Association of dietary type with fecal microbiota in vegetarians and omnivores in Slovenia

Eur J Nutr. 2014 Jun;53(4):1051-64. doi: 10.1007/s00394-013-0607-6. Epub 2013 Oct 31.


Purpose: The purpose of this study was to discover differences in the human fecal microbiota composition driven by long-term omnivore versus vegan/lacto-vegetarian dietary pattern. In addition, the possible association of demographic characteristics and dietary habits such as consumption of particular foods with the fecal microbiota was examined.

Methods: This study was conducted on a Slovenian population comprising 31 vegetarian participants (11 lacto-vegetarians and 20 vegans) and 29 omnivore participants. Bacterial DNA was extracted from the frozen fecal samples by Maxwell 16 Tissue DNA Purification Kit (Promega). Relative quantification of selected bacterial groups was performed by real-time PCR. Differences in fecal microbiota composition were evaluated by PCR-DGGE fingerprinting of the V3 16S rRNA region. Participants' demographic characteristics, dietary habits and health status information were collected through a questionnaire.

Results: Vegetarian diet was associated with higher ratio (% of group-specific DNA in relation to all bacterial DNA) of Bacteroides-Prevotella, Bacteroides thetaiotaomicron, Clostridium clostridioforme and Faecalibacterium prausnitzii, but with lower ratio (%) of Clostridium cluster XIVa. Real-time PCR also showed a higher concentration and ratio of Enterobacteriaceae (16S rDNA copies/g and %) in female participants (p < 0.05 and p < 0.01) and decrease in Bifidobacterium with age (p < 0.01). DGGE analysis of the 16S rRNA V3 region showed that relative quantity of DGGE bands from certain bacterial groups was lower (Bifidobacterium, Streptococus, Collinsella and Lachnospiraceae) or higher (Subdoligranulum) among vegetarians, indicating the association of dietary type with bacterial community composition. Sequencing of selected DGGE bands revealed the presence of common representatives of fecal microbiota: Bacteroides, Eubacterium, Faecalibacterium, Ruminococcaceae, Bifidobacterium and Lachnospiraceae. Up to 4 % of variance in microbial community analyzed by DGGE could be explained by the vegetarian type of diet.

Conclusions: Long-term vegetarian diet contributed to quantity and associated bacterial community shifts in fecal microbiota composition. Consumption of foods of animal origin (eggs, red meat, white meat, milk, yoghurt, other dairy products, fish and seafood) and vegetarian type of diet explained the largest share of variance in microbial community structure. Fecal microbiota composition was also associated with participants' age, gender and body mass.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Adult
  • Aged
  • Bacteroides / isolation & purification
  • Bifidobacterium / isolation & purification
  • Child
  • Child, Preschool
  • Clostridium / isolation & purification
  • DNA, Bacterial / isolation & purification
  • Diet
  • Diet, Vegetarian*
  • Feces / chemistry
  • Feces / microbiology*
  • Feeding Behavior*
  • Female
  • Healthy Volunteers
  • Humans
  • Infant
  • Male
  • Microbiota*
  • Middle Aged
  • RNA, Ribosomal, 16S / genetics
  • RNA, Ribosomal, 16S / isolation & purification
  • Real-Time Polymerase Chain Reaction
  • Slovenia
  • Surveys and Questionnaires
  • Young Adult


  • DNA, Bacterial
  • RNA, Ribosomal, 16S