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  1. Polymyxin is a cationic polypeptide antibiotic that can disrupt bacterial cell membrane by interacting with its lipopolysaccharide molecules and is used as a last resort drug against lethal infections by the c...

    Authors: Qingjing Wang, Jian Sun, Jun Li, Youfa Ding, Xing-Ping Li, Jingxia Lin, Bachar Hassan and Youjun Feng
    Citation: Microbiome 2017 5:70
    Content type: Research Published on:

  2. Advances in sequencing technologies and bioinformatics have made the analysis of microbial communities almost routine. Nonetheless, the need remains to improve on the techniques used for gathering such data, i...

    Authors: Eric J. de Muinck, Pål Trosvik, Gregor D. Gilfillan, Johannes R. Hov and Arvind Y. M. Sundaram
    Citation: Microbiome 2017 5:68
    Content type: Methodology Published on:

  3. Progressive, chronic bacterial infection of the airways is a leading cause of death in cystic fibrosis (CF). Culture-independent methods based on sequencing of the bacterial 16S rRNA gene describe a distinct m...

    Authors: Vaishnavi Narayanamurthy, John M. Sweetnam, Darcy R. Denner, Lena W. Chen, Edward T. Naureckas, Bharathi Laxman and Steven R. White
    Citation: Microbiome 2017 5:67
    Content type: Short report Published on:

  4. The correct establishment of the human gut microbiota represents a crucial development that commences at birth. Different hypotheses propose that the infant gut microbiota is derived from, among other sources,...

    Authors: Sabrina Duranti, Gabriele Andrea Lugli, Leonardo Mancabelli, Federica Armanini, Francesca Turroni, Kieran James, Pamela Ferretti, Valentina Gorfer, Chiara Ferrario, Christian Milani, Marta Mangifesta, Rosaria Anzalone, Moreno Zolfo, Alice Viappiani, Edoardo Pasolli, Ilaria Bariletti…
    Citation: Microbiome 2017 5:66
    Content type: Research Published on:

  5. The circadian clock regulates plant metabolic functions and is an important component in plant health and productivity. Rhizosphere bacteria play critical roles in plant growth, health, and development and are...

    Authors: Christopher Staley, Abigail P. Ferrieri, Malak M. Tfaily, Yaya Cui, Rosalie K. Chu, Ping Wang, Jared B. Shaw, Charles K. Ansong, Heather Brewer, Angela D. Norbeck, Meng Markillie, Fernanda do Amaral, Thalita Tuleski, Tomás Pellizzaro, Beverly Agtuca, Richard Ferrieri…
    Citation: Microbiome 2017 5:65
    Content type: Research Published on:

  7. Perturbation of commensal intestinal microbiota has been associated with several autoimmune diseases. Mice deficient in interleukin-1 receptor antagonist (Il1rn −/− mice) spontaneously ...

    Authors: Rebecca Rogier, Thomas H. A. Ederveen, Jos Boekhorst, Harm Wopereis, Jose U. Scher, Julia Manasson, Sanne J. C. M. Frambach, Jan Knol, Johan Garssen, Peter M. van der Kraan, Marije I. Koenders, Wim B. van den Berg, Sacha A. F. T. van Hijum and Shahla Abdollahi-Roodsaz
    Citation: Microbiome 2017 5:63
    Content type: Research Published on:

  8. Although culture-independent methods have paved the way for characterization of the lung microbiome, the dynamic changes in the lung microbiome from neonatal stage to adult age have not been investigated.

    Authors: Nisha Singh, Asheema Vats, Aditi Sharma, Amit Arora and Ashwani Kumar
    Citation: Microbiome 2017 5:61
    Content type: Research Published on:

    The Erratum to this article has been published in Microbiome 2017 5:124

  9. Grazing mammals rely on their ruminal microbial symbionts to convert plant structural biomass into metabolites they can assimilate. To explore how this complex metabolic system adapts to the host animal’s diet...

    Authors: Sara M. Wolff, Melinda J. Ellison, Yue Hao, Rebecca R. Cockrum, Kathy J. Austin, Michael Baraboo, Katherine Burch, Hyuk Jin Lee, Taylor Maurer, Rocky Patil, Andrea Ravelo, Tasia M. Taxis, Huan Truong, William R. Lamberson, Kristi M. Cammack and Gavin C. Conant
    Citation: Microbiome 2017 5:60
    Content type: Research Published on:

  10. Recent studies highlight the utility of quantitative trait locus (QTL) mapping for determining the contribution of host genetics to interindividual variation in the microbiota. We previously demonstrated that ...

    Authors: Meriem Belheouane, Yask Gupta, Sven Künzel, Saleh Ibrahim and John F. Baines
    Citation: Microbiome 2017 5:59
    Content type: Research Published on:

  11. Obligate bacterial primary (P-) endosymbionts that are maternally inherited and codiverge with hosts are widespread across insect lineages with nutritionally restricted diets. Secondary (S-) endosymbionts are ...

    Authors: Jennifer L. Morrow, Aidan A. G. Hall and Markus Riegler
    Citation: Microbiome 2017 5:58
    Content type: Research Published on:

  12. Bacteriophage–prokaryote dynamics and interaction are believed to be important in governing microbiome composition and ecosystem functions, yet our limited knowledge of the spatial and temporal variation in ph...

    Authors: Junyu Zhang, Qun Gao, Qiuting Zhang, Tengxu Wang, Haowei Yue, Linwei Wu, Jason Shi, Ziyan Qin, Jizhong Zhou, Jiane Zuo and Yunfeng Yang
    Citation: Microbiome 2017 5:57
    Content type: Research Published on:

  13. Interactions between pathogenic oomycetes and microbiota residing on the surface of the host plant root are unknown, despite being critical to inoculum constitution. The nature of these interactions was explor...

    Authors: Marie Larousse, Corinne Rancurel, Camille Syska, Ferran Palero, Catherine Etienne, Benoît Industri, Xavier Nesme, Marc Bardin and Eric Galiana
    Citation: Microbiome 2017 5:56
    Content type: Research Published on:

  14. Gut microbiota play a key role in maintaining homeostasis in the human gut. Alterations in the gut microbial ecosystem predispose to Clostridium difficile infection (CDI) and gut inflammatory disorders such as in...

    Authors: Sahil Khanna, Yoshiki Vazquez-Baeza, Antonio González, Sophie Weiss, Bradley Schmidt, David A. Muñiz-Pedrogo, John F. Rainey III, Patricia Kammer, Heidi Nelson, Michael Sadowsky, Alexander Khoruts, Stefan L. Farrugia, Rob Knight, Darrell S. Pardi and Purna C. Kashyap
    Citation: Microbiome 2017 5:55
    Content type: Report Published on:

  16. Chronic rhinosinusitis (CRS) is a heterogeneous disease characterized by persistent sinonasal inflammation and sinus microbiome dysbiosis. The basis of this heterogeneity is poorly understood. We sought to add...

    Authors: Emily K. Cope, Andrew N. Goldberg, Steven D. Pletcher and Susan V. Lynch
    Citation: Microbiome 2017 5:53
    Content type: Research Published on:

  17. Research on the human microbiome has yielded numerous insights into health and disease, but also has resulted in a wealth of experimental artifacts. Here, we present suggestions for optimizing experimental des...

    Authors: Dorothy Kim, Casey E. Hofstaedter, Chunyu Zhao, Lisa Mattei, Ceylan Tanes, Erik Clarke, Abigail Lauder, Scott Sherrill-Mix, Christel Chehoud, Judith Kelsen, Máire Conrad, Ronald G. Collman, Robert Baldassano, Frederic D. Bushman and Kyle Bittinger
    Citation: Microbiome 2017 5:52
    Content type: Review Published on:

  18. Aztreonam lysine for inhalation (AZLI) is an inhaled antibiotic used to treat chronic Pseudomonas aeruginosa infection in CF. AZLI improves lung function and quality of life, and reduces exacerbations-improvement...

    Authors: Alya A. Heirali, Matthew L. Workentine, Nicole Acosta, Ali Poonja, Douglas G. Storey, Ranjani Somayaji, Harvey R. Rabin, Fiona J. Whelan, Michael G. Surette and Michael D. Parkins
    Citation: Microbiome 2017 5:51
    Content type: Research Published on:

  19. Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection and shows promise for treating other medical conditions associated with intestinal dysbioses. However...

    Authors: Sonny T. M. Lee, Stacy A. Kahn, Tom O. Delmont, Alon Shaiber, Özcan C. Esen, Nathaniel A. Hubert, Hilary G. Morrison, Dionysios A. Antonopoulos, David T. Rubin and A. Murat Eren
    Citation: Microbiome 2017 5:50
    Content type: Research Published on:

  20. Preclinical and clinical evidence supports the concept of bidirectional brain-gut microbiome interactions. We aimed to determine if subgroups of irritable bowel syndrome (IBS) subjects can be identified based ...

    Authors: Jennifer S. Labus, Emily B. Hollister, Jonathan Jacobs, Kyleigh Kirbach, Numan Oezguen, Arpana Gupta, Jonathan Acosta, Ruth Ann Luna, Kjersti Aagaard, James Versalovic, Tor Savidge, Elaine Hsiao, Kirsten Tillisch and Emeran A. Mayer
    Citation: Microbiome 2017 5:49
    Content type: Research Published on:

  21. After more than a century of active research, the notion that the human fetal environment is sterile and that the neonate’s microbiome is acquired during and after birth was an accepted dogma. However, recent ...

    Authors: Maria Elisa Perez-Muñoz, Marie-Claire Arrieta, Amanda E. Ramer-Tait and Jens Walter
    Citation: Microbiome 2017 5:48
    Content type: Review Published on:

  22. Salmonella is one of the most significant food-borne pathogens to affect humans and agriculture. While it is well documented that Salmonella infection triggers host inflammation, the i...

    Authors: Mikayla A. Borton, Anice Sabag-Daigle, Jikang Wu, Lindsey M. Solden, Bridget S. O’Banion, Rebecca A. Daly, Richard A. Wolfe, Juan F. Gonzalez, Vicki H. Wysocki, Brian M. M. Ahmer and Kelly C. Wrighton
    Citation: Microbiome 2017 5:47
    Content type: Research Published on:

  23. Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is characterized by unexplained persistent fatigue, commonly accompanied by cognitive dysfunction, sleeping disturbances, orthostatic intolerance, fe...

    Authors: Dorottya Nagy-Szakal, Brent L. Williams, Nischay Mishra, Xiaoyu Che, Bohyun Lee, Lucinda Bateman, Nancy G. Klimas, Anthony L. Komaroff, Susan Levine, Jose G. Montoya, Daniel L. Peterson, Devi Ramanan, Komal Jain, Meredith L. Eddy, Mady Hornig and W. Ian Lipkin
    Citation: Microbiome 2017 5:44
    Content type: Research Published on:

  24. IL-17-producing γδT cells (γδT17) promote autoinflammatory diseases and cancers. Yet, γδT17 peripheral regulation has not been thoroughly explored especially in the context of microbiota-host interaction. The ...

    Authors: Chris Fleming, Yihua Cai, Xuan Sun, Venkatakrishna R. Jala, Feng Xue, Samantha Morrissey, Yu-ling Wei, Yueh-hsiu Chien, Huang-ge Zhang, Bodduluri Haribabu, Jian Huang and Jun Yan
    Citation: Microbiome 2017 5:46
    Content type: Research Published on:

  25. The role of the microbiota in human health and disease has been increasingly studied, gathering momentum through the use of high-throughput technologies. Further identification of the roles of specific microbe...

    Authors: Hyunwook Koh, Martin J. Blaser and Huilin Li
    Citation: Microbiome 2017 5:45
    Content type: Methodology Published on:

  26. It is well known that the microbiota of high-fat (HF) diet-induced obese mice differs from that of lean mice, but to what extent, this difference reflects the obese state or the diet is unclear. To dissociate ...

    Authors: Liang Xiao, Si Brask Sonne, Qiang Feng, Ning Chen, Zhongkui Xia, Xiaoping Li, Zhiwei Fang, Dongya Zhang, Even Fjære, Lisa Kolden Midtbø, Muriel Derrien, Floor Hugenholtz, Longqing Tang, Junhua Li, Jianfeng Zhang, Chuan Liu…
    Citation: Microbiome 2017 5:43
    Content type: Research Published on:

  28. Lake sediments harbor diverse microbial communities that cycle carbon and nutrients while being constantly colonized and potentially buried by organic matter sinking from the water column. The interaction of a...

    Authors: Christian Wurzbacher, Andrea Fuchs, Katrin Attermeyer, Katharina Frindte, Hans-Peter Grossart, Michael Hupfer, Peter Casper and Michael T. Monaghan
    Citation: Microbiome 2017 5:41
    Content type: Research Published on:

  29. Early-life exposure to household pets has the capacity to reduce risk for overweight and allergic disease, especially following caesarean delivery. Since there is some evidence that pets also alter the gut mic...

    Authors: Hein M. Tun, Theodore Konya, Tim K. Takaro, Jeffrey R. Brook, Radha Chari, Catherine J. Field, David S. Guttman, Allan B. Becker, Piush J. Mandhane, Stuart E. Turvey, Padmaja Subbarao, Malcolm R. Sears, James A. Scott and Anita L. Kozyrskyj
    Citation: Microbiome 2017 5:40
    Content type: Research Published on:

  30. The intestinal microbial communities and their temporal dynamics are gaining increasing interest due to the significant implications for human health. Recent studies have shown the dynamic behavior of the gut ...

    Authors: Silvia Turroni, Simone Rampelli, Elena Biagi, Clarissa Consolandi, Marco Severgnini, Clelia Peano, Sara Quercia, Matteo Soverini, Franck G. Carbonero, Giovanna Bianconi, Petra Rettberg, Francesco Canganella, Patrizia Brigidi and Marco Candela
    Citation: Microbiome 2017 5:39
    Content type: Research Published on:

  31. Symbiosis is a phenomenon that allows organisms to colonise a wide range of environments and occupy a variety of ecological niches in marine environments. Large benthic foraminifera (LBF) are crucial marine ca...

    Authors: Martina Prazeres, Tracy Ainsworth, T. Edward Roberts, John M. Pandolfi and William Leggat
    Citation: Microbiome 2017 5:38
    Content type: Research Published on:

  32. Deep terrestrial biosphere waters are separated from the light-driven surface by the time required to percolate to the subsurface. Despite biofilms being the dominant form of microbial life in many natural env...

    Authors: Xiaofen Wu, Karsten Pedersen, Johanna Edlund, Lena Eriksson, Mats Åström, Anders F. Andersson, Stefan Bertilsson and Mark Dopson
    Citation: Microbiome 2017 5:37
    Content type: Research Published on:

  34. Adult survivors of childhood cancers such as acute lymphoblastic leukemia (ALL) have health problems that persist or develop years after cessation of therapy. These late effects include chronic inflammation-re...

    Authors: Ling Ling Chua, Reena Rajasuriar, Mohamad Shafiq Azanan, Noor Kamila Abdullah, Mei San Tang, Soo Ching Lee, Yin Ling Woo, Yvonne Ai Lian Lim, Hany Ariffin and P’ng Loke
    Citation: Microbiome 2017 5:35
    Content type: Research Published on:

  35. Periodontitis results from the interaction between a subgingival biofilm and host immune response. Changes in biofilm composition are thought to disrupt homeostasis between the host and subgingival bacteria re...

    Authors: Jôice Dias Corrêa, Débora Cerqueira Calderaro, Gilda Aparecida Ferreira, Santuza Maria Souza Mendonça, Gabriel R. Fernandes, E. Xiao, Antônio Lúcio Teixeira, Eugene J. Leys, Dana T. Graves and Tarcília Aparecida Silva
    Citation: Microbiome 2017 5:34
    Content type: Research Published on:

  37. There is strong evidence indicating that gut microbiota have the potential to modify, or be modified by the drugs and nutritional interventions that we rely upon. This study aims to characterize the compositio...

    Authors: Paul M. Ryan, Lis E. E. London, Trent C. Bjorndahl, Rupasri Mandal, Kiera Murphy, Gerald F. Fitzgerald, Fergus Shanahan, R. Paul Ross, David S. Wishart, Noel M. Caplice and Catherine Stanton
    Citation: Microbiome 2017 5:30
    Content type: Research Published on:

  38. A critical aspect regarding the global dispersion of pathogenic microorganisms is associated with atmospheric movement of soil particles. Especially, desert dust storms can transport alien microorganisms over ...

    Authors: Tobias Weil, Carlotta De Filippo, Davide Albanese, Claudio Donati, Massimo Pindo, Lorenzo Pavarini, Federico Carotenuto, Massimiliano Pasqui, Luisa Poto, Jacopo Gabrieli, Carlo Barbante, Birgit Sattler, Duccio Cavalieri and Franco Miglietta
    Citation: Microbiome 2017 5:32
    Content type: Research Published on:

  39. Necrotizing enterocolitis (NEC) is a catastrophic disease of preterm infants, and microbial dysbiosis has been implicated in its pathogenesis. Studies evaluating the microbiome in NEC and preterm infants lack ...

    Authors: Mohan Pammi, Julia Cope, Phillip I. Tarr, Barbara B. Warner, Ardythe L. Morrow, Volker Mai, Katherine E. Gregory, J. Simon Kroll, Valerie McMurtry, Michael J Ferris, Lars Engstrand, Helene Engstrand Lilja, Emily B. Hollister, James Versalovic and Josef Neu
    Citation: Microbiome 2017 5:31
    Content type: Review Published on:

  41. Bacterial biocatalysts play a key role in our transition to a bio-based, post-petroleum economy. However, the discovery of new biocatalysts is currently limited by our ability to analyze genomic information an...

    Authors: Premankur Sukul, Sina Schäkermann, Julia E. Bandow, Anna Kusnezowa, Minou Nowrousian and Lars I. Leichert
    Citation: Microbiome 2017 5:28
    Content type: Short report Published on:

  42. Data from 16S ribosomal RNA (rRNA) amplicon sequencing present challenges to ecological and statistical interpretation. In particular, library sizes often vary over several ranges of magnitude, and the data co...

    Authors: Sophie Weiss, Zhenjiang Zech Xu, Shyamal Peddada, Amnon Amir, Kyle Bittinger, Antonio Gonzalez, Catherine Lozupone, Jesse R. Zaneveld, Yoshiki Vázquez-Baeza, Amanda Birmingham, Embriette R. Hyde and Rob Knight
    Citation: Microbiome 2017 5:27
    Content type: Research Published on:

  43. Children with high body mass index (BMI) at preschool age are at risk of developing obesity. Early identification of factors that increase the risk of excessive weight gain could help direct preventive actions...

    Authors: K. Korpela, M. A. C. Zijlmans, M. Kuitunen, K. Kukkonen, E. Savilahti, A. Salonen, C. de Weerth and W. M. de Vos
    Citation: Microbiome 2017 5:26
    Content type: Research Published on:

  44. The plant microbiome represents one of the key determinants of plant health and productivity by providing a plethora of functional capacities such as access to low-abundance nutrients, suppression of phytopath...

    Authors: Bram Beckers, Michiel Op De Beeck, Nele Weyens, Wout Boerjan and Jaco Vangronsveld
    Citation: Microbiome 2017 5:25
    Content type: Research Published on:

  45. Autism spectrum disorders (ASDs) are neurodevelopmental conditions characterized by social and behavioural impairments. In addition to neurological symptoms, ASD subjects frequently suffer from gastrointestina...

    Authors: Francesco Strati, Duccio Cavalieri, Davide Albanese, Claudio De Felice, Claudio Donati, Joussef Hayek, Olivier Jousson, Silvia Leoncini, Daniela Renzi, Antonio Calabrò and Carlotta De Filippo
    Citation: Microbiome 2017 5:24
    Content type: Research Published on:

  47. There is a paucity of data regarding the microbial constituents of tobacco products and their impacts on public health. Moreover, there has been no comparative characterization performed on the bacterial micro...

    Authors: Jessica Chopyk, Suhana Chattopadhyay, Prachi Kulkarni, Emma Claye, Kelsey R. Babik, Molly C. Reid, Eoghan M. Smyth, Lauren E. Hittle, Joseph N. Paulson, Raul Cruz-Cano, Mihai Pop, Stephanie S. Buehler, Pamela I. Clark, Amy R. Sapkota and Emmanuel F. Mongodin
    Citation: Microbiome 2017 5:22
    Content type: Research Published on:

  48. Authors: Cian J. Hill, Denise B. Lynch, Kiera Murphy, Marynka Ulaszewska, Ian B. Jeffery, Carol Anne O’Shea, Claire Watkins, Eugene Dempsey, Fulvio Mattivi, Kieran Tuohy, R. Paul Ross, C. Anthony Ryan, Paul W. O’Toole and Catherine Stanton
    Citation: Microbiome 2017 5:21
    Content type: Erratum Published on:

    The original article was published in Microbiome 2017 5:4

  49. Cystic fibrosis (CF) is a life-threatening genetic disorder, characterized by chronic microbial lung infections due to abnormally viscous mucus secretions within airways. The clinical management of CF typicall...

    Authors: Rounak Feigelman, Christian R. Kahlert, Florent Baty, Frank Rassouli, Rebekka L. Kleiner, Philipp Kohler, Martin H. Brutsche and Christian von Mering
    Citation: Microbiome 2017 5:20
    Content type: Research Published on:

  50. Community-level analysis of the human microbiota has culminated in the discovery of relationships between overall shifts in the microbiota and a wide range of diseases and conditions. However, existing work ha...

    Authors: Anna Plantinga, Xiang Zhan, Ni Zhao, Jun Chen, Robert R. Jenq and Michael C. Wu
    Citation: Microbiome 2017 5:17
    Content type: Methodology Published on:
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