Beyond 16S rRNA Community Profiling: Intra-Species Diversity in the Gut Microbiota
Published 2016 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Beyond 16S rRNA Community Profiling: Intra-Species Diversity in the Gut Microbiota
Authors
Keywords
-
Journal
Frontiers in Microbiology
Volume 7, Issue -, Pages -
Publisher
Frontiers Media SA
Online
2016-09-21
DOI
10.3389/fmicb.2016.01475
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- The Modern Synthesis in the Light of Microbial Genomics
- (2016) Austin Booth et al. Annual Review of Microbiology
- Temporal Stability of the Human Skin Microbiome
- (2016) Julia Oh et al. CELL
- Host Selection of Microbiota via Differential Adhesion
- (2016) Kirstie McLoughlin et al. Cell Host & Microbe
- Bartonella apis sp. nov., a honey bee gut symbiont of the class Alphaproteobacteria
- (2016) Lucie Kešnerová et al. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
- Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations
- (2016) Matthew L Bendall et al. ISME Journal
- Strain diversity and host specificity in a specialized gut symbiont of honeybees and bumblebees
- (2016) Elijah Powell et al. MOLECULAR ECOLOGY
- Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation
- (2016) Hilary P. Browne et al. NATURE
- Development of the gut microbiota and mucosal IgA responses in twins and gnotobiotic mice
- (2016) Joseph D. Planer et al. NATURE
- The evolution of cooperation within the gut microbiota
- (2016) Seth Rakoff-Nahoum et al. NATURE
- Strain-level microbial epidemiology and population genomics from shotgun metagenomics
- (2016) Matthias Scholz et al. NATURE METHODS
- Gut microbial communities of social bees
- (2016) Waldan K. Kwong et al. NATURE REVIEWS MICROBIOLOGY
- Durable coexistence of donor and recipient strains after fecal microbiota transplantation
- (2016) Simone S. Li et al. SCIENCE
- Cospeciation of gut microbiota with hominids
- (2016) A. H. Moeller et al. SCIENCE
- Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea
- (2016) Elisabeth M. Bik et al. Nature Communications
- Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling
- (2016) Jennifer T. Lau et al. Genome Medicine
- Adaptation in Natural Microbial Populations
- (2015) Britt Koskella et al. Annual Review of Ecology Evolution and Systematics
- Multiorganismal Insects: Diversity and Function of Resident Microorganisms
- (2015) Angela E. Douglas Annual Review of Entomology
- The Gut Microbiota of Termites: Digesting the Diversity in the Light of Ecology and Evolution
- (2015) Andreas Brune et al. Annual Review of Microbiology
- MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome
- (2015) Stephen Nayfach et al. BIOINFORMATICS
- Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data: Fig. 1.
- (2015) Kathrin P. Aßhauer et al. BIOINFORMATICS
- MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
- (2015) Dinghua Li et al. BIOINFORMATICS
- Gene-specific selective sweeps in bacteria and archaea caused by negative frequency-dependent selection
- (2015) Nobuto Takeuchi et al. BMC BIOLOGY
- Extensive intra-phylotype diversity in lactobacilli and bifidobacteria from the honeybee gut
- (2015) Kirsten M Ellegaard et al. BMC GENOMICS
- Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species
- (2015) Sharon Greenblum et al. CELL
- Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life
- (2015) Fredrik Bäckhed et al. Cell Host & Microbe
- Insights from 20 years of bacterial genome sequencing
- (2015) Miriam Land et al. FUNCTIONAL & INTEGRATIVE GENOMICS
- Assessing the Unseen Bacterial Diversity in Microbial Communities
- (2015) Alejandro Caro-Quintero et al. Genome Biology and Evolution
- Accurate, multi-kb reads resolve complex populations and detect rare microorganisms
- (2015) Itai Sharon et al. GENOME RESEARCH
- Innate and Adaptive Humoral Responses Coat Distinct Commensal Bacteria with Immunoglobulin A
- (2015) Jeffrey J. Bunker et al. IMMUNITY
- Species-Specific Dynamic Responses of Gut Bacteria to a Mammalian Glycan
- (2015) Varsha Raghavan et al. JOURNAL OF BACTERIOLOGY
- Ecological Succession in the Honey Bee Gut: Shift in Lactobacillus Strain Dominance During Early Adult Development
- (2015) Kirk E. Anderson et al. MICROBIAL ECOLOGY
- ConStrains identifies microbial strains in metagenomic datasets
- (2015) Chengwei Luo et al. NATURE BIOTECHNOLOGY
- Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome
- (2015) Volodymyr Kuleshov et al. NATURE BIOTECHNOLOGY
- MetaPhlAn2 for enhanced metagenomic taxonomic profiling
- (2015) Duy Tin Truong et al. NATURE METHODS
- A complete bacterial genome assembled de novo using only nanopore sequencing data
- (2015) Nicholas J Loman et al. NATURE METHODS
- Sequencing and beyond: integrating molecular 'omics' for microbial community profiling
- (2015) Eric A. Franzosa et al. NATURE REVIEWS MICROBIOLOGY
- Gut biogeography of the bacterial microbiota
- (2015) Gregory P. Donaldson et al. NATURE REVIEWS MICROBIOLOGY
- Metabolic dependencies drive species co-occurrence in diverse microbial communities
- (2015) Aleksej Zelezniak et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples
- (2015) T. Korem et al. SCIENCE
- The ecology of the microbiome: Networks, competition, and stability
- (2015) K. Z. Coyte et al. SCIENCE
- The Bacterium Frischella perrara Causes Scab Formation in the Gut of its Honeybee Host
- (2015) Philipp Engel et al. mBio
- Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores
- (2015) Jon G. Sanders et al. Nature Communications
- The outer mucus layer hosts a distinct intestinal microbial niche
- (2015) Hai Li et al. Nature Communications
- The human gut virome: a multifaceted majority
- (2015) Lesley A. Ogilvie et al. Frontiers in Microbiology
- Inter-individual differences in the gene content of human gut bacterial species
- (2015) Ana Zhu et al. GENOME BIOLOGY
- Gut Symbionts from Distinct Hosts Exhibit Genotoxic Activity via Divergent Colibactin Biosynthesis Pathways
- (2014) Philipp Engel et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Routes of Acquisition of the Gut Microbiota of the Honey Bee Apis mellifera
- (2014) J. Elijah Powell et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Genomic Encyclopedia of Type Strains of the Genus Bifidobacterium
- (2014) Christian Milani et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance
- (2014) Tae-Hyuk Ahn et al. BIOINFORMATICS
- Immune-directed support of rich microbial communities in the gut has ancient roots
- (2014) Larry J. Dishaw et al. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY
- MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning
- (2014) Afiahayati et al. DNA RESEARCH
- Lactobacillus apinorum sp. nov., Lactobacillus mellifer sp. nov., Lactobacillus mellis sp. nov., Lactobacillus melliventris sp. nov., Lactobacillus kimbladii sp. nov., Lactobacillus helsingborgensis sp. nov. and Lactobacillus kullabergensis sp. nov., isolated from the honey stomach of the honeybee Apis mellifera
- (2014) T. C. Olofsson et al. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
- Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes
- (2014) M. Kim et al. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
- Implications of streamlining theory for microbial ecology
- (2014) Stephen J Giovannoni et al. ISME Journal
- The Devil Lies in the Details: How Variations in Polysaccharide Fine-Structure Impact the Physiology and Evolution of Gut Microbes
- (2014) Eric C. Martens et al. JOURNAL OF MOLECULAR BIOLOGY
- Gut microbiota–generated metabolites in animal health and disease
- (2014) Won-Jae Lee et al. Nature Chemical Biology
- Prochlorococcus: the structure and function of collective diversity
- (2014) Steven J. Biller et al. NATURE REVIEWS MICROBIOLOGY
- Explaining microbial genomic diversity in light of evolutionary ecology
- (2014) Otto X. Cordero et al. NATURE REVIEWS MICROBIOLOGY
- The Bacterial Communities Associated with Honey Bee (Apis mellifera) Foragers
- (2014) Vanessa Corby-Harris et al. PLoS One
- Illumina TruSeq Synthetic Long-Reads Empower De Novo Assembly and Resolve Complex, Highly-Repetitive Transposable Elements
- (2014) Rajiv C. McCoy et al. PLoS One
- A theoretical analysis of how strain-specific viruses can control microbial species diversity
- (2014) T. F. Thingstad et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Genomics and host specialization of honey bee and bumble bee gut symbionts
- (2014) W. K. Kwong et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus
- (2014) N. Kashtan et al. SCIENCE
- Symbiosis as a General Principle in Eukaryotic Evolution
- (2014) A. E. Douglas Cold Spring Harbor Perspectives in Biology
- Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale
- (2014) Thomas S. B. Schmidt et al. PLoS Computational Biology
- Hidden Diversity in Honey Bee Gut Symbionts Detected by Single-Cell Genomics
- (2014) Philipp Engel et al. PLoS Genetics
- Characterizing the avian gut microbiota: membership, driving influences, and potential function
- (2014) David W. Waite et al. Frontiers in Microbiology
- PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples
- (2014) Changjin Hong et al. Microbiome
- The Genotypic View of Social Interactions in Microbial Communities
- (2013) Sara Mitri et al. Annual Review of Genetics
- Benchmarking short sequence mapping tools
- (2013) Ayat Hatem et al. BMC BIOINFORMATICS
- An Ecological Network of Polysaccharide Utilization among Human Intestinal Symbionts
- (2013) Seth Rakoff-Nahoum et al. CURRENT BIOLOGY
- Frischella perrara gen. nov., sp. nov., a gammaproteobacterium isolated from the gut of the honeybee, Apis mellifera
- (2013) P. Engel et al. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
- Gene-targeted metagenomic analysis of glucan-branching enzyme gene profiles among human and animal fecal microbiota
- (2013) Sunghee Lee et al. ISME Journal
- Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria
- (2013) Samay Pande et al. ISME Journal
- The Singular Quest for a Universal Tree of Life
- (2013) J. Sapp et al. MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
- Correlates of gut community composition across an ant species (Cephalotes varians) elucidate causes and consequences of symbiotic variability
- (2013) Yi Hu et al. MOLECULAR ECOLOGY
- Convergence of gut microbiomes in myrmecophagous mammals
- (2013) Frédéric Delsuc et al. MOLECULAR ECOLOGY
- Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
- (2013) Morgan G I Langille et al. NATURE BIOTECHNOLOGY
- Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
- (2013) Chen-Shan Chin et al. NATURE METHODS
- Animals in a bacterial world, a new imperative for the life sciences
- (2013) Margaret McFall-Ngai et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Bacteriophage adhering to mucus provide a non-host-derived immunity
- (2013) J. J. Barr et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The Long-Term Stability of the Human Gut Microbiota
- (2013) J. J. Faith et al. SCIENCE
- Establishment of Characteristic Gut Bacteria during Development of the Honeybee Worker
- (2012) Vincent G. Martinson et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
- (2012) Y. Peng et al. BIOINFORMATICS
- Population Genomics: How Bacterial Species Form and Why They Don't Exist
- (2012) W. Ford Doolittle CURRENT BIOLOGY
- Polyclonality of Concurrent Natural Populations of Alteromonas macleodii
- (2012) Aitor Gonzaga et al. Genome Biology and Evolution
- Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization
- (2012) I. Sharon et al. GENOME RESEARCH
- Cultivation and characterization of the gut symbionts of honey bees and bumble bees: description of Snodgrassella alvi gen. nov., sp. nov., a member of the family Neisseriaceae of the Betaproteobacteria, and Gilliamella apicola gen. nov., sp. nov., a member of Orbaceae fam. nov., Orbales ord. nov., a sister taxon to the order 'Enterobacteriales' of the Gammaproteobacteria
- (2012) W. K. Kwong et al. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
- Pyrosequencing analysis of the bacterial communities in the guts of honey bees Apis cerana and Apis mellifera in Korea
- (2012) Jae-Hyung Ahn et al. JOURNAL OF MICROBIOLOGY
- Do diet and taxonomy influence insect gut bacterial communities?
- (2012) D. R. Colman et al. MOLECULAR ECOLOGY
- Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis
- (2012) KAREN E. SULLAM et al. MOLECULAR ECOLOGY
- A metagenome-wide association study of gut microbiota in type 2 diabetes
- (2012) Junjie Qin et al. NATURE
- Genomic variation landscape of the human gut microbiome
- (2012) Siegfried Schloissnig et al. NATURE
- Metagenomic microbial community profiling using unique clade-specific marker genes
- (2012) Nicola Segata et al. NATURE METHODS
- Distinctive Gut Microbiota of Honey Bees Assessed Using Deep Sampling from Individual Worker Bees
- (2012) Nancy A. Moran et al. PLoS One
- Independent Studies Using Deep Sequencing Resolve the Same Set of Core Bacterial Species Dominating Gut Communities of Honey Bees
- (2012) Zakee L. Sabree et al. PLoS One
- Bifidobacterium asteroides PRL2011 Genome Analysis Reveals Clues for Colonization of the Insect Gut
- (2012) Francesca Bottacini et al. PLoS One
- Functional diversity within the simple gut microbiota of the honey bee
- (2012) P. Engel et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Population Genomics of Early Events in the Ecological Differentiation of Bacteria
- (2012) B. J. Shapiro et al. SCIENCE
- A Crypt-Specific Core Microbiota Resides in the Mouse Colon
- (2012) T. Pedron et al. mBio
- The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss
- (2012) J. J. Morris et al. mBio
- The Evolution of Mutualism in Gut Microbiota Via Host Epithelial Selection
- (2012) Jonas Schluter et al. PLOS BIOLOGY
- Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance
- (2012) Steven W. Kembel et al. PLoS Computational Biology
- Ray Meta: scalable de novo metagenome assembly and profiling
- (2012) Sébastien Boisvert et al. GENOME BIOLOGY
- Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment
- (2012) Xochitl C Morgan et al. GENOME BIOLOGY
- Eating For Two: How Metabolism Establishes Interspecies Interactions in the Gut
- (2011) Michael A. Fischbach et al. Cell Host & Microbe
- Species coexistence in a variable world
- (2011) Dominique Gravel et al. ECOLOGY LETTERS
- Bacterial species may exist, metagenomics reveal
- (2011) Alejandro Caro-Quintero et al. ENVIRONMENTAL MICROBIOLOGY
- Resource partitioning in relation to cohabitation of Lactobacillus species in the mouse forestomach
- (2011) Gerald W Tannock et al. ISME Journal
- Ecology drives a global network of gene exchange connecting the human microbiome
- (2011) Chris S. Smillie et al. NATURE
- Experimental and analytical tools for studying the human microbiome
- (2011) Justin Kuczynski et al. NATURE REVIEWS GENETICS
- Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans
- (2011) B. D. Muegge et al. SCIENCE
- The Evolution of Host Specialization in the Vertebrate Gut Symbiont Lactobacillus reuteri
- (2011) Steven A. Frese et al. PLoS Genetics
- Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes
- (2011) Todd J. Treangen et al. PLoS Genetics
- Spatial organization of intestinal microbiota in the mouse ascending colon
- (2010) Gerardo M Nava et al. ISME Journal
- A simple and distinctive microbiota associated with honey bees and bumble bees
- (2010) VINCENT G. MARTINSON et al. MOLECULAR ECOLOGY
- Viruses in the faecal microbiota of monozygotic twins and their mothers
- (2010) Alejandro Reyes et al. NATURE
- Gut Microbiota in Health and Disease
- (2010) Inna Sekirov et al. PHYSIOLOGICAL REVIEWS
- Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates
- (2009) Victor Kunin et al. ENVIRONMENTAL MICROBIOLOGY
- On the origin of prokaryotic species
- (2009) W. F. Doolittle et al. GENOME RESEARCH
- Explaining microbial population genomics through phage predation
- (2009) Francisco Rodriguez-Valera et al. NATURE REVIEWS MICROBIOLOGY
- Worlds within worlds: evolution of the vertebrate gut microbiota
- (2008) Ruth E. Ley et al. NATURE REVIEWS MICROBIOLOGY
- Evolution of Mammals and Their Gut Microbes
- (2008) R. E. Ley et al. SCIENCE
- Resource Partitioning and Sympatric Differentiation Among Closely Related Bacterioplankton
- (2008) D. E. Hunt et al. SCIENCE
Publish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn MoreAdd your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload Now