Merging Fungal and Bacterial Community Profiles via an Internal Control
Abstract
Integrated measurements of fungi and bacteria are critical to understand how interactions between these taxa drive key processes in ecosystems ranging from soils to animal guts. High-throughput amplicon sequencing is commonly used to census microbiomes, but the genetic markers targeted for fungi and bacteria (typically ribosomal regions) are domain-specific so profiling must be performed separately, obscuring relationships between these groups. To solve this problem, we developed a spike-in method with an internal control (IC) construct containing primer sites commonly used for bacterial and fungal taxonomic profiling. The internal control offers several advantages: estimation of absolute abundances, estimation of fungal to bacterial ratios (F:B), integration of bacterial and fungal profiles for holistic community analysis, and lower costs compared to other quantitation methods. To validate the IC as a scaling method, we compared IC-derived measures of F:B to measures from quantitative PCR (qPCR) using a commercial mock community (the ZymoBiomic Microbial Community DNA Standard II, containing two fungi and eight bacteria) and complex environmental samples. For both the mock community and the environmental samples, the IC produced F:B values that were statistically consistent with qPCR. Merging the environmental fungal and bacterial profiles based on the IC-derived F:B values revealed new relationships amongmore »
- Authors:
-
[1];
[2];
[1];
[1]
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Univ. of Montana, Missoula, MT (United States)
- Publication Date:
- Research Org.:
- Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC). Biological and Environmental Research (BER)
- OSTI Identifier:
- 1804396
- Report Number(s):
- LA-UR-20-24318
Journal ID: ISSN 0095-3628
- Grant/Contract Number:
- 89233218CNA000001; F255LANL2018
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Microbial Ecology
- Additional Journal Information:
- Journal Volume: 82; Journal ID: ISSN 0095-3628
- Publisher:
- Springer
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Biological science; community ecology; taxonomic profiles; fungi; bacteria; fungal-bacterial ratio; targeted metagenomics
Citation Formats
Hutchinson, Miriam I., Bell, Tisza A. S., Gallegos-Graves, La Verne, Dunbar, John, and Albright, Michaeline. Merging Fungal and Bacterial Community Profiles via an Internal Control. United States: N. p., 2021.
Web. doi:10.1007/s00248-020-01638-y.
Hutchinson, Miriam I., Bell, Tisza A. S., Gallegos-Graves, La Verne, Dunbar, John, & Albright, Michaeline. Merging Fungal and Bacterial Community Profiles via an Internal Control. United States. https://doi.org/10.1007/s00248-020-01638-y
Hutchinson, Miriam I., Bell, Tisza A. S., Gallegos-Graves, La Verne, Dunbar, John, and Albright, Michaeline. Thu .
"Merging Fungal and Bacterial Community Profiles via an Internal Control". United States. https://doi.org/10.1007/s00248-020-01638-y. https://www.osti.gov/servlets/purl/1804396.
@article{osti_1804396,
title = {Merging Fungal and Bacterial Community Profiles via an Internal Control},
author = {Hutchinson, Miriam I. and Bell, Tisza A. S. and Gallegos-Graves, La Verne and Dunbar, John and Albright, Michaeline},
abstractNote = {Integrated measurements of fungi and bacteria are critical to understand how interactions between these taxa drive key processes in ecosystems ranging from soils to animal guts. High-throughput amplicon sequencing is commonly used to census microbiomes, but the genetic markers targeted for fungi and bacteria (typically ribosomal regions) are domain-specific so profiling must be performed separately, obscuring relationships between these groups. To solve this problem, we developed a spike-in method with an internal control (IC) construct containing primer sites commonly used for bacterial and fungal taxonomic profiling. The internal control offers several advantages: estimation of absolute abundances, estimation of fungal to bacterial ratios (F:B), integration of bacterial and fungal profiles for holistic community analysis, and lower costs compared to other quantitation methods. To validate the IC as a scaling method, we compared IC-derived measures of F:B to measures from quantitative PCR (qPCR) using a commercial mock community (the ZymoBiomic Microbial Community DNA Standard II, containing two fungi and eight bacteria) and complex environmental samples. For both the mock community and the environmental samples, the IC produced F:B values that were statistically consistent with qPCR. Merging the environmental fungal and bacterial profiles based on the IC-derived F:B values revealed new relationships among samples in terms of community similarity. As a result, this IC method is the first spike-in method to employ a single construct for cross-domain amplicon sequencing, offering more reliable measurements.},
doi = {10.1007/s00248-020-01638-y},
journal = {Microbial Ecology},
number = ,
volume = 82,
place = {United States},
year = {Thu Jan 07 00:00:00 EST 2021},
month = {Thu Jan 07 00:00:00 EST 2021}
}
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