Enrichment of the microbial fraction from pig faeces

The microbial fraction from a faecal sample was enriched using an adaptation of a previously described method by Ikeda et al. [27]. Prior to the enrichment process, 0.5 g of faeces was re-suspended in 9 ml of saline and homogenised for 2 min in a Stomacher 80 (Seward) at high power. Debris was removed from the homogenised sample by centrifugation at 500 g for 1 min. The supernatant was then transferred on top of 3.5 ml of sterile 80% (w/v) Histodenz (Sigma) and centrifuged in a Beckman ultracentrifuge using a JLA 16.250 rotor at 10,000 g for 40 min at 4°C. After centrifugation, the layer on top of the insoluble debris was recovered into a new 15 ml tube (Falcon) and centrifuged at 500 g for 1 min to remove debris. The supernatant was moved to a new 15 ml tube (Falcon) and centrifuged at 10,000 g for 20 min at 4°C. The bacterial pellet was washed in 10 ml of TE buffer (Merck) and used for the generation of Hi-C libraries.