Strain analysis
SNP level analysis was performed across the subjects by mapping metagenomic reads to bacterial reference genomes and quantify nucleotide variation along the entire genomeĀ (i.e. the read depth and observed alleles at each position), to identify multiple strains of bacteria playing role in adaptation. Further SNP nucleotide variants from all the samples were pooled and filtered at 15X depth at a minor allele frequency of 0.01.
Strain level maximum likely hood phylogenetic tree was constructed (FASTTREEĀ  http://www.microbesonline.org/fasttree) (Figure5), using consensus alleles obtained from the core-genome sequences of Prevotella copri 61740 having nucleotide variation (multi-FASTA file in supplementary at H1, H3 to H2 and H4), which separates it from strain at H1, H3 versus H2 and H4 (High altitudes), respectively.
It is observed that the abundance of significantly appeared individual nine strains, Roseburia inulinivorans 61943, Faecalibacterium prausnitzii 62201, Oscillibacter sp 60799 and Eubacterium eligens 61678 had similar pattern of appearance as increase at H2, decrease at H3 and again increase at H4. Except Roseburia inulinivorans 61943 other three had a sharp decline at H3. Megamonas hypermegale 57114 and Eubacterium rectale 56927 decreased linearly at H2 and H3 with sudden increase at H4. Whereas, Bacteroides vulgatus 57955 showed a very different and declined pattern at H2, which persisted till H3, with a marginal increase at H4. Contrary to all these patterns Prevotella copri 61740 had sharp increment at H2 which further increased to H3 with a mild decrement at H4 (Figure 6).