Short-chain fatty acids (SCFAs) were determined by gas chromatography (GC-14B; Shimadzu, Kyoto, Japan). Succinate and d-/l-lactate were measured by commercial assay kits (Megazyme, Wicklow, Ireland). To monitor the growth of each bacterial strain in culture, copy number of 16S rRNA gene was quantified by real-time PCR. Repeated bead beating plus column method
(Yu & Morrison, www.selleckchem.com/products/VX-809.html 2004) was employed for DNA extraction and purification from 1 mL of inocula and cultures at 48 and 96 h. PCR targeting the 16S rRNA gene was performed with a LightCycler 480 system (Roche Applied Science, Mannheim, Germany) and a KAPA SYBR FAST qPCR kit (KAPA Biosystems, Woburn, MA). Primer sets specific to each bacterial strain were used as follows: U2_Fw (5′-CTAGGTGTAGGGGGTATC-3′) and U2_Rv (5′-GCTGCCCTCTGTCGTTG-3′) for strain R-25 (Koike et al., 2010), 193f (5′-GGTATGGGATGAGCTTGC-3′) and 654r (5′-GCCTGCCCCTGAACTATC-3′) for F. succinogenes S85 (Tajima et al., 2001) and Sele.rumi_Fw (5′-TGCTAATACCGAATGTTG-3′) and Sele.rumi_Rv (5′-TCCTGCACTCAAGAAAGA-3′) for S. ruminantium S137 (Tajima et al., 2001). All other quantification procedures, including the standard plasmids, PCR conditions, and calculations, were according to Koike et al. (2007, 2010). To measure the fibrolytic activity in culture, fibrolytic HIF inhibitor enzyme assays were carried out for extracellular and intracellular fractions.
Culture supernatant and bacterial cells from strains R-25 and F. succinogenes S85 monocultures and their coculture were separated by centrifugation (16 000 g, 4 °C, 10 min). The supernatant was placed in dialysis tubing (12 000- to 14 000-Da cut-off, Seamless Cellulose Tubing, Sanko-junyaku, Tokyo,
Japan) in potassium phosphate buffer (50 mM, pH 6.8) overnight. The dialyzed fraction was condensed with polyethylene glycol (MW 20,000) and used in extracellular enzyme assays. Cell-free extract was obtained by ultrasonic disruption of the cell pellet (10 × 1 min on ice, 20 kHz, 25 watts) using a VC-70 GNA12 Ultrasonic Processor (Sonics and Materials, Newton, CT) followed by centrifugation (16 000 g, 4 °C, 20 min) and was used in intracellular enzyme assay. The carboxymethylcellulase (CMCase) and xylanase activities were determined by monitoring the increase in reducing sugar formation from the substrates using dinitrosalicylic acid reagents, as described by Cotta (1988). Carboxymethylcellulose and oat spelt xylan were dissolved in 50 mM potassium phosphate buffer (pH 6.8) at 1% (w/v) and used as the substrates. The protein concentration was determined using Bio-Rad Protein Assay kit (Bio-Rad, Hercules, CA) with bovine gamma globulin as a standard. Enzyme activity was expressed as specific activity (formation of 1 nmol of sugar min−1 mg of protein−1) or total activity mL−1 culture (formation of 1 nmol of sugar min−1 mL−1 of original culture).