ArticleScientific reports2018
The impact of storage buffer, DNA extraction method, and polymerase on microbial analysis.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT04846361 (The Effectiveness of Vaginal Hygiene Wash as Adjunct Treatment in Bacterial Vaginosis- a Randomized Double Blind Controlled Trial With Microbial Analysis), which is not on this map. Cited by 41 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
The Effectiveness of Vaginal Hygiene Wash as Adjunct Treatment in Bacterial Vaginosis- a Randomized Double Blind Controlled Trial With Microbial Analysis
Who cites it
41 citing papers in PubMed, 88 citations in OpenAlex.
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- Maple and hickory leaf litter fungal communities reflect pre-senescent leaf communities.PeerJ · 2022Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-generation sequencing approaches used to characterize microbial communities are subject to technical caveats that can lead to major distortion of acquired data. Determining the optimal sample handling protocol is essential to minimize the bias for different sample types. Using a mock community composed of 22 bacterial strains of even concentration, we studied a combination of handling conditions to determine the optimal conditions for swab material. Examining a combination of effects simulates the reality of handling environmental samples and may thus provide a better foundation for the standardization of protocols. We found that the choice of storage buffer and extraction kit affects the detected bacterial composition, while different 16S rRNA amplification methods only had a minor effect. All bacterial genera present in the mock community were identified with minimal levels of contamination independent of the choice of sample processing. Despite this, the observed bacterial profile for all tested conditions were significantly different from the expected abundance. This highlights the need for proper validation and standardization for each sample type using a mock community and blank control samples, to assess the bias in the protocol and reduce variation across the datasets.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.