The species composition of the human intestinal microbiota differs between particle-associated and liquid phase communities

Alan W Walker, Sylvia H Duncan, Hermie J M Harmsen, Grietje Holtrop, Gjalt W Welling, Harry James Flint

Research output: Contribution to journalArticlepeer-review

107 Citations (Scopus)


Many of the substrates available as energy sources for microorganisms in the human colon, including dietary plant fibre and secreted mucin, are insoluble. It seems likely that such insoluble substrates support a specialized microbiota, and in order to test this hypothesis, faecal samples from four healthy subjects were fractionated into insoluble (washed particulate) and liquid fractions. Analysis of 1252 PCR-amplified 16S rRNA sequences revealed a significantly lower percentage of Bacteroidetes (P = 0.021) and a significantly higher percentage of Firmicutes (P = 0.029) among bacterial sequences amplified from particle-associated (mean 76.8% Firmicutes, 18.5% Bacteroidetes) compared with liquid phase (mean 65.8% Firmicutes, 28.5% Bacteroidetes). Within the Firmicutes, the most significant association with solid particles was found for relatives of Ruminococcus-related clostridial cluster IV species that include Ruminococcus flavefaciens and R. bromii, which together accounted for 12.2% of particle-associated, but only 3.3% of liquid phase, sequences. These findings were strongly supported by microscopy, using group-specific FISH probes able to detect these species. This work suggests that the primary colonizers of insoluble substrates found in the gut are restricted to certain specialized groups of bacteria. The abundance of such primary degraders may often be underestimated because of the difficulty in recovering these bacteria and their nucleic acids from the insoluble substrate.

Original languageEnglish
Pages (from-to)3275-3283
Number of pages9
JournalEnvironmental Microbiology
Issue number12
Early online date17 Aug 2008
Publication statusPublished - Dec 2008


  • in-situ hybridization
  • human colon
  • human gut
  • ruminococcus-flavefaciens
  • cell-surface
  • bacteroides-thetaiotaomicron
  • plant polysaccharides
  • bacterial-populations
  • sequence-analysis
  • dominant group
  • adult
  • bacteria
  • biodiversity
  • colon
  • DNA
  • bacterial
  • DNA, ribosomal
  • feces
  • genes
  • rRNA
  • humans
  • in situ hybridization
  • fluorescence
  • microscopy
  • fluorescence, molecular
  • sequence data
  • phylogeny
  • RNA, bacterial
  • RNA, ribosomal
  • 16S
  • sequence analysis, DNA
  • homology
  • nucleic acid


Dive into the research topics of 'The species composition of the human intestinal microbiota differs between particle-associated and liquid phase communities'. Together they form a unique fingerprint.

Cite this