Relating the metatranscriptome and metagenome of the human gut.

PubWeight™: 2.11‹?› | Rank: Top 2%

🔗 View Article (PMC 4050606)

Published in Proc Natl Acad Sci U S A on May 19, 2014

Authors

Eric A Franzosa1, Xochitl C Morgan1, Nicola Segata2, Levi Waldron2, Joshua Reyes2, Ashlee M Earl3, Georgia Giannoukos3, Matthew R Boylan4, Dawn Ciulla3, Dirk Gevers3, Jacques Izard5, Wendy S Garrett6, Andrew T Chan7, Curtis Huttenhower8

Author Affiliations

1: Biostatistics Department andThe Broad Institute, Cambridge, MA 02142;
2: Biostatistics Department and.
3: The Broad Institute, Cambridge, MA 02142;
4: Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114;
5: Department of Microbiology, The Forsyth Institute, Cambridge, MA 02142;Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, MA 02115;
6: The Broad Institute, Cambridge, MA 02142;Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115;Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215; and.
7: Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114;Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA 02115.
8: Biostatistics Department andThe Broad Institute, Cambridge, MA 02142; chuttenh@hsph.harvard.edu.

Articles citing this

Temporal Stability of the Human Skin Microbiome. Cell (2016) 2.41

Commensal bacteria make GPCR ligands that mimic human signalling molecules. Nature (2017) 2.01

Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks. Gut (2015) 1.63

Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases. Cell (2017) 1.46

Sequencing and beyond: integrating molecular 'omics' for microbial community profiling. Nat Rev Microbiol (2015) 1.41

Inflammatory bowel disease as a model for translating the microbiome. Immunity (2014) 1.39

An evaluation of the accuracy and speed of metagenome analysis tools. Sci Rep (2016) 1.36

Strain-level microbial epidemiology and population genomics from shotgun metagenomics. Nat Methods (2016) 1.30

Microbiota-mediated inflammation and antimicrobial defense in the intestine. Annu Rev Immunol (2015) 1.23

The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease. Cell Host Microbe (2014) 1.08

Breaking down the barriers: the gut microbiome, intestinal permeability and stress-related psychiatric disorders. Front Cell Neurosci (2015) 1.06

The human intestinal microbiome at extreme ages of life. Dietary intervention as a way to counteract alterations. Front Genet (2014) 1.05

Beyond microbial community composition: functional activities of the oral microbiome in health and disease. Microbes Infect (2015) 1.04

Library preparation methodology can influence genomic and functional predictions in human microbiome research. Proc Natl Acad Sci U S A (2015) 1.03

Uncovering oral Neisseria tropism and persistence using metagenomic sequencing. Nat Microbiol (2016) 1.01

Temporal and technical variability of human gut metagenomes. Genome Biol (2015) 1.00

Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome. Comput Struct Biotechnol J (2015) 1.00

Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls. PeerJ (2015) 0.99

Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies. mSystems (2016) 0.97

Reduction of butyrate- and methane-producing microorganisms in patients with Irritable Bowel Syndrome. Sci Rep (2015) 0.96

Dual RNA-seq reveals viral infections in asthmatic children without respiratory illness which are associated with changes in the airway transcriptome. Genome Biol (2017) 0.96

The role of the intestinal microbiota in type 1 diabetes mellitus. Nat Rev Endocrinol (2016) 0.93

Application of metagenomics in the human gut microbiome. World J Gastroenterol (2015) 0.90

Dual Transcriptomic Profiling of Host and Microbiota during Health and Disease in Pediatric Asthma. PLoS One (2015) 0.89

Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics. Front Microbiol (2016) 0.87

The players may change but the game remains: network analyses of ruminal microbiomes suggest taxonomic differences mask functional similarity. Nucleic Acids Res (2015) 0.86

Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes. Genome Med (2016) 0.84

Stool metatranscriptomics: A technical guideline for mRNA stabilisation and isolation. BMC Genomics (2015) 0.84

Integrating microbial and host transcriptomics to characterize asthma-associated microbial communities. BMC Med Genomics (2015) 0.83

Evidence-based recommendations on storing and handling specimens for analyses of insect microbiota. PeerJ (2015) 0.83

Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis. Evol Bioinform Online (2016) 0.83

Analysis of the mouse gut microbiome using full-length 16S rRNA amplicon sequencing. Sci Rep (2016) 0.82

MixMC: A Multivariate Statistical Framework to Gain Insight into Microbial Communities. PLoS One (2016) 0.82

Thermophilic microbial cellulose decomposition and methanogenesis pathways recharacterized by metatranscriptomic and metagenomic analysis. Sci Rep (2014) 0.82

Selective Manipulation of the Gut Microbiota Improves Immune Status in Vertebrates. Front Immunol (2015) 0.81

Intricacies of assessing the human microbiome in epidemiologic studies. Ann Epidemiol (2016) 0.80

Determining microbial products and identifying molecular targets in the human microbiome. Cell Metab (2014) 0.80

Studying Vertical Microbiome Transmission from Mothers to Infants by Strain-Level Metagenomic Profiling. mSystems (2017) 0.80

Comparison of Collection Methods for Fecal Samples in Microbiome Studies. Am J Epidemiol (2016) 0.79

MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota. Microbiome (2016) 0.79

Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis. Bioinformatics (2015) 0.79

Characterization of Intestinal Microbiota in Ulcerative Colitis Patients with and without Primary Sclerosing Cholangitis. J Crohns Colitis (2015) 0.79

No difference in small bowel microbiota between patients with irritable bowel syndrome and healthy controls. Sci Rep (2015) 0.79

Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant. Front Microbiol (2015) 0.79

Interplay between diet, gut microbiota, epigenetic events, and colorectal cancer. Mol Nutr Food Res (2016) 0.79

Defining the microbial transcriptional response to colitis through integrated host and microbiome profiling. ISME J (2016) 0.79

Taxonomic Assessment of Rumen Microbiota Using Total RNA and Targeted Amplicon Sequencing Approaches. Front Microbiol (2016) 0.78

Characterization of the gut microbiome in epidemiologic studies: the multiethnic cohort experience. Ann Epidemiol (2016) 0.78

Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota. Front Microbiol (2015) 0.78

Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants. Microbiome (2016) 0.78

How to Predict Molecular Interactions between Species? Front Microbiol (2016) 0.77

Transitioning From Descriptive to Mechanistic Understanding of the Microbiome: The Need for a Prospective Longitudinal Approach to Predicting Disease. J Pediatr (2016) 0.77

Metabolic modeling with Big Data and the gut microbiome. Appl Transl Genom (2016) 0.77

Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults. PLoS One (2016) 0.76

Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing. PLoS One (2016) 0.76

Bifidobacteria Abundance-Featured Gut Microbiota Compositional Change in Patients with Behcet's Disease. PLoS One (2016) 0.76

Emerging Technologies for Gut Microbiome Research. Trends Microbiol (2016) 0.76

Gut Microbiota as a Target for Preventive and Therapeutic Intervention against Food Allergy. Nutrients (2017) 0.76

Increasing Metagenomic Resolution of Microbiome Interactions Through Functional Phylogenomics and Bacterial Sub-Communities. Front Genet (2016) 0.75

Use of Metatranscriptomics in Microbiome Research. Bioinform Biol Insights (2016) 0.75

Circulating microbial RNA and health. Sci Rep (2015) 0.75

Intriguing Interaction of Bacteriophage-Host Association: An Understanding in the Era of Omics. Front Microbiol (2017) 0.75

Simultaneous purification of DNA and RNA from microbiota in a single colonic mucosal biopsy. BMC Res Notes (2016) 0.75

Function and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate Transferases and Their Diversity in the Proximal Colon of Swine. Appl Environ Microbiol (2016) 0.75

Periodontal and inflammatory bowel diseases: Is there evidence of complex pathogenic interactions? World J Gastroenterol (2016) 0.75

Comparison of Fecal Collection Methods for Microbiota Studies in Bangladesh. Appl Environ Microbiol (2017) 0.75

Transcriptional regulation and adaptation to a high-fiber environment in Bacillus subtilis HH2 isolated from feces of the giant panda. PLoS One (2015) 0.75

Diversity and enterotype in gut bacterial community of adults in Taiwan. BMC Genomics (2017) 0.75

IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses. Genome Biol (2016) 0.75

Diet affects arctic ground squirrel gut microbial metatranscriptome independent of community structure. Environ Microbiol (2017) 0.75

Characterization of CRISPR RNA transcription by exploiting stranded metatranscriptomic data. RNA (2016) 0.75

The Metagenome of Utricularia gibba's Traps: Into the Microbial Input to a Carnivorous Plant. PLoS One (2016) 0.75

Metatranscriptomic Profiling Reveals Linkages between the Active Rumen Microbiome and Feed Efficiency in Beef Cattle. Appl Environ Microbiol (2017) 0.75

SAMSA: a comprehensive metatranscriptome analysis pipeline. BMC Bioinformatics (2016) 0.75

Embracing the gut microbiota: the new frontier for inflammatory and infectious diseases. Clin Transl Immunology (2017) 0.75

Overexpression of antibiotic resistance genes in hospital effluents over time. J Antimicrob Chemother (2017) 0.75

Host-Microbiome Interaction and Cancer: Potential Application in Precision Medicine. Front Physiol (2016) 0.75

Fecal Microbiome in Epidemiologic Studies-Letter. Cancer Epidemiol Biomarkers Prev (2016) 0.75

Microbial bioinformatics 2020. Microb Biotechnol (2016) 0.75

Cross Talk: The Microbiota and Neurodevelopmental Disorders. Front Neurosci (2017) 0.75

Shaping functional gut microbiota using dietary bioactives to reduce colon cancer risk. Semin Cancer Biol (2017) 0.75

Community characteristics of the gut microbiomes of competitive cyclists. Microbiome (2017) 0.75

Evolutionary Biology Needs Wild Microbiomes. Front Microbiol (2017) 0.75

Capturing the genetic makeup of the active microbiome in situ. ISME J (2017) 0.75

Feasibility of Metatranscriptome Analysis from Infant Gut Microbiota: Adaptation to Solid Foods Results in Increased Activity of Firmicutes at Six Months. Int J Microbiol (2017) 0.75

Microbial Community Functional Potential and Composition Are Shaped by Hydrologic Connectivity in Riverine Floodplain Soils. Microb Ecol (2016) 0.75

Potential and active functions in the gut microbiota of a healthy human cohort. Microbiome (2017) 0.75

Fluoride Depletes Acidogenic Taxa in Oral but Not Gut Microbial Communities in Mice. mSystems (2017) 0.75

Articles cited by this

Accurate whole human genome sequencing using reversible terminator chemistry. Nature (2008) 90.20

A core gut microbiome in obese and lean twins. Nature (2008) 52.30

Search and clustering orders of magnitude faster than BLAST. Bioinformatics (2010) 51.97

Structure, function and diversity of the healthy human microbiome. Nature (2012) 30.40

KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res (2011) 30.20

Bacterial community variation in human body habitats across space and time. Science (2009) 24.84

Enterotypes of the human gut microbiome. Nature (2011) 24.36

A framework for human microbiome research. Nature (2012) 11.41

Metagenomic microbial community profiling using unique clade-specific marker genes. Nat Methods (2012) 8.37

Clostridium difficile infection: new developments in epidemiology and pathogenesis. Nat Rev Microbiol (2009) 7.89

Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc Natl Acad Sci U S A (2010) 7.09

Gut microbiomes of Malawian twin pairs discordant for kwashiorkor. Science (2013) 6.98

Peptidoglycan structure and architecture. FEMS Microbiol Rev (2008) 6.69

Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci U S A (2008) 6.50

Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol (2012) 6.27

A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries. Genome Biol (2011) 5.11

A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism. Proc Natl Acad Sci U S A (2006) 5.04

From the regulation of peptidoglycan synthesis to bacterial growth and morphology. Nat Rev Microbiol (2011) 4.98

Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol (2012) 4.68

Metabolic interactions between anaerobic bacteria in methanogenic environments. Antonie Van Leeuwenhoek (1994) 4.48

The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. Sci Transl Med (2011) 4.24

Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS One (2008) 3.83

Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell (2013) 3.26

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes. Genome Biol (2012) 3.02

Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut. Proc Natl Acad Sci U S A (2007) 2.79

Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column. Nature (2009) 2.72

Adaptation of Escherichia coli to high osmolarity environments: osmoregulation of the high-affinity glycine betaine transport system proU. FEMS Microbiol Rev (1994) 2.41

Metatranscriptomic approach to analyze the functional human gut microbiota. PLoS One (2011) 2.14

Proteasomes and other self-compartmentalizing proteases in prokaryotes. Trends Microbiol (1999) 1.86

Biodiversity and functional genomics in the human microbiome. Trends Genet (2012) 1.52

Chapter 12: Human microbiome analysis. PLoS Comput Biol (2012) 1.44

Metatranscriptome analysis of the human fecal microbiota reveals subject-specific expression profiles, with genes encoding proteins involved in carbohydrate metabolism being dominantly expressed. Appl Environ Microbiol (2010) 1.18

Dialister invisus sp. nov., isolated from the human oral cavity. Int J Syst Evol Microbiol (2003) 1.05

Functional profiling of the gut microbiome in disease-associated inflammation. Genome Med (2013) 0.93

Condensing the omics fog of microbial communities. Trends Microbiol (2013) 0.90

Antibiotics and anaerobes of gut origin. Curr Opin Microbiol (2003) 0.88

Microbial community analysis and identification of alternative host-specific fecal indicators in fecal and river water samples using pyrosequencing. J Microbiol (2011) 0.88