbiology 2020 20:211

    Content type: Research article

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  8. Shiga toxin-producing Escherichia coli (STEC) is a major source of food-borne illness around the world. E. coli O157 has been widely reported as the most common STEC serogroup and has emerged as an important ente...

    Authors: Dawood Al-Ajmi, Shafeeq Rahman and Sharmila Banu

    Citation: BMC Microbiology 2020 20:210

    Content type: Research article

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  9. Isolation of marine microorganisms is fundamental to gather information about their physiology, ecology and genomic content. To date, most of the bacterial isolation efforts have focused on the photic ocean le...

    Authors: Isabel Sanz-Sáez, Guillem Salazar, Pablo Sánchez, Elena Lara, Marta Royo-Llonch, Elisabet L. Sà, Teresa Lucena, María J. Pujalte, Dolors Vaqué, Carlos M. Duarte, Josep M. Gasol, Carlos Pedrós-Alió, Olga Sánchez and Silvia G. Acinas

    Citation: BMC Microbiology 2020 20:207

    Content type: Research article

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  10. The vertebrate gastrointestinal tract is colonised by microbiota that have a major effect on the host’s health, physiology and phenotype. Once introduced into captivity, however, the gut microbial composition ...

    Authors: Barbora Bendová, Jaroslav Piálek, Ľudovít Ďureje, Lucie Schmiedová, Dagmar Čížková, Jean-Francois Martin and Jakub Kreisinger

    Citation: BMC Microbiology 2020 20:194

    Content type: Research article

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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  41. 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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  42. 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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  43. 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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  44. 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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  45. 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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  46. 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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  47. 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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  48. 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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  49. 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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