Fig. 1

Relative abudance of the major taxonomic groups identified by MEGAN. a Eukaryotic groups (microbes and parasites) and b Bacteria in patients 1 (light blue); 2 (dark blue) and Controls (red collors). The Shannon and Simpson index calculated for Bacteria and Eukariotic domains, using Vegan R package, are shown in a right upper box. Controls, mean (±Standard Deviation) obtained from AF samples of 16 pregnant women collected in different times (“Prenatal”, “Late Preterm” and “Term”) deposited and available in SRA NCBI section (http://www.ncbi.nlm.nih.gov/bioproject/PRJNA281986). The Shannon and Simpson index were calculated with “Vegan” package from R language, using genus counts. In total, 170,928 and 166,717 eukaryotic sequences showed no hits or were not taxonomically assigned by MEGAN in samples from the patients 1 and 2, respectively. Unidentified Bacterial sequences were the most abundant group found in both samples (3483 reads in the sample from patient 1 and 6538 reads in the sample from patient 2). Shannon and Simpson indexes, for Eukariotic species (Fig. 1a), showed that Controls were more diverse than the two Zika infected AF samples, altough only the comparissons between Zika patients and Term Control (considering Simpson index); and Zika patients and Preterm Control (considering Shannon index) were statistically significant (Additional file 2: Table S2). The PERMANOVA analysis showed a statistical diference in the Eukaryotic composition between the samples types (Additional file 3: Table S3). Zika positive AF patients 1 and 2 were more diverse (Shannon index = 2.578 and 2.678; Simpson index = 0,91 and 0,90) than Prenatal and Preterm Controls samples (Shannon index = 2.44; Simpson index = 0.88 and Shannon index = 2.54; Simpson index = 0.9, respectivelly) (Fig. 1b). The Term samples were more diverse than Zika samples (Shannon index = 3.19; Simpson index = 0.94), however the difference were not statically significant in any comparisson (Additional file 2: Table S2). The PERMANOVA showed a statistical diference in the Bacterial species composition between the type of the samples (Additional file 3: Table S3), even as the NMDS analysis also showed that Zika patients clustering together, a part from the three controls groups (Additional file 4: Figure S1)