Multiomics Characterization of the Canada Goose Fecal Microbiome Reveals Selective Efficacy of Simulated Metagenomes
16S rRNA amplicon sequences are predominantly used to identify the taxonomic composition of a microbiome, but they can also be used to generate simulated metagenomes to circumvent costly empirical shotgun sequencing. The effectiveness of using “simulated metagenomes” (shotgun metagenomes simulated f...
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ftpubmed:oai:pubmedcentral.nih.gov:9769641 2023-05-15T15:46:21+02:00 Multiomics Characterization of the Canada Goose Fecal Microbiome Reveals Selective Efficacy of Simulated Metagenomes Gil, Joshua C. Hird, Sarah M. 2022-11-01 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9769641/ http://www.ncbi.nlm.nih.gov/pubmed/36318011 https://doi.org/10.1128/spectrum.02384-22 en eng American Society for Microbiology http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9769641/ http://www.ncbi.nlm.nih.gov/pubmed/36318011 http://dx.doi.org/10.1128/spectrum.02384-22 Copyright © 2022 Gil and Hird. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license (https://creativecommons.org/licenses/by/4.0/) . CC-BY Microbiol Spectr Research Article Text 2022 ftpubmed https://doi.org/10.1128/spectrum.02384-22 2022-12-25T02:03:26Z 16S rRNA amplicon sequences are predominantly used to identify the taxonomic composition of a microbiome, but they can also be used to generate simulated metagenomes to circumvent costly empirical shotgun sequencing. The effectiveness of using “simulated metagenomes” (shotgun metagenomes simulated from 16S rRNA amplicons using a database of full genomes closely related to the amplicons) in nonmodel systems is poorly known. We sought to determine the accuracy of simulated metagenomes in a nonmodel organism, the Canada goose (Branta canadensis), by comparing metagenomes and metatranscriptomes to simulated metagenomes derived from 16S amplicon sequencing. We found significant differences between the metagenomes, metatranscriptomes, and simulated metagenomes when comparing enzymes, KEGG orthologies (KO), and metabolic pathways. The simulated metagenomes accurately identified the majority (>70%) of the total enzymes, KOs, and pathways. The simulated metagenomes accurately identified the majority of the short-chain fatty acid metabolic pathways crucial to folivores. When narrowed in scope to specific genes of interest, the simulated metagenomes overestimated the number of antimicrobial resistance genes and underestimated the number of genes related to the breakdown of plant matter. Our results suggest that simulated metagenomes should not be used in lieu of empirical sequencing when studying the functional potential of a nonmodel organism’s microbiome. Regarding the function of the Canada goose microbiome, we found unexpected amounts of fermentation pathways, and we found that a few taxa are responsible for large portions of the functional potential of the microbiome. IMPORTANCE The taxonomic composition of a microbiome is predominately identified using amplicon sequencing of 16S rRNA genes, but as a single marker, it cannot identify functions (genes). Metagenome and metatranscriptome sequencing can determine microbiome function but can be cost prohibitive. Therefore, computational methods have been developed to ... Text Branta canadensis Canada Goose PubMed Central (PMC) Canada Kos ENVELOPE(143.432,143.432,75.709,75.709) Microbiology Spectrum 10 6 |
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Research Article Gil, Joshua C. Hird, Sarah M. Multiomics Characterization of the Canada Goose Fecal Microbiome Reveals Selective Efficacy of Simulated Metagenomes |
topic_facet |
Research Article |
description |
16S rRNA amplicon sequences are predominantly used to identify the taxonomic composition of a microbiome, but they can also be used to generate simulated metagenomes to circumvent costly empirical shotgun sequencing. The effectiveness of using “simulated metagenomes” (shotgun metagenomes simulated from 16S rRNA amplicons using a database of full genomes closely related to the amplicons) in nonmodel systems is poorly known. We sought to determine the accuracy of simulated metagenomes in a nonmodel organism, the Canada goose (Branta canadensis), by comparing metagenomes and metatranscriptomes to simulated metagenomes derived from 16S amplicon sequencing. We found significant differences between the metagenomes, metatranscriptomes, and simulated metagenomes when comparing enzymes, KEGG orthologies (KO), and metabolic pathways. The simulated metagenomes accurately identified the majority (>70%) of the total enzymes, KOs, and pathways. The simulated metagenomes accurately identified the majority of the short-chain fatty acid metabolic pathways crucial to folivores. When narrowed in scope to specific genes of interest, the simulated metagenomes overestimated the number of antimicrobial resistance genes and underestimated the number of genes related to the breakdown of plant matter. Our results suggest that simulated metagenomes should not be used in lieu of empirical sequencing when studying the functional potential of a nonmodel organism’s microbiome. Regarding the function of the Canada goose microbiome, we found unexpected amounts of fermentation pathways, and we found that a few taxa are responsible for large portions of the functional potential of the microbiome. IMPORTANCE The taxonomic composition of a microbiome is predominately identified using amplicon sequencing of 16S rRNA genes, but as a single marker, it cannot identify functions (genes). Metagenome and metatranscriptome sequencing can determine microbiome function but can be cost prohibitive. Therefore, computational methods have been developed to ... |
format |
Text |
author |
Gil, Joshua C. Hird, Sarah M. |
author_facet |
Gil, Joshua C. Hird, Sarah M. |
author_sort |
Gil, Joshua C. |
title |
Multiomics Characterization of the Canada Goose Fecal Microbiome Reveals Selective Efficacy of Simulated Metagenomes |
title_short |
Multiomics Characterization of the Canada Goose Fecal Microbiome Reveals Selective Efficacy of Simulated Metagenomes |
title_full |
Multiomics Characterization of the Canada Goose Fecal Microbiome Reveals Selective Efficacy of Simulated Metagenomes |
title_fullStr |
Multiomics Characterization of the Canada Goose Fecal Microbiome Reveals Selective Efficacy of Simulated Metagenomes |
title_full_unstemmed |
Multiomics Characterization of the Canada Goose Fecal Microbiome Reveals Selective Efficacy of Simulated Metagenomes |
title_sort |
multiomics characterization of the canada goose fecal microbiome reveals selective efficacy of simulated metagenomes |
publisher |
American Society for Microbiology |
publishDate |
2022 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9769641/ http://www.ncbi.nlm.nih.gov/pubmed/36318011 https://doi.org/10.1128/spectrum.02384-22 |
long_lat |
ENVELOPE(143.432,143.432,75.709,75.709) |
geographic |
Canada Kos |
geographic_facet |
Canada Kos |
genre |
Branta canadensis Canada Goose |
genre_facet |
Branta canadensis Canada Goose |
op_source |
Microbiol Spectr |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9769641/ http://www.ncbi.nlm.nih.gov/pubmed/36318011 http://dx.doi.org/10.1128/spectrum.02384-22 |
op_rights |
Copyright © 2022 Gil and Hird. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license (https://creativecommons.org/licenses/by/4.0/) . |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1128/spectrum.02384-22 |
container_title |
Microbiology Spectrum |
container_volume |
10 |
container_issue |
6 |
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1766381042051055616 |