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  1. Research

    Sputum DNA sequencing in cystic fibrosis: non-invasive access to the lung microbiome and to pathogen details

    Cystic fibrosis (CF) is a life-threatening genetic disorder, characterized by chronic microbial lung infections due to abnormally viscous mucus secretions within airways. The clinical management of CF typicall...

    Rounak Feigelman, Christian R. Kahlert, Florent Baty, Frank Rassouli, Rebekka L. Kleiner, Philipp Kohler, Martin H. Brutsche and Christian von Mering

    Microbiome 2017 5:20

    Published on: 10 February 2017

  2. Research

    Resistant starch can improve insulin sensitivity independently of the gut microbiota

    Obesity-related diseases, including type 2 diabetes and cardiovascular disease, have reached epidemic proportions in industrialized nations, and dietary interventions for their prevention are therefore importa...

    Laure B. Bindels, Rafael R. Segura Munoz, João Carlos Gomes-Neto, Valentin Mutemberezi, Inés Martínez, Nuria Salazar, Elizabeth A. Cody, Maria I. Quintero-Villegas, Hatem Kittana, Clara G de los Reyes-Gavilán, Robert J. Schmaltz, Giulio G. Muccioli, Jens Walter and Amanda E. Ramer-Tait

    Microbiome 2017 5:12

    Published on: 7 February 2017

  3. Letter to the Editor

    Gut metagenomes of type 2 diabetic patients have characteristic single-nucleotide polymorphism distribution in Bacteroides coprocola

    Gut microbes play a critical role in human health and disease, and researchers have begun to characterize their genomes, the so-called gut metagenome. Thus far, metagenomics studies have focused on genus- or s...

    Yaowen Chen, Zongcheng Li, Shuofeng Hu, Jian Zhang, Jiaqi Wu, Ningsheng Shao, Xiaochen Bo, Ming Ni and Xiaomin Ying

    Microbiome 2017 5:15

    Published on: 1 February 2017

  4. Research

    Gut microbiota dysbiosis contributes to the development of hypertension

    Recently, the potential role of gut microbiome in metabolic diseases has been revealed, especially in cardiovascular diseases. Hypertension is one of the most prevalent cardiovascular diseases worldwide, yet w...

    Jing Li, Fangqing Zhao, Yidan Wang, Junru Chen, Jie Tao, Gang Tian, Shouling Wu, Wenbin Liu, Qinghua Cui, Bin Geng, Weili Zhang, Ryan Weldon, Kelda Auguste, Lei Yang, Xiaoyan Liu, Li Chen…

    Microbiome 2017 5:14

    Published on: 1 February 2017

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

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