2021
DOI: 10.21203/rs.3.rs-321778/v1
|View full text |Cite
Preprint
|
Sign up to set email alerts
|

Metagenome-validated Parallel Amplicon Sequencing and Text Mining-based Annotations for Simultaneous Profiling of Bacteria and Fungi: Vaginal Microbiome and Mycobiota in Healthy Women

Abstract: Background: Amplicon sequencing of kingdom-specific tags such as 16S rRNA gene for bacteria and internal transcribed spacer (ITS) region for fungi are widely used for investigating microbial populations. So far most human studies have focused on bacteria while studies on host-associated fungi in health and disease have only recently started to accumulate. To enable cost-effective parallel analysis of bacterial and fungal communities in human and environmental samples, we developed a method where 16S rRNA gene … Show more

Help me understand this report

Search citation statements

Order By: Relevance

Paper Sections

Select...
2
2
1

Citation Types

0
7
0

Year Published

2021
2021
2023
2023

Publication Types

Select...
4
2

Relationship

5
1

Authors

Journals

citations
Cited by 7 publications
(7 citation statements)
references
References 65 publications
0
7
0
Order By: Relevance
“…The amplicon sequence variants (ASVs) obtained from dada2 were annotated using the taxminer R package workflow. 29 This consists of BLAST based sequence alignments followed by a text-mining based strategy that attaches ecosystem specificity to each alignment (host & isolation source) to probabilistically select the most likely taxonomic annotations.…”
Section: Methodsmentioning
confidence: 99%
“…The amplicon sequence variants (ASVs) obtained from dada2 were annotated using the taxminer R package workflow. 29 This consists of BLAST based sequence alignments followed by a text-mining based strategy that attaches ecosystem specificity to each alignment (host & isolation source) to probabilistically select the most likely taxonomic annotations.…”
Section: Methodsmentioning
confidence: 99%
“…were annotated using the taxminer R package work ow 57 . This consists of BLAST based sequence alignments followed by a text-mining based strategy that attaches ecosystem speci city to each alignment (host & isolation source) to probabilistically select the most likely taxonomic annotations.…”
Section: Sequence Preprocessing and Analysismentioning
confidence: 99%
“…71 To characterize the gut fungal community, we performed ITS-1 sequencing for the Pakistani samples using a two-step PCR protocol described in detail elsewhere. 72 PCR-amplicons of the ITS-1 region were generated using ITS1F and ITS2 primers. 72, 73…”
Section: Methodsmentioning
confidence: 99%