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  1. Research

    Associations among dietary non-fiber carbohydrate, ruminal microbiota and epithelium G-protein-coupled receptor, and histone deacetylase regulations in goats

    Diet-derived short-chain fatty acids (SCFAs) in the rumen have broad effects on the health and growth of ruminants. The microbe-G-protein-coupled receptor (GPR) and microbe-histone deacetylase (HDAC) axes migh...

    Hong Shen, Zhongyan Lu, Zhihui Xu, Zhan Chen and Zanming Shen

    Microbiome 2017 5:123

    Published on: 19 September 2017

  2. Research

    Feed in summer, rest in winter: microbial carbon utilization in forest topsoil

    Evergreen coniferous forests contain high stocks of organic matter. Significant carbon transformations occur in litter and soil of these ecosystems, making them important for the global carbon cycle. Due to se...

    Lucia Žifčáková, Tomáš Větrovský, Vincent Lombard, Bernard Henrissat, Adina Howe and Petr Baldrian

    Microbiome 2017 5:122

    Published on: 18 September 2017

  3. Research

    Profiling bacterial communities by MinION sequencing of ribosomal operons

    An approach utilizing the long-read capability of the Oxford Nanopore MinION to rapidly sequence bacterial ribosomal operons of complex natural communities was developed. Microbial fingerprinting employs domai...

    Lee J. Kerkhof, Kevin P. Dillon, Max M. Häggblom and Lora R. McGuinness

    Microbiome 2017 5:116

    Published on: 15 September 2017

  4. Research

    Recent urbanization in China is correlated with a Westernized microbiome encoding increased virulence and antibiotic resistance genes

    Urbanization is associated with an increased risk for a number of diseases, including obesity, diabetes, and cancer, which all also show associations with the microbiome. While microbial community composition ...

    Kathryn Winglee, Annie Green Howard, Wei Sha, Raad Z. Gharaibeh, Jiawu Liu, Donghui Jin, Anthony A. Fodor and Penny Gordon-Larsen

    Microbiome 2017 5:121

    Published on: 15 September 2017

  5. Research

    Treatment of biofilms in bacterial vaginosis by an amphoteric tenside pessary-clinical study and microbiota analysis

    Bacterial vaginosis (BV) is the most common vaginal syndrome among women in their reproductive years. It is associated with an increased risk of acquiring sexually transmitted infections and complications like...

    Cornelia Gottschick, Zhi-Luo Deng, Marius Vital, Clarissa Masur, Christoph Abels, Dietmar H. Pieper, Manfred Rohde, Werner Mendling and Irene Wagner-Döbler

    Microbiome 2017 5:119

    Published on: 13 September 2017

  6. Research

    More than 2500 years of oil exposure shape sediment microbiomes with the potential for syntrophic degradation of hydrocarbons linked to methanogenesis

    Natural oil seeps offer the opportunity to study the adaptation of ecosystems and the associated microbiota to long-term oil exposure. In the current study, we investigated a land-to-sea transition ecosystem c...

    Antonios Michas, Gisle Vestergaard, Kathleen Trautwein, Pavlos Avramidis, Dimitris G. Hatzinikolaou, Constantinos E. Vorgias, Heinz Wilkes, Ralf Rabus, Michael Schloter and Anne Schöler

    Microbiome 2017 5:118

    Published on: 11 September 2017

  7. Research

    Perilipin-2 modulates dietary fat-induced microbial global gene expression profiles in the mouse intestine

    Intestinal microbiota are critical determinants of obesity and metabolic disease risk. In previous work, we showed that deletion of the cytoplasmic lipid droplet (CLD) protein perilipin-2 (Plin2) modulates gut...

    Xuejian Xiong, Elise S. Bales, Diana Ir, Charles E. Robertson, James L. McManaman, Daniel N. Frank and John Parkinson

    Microbiome 2017 5:117

    Published on: 6 September 2017

  8. Research

    Collection of non-meconium stool on fecal occult blood cards is an effective method for fecal microbiota studies in infants

    Effective methods are needed to collect fecal samples from children for large-scale microbiota studies. Stool collected on fecal occult blood test (FOBT) cards that can be mailed provides an effective solution...

    Wendy S.W. Wong, Nicole Clemency, Elisabeth Klein, Marina Provenzano, Ramaswamy Iyer, John E. Niederhuber and Suchitra K. Hourigan

    Microbiome 2017 5:114

    Published on: 5 September 2017

  9. Research

    Pre-pregnancy weight, gestational weight gain, and the gut microbiota of mothers and their infants

    Recent evidence supports that the maternal gut microbiota impacts the initial infant gut microbiota. Since the gut microbiota may play a causal role in the development of obesity, it is important to understand...

    Maggie A. Stanislawski, Dana Dabelea, Brandie D. Wagner, Marci K. Sontag, Catherine A. Lozupone and Merete Eggesbø

    Microbiome 2017 5:113

    Published on: 4 September 2017

  10. Research

    The structure of the Brassica napus seed microbiome is cultivar-dependent and affects the interactions of symbionts and pathogens

    Although the plant microbiome is crucial for plant health, little is known about the significance of the seed microbiome. Here, we studied indigenous bacterial communities associated with the seeds in differen...

    Daria Rybakova, Riccardo Mancinelli, Mariann Wikström, Ann-Sofie Birch-Jensen, Joeke Postma, Ralf-Udo Ehlers, Simon Goertz and Gabriele Berg

    Microbiome 2017 5:104

    Published on: 1 September 2017

  11. Research

    Microbial regulation of microRNA expression in the amygdala and prefrontal cortex

    There is growing evidence for a role of the gut microbiome in shaping behaviour relevant to many psychiatric and neurological disorders. Preclinical studies using germ-free (GF) animals have been essential in ...

    Alan E. Hoban, Roman M. Stilling, Gerard M. Moloney, Rachel D. Moloney, Fergus Shanahan, Timothy G. Dinan, John F. Cryan and Gerard Clarke

    Microbiome 2017 5:102

    Published on: 25 August 2017

  12. Research

    Oxalobacter formigenes-associated host features and microbial community structures examined using the American Gut Project

    Increasing evidence shows the importance of the commensal microbe Oxalobacter formigenes in regulating host oxalate homeostasis, with effects against calcium oxalate kidney stone formation, and other oxalate-asso...

    Menghan Liu, Hyunwook Koh, Zachary D. Kurtz, Thomas Battaglia, Amanda PeBenito, Huilin Li, Lama Nazzal and Martin J. Blaser

    Microbiome 2017 5:108

    Published on: 25 August 2017

  13. Research

    Blood as a route of transmission of uterine pathogens from the gut to the uterus in cows

    Metritis is an inflammatory disease of the uterus caused by bacterial infection, particularly Bacteroides, Porphyromonas, and Fusobacterium. Bacteria from the environment, feces, or vagina are believed to be the ...

    Soo Jin Jeon, Federico Cunha, Achilles Vieira-Neto, Rodrigo C. Bicalho, Svetlana Lima, Marcela L. Bicalho and Klibs N. Galvão

    Microbiome 2017 5:109

    Published on: 25 August 2017

  14. Research

    Early gut mycobiota and mother-offspring transfer

    The fungi in the gastrointestinal tract, the gut mycobiota, are now recognised as a significant part of the gut microbiota, and they may be important to human health. In contrast to the adult gut mycobiota, the e...

    Kasper Schei, Ekaterina Avershina, Torbjørn Øien, Knut Rudi, Turid Follestad, Saideh Salamati and Rønnaug Astri Ødegård

    Microbiome 2017 5:107

    Published on: 24 August 2017

  15. Research

    Space-type radiation induces multimodal responses in the mouse gut microbiome and metabolome

    Space travel is associated with continuous low dose rate exposure to high linear energy transfer (LET) radiation. Pathophysiological manifestations after low dose radiation exposure are strongly influenced by non...

    David Casero, Kirandeep Gill, Vijayalakshmi Sridharan, Igor Koturbash, Gregory Nelson, Martin Hauer-Jensen, Marjan Boerma, Jonathan Braun and Amrita K. Cheema

    Microbiome 2017 5:105

    Published on: 18 August 2017

  16. Review

    Schrödinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems

    While often obvious for macroscopic organisms, determining whether a microbe is dead or alive is fraught with complications. Fields such as microbial ecology, environmental health, and medical microbiology eac...

    Joanne B. Emerson, Rachel I. Adams, Clarisse M. Betancourt Román, Brandon Brooks, David A. Coil, Katherine Dahlhausen, Holly H. Ganz, Erica M. Hartmann, Tiffany Hsu, Nicholas B. Justice, Ivan G. Paulino-Lima, Julia C. Luongo, Despoina S. Lymperopoulou, Cinta Gomez-Silvan, Brooke Rothschild-Mancinelli, Melike Balk…

    Microbiome 2017 5:86

    Published on: 16 August 2017

  17. Research

    Comparative gut microbiota and resistome profiling of intensive care patients receiving selective digestive tract decontamination and healthy subjects

    The gut microbiota is a reservoir of opportunistic pathogens that can cause life-threatening infections in critically ill patients during their stay in an intensive care unit (ICU). To suppress gut colonizatio...

    Elena Buelow, Teresita d. j. Bello González, Susana Fuentes, Wouter A. A. de Steenhuijsen Piters, Leo Lahti, Jumamurat R. Bayjanov, Eline A. M. Majoor, Johanna C. Braat, Maaike S. M. van Mourik, Evelien A. N. Oostdijk, Rob J. L. Willems, Marc J. M. Bonten, Mark W. J. van Passel, Hauke Smidt and Willem van Schaik

    Microbiome 2017 5:88

    Published on: 14 August 2017

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