Identifying group-specific primers for environmental Heterolobosa by high-throughput sequencing.
Journal
Microbial biotechnology
ISSN: 1751-7915
Titre abrégé: Microb Biotechnol
Pays: United States
ID NLM: 101316335
Informations de publication
Date de publication:
09 2022
09 2022
Historique:
revised:
29
04
2022
received:
15
09
2021
accepted:
09
05
2022
pubmed:
4
8
2022
medline:
9
9
2022
entrez:
3
8
2022
Statut:
ppublish
Résumé
Diversity of Heterolobosea (Excavata) in environments is poorly understood despite their ecological occurrence and health-associated risk, partly because this group tends to be under-covered by most universal eukaryotic primers used for sequencing. To overcome the limits of the traditional morpho-taxonomy-based biomonitoring, we constructed a primer database listing existing and newly designed specific primer pairs that have been evaluated for Heterolobosea 18S rRNA sequencing. In silico taxonomy performance against the current SILVA SSU database allowed the selection of primer pairs that were next evaluated on reference culture amoebal strains. Two primer pairs were retained for monitoring the diversity of Heterolobosea in freshwater environments, using high-throughput sequencing. Results showed that one of the newly designed primer pairs allowed species-level identification of most heterolobosean sequences. Such primer pair could enable informative, cultivation-free assays for characterizing heterolobosean populations in various environments.
Identifiants
pubmed: 35920130
doi: 10.1111/1751-7915.14080
pmc: PMC9437880
doi:
Substances chimiques
DNA Primers
0
RNA, Ribosomal, 18S
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
2476-2487Informations de copyright
© 2022 The Authors. Microbial Biotechnology published by Society for Applied Microbiology and John Wiley & Sons Ltd.
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