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  1. Research

    Diet shifts provoke complex and variable changes in the metabolic networks of the ruminal microbiome

    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...

    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

    Microbiome 2017 5:60

    Published on: 8 June 2017

  2. Research

    Bacteriophage–prokaryote dynamics and interaction within anaerobic digestion processes across time and space

    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...

    Junyu Zhang, Qun Gao, Qiuting Zhang, Tengxu Wang, Haowei Yue, Linwei Wu, Jason Shi, Ziyan Qin, Jizhong Zhou, Jiane Zuo and Yunfeng Yang

    Microbiome 2017 5:57

    Published on: 31 May 2017

  3. Research

    Tomato root microbiota and Phytophthora parasitica-associated disease

    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...

    Marie Larousse, Corinne Rancurel, Camille Syska, Ferran Palero, Catherine Etienne, Benoît Industri, Xavier Nesme, Marc Bardin and Eric Galiana

    Microbiome 2017 5:56

    Published on: 16 May 2017

  4. Report

    Changes in microbial ecology after fecal microbiota transplantation for recurrent C. difficile infection affected by underlying inflammatory bowel disease

    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...

    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

    Microbiome 2017 5:55

    Published on: 15 May 2017

  5. Research

    Compositionally and functionally distinct sinus microbiota in chronic rhinosinusitis patients have immunological and clinically divergent consequences

    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...

    Emily K. Cope, Andrew N. Goldberg, Steven D. Pletcher and Susan V. Lynch

    Microbiome 2017 5:53

    Published on: 12 May 2017

  6. Review

    Optimizing methods and dodging pitfalls in microbiome research

    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...

    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

    Microbiome 2017 5:52

    Published on: 5 May 2017

  7. Research

    The effects of inhaled aztreonam on the cystic fibrosis lung microbiome

    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...

    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

    Microbiome 2017 5:51

    Published on: 5 May 2017

  8. Research

    Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics

    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...

    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

    Microbiome 2017 5:50

    Published on: 4 May 2017

  9. Research

    Differences in gut microbial composition correlate with regional brain volumes in irritable bowel syndrome

    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 ...

    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

    Microbiome 2017 5:49

    Published on: 1 May 2017

  10. Review

    A critical assessment of the “sterile womb” and “in utero colonization” hypotheses: implications for research on the pioneer infant microbiome

    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 ...

    Maria Elisa Perez-Muñoz, Marie-Claire Arrieta, Amanda E. Ramer-Tait and Jens Walter

    Microbiome 2017 5:48

    Published on: 28 April 2017

  11. Research

    Chemical and pathogen-induced inflammation disrupt the murine intestinal microbiome

    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...

    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

    Microbiome 2017 5:47

    Published on: 27 April 2017

  12. Research

    Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome

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

    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

    Microbiome 2017 5:44

    Published on: 26 April 2017

  13. Research

    Microbiota-activated CD103+ DCs stemming from microbiota adaptation specifically drive γδT17 proliferation and activation

    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 ...

    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

    Microbiome 2017 5:46

    Published on: 24 April 2017

  14. Research

    Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment

    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...

    Christian Wurzbacher, Andrea Fuchs, Katrin Attermeyer, Katharina Frindte, Hans-Peter Grossart, Michael Hupfer, Peter Casper and Michael T. Monaghan

    Microbiome 2017 5:41

    Published on: 8 April 2017

  15. Research

    High-fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice

    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 ...

    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…

    Microbiome 2017 5:43

    Published on: 8 April 2017

  16. Research

    Novel soil-inhabiting clades fill gaps in the fungal tree of life

    Fungi are a diverse eukaryotic group of degraders, pathogens, and symbionts, with many lineages known only from DNA sequences in soil, sediments, air, and water.

    Leho Tedersoo, Mohammad Bahram, Rasmus Puusepp, R. Henrik Nilsson and Timothy Y. James

    Microbiome 2017 5:42

    Published on: 8 April 2017

  17. Research

    Exposure to household furry pets influences the gut microbiota of infants at 3–4 months following various birth scenarios

    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...

    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

    Microbiome 2017 5:40

    Published on: 6 April 2017

  18. Research

    Temporal dynamics of the gut microbiota in people sharing a confined environment, a 520-day ground-based space simulation, MARS500

    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 ...

    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

    Microbiome 2017 5:39

    Published on: 24 March 2017

  19. Research

    Potential for hydrogen-oxidizing chemolithoautotrophic and diazotrophic populations to initiate biofilm formation in oligotrophic, deep terrestrial subsurface waters

    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...

    Xiaofen Wu, Karsten Pedersen, Johanna Edlund, Lena Eriksson, Mats Åström, Anders F. Andersson, Stefan Bertilsson and Mark Dopson

    Microbiome 2017 5:37

    Published on: 23 March 2017

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