Depth-dependent differences in community structure of the human colonic microbiota in health.
OBJECTIVE
The aims of this study were to develop techniques for spatial microbial assessment in humans and to establish colonic luminal and mucosal spatial ecology, encompassing longitudinal and cross-sectional axes.


METHODS
A microbiological protected specimen brush was used in conjunction with a biopsy forceps to sample the colon in nine healthy volunteers undergoing colonoscopy. Terminal Restriction Fragment Length Polymorphism analysis was used to determine the major variables in the spatial organization of the colonic microbiota.


RESULTS
Protected Specimen Brush sampling retrieved region-specific, uncontaminated samples that were enriched for bacterial DNA and depleted in human DNA when compared to biopsy samples. Terminal Restriction Fragment Length Polymorphism analysis revealed a segmentation of bacterial communities between the luminal brush and biopsy-associated ecological niches with little variability across the longitudinal axis of the colon and reduced diversity in brush samples.


CONCLUSIONS
These results support the concept of a microbiota with little longitudinal variability but with some degree of segregation between luminal and mucosal communities.
University College Dublin, School of Medicine and Medical Science, Dublin, Ireland ; Centre for Colorectal Disease, St Vincent's University Hospital, Dublin, Ireland.
Aonghus
A
Lavelle
Grainne
G
Lennon
Neil
N
Docherty
Aine
A
Balfe
Hugh E
HE
Mulcahy
Glen
G
Doherty
Diarmuid
D
O Donoghue
John M
JM
Hyland
Fergus
F
Shanahan
Kieran
K
Sheahan
J Calvin
JC
Coffey
Desmond C
DC
Winter
P Ronan
PR
O Connell
D000328:Adult; D000368:Aged; D054458:Amplified Fragment Length Polymorphism Analysis / Q000379:methods; D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D001432:Bacteriology / Q000295:instrumentation; D044822:Biodiversity; D016000:Cluster Analysis; D003106:Colon / Q000382:microbiology*; D003113:Colonoscopy; D004269:DNA, Bacterial / Q000235:genetics; D017753:Ecosystem; D005260:Female; D014644:Genetic Variation; D064368:Healthy Volunteers; D006801:Humans; D008297:Male; D064307:Microbiota / Q000235:genetics*; D008875:Middle Aged; D009092:Mucous Membrane / Q000382:microbiology*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D013525:Surgical Instruments
D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S