ArticlePloS one2018
Combined bacterial and fungal intestinal microbiota analyses: Impact of storage conditions and DNA extraction protocols.
Article in PloS one, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers, 1 of them a synthesis that pooled it.
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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.
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Who cites it
25 citing papers in PubMed, 1 synthesis or guideline pooled it, 46 citations in OpenAlex.
- Effects of Stool Sample Preservation Methods on Gut Microbiota Biodiversity: New Original Data and Systematic Review with Meta-Analysis.Microbiology spectrum · 2023Pooled it
- Gut Dysbiosis in Selected Gynecological Diseases Associated with Female Infertility: A Scoping Review.Journal of clinical medicine · 2026Review
- Role of Fungi in Tumorigenesis: Promises and Challenges.Annual review of pathology · 2025Review
- Understanding dysbiosis and resilience in the human gut microbiome: biomarkers, interventions, and challenges.Frontiers in microbiology · 2025Review
- Article
- Metagenomics Applied to the Respiratory Mycobiome in Cystic Fibrosis.Mycopathologia · 2024Review
- Assessing the feasibility of free DNA for disaster victim identification and forensic applications.Scientific reports · 2024Article
- Assessment of DNA extraction methods for human gut mycobiome analysis.Royal Society open science · 2024Article
- Fungal Gut Microbiome in Myasthenia Gravis: A Sub-Analysis of the MYBIOM Study.Journal of fungi (Basel, Switzerland) · 2023Article
- Towards standardized and reproducible research in skin microbiomes.Environmental microbiology · 2022Review
- ClinicalJournal of fungi (Basel, Switzerland) · 2022Review
- Analyzing the human gut mycobiome - A short guide for beginners.Computational and structural biotechnology journal · 2022Review
- The impact of the Fungus-Host-Microbiota interplay upon Candida albicans infections: current knowledge and new perspectives.FEMS microbiology reviews · 2021Review
- Development of a robust protocol for the characterization of the pulmonary microbiota.Communications biology · 2021Article
- Tumor-Associated Microbiome: Where Do We Stand?International journal of molecular sciences · 2021Review
- Symbiosis and Dysbiosis of the Human Mycobiome.Frontiers in microbiology · 2021Review
- Whole-Genome Metagenomic Analysis of the Gut Microbiome in HIV-1-Infected Individuals on Antiretroviral Therapy.Frontiers in microbiology · 2021Article
- The Dynamics of Interacting Bacterial and Fungal Communities of the Mouse Colon Following Antibiotics.Microbial ecology · 2020Article
- The gut mycobiome: The overlooked constituent of clinical outcomes and treatment complications in patients with cancer and other immunosuppressive conditions.PLoS pathogens · 2020Article
- The Mycobiome in Health and Disease: Emerging Concepts, Methodologies and Challenges.Mycopathologia · 2020Review
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe human intestinal microbiota contains a vast community of microorganisms increasingly studied using high-throughput DNA sequencing. Standardized protocols for storage and DNA extraction from fecal samples have been established mostly for bacterial microbiota analysis. Here, we investigated the impact of storage and DNA extraction on bacterial and fungal community structures detected concomitantly.
methodsFecal samples from healthy adults were stored at -80°C as such or diluted in RNAlater® and subjected to 2 extraction protocols with mechanical lysis: the Powersoil® MoBio kit or the International Human Microbiota Standard (IHMS) Protocol Q. Libraries of the 12 samples targeting the V3-V4 16S and the ITS1 regions were prepared using Metabiote® (Genoscreen) and sequenced on GS-FLX-454. Sequencing data were analysed using SHAMAN (http://shaman.pasteur.fr/). The bacterial and fungal microbiota were compared in terms of diversity and relative abundance.
resultsWe obtained 171869 and 199089 quality-controlled reads for 16S and ITS, respectively. All 16S reads were assigned to 41 bacterial genera; only 52% of ITS reads were assigned to 40 fungal genera/section. Rarefaction curves were satisfactory in 3/3 and 2/3 subjects for 16S and ITS, respectively. PCoA showed important inter-individual variability of intestinal microbiota largely overweighing the effect of storage or extraction. Storage in RNAlater® impacted (downward trend) the relative abundances of 7/41 bacterial and 6/40 fungal taxa, while extraction impacted randomly 18/41 bacterial taxa and 1/40 fungal taxon.
conclusionOur results showed that RNAlater® moderately impacts bacterial or fungal community structures, while extraction significantly influences the bacterial composition. For combined bacterial and fungal intestinal microbiota analysis, immediate sample freezing should be preferred when feasible, but storage in RNAlater® remains an option under unfavourable conditions or for concomitant metatranscriptomic analysis; and extraction should rely on protocols validated for bacterial analysis, such as IHMS Protocol Q, and including a powerful mechanical lysis, essential for fungal extraction.
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