Computational protocol: Long-term irritable bowel syndrome symptom control with reintroduction of selected FODMAPs

Similar protocols

Protocol publication

[…] Stool samples were collected at baseline, three and six months from participants and within 4 h frozen and stored at -20 °C. DNA was extracted using the MoBio 96-well Soil DNA Extraction kit (MoBio Laboratories Inc., Carlsbad, CA, United States) according to the Earth Microbiome Projects protocols (www.earthmicrobiome.org). Samples were then amplified using primers based on the bacterial/archael primers 515F/806R and amplified, sequenced and analyzed as before[]. Taxonomy was assigned using the RDP classifier[] to assign taxonomy to genus level with any taxonomic level with a ≤ 0.80 confidence score assigned “unclassified”. Tests for significance of individual taxa were carried out using ALDEx2 version 0.99[] and community analysis with the Quantitative Insights into Microbial Ecology package[]. […]

Pipeline specifications

Software tools RDP Classifier, ALDEx, QIIME
Application 16S rRNA-seq analysis
Organisms Homo sapiens
Diseases Irritable Bowel Syndrome