ArticleeLife2021
Host-associated microbe PCR (hamPCR) enables convenient measurement of both microbial load and community composition.
Article in eLife, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Bacterial degradation of a plant toxin and nutrient competition with commensals trade off to constrain pathogen growth.mSystems · 2026Article
- Applying ecological principles to microbiome engineering.Nature microbiology · 2025Review
- A major trade-off between growth and defense in Arabidopsis thaliana can vanish in field conditions.PLoS biology · 2025Article
- Glucosinolate structural diversity shapes recruitment of a metabolic network of leaf-associated bacteria.Nature communications · 2024Article
- Embracing complexity in plant-microbiome systems.Environmental microbiology reports · 2024Review
- Chromosomal barcodes for simultaneous tracking of near-isogenic bacterial strains in plant microbiota.Nature microbiology · 2024Article
- Primer pairs, PCR conditions, and peptide nucleic acid clamps affect fungal diversity assessment from plant root tissues.Mycology · 2024Article
- Evolutionary implications of host genetic control for engineering beneficial microbiomes.Current opinion in systems biology · 2023Review
- The Arabidopsis holobiont: a (re)source of insights to understand the amazing world of plant-microbe interactions.Environmental microbiome · 2023Review
- Optimization of Molecular Methods for Detecting Duckweed-Associated Bacteria.Plants (Basel, Switzerland) · 2023Article
- Article
- Extracting abundance information from DNA-based data.Molecular ecology resources · 2023Review
- Contrasting patterns of microbial dominance in theProceedings of the National Academy of Sciences of the United States of America · 2022Article
- Investigating plant-microbe interactions within the root.Archives of microbiology · 2022Review
- The coral symbiont Candidatus Aquarickettsia is variably abundant in threatened Caribbean acroporids and transmitted horizontally.The ISME journal · 2022Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The ratio of microbial population size relative to the amount of host tissue, or 'microbial load', is a fundamental metric of colonization and infection, but it cannot be directly deduced from microbial amplicon data such as 16S rRNA gene counts. Because existing methods to determine load, such as serial dilution plating, quantitative PCR, and whole metagenome sequencing add substantial cost and/or experimental burden, they are only rarely paired with amplicon sequencing. We introduce host-associated microbe PCR (hamPCR), a robust strategy to both quantify microbial load and describe interkingdom microbial community composition in a single amplicon library. We demonstrate its accuracy across multiple study systems, including nematodes and major crops, and further present a cost-saving technique to reduce host overrepresentation in the library prior to sequencing. Because hamPCR provides an accessible experimental solution to the well-known limitations and statistical challenges of compositional data, it has far-reaching potential in culture-independent microbiology.
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