Mp fastprep homogenizer

Samples were processed in BSL2 conditions using either the Miniprep (0.25 g of starting material) or Maxiprep (20 g of starting material) version of the DNeasy PowerSoil Kit from Qiagen (Venlo, Netherlands). Extractions were repeated until ∼1 μg (or more) of raw DNA was obtained for each sample (Table S1, Supporting Information). Samples B, C, D, E were processed using the Miniprep kit, following the manufacturer's protocol and by adding dithiothréitol (DTT) to the C1 buffer at a 10 mM final concentration. All other samples (K, L, M, N, O, P, Q, R) were processed using the Maxiprep kit, including the addition of DTT to the C1 buffer at a 10 mM final. Samples were ground for 20 s in an MP FastPrep homogenizer (MP Biomedicals, Santa Ana, California, USA) at a speed of 4 m/s then incubated for 30 min at 65°C and finally ground again for 20 s at 4 m/s. After elution in 5 ml of elution buffer the extracted raw DNA was concentrated on a silica column from the Monarch Genomic DNA purification Kit from New England Biolabs (Ipswich, MA, USA). The DNA contents were then quantified using Qubit (Thermo Fisher Scientific, Waltham, MA, USA) and NanoDrop (Thermo Fisher Scientific) assays (Table S1, Supporting Information) prior sequencing.

For screening of native bacterial isolates, the R2 agar was supplemented with 0.2% lactose and either 20 µg/ml 5‐bromo‐4‐chloro‐3‐indolyl β‐d‐galactopyranoside (X‐gal) for β‐d‐galactosidase activity or 20 µg/ml 5‐bromo‐4‐chloro‐3‐indolyl β‐d‐fucopyranoside (X‐fuc) for α‐l‐fucosidase activity. Cultures were incubated at 50°C overnight, and positive colonies were re‐inoculated until pure colonies with enzymatic activity were obtained.
Crude protein extract was made by bead beating of cells harvested from an overnight culture (50°C, 200 rpm) in a MP FastPrep Homogenizer (MP Biomedicals) at speed 5.5 for 3 × 25 s in 2‐ml Micro tubes PP (Sarstedt, Nümbrecht) supplemented with approx. 250 µl acid‐washed glass beads (212–300 µm, 425–600 µm, ratio 1:1). Extracts were tested for hydrolytic activity with 1 mM oNPG and 1 mM pNP‐fucose at 50°C until visible yellow color was developed (10–35 min). Reactions were stopped with 0.5 M Na₂CO₃, and OD₄₀₅ was measured in an EL808 Ultra Microplate Reader (BioTek Instruments, Inc.,).