Genomic DNA was isolated using an Easy-DNA (Invitrogen) kit. PCR
reaction conditions were described above and PCR product cleanup was performed
using ExoSAP-IT (Affymetrix) per the manufactures protocol. Near full-length 16S
rRNA amplicons were sequenced at the University of Michigan DNA Sequencing Core
using primers 8F (5′-AGA GTT TGA TCC TGG CTC AG- 3′), 515F
(5′-GTG CCA GCM GCC GCG GTA- 3′), E939R (5′-CTT GTG CGG
GCC CCC GTC AAT TC- 3′), and 1492R (5′-GGT TAC CTT GTT ACG ACT
T- 3′). CLUSTALW multiple-sequence alignments were generated for each
isolate and a near-full length 16S rRNA gene consensus sequence was obtained.
The consensus sequence was taxonomically classified using the RDP classifier
(https://rdp.cme.msu.edu/classifier/classifier.jsp accessed
between 6-29-2012 and 3-7-2013)50 (link). Bacterial strains that classified to the family
Lachnospiraceae were used in this study ((Supplementary Table 7 )).
reaction conditions were described above and PCR product cleanup was performed
using ExoSAP-IT (Affymetrix) per the manufactures protocol. Near full-length 16S
rRNA amplicons were sequenced at the University of Michigan DNA Sequencing Core
using primers 8F (5′-AGA GTT TGA TCC TGG CTC AG- 3′), 515F
(5′-GTG CCA GCM GCC GCG GTA- 3′), E939R (5′-CTT GTG CGG
GCC CCC GTC AAT TC- 3′), and 1492R (5′-GGT TAC CTT GTT ACG ACT
T- 3′). CLUSTALW multiple-sequence alignments were generated for each
isolate and a near-full length 16S rRNA gene consensus sequence was obtained.
The consensus sequence was taxonomically classified using the RDP classifier
(
between 6-29-2012 and 3-7-2013)50 (link). Bacterial strains that classified to the family
Lachnospiraceae were used in this study ((