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Novel data from Italian Vermamoeba vermiformis isolates from multiple sources add to genetic diversity within the genus

  • M. Montalbano Di Filippo
  • F. BerrilliEmail author
  • D. Di Cave
  • A. Novelletto
Genetics, Evolution, and Phylogeny - Original Paper
  • 23 Downloads

Abstract

Vermamoeba vermiformis represents one of the most common free-living amoebae identified in worldwide environmental surveys. We analyzed 56 water samples with varying characteristics, including temperature and the particular settings in which humans may be exposed to water, plus one corneal scraping from a keratitis patient, with the following aims: (i) to investigate the presence of V. vermiformis; (ii) to identify the isolate subtypes; (iii) to place the Italian isolates in the broader picture of the genetic diversity within V. vermiformis. Twenty-two isolates were identified upon culturing and sequencing of > 600 bp in the 18S ribosomal RNA (rRNA) gene sequence, bringing to 27 the number of sequences recovered from Italian sources. By adding deposited sequences, we assembled a dataset of 74 isolates. Three of our isolates were characterized by allelic code 7-5-1-1, never reported before, and two showed 100% identity with an uncultured eukaryote and carried the 719T>C variant. We show that the variable segments E5, E3, F, and G convey most of the information on diversity, enabling the clustering of the isolates in a replicable fashion. The presence of different strains in natural thermal waters and in distribution systems indicated heterogeneity of the amoebic populations. Also, ours and the only other sequence from human infection were mapped in different clades. Overall, we enlarged the repertoire of single nucleotide and indel variants and the list of allelic codes, proceeding one step further in the description of the diversity within the genus.

Keywords

Amoebozoa Vermamoeba vermiformis 18S rRNA Allelic variants Dynamic homology 

Notes

Funding

This study was partially funded by the University of Rome Tor Vergata, Italy (Ricerca Scientifica di Ateneo 2016 “Mission: Sustainability”).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki Declaration and its later amendments or comparable standards.

Supplementary material

436_2019_6294_MOESM1_ESM.xlsx (22 kb)
Online Resource 1 The implicit alignment corresponding to Fig. 1 in Fasta format (74 Vermamoeba sequences, outgrouped with 3 Echinamoeba sequences). Heatmap of the pairwise distances matrix produced in Excel environment. Pairwise distance matrix was generated from aligned sequences (74 Vermamoeba sequences) in MEGA v5, with equal weights for transitions and transversions. (XLSX 21 kb)
436_2019_6294_MOESM2_ESM.pdf (388 kb)
ESM 1 (PDF 387 kb)
436_2019_6294_MOESM3_ESM.fas (127 kb)
Video 1 (FAS 126 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Clinical Sciences and Translational MedicineUniversity of Rome Tor VergataRomeItaly
  2. 2.Department of BiologyUniversity of Rome Tor VergataRomeItaly

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