| Method |
p.14695 right column 4th paragraph:"Taxonomic Assignment to 16S Reads: RDP classifier (v 2.1) software was used (ref 29) to classify the sequences according to the taxonomy proposed by Garrity et al. (ref 30), maintained at the Ribosomal Database Project (RDP 10 database, Update 18). RDP classifier also emits, for each taxonomic rank, a confidence estimate (CE) based on a bootstrapping procedure, allowing to append the notation of “_uncertain” to assignments with CE lower than a defined cutoff , usually 50% (Table S4). Bacterial species were assigned using a speed-optimized procedure based on BLAST and on the creation of genus specific subsamples of the RDP 10 database (details in SI Materials and Methods)." |
| Comments |
p.14693 left column bottom paragraph:"Firmicutes are twice as abundant in the EU [European Union, Florence, Italy] children as evidenced by the different ratio between Firmicutes and Bacteroidetes (F/B ratio ± SD, 2.8 ± 0.06 in EU and 0.47 ± 0.05 in BF [Burkina Faso, from rural African village]), suggesting a dramatically different bacterial colonization of the human gut in the two populations. Interestingly, Prevotella, Xylanibacter (Bacteroidetes) and Treponema (Spirochaetes) are present exclusively in BF children microbiota (Figs. 2 A and B, Fig. S2, and Table S5). [Investigators] can hypothesize that among the environmental factors separating the two populations (diet, sanitation, hygiene, geography, and climate) the presence of these three genera could be a consequence of high fiber intake, maximizing metabolic energy extraction from ingested plant polysaccharides." |