Quantitative, longitudinal profiling of the primate fecal microbiota reveals idiosyncratic, dynamic communities.
We used slot blot hybridization, quantitative polymerase chain reaction (qPCR), and flow cytometry microarrays to quantify specific 16S rDNAs in weekly fecal specimens from four monkeys housed in a research vivarium for periods ranging from five to 8 months. Even in these uniformly housed and fed animals the gut microbiota is idiosyncratic, very dynamic on short timescales, and shows significant positive and negative correlations among some bacteria as well as responses to heavy metal exposure. The relative quantification (fmol targets per total fmol bacterial 16S rDNA) afforded by flow cytometry microarrays agreed well with the absolute quantification (nanogram of target DNA per nanogram of fecal DNA) afforded by slot blots and qPCR. We also noted strengths and weaknesses in inter-method comparisons for DNA-based quantification of these complex bacterial communities.
Department of Microbiology, The University of Georgia, Athens, GA 30602, USA.
Joy
J
Wireman
Mary
M
Lowe
Alex
A
Spiro
Yu-Zhong
YZ
Zhang
Andrew
A
Sornborger
Anne O
AO
Summers
D000818:Animals; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001419:Bacteria / Q000254:growth & development*; D044822:Biodiversity; D015169:Colony Count, Microbial; D004269:DNA, Bacterial / Q000032:analysis; D004275:DNA, Ribosomal / Q000032:analysis; D005243:Feces / Q000382:microbiology*; D005434:Flow Cytometry; D000882:Haplorhini / Q000382:microbiology*; D008297:Male; D019216:Metals, Heavy / Q000494:pharmacology; D009693:Nucleic Acid Hybridization; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics
D000900:Anti-Bacterial Agents; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D019216:Metals, Heavy; D012336:RNA, Ribosomal, 16S