This organism is one of the very few for which a single strain (found for example in infant #5, sample 1 shown here) was detected in multiple infants. Consensus sequence for the alignments (shown at the top of each alignment) represents the calculated order of the most frequent nucleotide residues. Alignments were done in Geneious v7.1.7 (Kearse et al., 2012), using MAFFT v7.017 (Katoh et al., 2002) with default parameters. Samples are ordered by similarity. For each sample, SNPs and indel locations relative to the multiple alignment are marked by black lines or boxes. Reads from three samples, from which different Clostridium paraputrificum strains were recovered (infant #5 samples 1 and 7, infant #6 sample 3) were mapped to three 100–200 Kbp scaffolds (infant #5 sample 1, scaffolds 3 and 8, and infant #5 sample 7, scaffold 41). Shown is a multiple alignment of the consensus sequences derived for each sample from these mappings. The different strains are very closely related, yet multiple SNPs and short indels are detected throughout the sequence. Large indels shown in the bottom panels are both associated with mobile elements.