design: Faeces was suspended 1:10 PBS V/V and homogenized in a Tissuelyzer at 25Hz for 2 min. Sample was centrifuged at 17000xg for 3 min. 500ul of supernatant was filtered through a 0.8uM Vivaclear mini spin filter at 2000x g for 2 min. A quantity of 450 L of the filtrate was then ultracentrifuged at 178,000 g for 1 h at room temperature. The resulting pellet was re-suspended in 130 L of PBS, and treated with benzococcal and micrococcal nucleases for 2 h. PMAxx dye was then added to a concentration of 200 M to each suspension and incubated for 10 min in the dark, before being exposed to blue light for 30 min. Reverse transcription and amplification were performed using the Seqplex RNA Amplification Kit as per the manufacturers instructions, except that the RNA and library synthesis solution incubation temperature was increased from 70C to 95C to denature the RNA, and the number of amplification PCR reaction cycles increased to 25 cycles.  Barcoded libraries were prepared using the Ion Plus Fragment Library Kit and IonXpress barcodes.