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Computer simulations by Liu et al. As with the established approach of generating data from clone libraries, the actual performance of tag pyrosequencing for the goals of a particular study will depend on the region of the 16 S rRNA gene analyzed, the PCR primers used, and the composition of the microbial communities in the samples.
In the present study, we used pyrosequencing tags spanning the V 6 and V 3 regions as well as full-length 16 S rRNA sequences to analyze the bacterial community composition in a time series of stool samples obtained from three healthy adults before,, and after a short course of the antibiotic ciprofloxacin Cp.
A companion paper reports a high degree of similarity in the community composition inferred from the two variable regions and from full-length sequences. Here we describe the diversity of human intestinal bacteria more completely and with more precision than has previously been possible.
Cp has an extensive and individualized effect on the composition of these communities, but most members of the community returned to their pretreatment abundance within weeks.
Methods Participants, Treatment, and Sampling Healthy adults who had not taken any antibiotics within the previous year were recruited to donate stool samples before,, and after a short course of ciprofloxacin Cp 500 mg twice a day for 5 d, typical of the treatment prescribed.
From a larger number of samples collected, we chose five time points spanning an 8-mo interval from each of three participants for analyses using full-length 16 S rRNA clone libraries and pyrosequencing of the V 6 variable region of 16 S rRNA.
An additional three samples from one of the participants were analyzed along with the original 15 samples using V 3 tag pyrosequencing. The safety profile was similar to that seen in adults.
Not known: Study 2 was an open-label, single-dose pharmacokinetic, multiple-dose safety study of famciclovir experimental granules mixed with OraSweet in famciclovir cat dose 1 to less than 12 years of age with clinically suspected HSV or varicella zoster virus VZV infection.
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