Extended Data Fig. 3: Perinatal antibiotics alter diversity of the intestinal microbiome.
From: Preventing dysbiosis of the neonatal mouse intestinal microbiome protects against late-onset sepsis
(a) Initial Shannon entropy analysis of reads classified to Gammapreoteobacteria (left) or Lactobacillales (right). Oligotyping analysis was performed to resolve Lactobacillales oligotypes, but not carried out on Gammaproteobacteria reads due to low entropy. Shannon entropy by nucleotide position was calculated from the combined sequencing data described in Fig. 3e using the standard oligotyping pipeline. (b) Ratio (top) and absolute counts (bottom) of Lactobacillales reads in each sample aligning to any of the 8 oligotypes compared with reads failing to align. 465,160 reads from 36 samples were input and 453,693 were used in the final analysis after quality filtering. (c) 26 isolates from P5 intestinal samples were identified via BLAST of full length 16S gene sequence. Sequences from the V4 region of each oligotype resolved from previous analysis were aligned to each isolate. Table shows the number of isolates with > 98% match to a previously identified oligotype and the Shannon entropy measurements following oligotyping to highlight any unresolved diversity.
