Host-associated microbe PCR (hamPCR) enables convenient measurement of both microbial load and community composition
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 s...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2021-07-01
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| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/66186 |
| _version_ | 1828221487561048064 |
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| author | Derek S Lundberg Pratchaya Pramoj Na Ayutthaya Annett Strauß Gautam Shirsekar Wen-Sui Lo Thomas Lahaye Detlef Weigel |
| author_facet | Derek S Lundberg Pratchaya Pramoj Na Ayutthaya Annett Strauß Gautam Shirsekar Wen-Sui Lo Thomas Lahaye Detlef Weigel |
| author_sort | Derek S Lundberg |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-12T16:41:51Z |
| format | Article |
| id | doaj.art-ef683d00321945a8bcfe93a7820b23af |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-12T16:41:51Z |
| publishDate | 2021-07-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-ef683d00321945a8bcfe93a7820b23af2022-12-22T03:24:45ZengeLife Sciences Publications LtdeLife2050-084X2021-07-011010.7554/eLife.66186Host-associated microbe PCR (hamPCR) enables convenient measurement of both microbial load and community compositionDerek S Lundberg0https://orcid.org/0000-0001-7970-1595Pratchaya Pramoj Na Ayutthaya1Annett Strauß2Gautam Shirsekar3Wen-Sui Lo4Thomas Lahaye5Detlef Weigel6https://orcid.org/0000-0002-2114-7963Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, GermanyDepartment of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, GermanyDepartment of Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, GermanyDepartment of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, GermanyZMBP-General Genetics, University of Tübingen, Tübingen, GermanyZMBP-General Genetics, University of Tübingen, Tübingen, GermanyDepartment of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, GermanyThe 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.https://elifesciences.org/articles/66186amplicon sequencingmicrobiomeabsolute abundancenematodecrop plantsquantitative |
| spellingShingle | Derek S Lundberg Pratchaya Pramoj Na Ayutthaya Annett Strauß Gautam Shirsekar Wen-Sui Lo Thomas Lahaye Detlef Weigel Host-associated microbe PCR (hamPCR) enables convenient measurement of both microbial load and community composition eLife amplicon sequencing microbiome absolute abundance nematode crop plants quantitative |
| title | Host-associated microbe PCR (hamPCR) enables convenient measurement of both microbial load and community composition |
| title_full | Host-associated microbe PCR (hamPCR) enables convenient measurement of both microbial load and community composition |
| title_fullStr | Host-associated microbe PCR (hamPCR) enables convenient measurement of both microbial load and community composition |
| title_full_unstemmed | Host-associated microbe PCR (hamPCR) enables convenient measurement of both microbial load and community composition |
| title_short | Host-associated microbe PCR (hamPCR) enables convenient measurement of both microbial load and community composition |
| title_sort | host associated microbe pcr hampcr enables convenient measurement of both microbial load and community composition |
| topic | amplicon sequencing microbiome absolute abundance nematode crop plants quantitative |
| url | https://elifesciences.org/articles/66186 |
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