ArticleMicrobiologyOpen2021
Optimized bacterial DNA isolation method for microbiome analysis of human tissues.
Article in MicrobiologyOpen, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 42 citations in OpenAlex.
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- Preliminary microbiome characterization of shrimp gut and pond water in Egyptian aquaculture farms: Implications for pathogen dynamics and management practices.Veterinary research communications · 2026Article
- Advancing Plant Microbiome Research Through Host DNA Depletion Techniques.Plant biotechnology journal · 2026Review
- IntratumoralScience advances · 2026Article
- Effects of aquaculture practices onApplied and environmental microbiology · 2026Article
- Standardizing vaginal microbial profiling: evaluating swab materials, storage conditions, and host DNA depletion strategies.BMC microbiology · 2026Article
- Development and optimization of host DNA depletion in blood cultures using a saponin and salt-activated nuclease-based method.Frontiers in microbiology · 2026Article
- Mucosal washes are useful for sampling intestinal mucus-associated microbiota despite low biomass.Gut microbes · 2025Article
- Metagenomic Applications to Herbivore Gut Microbiomes: A Comprehensive Review of Microbial Diversity and Host Interactions.Animals : an open access journal from MDPI · 2025Review
- Benefits and challenges of host depletion methods in profiling the upper and lower respiratory microbiome.NPJ biofilms and microbiomes · 2025Article
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- Microbiome dysbiosis and endometriosis: a systematic scoping review of current literature and knowledge gaps.Human reproduction open · 2025Review
- State-of-the-art approaches in the investigation of human seminal bacteriome using metagenomic methods.Frontiers in reproductive health · 2025Review
- Geographical Differences and Temporal Dynamics of Intestinal Microbiota in Endangered Great BustardInternational journal of microbiology · 2025Article
- Bacterial profiling of colorectal cancer biopsies: a culture-based study in Indian patients.Frontiers in cellular and infection microbiology · 2025Article
- Analysis of metagenomic data.Nature reviews. Methods primers · 2025Article
- Methods for identification of the opportunistic gut mycobiome from colorectal adenocarcinoma biopsy tissues.MethodsX · 2024Article
- Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments.Nature protocols · 2024Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent advances in microbiome sequencing have rendered new insights into the role of the microbiome in human health with potential clinical implications. Unfortunately, the presence of host DNA in tissue isolates has hampered the analysis of host-associated bacteria. Here, we present a DNA isolation protocol for tissue, optimized on biopsies from resected human colons (~2-5 mm in size), which includes reduction of human DNA without distortion of relative bacterial abundance at the phylum level. We evaluated which concentrations of Triton and saponin lyse human cells and leave bacterial cells intact, in combination with DNAse treatment to deplete released human DNA. Saponin at a concentration of 0.0125% in PBS lysed host cells, resulting in a 4.5-fold enrichment of bacterial DNA while preserving the relative abundance of Firmicutes, Bacteroidetes, γ-Proteobacteria, and Actinobacteria assessed by qPCR. Our optimized protocol was validated in the setting of two large clinical studies on 521 in vivo acquired colon biopsies of 226 patients using shotgun metagenomics. The resulting bacterial profiles exhibited alpha and beta diversities that are similar to the diversities found by 16S rRNA amplicon sequencing. A direct comparison between shotgun metagenomics and 16S rRNA amplicon sequencing of 15 forceps tissue biopsies showed similar bacterial profiles and a similar Shannon diversity index between the sequencing methods. Hereby, we present the first protocol for enriching bacterial DNA from tissue biopsies that allows efficient isolation of all bacteria. Our protocol facilitates analysis of a wide spectrum of bacteria of clinical tissue samples improving their applicability for microbiome research.
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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.