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  1. Antibiotic-resistant pathogens are challenging treatment of infections worldwide. Urban sewage is potentially a major conduit for dissemination of antibiotic resistance genes into various environmental compart...

    Authors: Jian-Qiang Su, Xin-Li An, Bing Li, Qing-Lin Chen, Michael R. Gillings, Hong Chen, Tong Zhang and Yong-Guan Zhu
    Citation: Microbiome 2017 5:84
    Content type: Research Published on:

    The Correction to this article has been published in Microbiome 2018 6:127

  2. The Antarctic continent is considered the coldest and driest place on earth with simple ecosystems, devoid of higher plants. Soils in the ice-free regions of Antarctica are known to harbor a wide range of micr...

    Authors: Evelien M. Adriaenssens, Rolf Kramer, Marc W. Van Goethem, Thulani P. Makhalanyane, Ian Hogg and Don A. Cowan
    Citation: Microbiome 2017 5:83
    Content type: Research Published on:

  3. The built environment of the International Space Station (ISS) is a highly specialized space in terms of both physical characteristics and habitation requirements. It is unique with respect to conditions of mi...

    Authors: Nicholas A. Be, Aram Avila-Herrera, Jonathan E. Allen, Nitin Singh, Aleksandra Checinska Sielaff, Crystal Jaing and Kasthuri Venkateswaran
    Citation: Microbiome 2017 5:81
    Content type: Research Published on:

    The Erratum to this article has been published in Microbiome 2017 5:111

  5. The study of the gut microbiota (GM) is rapidly moving towards its functional characterization by means of shotgun meta-omics. In this context, there is still no consensus on which microbial functions are cons...

    Authors: Alessandro Tanca, Marcello Abbondio, Antonio Palomba, Cristina Fraumene, Valeria Manghina, Francesco Cucca, Edoardo Fiorillo and Sergio Uzzau
    Citation: Microbiome 2017 5:79
    Content type: Research Published on:

  6. The human gut is colonized with a myriad of microbes, with substantial interpersonal variation. This complex ecosystem is an integral part of the gastrointestinal tract and plays a major role in the maintenanc...

    Authors: Kees C. H. van der Ark, Ruben G. A. van Heck, Vitor A. P. Martins Dos Santos, Clara Belzer and Willem M. de Vos
    Citation: Microbiome 2017 5:78
    Content type: Review Published on:

  7. The gut microbiota of breast-fed and formula-fed infants differ significantly, as do the risks for allergies, gut dysfunction, and upper respiratory tract infections. The connections between breast milk, vario...

    Authors: Manish Kumar Saraf, Brian D. Piccolo, Anne K. Bowlin, Kelly E. Mercer, Tanya LeRoith, Sree V. Chintapalli, Kartik Shankar, Thomas M. Badger and Laxmi Yeruva
    Citation: Microbiome 2017 5:77
    Content type: Research Published on:

  8. The concept of hygiene is rooted in the relationship between cleanliness and the maintenance of good health. Since the widespread acceptance of the germ theory of disease, hygiene has become increasingly confl...

    Authors: Roo Vandegrift, Ashley C. Bateman, Kyla N. Siemens, May Nguyen, Hannah E. Wilson, Jessica L. Green, Kevin G. Van Den Wymelenberg and Roxana J. Hickey
    Citation: Microbiome 2017 5:76
    Content type: Review Published on:

  9. Late onset sepsis (LOS) in preterm infants is associated with considerable morbidity and mortality. While studies have implicated gut bacteria in the aetiology of the disease, functional analysis and mechanist...

    Authors: Christopher J. Stewart, Nicholas D. Embleton, Emma C. L. Marrs, Daniel P. Smith, Tatiana Fofanova, Andrew Nelson, Tom Skeath, John D. Perry, Joseph F. Petrosino, Janet E. Berrington and Stephen P. Cummings
    Citation: Microbiome 2017 5:75
    Content type: Research Published on:

  10. The use of antimicrobials in food animals and the emergence of antimicrobial resistance are global concerns. Ceftiofur is the only third-generation cephalosporin labeled for veterinary use in the USA, and it i...

    Authors: Erika K. Ganda, Natalia Gaeta, Anja Sipka, Brianna Pomeroy, Georgios Oikonomou, Ynte H. Schukken and Rodrigo C. Bicalho
    Citation: Microbiome 2017 5:74
    Content type: Research Published on:

  11. Systemic lupus erythematosus, characterized by persistent inflammation, is a complex autoimmune disorder with no known cure. Immunosuppressants used in treatment put patients at a higher risk of infections. Ne...

    Authors: Qinghui Mu, Husen Zhang, Xiaofeng Liao, Kaisen Lin, Hualan Liu, Michael R. Edwards, S. Ansar Ahmed, Ruoxi Yuan, Liwu Li, Thomas E. Cecere, David B. Branson, Jay L. Kirby, Poorna Goswami, Caroline M. Leeth, Kaitlin A. Read, Kenneth J. Oestreich…
    Citation: Microbiome 2017 5:73
    Content type: Research Published on:

  13. Establishment of the human gut microbiota begins at birth. This early-life microbiota development can impact host physiology during infancy and even across an entire life span. However, the functional stabilit...

    Authors: Weili Xiong, Christopher T. Brown, Michael J. Morowitz, Jillian F. Banfield and Robert L. Hettich
    Citation: Microbiome 2017 5:72
    Content type: Research Published on:

  14. Effective treatment of Mycobacterium tuberculosis (Mtb) infection requires at least 6 months of daily therapy with multiple orally administered antibiotics. Although this drug regimen is administered annually to ...

    Authors: Sivaranjani Namasivayam, Mamoudou Maiga, Wuxing Yuan, Vishal Thovarai, Diego L. Costa, Lara R. Mittereder, Matthew F. Wipperman, Michael S. Glickman, Amiran Dzutsev, Giorgio Trinchieri and Alan Sher
    Citation: Microbiome 2017 5:71
    Content type: Research Published on:

  15. 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:

  16. Identifying viral sequences in mixed metagenomes containing both viral and host contigs is a critical first step in analyzing the viral component of samples. Current tools for distinguishing prokaryotic virus ...

    Authors: Jie Ren, Nathan A. Ahlgren, Yang Young Lu, Jed A. Fuhrman and Fengzhu Sun
    Citation: Microbiome 2017 5:69
    Content type: Methodology Published on:

  17. 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:

  18. 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:

  19. 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:

  20. 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:

  22. 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:

  23. 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

  24. 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:

  25. 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:

  26. 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:

  27. 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:

  28. 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:

  29. 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:

  31. 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:

  32. 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:

  33. 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:

  34. 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:

  35. 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:

  36. 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:

  37. 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:

  38. 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:

  39. 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:

  40. 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:

  41. 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:

  43. 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:

  44. 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:

  45. 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:

  46. 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:

  47. 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:

  49. 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:

  50. 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:
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