Molecular biological methods for studying the gut microbiota: the EU human gut flora project

• Published in: British journal of nutrition Vol. 87; no. S2; pp. S203 - S211
• Main Authors: Blaut, M., Collins, M.D., Welling, G. W., Doré, J., van Loo, J., de Vos, W.
• Format: Journal Article Conference Proceeding
• Language: English
• Published: Cambridge, UK Cambridge University Press 01.05.2002; Cambridge University Press (CUP)
• Subjects: Adult; Aged; Aging; Animal, plant and microbial ecology; Bacteria; Bacteria - genetics; Biological and medical sciences; Cloning; Databases, Factual; Diet; European Union; Feces - microbiology; Flora; Food and Nutrition; Fundamental and applied biological sciences. Psychology; Genes, Bacterial; Genotype; Humans; In Situ Hybridization; Infant; Intestines - microbiology; Laboratories; Laboratorium voor Microbiologie; Life Sciences; Microbial ecology; Microbiological Laboratory; Microbiologie; Microbiology; Microbiota; Normal microflora of man and animals. Rumen; Nutrition; Oligonucleotide Probes - genetics; Phylogenetics; Phylogeny; Polymerase chain reaction; Polymerase Chain Reaction - methods; Probes; RNA, Ribosomal, 16S; Species diversity; Taxonomy; VLAG; Netherlands; Intestinal flora; Ribosomal RNA; Gut microbiology; Genotypic identification of bacteria; Human; Methodology; Digestive system; Taxonomy; Gut; Chemotaxonomy; Genotype; Microflora; Species diversity; Investigation method; Bacteria; Genetic identification; Specific identification; Microbial community; TUBE DIGESTIF
• ISSN: 0007-1145; 1475-2662
• DOI: 10.1079/BJN/2002539

Seven European laboratories co-operated in a joint project (FAIR CT97-3035) to develop, refine and apply molecular methods towards facilitating elucidation of the complex composition of the human intestinal microflora and to devise robust methodologies for monitoring the gut flora in response to diet. An extensive database of 16S rRNA sequences for tracking intestinal bacteria was generated by sequencing the 16S rRNA genes of new faecal isolates and of clones obtained by amplification with polymerase chain reaction (PCR) on faecal DNA from subjects belonging to different age groups. The analyses indicated that the number of different species (diversity) present in the human gut increased with age. The sequence information generated, provided the basis for design of 16S rRNA-directed oligonucleotide probes to specifically detect bacteria at various levels of phylogenetic hierarchy. The probes were tested for their specificity and used in whole-cell and dot-blot hybridisations. The applicability of the developed methods was demonstrated in several studies and the major outcomes are described.