Evidence map›Paper›PMID 41292709›Full record

ArticlebioRxiv : the preprint server for biology2025

Optimizing Tissue Lysis and DNA Extraction Protocols to Enhance Bacterial Diversity Profiling in the

Carlos L Quiñones-Sanchez, Jan L Bilbao-Del Valle, Miguel A Urdaneta-Colon, Tasha M Santiago-Rodriguez, Imilce A Rodriguez-Fernandez

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 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

5 authors.

Carlos L Quiñones-SanchezDepartment of Biology, College of Natural Sciences, University of Puerto Rico, Rio Piedras, San Juan 00925, Puerto Rico.ORCID 0009-0004-5654-6640
Jan L Bilbao-Del ValleDepartment of Biology, College of Natural Sciences, University of Puerto Rico, Rio Piedras, San Juan 00925, Puerto Rico.ORCID 0009-0006-4049-6612
Miguel A Urdaneta-ColonDepartment of Biology, College of Natural Sciences, University of Puerto Rico, Rio Piedras, San Juan 00925, Puerto Rico.
Tasha M Santiago-RodriguezThe Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.ORCID 0000-0003-2738-9784
Imilce A Rodriguez-FernandezDepartment of Biology, College of Natural Sciences, University of Puerto Rico, Rio Piedras, San Juan 00925, Puerto Rico.ORCID 0000-0002-5112-4834

Funding

The Role of Sensory Input to Mammalian Locomotion After the Loss of supraspinal.P20GM103642 · NIGMS · UNIVERSITY OF PUERTO RICO MED SCIENCES · PI LASALDE-DOMINICCI, JOSE ANTONIO · 2013 to 2023
$20.6M
Research Projects CoreP30GM149367 · NIGMS · UNIVERSITY OF PUERTO RICO MED SCIENCES · PI JOSE Antonio LASALDE-DOMINICCI · 2023 to 2026
$5.6M
Increasing Diversity in Genomics for the Next generation (IDGeNe)R25HG012702 · NHGRI · UNIVERSITY OF PUERTO RICO RIO PIEDRAS · PI JOSE E GARCIA-ARRARAS · 2022 to 2026
$1.7M
NHGRI NIH HHS R25 HG012702NIGMS NIH HHS P20 GM103642NIGMS NIH HHS P30 GM149367
6 · The paper itself

Abstract

The gut microbiota is a dynamic community that influences host metabolism, immunity, and overall health. Accurate characterization of this community requires robust and reproducible DNA extraction methods; however, technical biases introduced during tissue lysis and DNA isolation remain major challenges in microbiome research, particularly in animal model systems. In this study, we compared two commercial DNA extraction kits (Qiagen and Zymo) and two lysis methods (manual pestle homogenization and bead-beating) to evaluate their impact on microbiota profiling in a microbial community standard (MCS) and

Indexed as

DNA extraction methodsDrosophila melanogasterGut microbiomeMicrobial community profilingMicrobial diversityNanopore full-length 16S rRNA sequencing

Identifiers

PMID41292709
PMCPMC12642230

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.