Impact of Pre-Extraction Methods on Apple Blossom Microbiome Analysis.

Nikhil N Patel, Jonathan R Gaiero, Muhammad Sulman, Paul Moote, Darlene Nesbitt, Antonet M Svircev, Walid Ellouze

Abstract read

In one paragraph

Article in Microorganisms, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it

0cells of the map it votes in

0citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

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.

2 · The registry

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.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors.

Nikhil N PatelAgriculture and Agri-Food Canada, London Research and Development Centre, 4902 Victoria Avenue North, Vineland Station, ON L0R 2E0, Canada.

Jonathan R GaieroAgriculture and Agri-Food Canada, London Research and Development Centre, 4902 Victoria Avenue North, Vineland Station, ON L0R 2E0, Canada.

Muhammad SulmanAgriculture and Agri-Food Canada, London Research and Development Centre, 4902 Victoria Avenue North, Vineland Station, ON L0R 2E0, Canada.

Paul MooteAgriculture and Agri-Food Canada, London Research and Development Centre, 4902 Victoria Avenue North, Vineland Station, ON L0R 2E0, Canada.ORCID 0009-0007-4359-4872

Darlene NesbittAgriculture and Agri-Food Canada, London Research and Development Centre, 4902 Victoria Avenue North, Vineland Station, ON L0R 2E0, Canada.

Antonet M SvircevAgriculture and Agri-Food Canada, London Research and Development Centre, 4902 Victoria Avenue North, Vineland Station, ON L0R 2E0, Canada.

Walid EllouzeAgriculture and Agri-Food Canada, London Research and Development Centre, 4902 Victoria Avenue North, Vineland Station, ON L0R 2E0, Canada.ORCID 0000-0002-8749-9486

Funding

Agriculture and Agri-Food Canada J-002617; J-002861

6 · The paper itself

Abstract

This study examines the effect of pre-extraction methods, namely, sonication, grinding, and lyophilization, and the use of peptide nucleic acid (PNA) blockers on the DNA recovery, diversity, and taxonomic resolution of bacterial and fungal communities in apple blossoms. Sonication was the most successful in recovering bacterial 16S and fungal ITS reads across all the collection points and plots. Lyophilization and grinding led to a significant reduction in fungal read counts, while PNA enhanced the recovery of bacterial 16S reads. Sonication improved the efficiency of DNA extraction and yielded greater diversity in the recovered microbial community. Sonicated samples showed greater sensitivity to temporal shifts in microbial community composition. Communities in sonicated samples contained a larger number of bacterial genera, such as

Indexed as

bacterial 16SDNA recoveryfungal ITSgrindinglyophilizationmicrobial community compositionmicrobial diversitypeptide nucleic acid (PNA) blockerssonicationtaxonomic resolution

Identifiers

PMID40284759

DOI10.3390/microorganisms13040923

PMCPMC12029539

What OpenQuestion holds

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Registered trials

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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.