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Longhi et al. Microbiome Res Rep 2024;3:4 Microbiome Research
DOI: 10.20517/mrr.2023.02
Reports

Original Article Open Access

Saponin treatment for eukaryotic DNA depletion
alters the microbial DNA profiles by reducing the

abundance of Gram-negative bacteria in
metagenomics analyses

1
1,2
1,2
1
3,4
Giulia Longhi , Chiara Argentini , Federico Fontana , Chiara Tarracchini , Leonardo Mancabelli ,
1
1
1,4
5
5
Gabriele Andrea Lugli , Giulia Alessandri , Edith Lahner , Giulia Pivetta , Francesca Turroni , Marco
1,4
Ventura , Christian Milani 1,4
1
Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma,
Parma 43124, Italy.
2
GenProbio Srl, Parma 43124, Italy.
3
Department of Medicine and Surgery, University of Parma, Parma 43124, Italy.
4
Microbiome Research Hub, University of Parma, Parma 43124, Italy.
5
Medical-Surgical Department of Clinical Sciences and Translational Medicine, Sant’Andrea Hospital, School of Medicine,
University Sapienza, Rome 00185, Italy.
Correspondence to: Prof. Christian Milani, Prof. Marco Ventura, Laboratory of Probiogenomics, Department of Chemistry, Life
Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, Parma 43124, Italy. E-mail:
christian.milani@unipr.it; marco.ventura@unipr.it
How to cite this article: Longhi G, Argentini C, Fontana F, Tarracchini C, Mancabelli L, Lugli GA, Alessandri G, Lahner E, Pivetta
G, Turroni F, Ventura M, Milani C. Saponin treatment for eukaryotic DNA depletion alters the microbial DNA profiles by reducing
the abundance of Gram-negative bacteria in metagenomics analyses. Microbiome Res Rep 2024;3:4. https://dx.doi.org/10.
20517/mrr.2023.02
Received: 12 Jan 2023 First Decision: 11 Oct 2023 Revised: 1 Nov 2023 Accepted: 10 Nov 2023 Published: 15 Nov 2023
Academic Editor: Rodolphe Barrangou Copy Editor: Dong-Li Li Production Editor: Dong-Li Li
Abstract
Background: Recent advances in microbiome sequencing techniques have provided new insights into the role of
the microbiome on human health with potential diagnostic implications. However, these developments are often
hampered by the presence of a large amount of human DNA interfering with the analysis of the bacterial content.
Nowadays, extensive scientific literature focuses on eukaryotic DNA depletion methods, which successfully
remove host DNA in microbiome studies, even if a precise assessment of the impact on bacterial DNA is often
missing.

© The Author(s) 2023. Open Access This article is licensed under a Creative Commons Attribution 4.0
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