Quantifying the metabolic activities of human-associated microbial communities across multiple ecological scales.

No abstract is available for this paper.

• Publication year

  2013

• Venue

  FEMS Microbiology Reviews

• Publication date

  2013-09-01

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1111/1574-6976.12022PMID 23550823PMCID PMC3729610
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Conserved Shifts in the Gut Microbiota Due to Gastric Bypass Reduce Host Weight and Adiposity

  2013cited by this paper
• The future is now: single-cell genomics of bacteria and archaea.

  2013cited by this paper
• Impact of chronic exposure to low doses of chlorpyrifos on the intestinal microbiota in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®) and in the rat

  2013influential reference
• Developing a metagenomic view of xenobiotic metabolism.

  2013cited by this paper
• Xenobiotics shape the physiology and gene expression of the active human gut microbiome.

  2013influential reference
• Molecular Microbial Ecology Manual

  2013cited by this paper
• Infant antibiotic exposures and early-life body mass

  2013cited by this paper
• Genomic analysis identifies association of Fusobacterium with colorectal carcinoma.

  2012cited by this paper
• Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish.

  2012cited by this paper
• Regulated Virulence Controls the Ability of a Pathogen to Compete with the Gut Microbiota

  2012cited by this paper
• Gut immune maturation depends on colonization with a host-specific microbiota.

  2012cited by this paper
• Dietary fat-induced taurocholic acid production promotes pathobiont and colitis in IL-10−/− mice

  2012cited by this paper
• Structure, Function and Diversity of the Healthy Human Microbiome

  2012influential reference
• Antibiotics in early life alter the murine colonic microbiome and adiposity

  2012cited by this paper
• Detecting metabolic activities in single cells, with emphasis on nanoSIMS.

  2012influential reference
• A metagenome-wide association study of gut microbiota in type 2 diabetes

  2012cited by this paper
• Human gut microbiome viewed across age and geography

  2012influential reference
• Microbial Co-occurrence Relationships in the Human Microbiome

  2012cited by this paper
• Metabolic Syndrome and Altered Gut Microbiota in Mice Lacking Toll-Like Receptor 5

  2012cited by this paper
• Multidomain Carbohydrate-binding Proteins Involved in Bacteroides thetaiotaomicron Starch Metabolism*

  2012cited by this paper
• Anthropology of microbes

  2012cited by this paper
• Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts

  2012cited by this paper
• Bacteria of the human gut microbiome catabolize red seaweed glycans with carbohydrate-active enzyme updates from extrinsic microbes

  2012cited by this paper
• Outer membrane vesicles of a human commensal mediate immune regulation and disease protection.

  2012cited by this paper
• Molecular analysis of model gut microbiotas by imaging mass spectrometry and nanodesorption electrospray ionization reveals dietary metabolite transformations.

  2012cited by this paper
• Microbial interactions: from networks to models

  2012cited by this paper
• Honor Thy Gut Symbionts Redux

  2012cited by this paper
• Is It Time for a Metagenomic Basis of Therapeutics?

  2012cited by this paper
• Galacto-oligosaccharides have prebiotic activity in a dynamic in vitro colon model using a (13)C-labeling technique.

  2012cited by this paper
• Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB)

  2012cited by this paper
• Induction of Colonic Regulatory T Cells by Indigenous Clostridium Species

  2011cited by this paper
• Predicting a Human Gut Microbiota’s Response to Diet in Gnotobiotic Mice

  2011cited by this paper
• Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging

  2011cited by this paper
• Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease

  2011cited by this paper
• The Toll-Like Receptor 2 pathway Establishes Colonization by a Commensal of the Human Microbiota

  2011cited by this paper
• The Toll-Like Receptor 2 Pathway Establishes Colonization by a Commensal of the Human Microbiota

  2011cited by this paper
• The Active Human Gut Microbiota Differs from the Total Microbiota

  2011cited by this paper
• The Evolution of Host Specialization in the Vertebrate Gut Symbiont Lactobacillus reuteri

  2011cited by this paper
• The Intestinal Microbiota and Viral Susceptibility

  2011cited by this paper
• Flow cytometry to assess biochemical pathways in heat‐stressed Cronobacter spp. (formerly Enterobacter sakazakii)

  2011cited by this paper
• Detecting Novel Associations in Large Data Sets

  2011cited by this paper
• Bacteroides in the infant gut consume milk oligosaccharides via mucus-utilization pathways.

  2011cited by this paper
• Genomic analysis at the single-cell level.

  2011cited by this paper
• Recognition and Degradation of Plant Cell Wall Polysaccharides by Two Human Gut Symbionts

  2011cited by this paper
• Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice

  2011cited by this paper
• Spatial organization of intestinal microbiota in the mouse ascending colon

  2011cited by this paper
• Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease

  2011cited by this paper
• Sulfatases and a Radical S-Adenosyl-l-methionine (AdoMet) Enzyme Are Key for Mucosal Foraging and Fitness of the Prominent Human Gut Symbiont, Bacteroides thetaiotaomicron*

  2011cited by this paper
• Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

  2011cited by this paper
• Use of Stable Isotopes To Measure the Metabolic Activity of the Human Intestinal Microbiota

  2011influential reference
• Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins

  2011cited by this paper
• Enterotypes of the human gut microbiome

  2011cited by this paper
• Dark Matter

  2011cited by this paper
• Trade-Off between Bile Resistance and Nutritional Competence Drives Escherichia coli Diversification in the Mouse Gut

  2011cited by this paper
• The Impact of a Consortium of Fermented Milk Strains on the Gut Microbiome of Gnotobiotic Mice and Monozygotic Twins

  2011cited by this paper
• Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

  2010influential reference
• Alleviating Cancer Drug Toxicity by Inhibiting a Bacterial Enzyme

  2010cited by this paper
• Viewing the human microbiome through three-dimensional glasses: integrating structural and functional studies to better define the properties of myriad carbohydrate-active enzymes

  2010cited by this paper
• Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota

  2010cited by this paper
• Virus-plus-susceptibility gene interaction determines Crohn's disease gene Atg16L1 phenotypes in intestine.

  2010cited by this paper
• Flow cytometry for bacteria: enabling metabolic engineering, synthetic biology and the elucidation of complex phenotypes.

  2010cited by this paper
• Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns

  2010cited by this paper
• Metabolic Syndrome and Altered Gut Microbiota in Mice Lacking Toll-Like Receptor 5

  2010cited by this paper
• Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins

  2010cited by this paper
• Creating and characterizing communities of human gut microbes in gnotobiotic mice

  2010cited by this paper
• Detection of Mycoplasma pneumoniae in Simulated and True Clinical Throat Swab Specimens by Nanorod Array-Surface-Enhanced Raman Spectroscopy

  2010cited by this paper
• A human gut microbial gene catalogue established by metagenomic sequencing

  2010cited by this paper
• Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota

  2010cited by this paper
• Raman tweezers sorting of single microbial cells.

  2009cited by this paper
• Direct analysis of clinical relevant single bacterial cells from cerebrospinal fluid during bacterial meningitis by means of micro‐Raman spectroscopy

  2009cited by this paper
• Comprar Surface Analysis: The Principal Techniques | John C. Vickerman | 9780470017630 | Wiley

  2009cited by this paper
• Towards a nondestructive chemical characterization of biofilm matrix by Raman microscopy

  2009cited by this paper
• Surface analysis : the principal techniques

  2009cited by this paper
• Global diversity in the human salivary microbiome.

  2009cited by this paper
• Single-cell ecophysiology of microbes as revealed by Raman microspectroscopy or secondary ion mass spectrometry imaging.

  2009influential reference
• Identifying genetic determinants needed to establish a human gut symbiont in its habitat.

  2009cited by this paper
• Bacterial Community Variation in Human Body Habitats Across Space and Time

  2009influential reference
• Microbiome Metagenomic Analysis of the Human Distal Gut

  2009influential reference
• Isolation and characterization of low nucleic acid (LNA)-content bacteria

  2009cited by this paper
• The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice

  2009influential reference
• Induction of intestinal Th17 cells by segmented filamentous bacteria.

  2009cited by this paper
• Changes in the Composition of the Human Fecal Microbiome After Bacteriotherapy for Recurrent Clostridium difficile-associated Diarrhea

  2009cited by this paper
• Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome.

  2008cited by this paper
• A core gut microbiome in obese and lean twins

  2008influential reference
• Eubacterium limosum activates isoxanthohumol from hops (Humulus lupulus L.) into the potent phytoestrogen 8-prenylnaringenin in vitro and in rat intestine.

  2008cited by this paper
• Physiological Structure and Single‐Cell Activity in Marine Bacterioplankton

  2008cited by this paper
• Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes

  2008cited by this paper
• Linking Microbial Phylogeny to Metabolic Activity at the Single-Cell Level by Using Enhanced Element Labeling-Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (EL-FISH) and NanoSIMS

  2008cited by this paper
• Barcoding bacterial cells: A SERS based methodology for pathogen identification.

  2008cited by this paper
• Alternatively Activated Macrophages in Intestinal Helminth Infection: Effects on Concurrent Bacterial Colitis1

  2007cited by this paper
• Raman-FISH: combining stable-isotope Raman spectroscopy and fluorescence in situ hybridization for the single cell analysis of identity and function.

  2007influential reference
• A comparative study of the cytometric characteristics of high and low nucleic-acid bacterioplankton cells from different aquatic ecosystems.

  2007cited by this paper
• Identification of glucose-fermenting bacteria present in an in vitro model of the human intestine by RNA-stable isotope probing.

  2007cited by this paper
• Human gut microbes associated with obesity

  2007cited by this paper
• Methodological Considerations for the Use of Stable Isotope Probing in Microbial Ecology

  2007cited by this paper
• DNA stable-isotope probing

  2007cited by this paper
• Quantitative Imaging of Nitrogen Fixation by Individual Bacteria Within Animal Cells

  2007cited by this paper
• Comparative Metagenomics Revealed Commonly Enriched Gene Sets in Human Gut Microbiomes

  2007influential reference
• Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth

  2007cited by this paper
• The future of single-cell environmental microbiology.

  2007cited by this paper

• Machine Learning Models for High-Throughput Screening of Obesogens Based on Pathway Network

  2025cites this paper
• A Fecal Metabolite Signature of Impaired Fasting Glucose: Results From Two Independent Population-Based Cohorts

  2023cites this paper
• Microbiota and probiotics: chances and challenges – a symposium report

  2023cites this paper
• MetaLP: An integrative linear programming method for protein inference in metaproteomics

  2022cites this paper
• Massively parallel single-cell sequencing of genetic loci in diverse microbial populations

  2022cites this paper
• d‐Amino Acid‐Based Metabolic Labeling Enables a Fast Antibiotic Susceptibility Test of Both Isolated Bacteria and Bronchoalveolar Lavage Fluid

  2021cites this paper
• Effects of oxygen exposure on relative nucleic acid content and membrane integrity in the human gut microbiota

  2021cites this paper
• Quantification of Bacterial Metabolic Activities in the Gut by D-Amino Acid-based in vivo Labeling.

  2020cites this paper
• Translational activity is uncoupled from nucleic acid content in bacterial cells of the human gut microbiota

  2020cites this paper
• Towards a rational design of faecal transplant analogues

  2019cites this paper
• Microbial Interaction Network Inference in Microfluidic Droplets.

  2019cites this paper
• Less Is More: Genome Reduction and the Emergence of Cooperation—Implications into the Coevolution of Microbial Communities

  2019cites this paper
• The mechanistic link between health and gut microbiota diversity

  2018cites this paper
• Methods for microbiota analysis: sample collection and laboratory methods

  2018cites this paper
• Gut microbial functional maturation and succession during human early life

  2018cites this paper
• The aryl hydrocarbon receptor as a moderator of host-microbiota communication.

  2017cites this paper
• Investigation of bacterial viability from incubated saliva by application of flow cytometry and hyphenated separation techniques

  2017cites this paper
• Gut microbiota, metabolites and host immunity

  2016cites this paper
• The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism

  2016cites this paper
• MICROBIAL FORENSIC'S - MICROBES AS A PART OF FORENSIC INVESTIGATION

  2016cites this paper
• Present and foreseeable future of metabolomics in forensic analysis.

  2016cites this paper
• Constraint-based modeling of host-microbe and microbe-microbe metabolic interactions in the human gut

  2015cites this paper
• Mapping Metabolic Interactions Between S . cerevisiae and Lactic Acid Bacteria

  2015influential citation
• Metabolic interactions in microbial communities: untangling the Gordian knot.

  2015cites this paper
• Novel Applications of Molecular Biological and Microscopic Tools in Environmental Engineering

  2013cites this paper
• Quantifying and identifying the active and damaged subsets of indigenous microbial communities.

  2013cites this paper