title: Microbiome analysis of stool samples from African Americans with colon polyps.
abstract: BACKGROUND
  Colonic polyps are common tumors occurring in ~50% of Western populations with ~10% risk of malignant progression. Dietary agents have been considered the primary environmental exposure to promote colorectal cancer (CRC) development. However, the colonic mucosa is permanently in contact with the microbiota and its metabolic products including toxins that also have the potential to trigger oncogenic transformation.
  
  
  OBJECTIVE
  To analyze fecal DNA for microbiota composition and functional potential in African Americans with pre-neoplastic lesions.
  
  
  METHODS
  We analyzed the bacterial composition of stool samples from 6 healthy individuals and 6 patients with colon polyps using 16S ribosomal RNA-based phylogenetic microarray; the Human intestinal Tract Chip (HITChip) and 16S rRNA gene barcoded 454 pyrosequencing. The functional potential was determined by sequence-based metagenomics using 454 pyrosequencing.
  
  
  RESULTS
  Fecal microbiota profiling of samples from the healthy and polyp patients using both a phylogenetic microarraying (HITChip) and barcoded 454 pyrosequencing generated similar results. A distinction between both sets of samples was only obtained when the analysis was performed at the sub-genus level. Most of the species leading to the dissociation were from the Bacteroides group. The metagenomic analysis did not reveal major differences in bacterial gene prevalence/abundances between the two groups even when the analysis and comparisons were restricted to available Bacteroides genomes.
  
  
  CONCLUSIONS
  This study reveals that at the pre-neoplastic stages, there is a trend showing microbiota changes between healthy and colon polyp patients at the sub-genus level. These differences were not reflected at the genome/functions levels. Bacteria and associated functions within the Bacteroides group need to be further analyzed and dissected to pinpoint potential actors in the early colon oncogenic transformation in a large sample size.
authors.affiliation: Department of Pathology, Department of Medicine and Cancer Center, Howard University, College of Medicine, Washington, District of Columbia, United States of America.
authors.forename: Hassan
authors.initials: H
authors.lastname: Brim
authors.affiliation: JCVI, San Diego, California, United States of America.
authors.forename: Shibu
authors.initials: S
authors.lastname: Yooseph
authors.affiliation: Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
authors.forename: Erwin G
authors.initials: EG
authors.lastname: Zoetendal
authors.affiliation: Department of Pathology, Department of Medicine and Cancer Center, Howard University, College of Medicine, Washington, District of Columbia, United States of America.
authors.forename: Edward
authors.initials: E
authors.lastname: Lee
authors.affiliation: JCVI, Rockville, Maryland, United States of America.
authors.forename: Manolito
authors.initials: M
authors.lastname: Torralbo
authors.affiliation: Department of Pathology, Department of Medicine and Cancer Center, Howard University, College of Medicine, Washington, District of Columbia, United States of America.
authors.forename: Adeyinka O
authors.initials: AO
authors.lastname: Laiyemo
authors.affiliation: Department of Pathology, Department of Medicine and Cancer Center, Howard University, College of Medicine, Washington, District of Columbia, United States of America.
authors.forename: Babak
authors.initials: B
authors.lastname: Shokrani
authors.affiliation: JCVI, Rockville, Maryland, United States of America.
authors.forename: Karen
authors.initials: K
authors.lastname: Nelson
authors.affiliation: Department of Pathology, Department of Medicine and Cancer Center, Howard University, College of Medicine, Washington, District of Columbia, United States of America.
authors.forename: Hassan
authors.initials: H
authors.lastname: Ashktorab
mesh_terms: D001741:Black or African American; D001419:Bacteria / Q000145:classification; D003111:Colonic Polyps / Q000382:microbiology*; D005243:Feces / Q000382:microbiology*; D006801:Humans; D056186:Metagenomics; D064307:Microbiota / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D010802:Phylogeny; D017422:Sequence Analysis, DNA