Computational protocol: Oral supplementation of healthy adults with2′-O-fucosyllactose and lacto-N-neotetraose is welltolerated and shifts the intestinal microbiota

Similar protocols

Protocol publication

[…] The paired-end reads were merged, and low-quality sequences were discarded (truncating reads at a quality score of 4 or less and requiring 100-bp overlap between paired reads, perfect match to primers, a merged sequence length of 300–600 bp, a maximum of five expected errors and a minimum of 5 identical sequences in the data set). Sequences were clustered into operational taxonomic units (OTU) at 97 % sequence similarity using USEARCH( ), and suspected chimeric sequences were discarded on the basis of UCHIME( ). Taxonomic assignment of OTU was performed on the basis of comparison with a database of curated sequences derived from the Ribosomal Database Project( ). Samples were rarified to the lowest sequence number found in a sample (11 568 sequences). Both negative controls and mock communities were included in the analysis as quality controls. […]

Pipeline specifications

Software tools USEARCH, UCHIME
Application 16S rRNA-seq analysis
Organisms Homo sapiens
Diseases Neisseriaceae Infections