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  1. Methodology

    Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads

    Microbiome sequencing projects typically collect tens of millions of short reads per sample. Depending on the goals of the project, the short reads can either be subjected to direct sequence analysis or be ass...

    Daniel H. Huson, Rewati Tappu, Adam L Bazinet, Chao Xie, Michael P. Cummings, Kay Nieselt and Rohan Williams

    Microbiome 2017 5:11

    Published on: 25 January 2017

  2. Research

    Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data

    A variety of bacteria are known to influence carcinogenesis. Therefore, we sought to investigate if publicly available whole genome and whole transcriptome sequencing data generated by large public cancer geno...

    Kelly M. Robinson, Jonathan Crabtree, John S. A. Mattick, Kathleen E. Anderson and Julie C. Dunning Hotopp

    Microbiome 2017 5:9

    Published on: 25 January 2017

  3. Research

    Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study

    Autism spectrum disorders (ASD) are complex neurobiological disorders that impair social interactions and communication and lead to restricted, repetitive, and stereotyped patterns of behavior, interests, and ...

    Dae-Wook Kang, James B. Adams, Ann C. Gregory, Thomas Borody, Lauren Chittick, Alessio Fasano, Alexander Khoruts, Elizabeth Geis, Juan Maldonado, Sharon McDonough-Means, Elena L. Pollard, Simon Roux, Michael J. Sadowsky, Karen Schwarzberg Lipson, Matthew B. Sullivan, J. Gregory Caporaso…

    Microbiome 2017 5:10

    Published on: 23 January 2017

  4. Research

    The interaction between vaginal microbiota, cervical length, and vaginal progesterone treatment for preterm birth risk

    Preterm birth is the primary cause of infant death worldwide. A short cervix in the second trimester of pregnancy is a risk factor for preterm birth. In specific patient cohorts, vaginal progesterone reduces t...

    Lindsay M. Kindinger, Phillip R. Bennett, Yun S Lee, Julian R. Marchesi, Ann Smith, Stefano Cacciatore, Elaine Holmes, Jeremy K. Nicholson, T. G. Teoh and David A. MacIntyre

    Microbiome 2017 5:6

    Published on: 19 January 2017

  5. Methodology

    A fast and robust protocol for metataxonomic analysis using RNAseq data

    Metagenomics is a rapidly emerging field aimed to analyze microbial diversity and dynamics by studying the genomic content of the microbiota. Metataxonomics tools analyze high-throughput sequencing data, prima...

    Jeremy W. Cox, Richard A. Ballweg, Diana H. Taft, Prakash Velayutham, David B. Haslam and Aleksey Porollo

    Microbiome 2017 5:7

    Published on: 19 January 2017

  6. Research

    The effect of cigarette smoking on the oral and nasal microbiota

    The goal of the study was to investigate whether cigarette smoking alters oral and nasal microbial diversity, composition, and structure. Twenty-three current smokers and 20 never smokers were recruited. From ...

    Guoqin Yu, Stephen Phillips, Mitchell H. Gail, James J. Goedert, Michael S. Humphrys, Jacques Ravel, Yanfang Ren and Neil E. Caporaso

    Microbiome 2017 5:3

    Published on: 17 January 2017

  7. Research

    Ancient bacteria of the Ötzi’s microbiome: a genomic tale from the Copper Age

    Ancient microbiota information represents an important resource to evaluate bacterial evolution and to explore the biological spread of infectious diseases in history. The soft tissue of frozen mummified human...

    Gabriele Andrea Lugli, Christian Milani, Leonardo Mancabelli, Francesca Turroni, Chiara Ferrario, Sabrina Duranti, Douwe van Sinderen and Marco Ventura

    Microbiome 2017 5:5

    Published on: 17 January 2017

    The Erratum to this article has been published in Microbiome 2017 5:23

  8. Research

    Evolution of gut microbiota composition from birth to 24 weeks in the INFANTMET Cohort

    The gut is the most extensively studied niche of the human microbiome. The aim of this study was to characterise the initial gut microbiota development of a cohort of breastfed infants (n = 192) from 1 to 24 wee...

    Cian J. Hill, Denise B. Lynch, Kiera Murphy, Marynka Ulaszewska, Ian B. Jeffery, Carol Anne O’Shea, Claire Watkins, Eugene Dempsey, Fulvio Mattivi, Kieran Tuohy, R. Paul Ross, C. Anthony Ryan, Paul W. O’ Toole and Catherine Stanton

    Microbiome 2017 5:4

    Published on: 17 January 2017

    The Erratum to this article has been published in Microbiome 2017 5:21

  9. Research

    Deciphering composition and function of the root microbiome of a legume plant

    Diverse assemblages of microbes colonize plant roots and collectively function as a microbiome. Earlier work has characterized the root microbiomes of numerous plant species, but little information is availabl...

    Kyle Hartman, Marcel GA van der Heijden, Valexia Roussely-Provent, Jean-Claude Walser and Klaus Schlaeppi

    Microbiome 2017 5:2

    Published on: 17 January 2017

  10. Research

    The gut microbiota in conventional and serrated precursors of colorectal cancer

    Colorectal cancer is a heterogeneous disease arising from at least two precursors—the conventional adenoma (CA) and the serrated polyp. We and others have previously shown a relationship between the human gut ...

    Brandilyn A. Peters, Christine Dominianni, Jean A. Shapiro, Timothy R. Church, Jing Wu, George Miller, Elizabeth Yuen, Hal Freiman, Ian Lustbader, James Salik, Charles Friedlander, Richard B. Hayes and Jiyoung Ahn

    Microbiome 2016 4:69

    Published on: 30 December 2016

    The Erratum to this article has been published in Microbiome 2017 5:29

  11. Research

    The developing hypopharyngeal microbiota in early life

    The airways of healthy humans harbor a distinct microbial community. Perturbations in the microbial community have been associated with disease, yet little is known about the formation and development of a hea...

    Martin Steen Mortensen, Asker Daniel Brejnrod, Michael Roggenbuck, Waleed Abu Al-Soud, Christina Balle, Karen Angeliki Krogfelt, Jakob Stokholm, Jonathan Thorsen, Johannes Waage, Morten Arendt Rasmussen, Hans Bisgaard and Søren Johannes Sørensen

    Microbiome 2016 4:70

    Published on: 30 December 2016

  12. Research

    Influence of maternal breast milk ingestion on acquisition of the intestinal microbiome in preterm infants

    The initial acquisition and early development of the intestinal microbiome during infancy are important to human health across the lifespan. Mode of birth, antibiotic administration, environment of care, and n...

    Katherine E. Gregory, Buck S. Samuel, Pearl Houghteling, Guru Shan, Frederick M. Ausubel, Ruslan I. Sadreyev and W. Allan Walker

    Microbiome 2016 4:68

    Published on: 30 December 2016

  13. Research

    Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease

    The preterm microbiome is crucial to gut health and may contribute to necrotising enterocolitis (NEC), which represents the most significant pathology affecting preterm infants. From a cohort of 318 infants, <...

    Christopher J. Stewart, Nicholas D. Embleton, Emma C. L. Marrs, Daniel P. Smith, Andrew Nelson, Bashir Abdulkadir, Tom Skeath, Joseph F. Petrosino, John D. Perry, Janet E. Berrington and Stephen P. Cummings

    Microbiome 2016 4:67

    Published on: 29 December 2016

  14. Research

    Disruption of the microbiota across multiple body sites in critically ill children

    Despite intense interest in the links between the microbiome and human health, little has been written about dysbiosis among ICU patients. We characterized microbial diversity in samples from 37 children in a ...

    Matthew B. Rogers, Brian Firek, Min Shi, Andrew Yeh, Rachel Brower-Sinning, Victoria Aveson, Brittany L. Kohl, Anthony Fabio, Joseph A. Carcillo and Michael J. Morowitz

    Microbiome 2016 4:66

    Published on: 29 December 2016

  15. Research

    Resilient microorganisms in dust samples of the International Space Station—survival of the adaptation specialists

    The International Space Station (ISS) represents a unique biotope for the human crew but also for introduced microorganisms. Microbes experience selective pressures such as microgravity, desiccation, poor nutr...

    Maximilian Mora, Alexandra Perras, Tatiana A. Alekhova, Lisa Wink, Robert Krause, Alina Aleksandrova, Tatiana Novozhilova and Christine Moissl-Eichinger

    Microbiome 2016 4:65

    Published on: 20 December 2016

  16. Research

    Staphylococcal species heterogeneity in the nasal microbiome following antibiotic prophylaxis revealed by tuf gene deep sequencing

    Staphylococci are a major constituent of the nasal microbiome and a frequent cause of hospital-acquired infection. Antibiotic surgical prophylaxis is administered prior to surgery to reduce a patient’s risk of...

    Claire L. McMurray, Katherine J. Hardy, Szymon T. Calus, Nicholas J. Loman and Peter M. Hawkey

    Microbiome 2016 4:63

    Published on: 2 December 2016

  17. Research

    Transmission of viruses via our microbiomes

    Bacteria inhabiting the human body have important roles in a number of physiological processes and are known to be shared amongst genetically-related individuals. Far less is known about viruses inhabiting the...

    Melissa Ly, Marcus B. Jones, Shira R. Abeles, Tasha M. Santiago-Rodriguez, Jonathan Gao, Ivan C. Chan, Chandrabali Ghose and David T. Pride

    Microbiome 2016 4:64

    Published on: 2 December 2016

  18. Research

    Extending colonic mucosal microbiome analysis—assessment of colonic lavage as a proxy for endoscopic colonic biopsies

    Sequencing-based analysis has become a well-established approach to deciphering the composition of the gut microbiota. However, due to the complexity of accessing sufficient material from colonoscopic biopsy s...

    Euan Watt, Matthew R. Gemmell, Susan Berry, Mark Glaire, Freda Farquharson, Petra Louis, Graeme I. Murray, Emad El-Omar and Georgina L. Hold

    Microbiome 2016 4:61

    Published on: 25 November 2016

  19. Methodology

    Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies

    There is an immense scientific interest in the human microbiome and its effects on human physiology, health, and disease. A common approach for examining bacterial communities is high-throughput sequencing of ...

    Jonathan Thorsen, Asker Brejnrod, Martin Mortensen, Morten A. Rasmussen, Jakob Stokholm, Waleed Abu Al-Soud, Søren Sørensen, Hans Bisgaard and Johannes Waage

    Microbiome 2016 4:62

    Published on: 25 November 2016

  20. Research

    The lung microbiota in early rheumatoid arthritis and autoimmunity

    Airway abnormalities and lung tissue citrullination are found in both rheumatoid arthritis (RA) patients and individuals at-risk for disease development. This suggests the possibility that the lung could be a ...

    Jose U. Scher, Vijay Joshua, Alejandro Artacho, Shahla Abdollahi-Roodsaz, Johan Öckinger, Susanna Kullberg, Magnus Sköld, Anders Eklund, Johan Grunewald, Jose C. Clemente, Carles Ubeda, Leopoldo N. Segal and Anca I. Catrina

    Microbiome 2016 4:60

    Published on: 17 November 2016

  21. Research

    DNA from fecal immunochemical test can replace stool for detection of colonic lesions using a microbiota-based model

    There is a significant demand for colorectal cancer (CRC) screening methods that are noninvasive, inexpensive, and capable of accurately detecting early stage tumors. It has been shown that models based on the...

    Nielson T. Baxter, Charles C. Koumpouras, Mary A. M. Rogers, Mack T. Ruffin and Patrick D. Schloss

    Microbiome 2016 4:59

    Published on: 14 November 2016

  22. Review

    The vaginal microbiota, human papillomavirus infection and cervical intraepithelial neoplasia: what do we know and where are we going next?

    The vaginal microbiota plays a significant role in health and disease of the female reproductive tract. Next-generation sequencing techniques based upon the analysis of bacterial 16S rRNA genes permit in-depth...

    Anita Mitra, David A. MacIntyre, Julian R. Marchesi, Yun S. Lee, Phillip R. Bennett and Maria Kyrgiou

    Microbiome 2016 4:58

    Published on: 1 November 2016

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