Much ado about nothing? Off-target amplification can lead to false-positive bacterial brain microbiome detection in healthy and Parkinson's disease individuals.
Level 4 - case-series / case-control
Case-control laboratory study comparing post-mortem human tissue from Parkinson's disease and healthy subjects along with murine controls.
PubMed 33771222 · doi:10.1186/s40168-021-01012-1
What was done
Researchers tested for a bacterial brain microbiome by analyzing brain samples (olfactory bulb and pre-frontal cortex) from healthy human subjects, individuals with Parkinson's disease (PD), and mice using 16S rRNA gene amplicon sequencing. They measured total bacterial biomass via 16S rRNA gene qPCR, incorporated negative and positive controls, and re-analyzed sequencing data across standard amplicon processing pipelines while checking for cross-reactivity against host genomes.
What was found
Initial 16S amplicon sequencing detected bacterial signals in human and murine samples, but qPCR confirmed extremely low bacterial biomass in all specimens. Detailed reanalysis showed that detected bacterial signals were driven by exogenous DNA contamination (54.8%) and off-target amplification of host DNA (34.2%). Most tested amplicon sequencing pipelines falsely assigned these amplified host DNA sequences to bacterial taxa, creating apparent brain-enriched signals. With rigorous artifact filtering, no evidence supported the presence of a brain microbiome or bacterial infection in PD brains.
Why it matters
This study demonstrates that host DNA off-target amplification and reagent contamination can produce false-positive bacterial signals in low-biomass tissues. It provides strong evidence against the existence of a bona fide brain microbiome or bacterial driver of Parkinson's pathology in the analyzed tissue types.
Limits
The abstract does not state the number of human donors, clinical characteristics, or mouse sample sizes ($n$ = ?). The analysis is focused on 16S rRNA amplicon sequencing and may not address non-bacterial microorganisms or evaluate other brain regions.
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- context Individuals with dementia have up to fourfold more bacteria in their brain compared to people without dementia.