Polymorphic sites present in all loci among the <i>S</i>. <i>haemolyticus</i> isolates.

<p>For allele one, the nucleotide designation at the variable site is shown. For the rest of the alleles, only those sites that differ from allele one is shown. The position of the polymorphic site within the sequenced fragment is shown above (in vertical format), and synonymous (S) and non-synonymous (N) polymorphisms are shown below the figure.</p

Minimum spanning tree generated using sequences of housekeeping genes consisting: <i>arc</i>, SH1200, <i>hemH</i>, <i>leuB</i>, SH1431, <i>cfxE</i> and <i>Ribose ABC</i>.

<p><b>(A)</b><i>S</i>. <i>haemolyticus</i> (34 isolates) collected during 2007–2016 from different places in India and reference <i>S</i>. <i>haemolyticus</i> strain ATCC 29970, <b>(B)</b> Combination of strains includes previously reported STs (ST1-ST17; pink circles) and new STs (ST18-ST41; yellow circles) found in this study. Minimum difference in two alleles separates the nodes into different clusters.</p

Allelic profiles of sequence types (STs) of <i>S</i>. <i>haemolyticus</i> strains isolated from a variety of infections and also included previously reported STs (ST1-ST17).

<p>Allelic profiles of sequence types (STs) of <i>S</i>. <i>haemolyticus</i> strains isolated from a variety of infections and also included previously reported STs (ST1-ST17).</p

Additional file 1 of Assessment of genotypes, endosymbionts and clinical characteristics of Acanthamoeba recovered from ocular infection

Additional file 1: Table S1: Reference Acanthamoeba strains used in this study for phylogenetic analysis. Table 2: Genotype and species identification of Acanthamoeba isolates recovered from AK patients. Map 1: Map showing the states of the AK patients from different states of India with sample codes and identified genotypes of Acanthamoeba from AK patients. The map was created using ArcGIS (Esri GIS, California, USA). Fig. S1. Monthly distribution of AK cases during study period. Fig. S2. Sequence alignment of Acanthamoeba 18S rDNA DF3 region using ClustalW. Table S3. Overall clinical presentation of the keratitis patients infected with Acanthamoeba spp. Fig S3. Phylogenetic tree inferred from the 18S (ITS1) rDNA sequence of fungi; tree was created using the neighbour-joining approach with the Kimura 2-parameter based on 1000 replicates bootstrap values. Fig. S4. Agarose (1%) gel image of PCR amplicons of 13 Acanthamoeba isolates (18S rRNA), PCR assay was performed using Acanthamoeba genus specific primer pair JDPFw and JDPRv which yielded ~450bp amplicons. Fig. S5: Agarose (1%) gel image of PCR amplicons of 13 Acanthamoeba isolates targeting intracellular bacteria 16S rRNA, primer pair 515Fw and 806Rv (V4, 16S rRNA) was used which yielded ~293bp amplicons

Taxonomic abundance of different bacterial phyla, across HC and FK samples.

<p>Only those phyla with > 1% mean abundance are depicted in the plot.</p

Box plots indicating relative abundance of different bacterial genera which exhibited significant (BH corrected P < 0.05) differential abundance across HC and FK samples.

<p>Differentially abundant genera having a median abundance > 0.1% in at least one group of samples has been depicted. Median abundances and interquartile ranges have been indicated in the plots.</p

Box-plots illustrating alpha diversity indices (Shannon diversity, Simpson index and Observed OTUs) in bacterial microbiomes of FK and HC samples.

<p>Median values and interquartile ranges have been indicated in the plots. * indicates significant difference between HC and FK (p-value <0.05).</p

Discriminating functional pathways (KEGG) between HC and FK samples.

<p>Discriminating functional pathways (KEGG) between HC and FK samples.</p