For this comparison, two aliquots from each volunteer (#1 to #8, named L1 to L8) and for each condition were used. Thus, a total of 48 samples were prepared for microbial composition analysis. To evaluate the effect of stool water content and the bead-beating technique on the integrity of microbial DNA and, therefore, on microbial composition analysis, fresh stool samples were homogenised

with an increasing proportion of phosphate-buffered saline (PBS), as indicated in Table 1. Assuming that a normal stool contains 75% (range 56.6%–84.9%) of water, the dilutions tested corresponded to 75%, 80%, 87.5%, 93.8%, 97.5% and 99.5% of water content, respectively, which reflect the range of typical diarrhoeic samples [9, 12]. Similar amounts of each diluted sample were then disrupted CX-4945 molecular weight with and without a bead-beating step. This procedure was carried out for four of the eight volunteers

cited above (#1, #3, #5 and #8, named DL1, DL3, DL5 and DL8). Thus, a total of 46 samples were collected for microbiome analysis. Table 1 Addition of PBS to obtain stools with a range of water content ID Weight (mg) Presence of beads PBS (μl) Water content L# 250 yes – 75.0% DL#.00 250 yes 0 75.0% DL#.25 187.5 yes 62.5 80.0% DL#.50 125 yes 125.0 87.5% DL#.75 62.5 yes MM-102 manufacturer 187.5 93.8% DL#.90 25 yes 225.0 97.5% DL#.98 5 yes 245.0 99.5% DL#B.00 250 yes – 75.0% DL#B.25 187.5 Dichloromethane dehalogenase yes – 75.0% DL#B.50 125 yes – 75.0% DL#B.75 62.5 yes – 75.0% DL#B.90 25 yes – 75.0% DL#B.98 5 yes – 75.0% DL#P.50 125 – 125.0 87.5% DL#P.75 62.5 – 187.5 93.8%

DL#P.90 25 – 225.0 97.5% DL#P.98 5 – 245.0 99.5% DL#C.50 125 – - 75.0% DL#C.75 62.5 – - 75.0% DL#C.90 25 – - 75.0% DL#C.98 5 – - 75.0% # indicates the identification number for each subject. L# = stands for layer in the homogenisation study. DL# = the “D” stands for diarrhoea in the water content study; the “L” refers to samples that have been also used in the homogenisation study, that contained PBS and underwent a bead-beating step. DL#B = samples that did not contain PBS but underwent a bead-beating step. DL#P = samples that contained PBS but did not undergo a bead-beating step. DL#C = samples that did not contain PBS and did not undergo a bead-beating step. Effect of stool homogenisation during collection Usually, participants are instructed to homogenise their stool samples during collection. However, given the laborious and unpleasant nature of this task, it is possible that they might not have fully complied with this procedure. To evaluate the impact of homogenisation on the composition of the microbial community, we analysed the 48 samples as specified in the experimental design cited above (L#) by means of pyrosequencing the 16S rRNA gene at a normalised depth of 6173 sequences of 290 bp per sample.