High temporal and inter-individual variation detected in the human ileal microbiota.

The diversity and temporal stability of the predominant bacteria in the human ileum was studied with the use of ileal effluent samples of seven individuals with Brooke ileostomies. The total number of bacteria within the ileal effluent was in the range of 10⁷ -10⁸ bacteria per gram (wet weight). The diversity of the bacteria in the ileal effluent showed marked differences compared with that in faecal samples from age-matched healthy adults. The ileal effluent had a higher relative abundance of species within the orders Lactobacillales and Clostridiales, mainly Streptococcus bovis-related species, and the Veillonella group, and a lower proportion of species related to Ruminococcus gnavus, R. obeum and Bacteroides plebeius. In addition, inter-individual differences were found, indicative of a highly personal ileal microbiota profile. Furthermore, temporal profiles showed large fluctuations per individual over a period of 9-28 days (average similarity over a period of 9 days was as low as 44%), and differences between morning and afternoon profiles were observed. Parallel cloning and sequencing efforts revealed several phylotypes that were not identified in previous studies (12 out of 65 phylotypes showed less than 97% sequence similarity with previously reported sequences). Achaea were found to be below detection limit by quantitative PCR. Overall, the results indicate that the microbiota of the human ileum is relatively unstable, less complex and consisting of different dominating phylotypes when compared with the colonic microbiota.

[1]  H. Hayashi,et al.  Molecular Analysis of Fecal Microbiota in Elderly Individuals Using 16S rDNA Library and T‐RFLP , 2003, Microbiology and immunology.

[2]  M. Pop,et al.  Metagenomic Analysis of the Human Distal Gut Microbiome , 2006, Science.

[3]  C. Neut,et al.  Changes in the bacterial flora of the neoterminal ileum after ileocolonic resection for Crohn's disease , 2002, American Journal of Gastroenterology.

[4]  M. Nadkarni,et al.  Quantitative Analysis of Diverse Lactobacillus Species Present in Advanced Dental Caries , 2004, Journal of Clinical Microbiology.

[5]  Jonathan A. Eisen,et al.  Human gut microbiome adopts an alternative state following small bowel transplantation , 2009, Proceedings of the National Academy of Sciences.

[6]  E. Zoetendal,et al.  High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota , 2008, Gut.

[7]  A. Hope.  A Simplified Monte Carlo Significance Test Procedure , 1968 .

[8]  L. van Lieshout,et al.  Changes in bacterial composition and enzymatic activity in ileostomy and ileal reservoir during intermittent occlusion: a study using dogs , 1992, Applied and environmental microbiology.

[9]  C. Pollitt,et al.  Streptococcus henryi sp. nov. and Streptococcus caballi sp. nov., isolated from the hindgut of horses with oligofructose-induced laminitis. , 2008, International journal of systematic and evolutionary microbiology.

[10]  A. Simpson,et al.  Rapid silver staining and recovery of PCR products separated on polyacrylamide gels. , 1994, BioTechniques.

[11]  W. D. de Vos,et al.  Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults , 2009, Environmental microbiology.

[12]  E. Zoetendal,et al.  Temperature Gradient Gel Electrophoresis Analysis of 16S rRNA from Human Fecal Samples Reveals Stable and Host-Specific Communities of Active Bacteria , 1998, Applied and Environmental Microbiology.

[13]  Martin Wiedmann,et al.  Culture independent analysis of ileal mucosa reveals a selective increase in invasive Escherichia coli of novel phylogeny relative to depletion of Clostridiales in Crohn's disease involving the ileum , 2007, The ISME Journal.

[14]  P. Turnbaugh,et al.  Microbial ecology: Human gut microbes associated with obesity , 2006, Nature.

[15]  H. Andersson.  The ileostomy model for the study of carbohydrate digestion and carbohydrate effects on sterol excretion in man. , 1992, European journal of clinical nutrition.

[16]  R. Amann,et al.  Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis , 1996, Journal of bacteriology.

[17]  M. Rajilić-Stojanović.  Diversity of the human gastrointestinal microbiota : novel perspectives from high throughput analyses , 2007 .

[18]  E. Delong,et al.  Quantitative Analysis of Small-Subunit rRNA Genes in Mixed Microbial Populations via 5′-Nuclease Assays , 2000, Applied and Environmental Microbiology.

[19]  S. Gorbach,et al.  Studies of intestinal microflora. IV. The microflora of ileostomy effluent: a unique microbial ecology. , 1967, Gastroenterology.

[20]  K. Schleifer,et al.  ARB: a software environment for sequence data. , 2004, Nucleic acids research.

[21]  T. Florin,et al.  Molecular characterization of the microbial species that colonize human ileal and colonic mucosa by using 16S rDNA sequence analysis , 2003, Journal of applied microbiology.

[22]  D. Stahl,et al.  Monitoring the enrichment and isolation of sulfate-reducing bacteria by using oligonucleotide hybridization probes designed from environmentally derived 16S rRNA sequences , 1993, Applied and environmental microbiology.

[23]  H. C. Douglas,et al.  Studies on the Anaerobic Micrococci , 1948, Journal of bacteriology.

[24]  D. Relman,et al.  Assembly of the human intestinal microbiota. , 2006, Trends in ecology & evolution.

[25]  Maria Saarela,et al.  Intra-individual diversity and similarity of salivary and faecal microbiota. , 2008, Journal of medical microbiology.

[26]  D. Cowan,et al.  Review and re-analysis of domain-specific 16S primers. , 2003, Journal of microbiological methods.

[27]  A. Uitterlinden,et al.  Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA , 1993, Applied and environmental microbiology.

[28]  B. Roe,et al.  A core gut microbiome in obese and lean twins , 2008, Nature.

[29]  Willem M. de Vos,et al.  The Host Genotype Affects the Bacterial Community in the Human Gastrointestinal Tract , 2001 .

[30]  F. Gillet,et al.  Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns. , 2002, Environmental microbiology.

[31]  Hauke Smidt,et al.  Diversity of the human gastrointestinal tract microbiota revisited. , 2007, Environmental microbiology.

[32]  Jan Lepš,et al.  Multivariate Analysis of Ecological Data using CANOCO , 2003 .

[33]  W. D. de Vos,et al.  Comparative Analysis of Pyrosequencing and a Phylogenetic Microarray for Exploring Microbial Community Structures in the Human Distal Intestine , 2009, PloS one.

[34]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[35]  Janet K. Jansson,et al.  Twin studies reveal specific imbalances in the mucosa‐associated microbiota of patients with ileal Crohn's disease , 2009, Inflammatory bowel diseases.

[36]  H. Drexler,et al.  The Pearson product‐moment correlation coefficient is better suited for identification of DNA fingerprint profiles than band matching algorithms , 1993, Electrophoresis.

[37]  Christophe Caron,et al.  Towards the human intestinal microbiota phylogenetic core. , 2009, Environmental microbiology.

[38]  Hiroshi Mori,et al.  Comparative Metagenomics Revealed Commonly Enriched Gene Sets in Human Gut Microbiomes , 2007, DNA research : an international journal for rapid publication of reports on genes and genomes.

[39]  E. Zoetendal,et al.  Molecular Diversity of Lactobacillus spp. and Other Lactic Acid Bacteria in the Human Intestine as Determined by Specific Amplification of 16S Ribosomal DNA , 2002, Applied and Environmental Microbiology.

[40]  J. Fujimoto,et al.  Use of 16S rRNA Gene-Targeted Group-Specific Primers for Real-Time PCR Analysis of Predominant Bacteria in Human Feces , 2004, Applied and Environmental Microbiology.

[41]  Michiel Kleerebezem,et al.  Isolation of DNA from bacterial samples of the human gastrointestinal tract , 2006, Nature Protocols.

[42]  S. Ahrné,et al.  Comparison of bacterial diversity along the human intestinal tract by direct cloning and sequencing of 16S rRNA genes. , 2005, FEMS microbiology ecology.

[43]  J. Doré,et al.  Food, GI-tract Functionality and Human Health Cluster: PROEUHEALTH , 2002 .

[44]  S. Gorbach,et al.  The microflora of the human ileum and intrabdominal colon: results of direct needle aspiration at surgery and evaluation of the technique. , 1972, The Journal of laboratory and clinical medicine.

[45]  J. Swings,et al.  Temporal stability analysis of the microbiota in human feces by denaturing gradient gel electrophoresis using universal and group-specific 16S rRNA gene primers. , 2004, FEMS microbiology ecology.

[46]  J. Jansson,et al.  Molecular analysis of the gut microbiota of identical twins with Crohn's disease , 2008, The ISME Journal.

[47]  E. H. Simpson.  Measurement of Diversity , 1949, Nature.

[48]  G. Macfarlane,et al.  Mucosa-Associated Bacterial Diversity in Relation to Human Terminal Ileum and Colonic Biopsy Samples , 2007, Applied and Environmental Microbiology.

[49]  Mitsuo Sakamoto,et al.  Molecular analysis of jejunal, ileal, caecal and recto-sigmoidal human colonic microbiota using 16S rRNA gene libraries and terminal restriction fragment length polymorphism. , 2005, Journal of medical microbiology.