• Publications
  • Influence
Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla
Bacterial PERegrinations Many branches of the bacterial domain of life are only known from sequences that turn up in metagenomic analyses and are still only named by acronym—for example, theExpand
  • 465
  • 33
  • PDF
Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla
The adult human distal gut microbial community is typically dominated by 2 bacterial phyla (divisions), the Firmicutes and the Bacteroidetes. Little is known about the factors that govern theExpand
  • 527
  • 23
  • PDF
Shotgun metaproteomics of the human distal gut microbiota
The human gut contains a dense, complex and diverse microbial community, comprising the gut microbiome. Metagenomics has recently revealed the composition of genes in the gut microbiome, but providesExpand
  • 463
  • 22
  • PDF
Community proteomics of a natural microbial biofilm.
Using genomic and mass spectrometry-based proteomic methods, we evaluated gene expression, identified key activities, and examined partitioning of metabolic functions in a natural acid mine drainageExpand
  • 386
  • 21
  • PDF
Enigmatic, ultrasmall, uncultivated Archaea
Metagenomics has provided access to genomes of as yet uncultivated microorganisms in natural environments, yet there are gaps in our knowledge—particularly for Archaea—that occur at relatively lowExpand
  • 220
  • 19
  • PDF
Detecting differential and correlated protein expression in label-free shotgun proteomics.
Recent studies have revealed a relationship between protein abundance and sampling statistics, such as sequence coverage, peptide count, and spectral count, in label-free liquid chromatography-tandemExpand
  • 396
  • 17
  • PDF
Integrated Metagenomics/Metaproteomics Reveals Human Host-Microbiota Signatures of Crohn's Disease
Crohn's disease (CD) is an inflammatory bowel disease of complex etiology, although dysbiosis of the gut microbiota has been implicated in chronic immune-mediated inflammation associated with CD.Expand
  • 325
  • 13
  • PDF
Effects of Diet on Resource Utilization by a Model Human Gut Microbiota Containing Bacteroides cellulosilyticus WH2, a Symbiont with an Extensive Glycobiome
Artificial human gut microbial communities implanted into germ-free mice provide insights into how species-level responses to changes in diet give rise to community-level structural and functionalExpand
  • 171
  • 10
  • PDF
Molecular Dynamics of the Shewanella oneidensis Response to Chromate Stress*S
Temporal genomic profiling and whole-cell proteomic analyses were performed to characterize the dynamic molecular response of the metal-reducing bacterium Shewanella oneidensis MR-1 to an acuteExpand
  • 162
  • 10
  • PDF
Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages.
Nitrogen, sulfur and carbon fluxes in the terrestrial subsurface are determined by the intersecting activities of microbial community members, yet the organisms responsible are largely unknown.Expand
  • 110
  • 10