MinION Sequencing of Yeast Mock Communities To Assess the Effect of Databases and ITS-LSU Markers on the Reliability of Metabarcoding Analysis

Conti, Angela; Pierantoni, Debora Casagrande; Corte, Laura Della; Cardinali, Gianluigi

doi:10.1128/spectrum.01052-22

Cited by 3 publications

(1 citation statement)

References 51 publications

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“…Our analysis was based on 16S rRNA and ITS sequencing rather than metagenomic data. ITS sequencing is widely accepted for studying fungal composition owing to its reasonable discriminatory power and well-defined reference databases (Conti et al, 2023; Schoch et al, 2012). However, metagenomic sequencing offers additional advantages, as it enhances strain- level resolution, which is somewhat challenging with 16S rRNA and ITS sequencing.…”

Section: Discussionmentioning

confidence: 99%

Role of socioeconomic factors and interkingdom crosstalk in the dental plaque microbiome in early childhood caries

Khan,

de Jesus,

Mittermuller

et al. 2024

Preprint

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Early childhood caries (ECC) is influenced by microbial and host factors, including social, behavioral, and oral health. In this cross-sectional study, we analyzed interkingdom dynamics in the dental plaque microbiome and its association with host variables. The samples collected from the preschool children underwent 16S rRNA and ITS1 rRNA gene sequencing. The questionnaire data were analyzed for social determinants of oral health. The results indicated a significant enrichment of Streptococcus mutans and Candida dubliniensis in ECC samples, in contrast to Neisseria oralis in caries-free children. Our interkingdom correlation analysis revealed that Candida dubliniensis was strongly correlated with both Neisseria bacilliformis and Prevotella veroralis in ECC. Additionally, ECC showed significant associations with host variables, including oral health status, age, place of residence, and mode of childbirth. This study provides empirical evidence associating the oral microbiome with socioeconomic and behavioral factors in relation to ECC, offering insights for developing targeted prevention strategies.

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Section: Discussionmentioning

confidence: 99%

Role of socioeconomic factors and interkingdom crosstalk in the dental plaque microbiome in early childhood caries

Khan,

de Jesus,

Mittermuller

et al. 2024

Preprint

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A comparison of microbiota isolation methods reveals habitat preferences for fermentative yeasts and plant pathogenic fungi in the grape berry

Martins,

Teixeira,

Gerós

2024

Food Microbiology

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Nanopore sequencing of DNA barcodes succeeds in unveilling the diversity of fungal mock communities

Pedroso-Roussado¹,

Guppy²,

Bowler³

et al. 2023

Open Res Europe

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Background: The fungal component of the gut microbiome has been underrepresented in most gut microbiome studies. While metabarcoding approaches have been used to assess the diversity and role of the gut mycobiome, differences in experimental design and downstream analyses may induce bias and differential outcomes. This study assessed the capacity of nanopore sequencing to retrieve the microbial profile and relative abundance of a mock fungal community comprised of Candida glabrata, Meyerozyma guilliermondii, Pichia kudriavzevii, Clavispora lusitaniae and Candida parapsilosis. Methods: The approach was implemented using the MinION system and involved the analysis of sequencing libraries made from equimolar mixtures of the PCR-amplified nuclear ribosomal internal transcribed spacer (ITS) of the target species. Results: Nanopore sequencing successfully retrieved the composition of the fungal mock community in terms of the different taxa present. However, the approach was unable to correctly assess the expected relative abundances of each species in the same community, showing some yet undetermined bias that may be related to the size of the respective target DNA fragments. Clavispora lusitaniae was consistently overrepresented in the mixtures, while C. glabrata was underrepresented. The remaining three species showed relative abundances more aligned with the expected values of an equimolar mixture. Conclusions: Although not yielding the expected results for the relative abundances, the values obtained from independent sequencing runs were similar for all species, suggesting a good reliability but questionable accuracy in this sequencing approach.

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MinION Sequencing of Yeast Mock Communities To Assess the Effect of Databases and ITS-LSU Markers on the Reliability of Metabarcoding Analysis

Cited by 3 publications

References 51 publications

Role of socioeconomic factors and interkingdom crosstalk in the dental plaque microbiome in early childhood caries

Role of socioeconomic factors and interkingdom crosstalk in the dental plaque microbiome in early childhood caries

A comparison of microbiota isolation methods reveals habitat preferences for fermentative yeasts and plant pathogenic fungi in the grape berry

Nanopore sequencing of DNA barcodes succeeds in unveilling the diversity of fungal mock communities

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