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  1. Research

    Influence of the pneumococcal conjugate vaccines on the temporal variation of pneumococcal carriage and the nasal microbiota in healthy infants: a longitudinal analysis of a case–control study

    Bacterial colonization of the upper airways is a prerequisite for subsequent invasive disease. With the introduction of the 7- and 13-valent pneumococcal conjugate vaccines (PCV7 and PCV13), changes in pneumoc...

    Moana Mika, Josua Maurer, Insa Korten, Aurélie Allemann, Suzanne Aebi, Silvio D. Brugger, Weihong Qi, Urs Frey, Philipp Latzin and Markus Hilty

    Microbiome 2017 5:85

    Published on: 24 July 2017

  2. Research

    Deciphering functional diversification within the lichen microbiota by meta-omics

    Recent evidence of specific bacterial communities extended the traditional concept of fungal-algal lichen symbioses by a further organismal kingdom. Although functional roles were already assigned to dominant ...

    Tomislav Cernava, Armin Erlacher, Ines Aline Aschenbrenner, Lisa Krug, Christian Lassek, Katharina Riedel, Martin Grube and Gabriele Berg

    Microbiome 2017 5:82

    Published on: 19 July 2017

  3. Research

    Whole metagenome profiles of particulates collected from the International Space Station

    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...

    Nicholas A. Be, Aram Avila-Herrera, Jonathan E. Allen, Nitin Singh, Aleksandra Checinska Sielaff, Crystal Jaing and Kasthuri Venkateswaran

    Microbiome 2017 5:81

    Published on: 17 July 2017

  4. Research

    Potential and active functions in the gut microbiota of a healthy human cohort

    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...

    Alessandro Tanca, Marcello Abbondio, Antonio Palomba, Cristina Fraumene, Valeria Manghina, Francesco Cucca, Edoardo Fiorillo and Sergio Uzzau

    Microbiome 2017 5:79

    Published on: 14 July 2017

  5. Review

    Cleanliness in context: reconciling hygiene with a modern microbial perspective

    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...

    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

    Microbiome 2017 5:76

    Published on: 14 July 2017

  6. Review

    More than just a gut feeling: constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes

    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...

    Kees C. H. van der Ark, Ruben G. A. van Heck, Vitor A. P. Martins Dos Santos, Clara Belzer and Willem M. de Vos

    Microbiome 2017 5:78

    Published on: 14 July 2017

  7. Research

    Formula diet driven microbiota shifts tryptophan metabolism from serotonin to tryptamine in neonatal porcine colon

    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...

    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

    Microbiome 2017 5:77

    Published on: 14 July 2017

  8. Research

    Longitudinal development of the gut microbiome and metabolome in preterm neonates with late onset sepsis and healthy controls

    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...

    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

    Microbiome 2017 5:75

    Published on: 12 July 2017

  9. Research

    Normal milk microbiome is reestablished following experimental infection with Escherichia coli independent of intramammary antibiotic treatment with a third-generation cephalosporin in bovines

    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...

    Erika K. Ganda, Natalia Gaeta, Anja Sipka, Brianna Pomeroy, Georgios Oikonomou, Ynte H. Schukken and Rodrigo C. Bicalho

    Microbiome 2017 5:74

    Published on: 12 July 2017

  10. Research

    Human presence impacts fungal diversity of inflated lunar/Mars analog habitat

    An inflatable lunar/Mars analog habitat (ILMAH), simulated closed system isolated by HEPA filtration, mimics International Space Station (ISS) conditions and future human habitation on other planets except for...

    A. Blachowicz, T. Mayer, M. Bashir, T. R. Pieber, P. De León and K. Venkateswaran

    Microbiome 2017 5:62

    Published on: 11 July 2017

  11. Research

    Control of lupus nephritis by changes of gut microbiota

    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...

    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…

    Microbiome 2017 5:73

    Published on: 11 July 2017

  12. Research

    Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life

    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...

    Weili Xiong, Christopher T. Brown, Michael J. Morowitz, Jillian F. Banfield and Robert L. Hettich

    Microbiome 2017 5:72

    Published on: 10 July 2017

  13. Research

    Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy

    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 ...

    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

    Microbiome 2017 5:71

    Published on: 7 July 2017

  14. Methodology

    A novel ultra high-throughput 16S rRNA gene amplicon sequencing library preparation method for the Illumina HiSeq platform

    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...

    Eric J. de Muinck, Pål Trosvik, Gregor D. Gilfillan, Johannes R. Hov and Arvind Y. M. Sundaram

    Microbiome 2017 5:68

    Published on: 6 July 2017

  15. Research

    Expanding landscapes of the diversified mcr-1-bearing plasmid reservoirs

    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...

    Qingjing Wang, Jian Sun, Jun Li, Youfa Ding, Xing-Ping Li, Jingxia Lin, Bachar Hassan and Youjun Feng

    Microbiome 2017 5:70

    Published on: 6 July 2017

  16. Short report

    The metabolic footprint of the airway bacterial community in cystic fibrosis

    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...

    Vaishnavi Narayanamurthy, John M. Sweetnam, Darcy R. Denner, Lena W. Chen, Edward T. Naureckas, Bharathi Laxman and Steven R. White

    Microbiome 2017 5:67

    Published on: 30 June 2017

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

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