ArticleScientific reports2016
Glycans affect DNA extraction and induce substantial differences in gut metagenomic studies.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers, 1 of them a synthesis that pooled it.
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Who cites it
34 citing papers in PubMed, 1 synthesis or guideline pooled it, 57 citations in OpenAlex.
- The Human Microbiota and Obesity: A Literature Systematic Review of In Vivo Models and Technical Approaches.International journal of molecular sciences · 2018Pooled it
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- Comparison of 6 DNA extraction methods for isolation of high yield of high molecular weight DNA suitable for shotgun metagenomics Nanopore sequencing to detect bacteria.BMC genomics · 2023Article
- Prolonged dysbiosis and altered immunity under nutritional intervention in a physiological mouse model of severe acute malnutrition.iScience · 2023Article
- Culturing the Human Oral Microbiota, Updating Methodologies and Cultivation Techniques.Microorganisms · 2023Review
- Formyl peptide receptor-1 (FPR1) represses intestinal oncogenesis.Oncoimmunology · 2023Article
- Standards for Collection, Preservation, and Transportation of Fecal Samples in TCM Clinical Trials.Frontiers in cellular and infection microbiology · 2022Article
- Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels.Frontiers in microbiology · 2022Review
- Profile of the Nasopharyngeal Microbiota Affecting the Clinical Course in COVID-19 Patients.Frontiers in microbiology · 2022Article
- Gut Microbiota in Military International Travelers with Doxycycline Malaria Prophylaxis: Towards the Risk of a Simpson Paradox in the Human Microbiome Field.Pathogens (Basel, Switzerland) · 2021Article
- Gut microbiota signatures are associated with toxicity to combined CTLA-4 and PD-1 blockade.Nature medicine · 2021Article
- A Listeria monocytogenes clone in human breast milk associated with severe acute malnutrition in West Africa: A multicentric case-controlled study.PLoS neglected tropical diseases · 2021Article
- Article
- State of the Art in the Culture of the Human Microbiota: New Interests and Strategies.Clinical microbiology reviews · 2020Review
- Full-repertoire comparison of the microscopic objects composing the human gut microbiome with sequenced and cultured communities.Journal of microbiology (Seoul, Korea) · 2020Article
- Toward Standards in Clinical Microbiota Studies: Comparison of Three DNA Extraction Methods and Two Bioinformatic Pipelines.mSystems · 2020Article
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- Successful Fecal Microbiota Transplantation in a Patient Suffering From Irritable Bowel Syndrome and Recurrent Urinary Tract Infections.Open forum infectious diseases · 2019Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Exopolysaccharides produced by bacterial species and present in feces are extremely inhibitory to DNA restriction and can cause discrepancies in metagenomic studies. We determined the effects of different DNA extraction methods on the apparent composition of the gut microbiota using Illumina MiSeq deep sequencing technology. DNA was extracted from the stool from an obese female using 10 different methods and the choice of DNA extraction method affected the proportional abundance at the phylum level, species richness (Chao index, 227 to 2,714) and diversity (non parametric Shannon, 1.37 to 4.4). Moreover DNA was extracted from stools obtained from 83 different individuals by the fastest extraction assay and by an extraction assay that degradated exopolysaccharides. The fastest extraction method was able to detect 68% to 100% genera and 42% to 95% species whereas the glycan degradation extraction method was able to detect 56% to 93% genera and 25% to 87% species. To allow a good liberation of DNA from exopolysaccharides commonly presented in stools, we recommend the mechanical lysis of stools plus glycan degradation, used here for the first time. Caution must be taken in the interpretation of current metagenomic studies, as the efficiency of DNA extraction varies widely among stool samples.
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