Studies of uncultured eukaryotes identified as Vermamoeba

(updated July 2021)

A substantial portion of the DNA database for V. vermiformis has been collected as sequences obtained in generalized environmental studies of unknown and/or uncultivated eukaryotic organisms.  Of the 930 sequences attributed to V. vermiformis, 376 (47%) are identified as some type of uncultured organism. 

Among the sequences from uncultured environmental sources, three sequences exceeded 1600 bp in length and thus overlap almost all of the 18S rRNA gene sequence from V. vermiformis.   For the remaining environmental survey sequences, 338 of the 376 sequences are between 480 and 622 bases in length, while only 26 sequences were less than 420 bases in length.  Although fairly similar in length, this large group of sequences actually represents at least two assemblages of sequences.  The largest group of sequences, involving 263 of the 371 partial sequences, overlap the gene region between about base 100 and base 600 of the complete sequence. A second group, encompassing 25 sequences, overlap bases ~600-1100 of the complete sequence.  The two groups have almost no overlap in extent.

As far as can be determined, the sequences from uncultured environmental isolates contain similar genetic variation, in terms of variants and their frequency, as that which occurs in the collection of  isolates that were identified through targeted studies aimed at identifying the presence of V. vermiformis.  More detailed studies should be carried out to determine whether any more subtle differences in the occurrence of genetic variants may be present.  

Initial comparison suggests that the proportion of isolates of Vermamoeba that were identified through anonymous eukaryotic environmental surveys substantially exceeds the proportion of isolates that were identified in Acanthamoeba using the same approaches.   Whereas uncultured eukaryotic sequences represent 40% (376/931) of all 18S rRNA gene sequences from Vermamoeba, they represent only 7% (426/6030) of the total sequences of Acanthamoeba.  (results for Acanthamoeba in July 2021).  The percentage of anonymous uncultured sequences from Vermamoeba is similar to that observed in Protacanthamoeba, although the number of sequences attributed to uncultured Vermamoeba greatly exceeds the equivalent group in Protacanthamoeba.

Does this disparity in the percentage of sequences from uncultured material in Vermamoeba compared to Acanthamoeba suggest that Vermamoeba occurs much more frequently in the environment?  Not necessarily.  Several explanations for the disparity can be proposed.   First, the use of universal eukaryotic rRNA PCR primers to amplify sequences from free-living amoeba may be more effective in the study of Vermamoeba than in Acanthamoeba.  This is because several additional hypervariable segments occur in the 18S rRNA gene of Acanthamoeba, segments that are absent in the gene of Vermamoeba.  Differences in the length of the subsequent PCR product would favor recovering Vermamoeba sequences compared to Acanthamoeba sequences.  Secondly, a substantial proportion of the sequences for Acanthamoeba were obtained from clinical studies, or studies that targeted localities which were associated with the occurrence of infections by free-living amoebae.  Very few such studies have implicated Vermamoeba

If we restrict our comparison to environmental studies of Acanthamoeba, 3413 isolates of Acanthamoeba would be classified as identified solely as part of an environmental screen with no clinical component (July 2021).  Uncultured eukaryotes would thus still represent only ~12% of this subset of isolates, continuing to be greatly less frequent than in the equivalent comparison for Vermamoeba.

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