Bidirectional interactions between indomethacin and the murine intestinal microbiota
Samples were collected along the intestine of mice treated with or without indomethacin. An independent set of fecal samples were collected from mice treated with or without antibiotics. Amplicon libraries were constructed by amplifying the 16S V1-V2 region of the bacterial genome, and sequencing was performed with 454/Roche GS FLX Titanium chemistry.
Each amplicon library was constructed by amplifying the 16S rRNA gene using the BSF8 and and the BSR357 primer pair. Primers contained DNA barcode sequences such as those described by Hamady et al. 2008, and the recommended 454 adapter sequences. Amplification conditions are described in McKenna et al 2007, with exception that the polymerase used was AccuPrime (Invitrogen, Carlsbad, CA, USA).