Genome Biology | Tags

Submit a manuscript Register Contact us Follow us on Twitter

Explore Genome Biology

Advertisement

Articles

Search microbiome on BioMed Central

#microbiome

25 items(s) found

Display/download options Articles per page: 25 | 50 | 100

Display options

Editor's summary Citation

Download options

Send
To

	All
	1.	Research highlight Microbiota's 'little helpers': bacteriophages and antibiotic-associated responses in the gut microbiome Christine L Sun, David A Relman Genome Biology 2013, 14:127 (30 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary David Relman and Christine Sun discuss recent research into how bacteriophage mediate the impact of antibiotics on the gut microbiome
	2.	Review The plant microbiome Thomas R Turner, Euan K James, Philip S Poole Genome Biology 2013, 14:209 (25 June 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Philip Poole and colleagues discuss how genomics approaches are unraveling the complex interactions between plant hosts and microbiome communities
	3.	Research CRISPR-Cas systems target a diverse collection of invasive mobile genetic elements in human microbiomes Quan Zhang, Mina Rho, Haixu Tang, Thomas G Doak, Yuzhen Ye Genome Biology 2013, 14:R40 (29 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of CRISPR sequences contained in human metagenomic datasets reveals a variety of different targeted mobile genetic elements
	4.	Review Studying the microbiology of the indoor environment Scott T Kelley, Jack A Gilbert Genome Biology 2013, 14:202 (28 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Scott Kelley and Jack Gilbert review the microbiology of the built environment, and highlight how genomics can empower its study
	5.	Research Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice Falk Hildebrand, Thi Loan Anh Nguyen, Brigitta Brinkman, Roberto Yunta, Benedicte Cauwe, Peter Vandenabeele, Adrian Liston, Jeroen Raes Genome Biology 2013, 14:R4 (24 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new study finds that enterotypes are not only present in mice, but also similar to those in humans
	6.	Software MetAMOS: a modular and open source metagenomic assembly and analysis pipeline Todd J Treangen, Sergey Koren, Daniel D Sommer, Bo Liu, Irina Astrovskaya, Brian Ondov, Aaron E Darling, Adam M Phillippy, Mihai Pop Genome Biology 2013, 14:R2 (15 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A modular, metagenomic analysis and assembly pipeline that inputs next-generation sequencing reads to generate genomic scaffolds and open reading frames
	7.	Research Biogeography of the ecosystems of the healthy human body Yanjiao Zhou, Hongyu Gao, Kathie A Mihindukulasuriya, Patricio S La Rosa, Kristine M Wylie, Tatiana Vishnivetskaya, Mircea Podar, Barb Warner, Phillip I Tarr, David E Nelson, J Fortenberry, Martin J Holland, Sarah E Burr, William D Shannon, Erica Sodergren, George M Weinstock Genome Biology 2013, 14:R1 (14 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary As part of the Human Microbiome Project, taxonomic analyses were performed on the bacteria from 22 body sites on 279 subjects
	8.	Research Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus Santiago Castillo-Ramírez, Jukka Corander, Pekka Marttinen, Mona Aldeljawi, William P Hanage, Henrik Westh, Kit Boye, Zeynep Gulay, Stephen D Bentley, Julian Parkhill, Matthew T Holden, Edward J Feil Genome Biology 2012, 13:R126 (27 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Different evolution rates of methicillin-resistant Staphylococcus aureus clone ST239 collected in different geographical locations are caused by fast global dissemination
	9.	Method *Ray Meta: scalable de novo* metagenome assembly and profiling** Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette, Jacques Corbeil Genome Biology 2012, 13:R122 (22 December 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A scalable, de novo metagenomic assembly method that couples taxonomic and ontology profiling
	10.	Research *Microevolutionary analysis of Clostridium difficile* genomes to investigate transmission** Xavier Didelot, David W Eyre, Madeleine Cule, Camilla LC Ip, M Ansari, David Griffiths, Alison Vaughan, Lily O'Connor, Tanya Golubchik, Elizabeth M Batty, Paolo Piazza, Daniel J Wilson, Rory Bowden, Peter J Donnelly, Kate E Dingle, Mark Wilcox, A Walker, Derrick W Crook, Tim E A Peto, Rosalind M Harding Genome Biology 2012, 13:R118 (21 December 2012) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary Transmission events of Clostridium difficile are inferred from whole-genome sequencing of isolates and estimating divergence time of bacterial strains
	11.	Research Microbiome dynamics of human epidermis following skin barrier disruption Patrick LJM Zeeuwen, Jos Boekhorst, Ellen H van den Bogaard, Heleen D de Koning, Peter MC van de Kerkhof, Delphine M Saulnier, Iris I van Swam, Sacha AFT van Hijum, Michiel Kleerebezem, Joost Schalkwijk, Harro M Timmerman Genome Biology 2012, 13:R101 (15 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An analysis of the microbiota of the surface and deeper layers of skin, and how it changes following skin barrier disruption
	12.	Research highlight Functional predictions from inference and observation in sequence-based inflammatory bowel disease research Folker Meyer, William L Trimble, Eugene B Chang, Kim M Handley Genome Biology 2012, 13:169 (26 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Research Highlight: important advances in understanding the gut microbiome composition and microbial metabolism in patients with IBD
	13.	Research Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment Xochitl C Morgan, Timothy L Tickle, Harry Sokol, Dirk Gevers, Kathryn L Devaney, Doyle V Ward, Joshua A Reyes, Samir A Shah, Neal LeLeiko, Scott B Snapper, Athos Bousvaros, Joshua Korzenik, Bruce E Sands, Ramnik J Xavier, Curtis Huttenhower Genome Biology 2012, 13:R79 (26 September 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of the microbes and microbial metabolism present in intestinal biopsies and stool samples from 231 IBD and healthy subjects
	14.	Research Staphylococcus epidermidis pan-genome sequence analysis reveals diversity of skin commensal and hospital infection-associated isolates Sean Conlan, Lilia A Mijares, Jesse Becker, Robert W Blakesley, Gerard G Bouffard, Shelise Brooks, Holly Coleman, Jyoti Gupta, Natalie Gurson, Morgan Park, Brian Schmidt, Pamela J Thomas, Michael Otto, Heidi H Kong, Patrick R Murray, Julia A Segre Genome Biology 2012, 13:R64 (25 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparative genomics of skin commensal and hospital infection-associated isolates uncovers a putative clinical biomarker
	15.	Method A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples Serena Dollive, Gregory L Peterfreund, Scott Sherrill-Mix, Kyle Bittinger, Rohini Sinha, Christian Hoffmann, Christopher S Nabel, David A Hill, David Artis, Michael A Bachman, Rebecca Custers-Allen, Stephanie Grunberg, Gary D Wu, James D Lewis, Frederic D Bushman Genome Biology 2012, 13:R60 (3 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary BROCC, a pipeline for the analysis of eukaryotes of microbiomes using conserved ribosomal rDNA sequences as markers
	16.	Research Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples Nicola Segata, Susan Haake, Peter Mannon, Katherine P Lemon, Levi Waldron, Dirk Gevers, Curtis Huttenhower, Jacques Izard Genome Biology 2012, 13:R42 (14 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Human Microbiome Project's analysis of ten sites in the digestive tract of healthy human adults
	17.	Research highlight We are what we eat: how the diet of infants affects their gut microbiome Mihai Pop Genome Biology 2012, 13:152 (30 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary We are what we eat: Mihai Pop highlights our Research article investigating the impact of diet on an infant's gut
	18.	Research A metagenomic study of diet-dependent interaction between gut microbiota and host in infants reveals differences in immune response Scott Schwartz, Iddo Friedberg, Ivan V Ivanov, Laurie A Davidson, Jennifer S Goldsby, David B Dahl, Damir Herman, Mei Wang, Sharon M Donovan, Robert S Chapkin Genome Biology 2012, 13:r32 (30 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A novel host-microbiome analysis method reveals a transcriptional immune response in the breast-fed infant gut associated with diet-specific microbiota
	19.	Method Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes Georgia Giannoukos, Dawn M Ciulla, Katherine Huang, Brian J Haas, Jacques Izard, Joshua Z Levin, Jonathan Livny, Ashlee M Earl, Dirk Gevers, Doyle V Ward, Chad Nusbaum, Bruce W Birren, Andreas Gnirke Genome Biology 2012, 13:r23 (28 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method is presented for transcriptome sequencing of complex bacterial mixtures or communities
	20.	Method Metagenomic biomarker discovery and explanation Nicola Segata, Jacques Izard, Levi Waldron, Dirk Gevers, Larisa Miropolsky, Wendy S Garrett, Curtis Huttenhower Genome Biology 2011, 12:R60 (24 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for distinguishing microbial populations from metagenomic data is presented
	21.	Research highlight The volatile microbiome George M Weinstock Genome Biology 2011, 12:114 (30 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary George Weinstock highlights Genome Biology's latest research article on human microbiota
	22.	Research Moving pictures of the human microbiome J Gregory Caporaso, Christian L Lauber, Elizabeth K Costello, Donna Berg-Lyons, Antonio Gonzalez, Jesse Stombaugh, Dan Knights, Pawel Gajer, Jacques Ravel, Noah Fierer, Jeffrey I Gordon, Rob Knight Genome Biology 2011, 12:R50 (30 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The dynamism of microbiome populations is seen in daily samples from a landmark multi-body site, multi-individual study
	23.	Method EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data Christopher S Miller, Brett J Baker, Brian C Thomas, Steven W Singer, Jillian F Banfield Genome Biology 2011, 12:R44 (19 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Reconstructing full length rRNA sequences from short reads to estimate microbial community structure
	24.	Review Direct sequencing of the human microbiome readily reveals community differences Justin Kuczynski, Elizabeth K Costello, Diana R Nemergut, Jesse Zaneveld, Christian L Lauber, Dan Knights, Omry Koren, Noah Fierer, Scott T Kelley, Ruth E Ley, Jeffrey I Gordon, Rob Knight Genome Biology 2010, 11:210 (5 May 2010) This article is part of a collection on 10th Anniversary... Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Future sequencing of the human microbiota will require greater breadth rather than depth.
	25.	Research Community-wide analysis of microbial genome sequence signatures Gregory J Dick, Anders F Andersson, Brett J Baker, Sheri L Simmons, Brian C Thomas, A Pepper Yelton, Jillian F Banfield Genome Biology 2009, 10:R85 (21 August 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome signatures are used to identify and cluster sequences de novo from an acid biofilm microbial community metagenomic dataset, revealing information about the low-abundance community members.