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  1. Research

    Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission

    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,...

    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…

    Microbiome 2017 5:66

    Published on: 26 June 2017

  2. Commentary

    How holobionts get sick—toward a unifying scheme of disease

    All humans, animals, and plants are holobionts. Holobionts comprise the host and a myriad of interacting microorganisms—the microbiota. The hologenome encompasses the genome of the host plus the composite of a...

    Silvio D. Pitlik and Omry Koren

    Microbiome 2017 5:64

    Published on: 24 June 2017

  3. Research

    Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism

    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...

    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…

    Microbiome 2017 5:65

    Published on: 24 June 2017

  4. Research

    Aberrant intestinal microbiota due to IL-1 receptor antagonist deficiency promotes IL-17- and TLR4-dependent arthritis

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

    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

    Microbiome 2017 5:63

    Published on: 23 June 2017

  5. Research

    The development of lower respiratory tract microbiome in mice

    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.

    Nisha Singh, Asheema Vats, Aditi Sharma, Amit Arora and Ashwani Kumar

    Microbiome 2017 5:61

    Published on: 21 June 2017

  6. 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

  7. 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

  8. 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

  9. 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, 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

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