"gut origin: Human colon"	"characteristics_ch1.1"
"Fluorescence intensities of oligonucleotide spots were extracted from the scanned images using the Feature Extraction software (V11.0, Agilent Technologies). Then data were processed with dedicated scripts based on C++ and Delphi languages. For each probe, median intensity value of the 3 replicates was conserved and used as the probe signal value. The SNR (Signal-to-Noise Ratio), similar to the detection threshold response (positive hybridization) and corresponding to the probe signal value divided by the local background intensity value, was calculated for each probe. The SNR thresholds were set to 3 for 25-mer probes and 6 for 54-mer probes. Such SNR threshold values ensured a very specific response of the FibroChip, except for genes belonging to very close strains from the same species. Results for 25- and 54-mer probes were treated independently and for each probe type, a gene was considered as detected when 65% of probes were positive. The SNR value of a detected gene was then calculated by the mean of the SNR of all 25- or 54-mer probes targeting this gene, meeting or not the defined SNR threshold."	"data_processing.1"
"Culture of bacterial strains (10 mL) were centrifuged 20 min at 10,000 g and bacterial pellets were washed 3 times with 2 mL of phosphate buffered saline (PBS). DNA extraction was performed using the EasyDNA kit (Invitrogen) following the manufacturer instructions slightly modified. Briefly, the bacterial pellet was incubated 5 min in 200 μL of PBS and 1 μL of protéinase K (20 mg/mL, Invitrogen). Then, bacteria were grinded 3 min with ~100 mg of 0.1 mm zirconia beads (BioSpec Products) using the model MM2000 BeadBeater instrument (Retsch). Concentration and quality of isolated gDNA were checked with the spectrophotometer Nanodrop 1000 (Thermo Fisher Scientific). Their integrity was verified by 1% agarose gel electrophoresis. gDNA were kept at -20°C."	"extract_protocol_ch1.1"
"Genomic DNA was extracted from 4 bacteria strains. Strains Fibrobacter succinogenes S85 (ATCC 19169), Ruminococcus albus 20 (ATCC 27211) and Bacteroides xylanisolvens XB1A (DSM 18836T) were grown 15 h under strictly anaerobic conditions (Hungate, 1950) in a complex medium containing 20% of clarified rumen fluid (Béra-Maillet et al., 2000) and 0.2 g of cellobiose (Sigma-Aldrich) as carbon source, at 39°C for the two first ones and 37°C for the third one. The strain Escherichia coli K12 (ATCC 10798) was cultivated 15 h at 37°C in Luria-Bertani medium under shaking and aerobic conditions. ("	"growth_protocol_ch1.1"
"Escherichia coli K-12"	"organism_ch1.1"
"Bacteria"	"source_name_ch1.1"
"gDNA_Ecoli_K12"	"title.1"
"No treatment"	"treatment_protocol_ch1.1"
"gut origin: Human colon"	"characteristics_ch1.1"
"Genomic DNA was extracted from 4 bacteria strains. Strains Fibrobacter succinogenes S85 (ATCC 19169), Ruminococcus albus 20 (ATCC 27211) and Bacteroides xylanisolvens XB1A (DSM 18836T) were grown 15 h under strictly anaerobic conditions (Hungate, 1950) in a complex medium containing 20% of clarified rumen fluid (Béra-Maillet et al., 2000) and 0.2 g of cellobiose (Sigma-Aldrich) as carbon source, at 39°C for the two first ones and 37°C for the third one. The strain Escherichia coli K12 (ATCC 10798) was cultivated 15 h at 37°C in Luria-Bertani medium under shaking and aerobic conditions. ("	"growth_protocol_ch1.1"
"Escherichia coli K-12"	"organism_ch1.1"
"Bacteria"	"source_name_ch1.1"
"No treatment"	"treatment_protocol_ch1.1"