MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations
Abstract Background Microbes and their viruses are hidden engines driving Earth’s ecosystems from the oceans and soils to humans and bioreactors. Though gene marker approaches can now be complemented by genome-resolved studies of inter-(macrodiversity) and intra-(microdiversity) population variation...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-03-01
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| Series: | Microbiome |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s40168-022-01231-0 |
| _version_ | 1818571714223669248 |
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| author | Ann C. Gregory Kenji Gerhardt Zhi-Ping Zhong Benjamin Bolduc Ben Temperton Konstantinos T. Konstantinidis Matthew B. Sullivan |
| author_facet | Ann C. Gregory Kenji Gerhardt Zhi-Ping Zhong Benjamin Bolduc Ben Temperton Konstantinos T. Konstantinidis Matthew B. Sullivan |
| author_sort | Ann C. Gregory |
| collection | DOAJ |
| description | Abstract Background Microbes and their viruses are hidden engines driving Earth’s ecosystems from the oceans and soils to humans and bioreactors. Though gene marker approaches can now be complemented by genome-resolved studies of inter-(macrodiversity) and intra-(microdiversity) population variation, analytical tools to do so remain scattered or under-developed. Results Here, we introduce MetaPop, an open-source bioinformatic pipeline that provides a single interface to analyze and visualize microbial and viral community metagenomes at both the macro- and microdiversity levels. Macrodiversity estimates include population abundances and α- and β-diversity. Microdiversity calculations include identification of single nucleotide polymorphisms, novel codon-constrained linkage of SNPs, nucleotide diversity (π and θ), and selective pressures (pN/pS and Tajima’s D) within and fixation indices (F ST) between populations. MetaPop will also identify genes with distinct codon usage. Following rigorous validation, we applied MetaPop to the gut viromes of autistic children that underwent fecal microbiota transfers and their neurotypical peers. The macrodiversity results confirmed our prior findings for viral populations (microbial shotgun metagenomes were not available) that diversity did not significantly differ between autistic and neurotypical children. However, by also quantifying microdiversity, MetaPop revealed lower average viral nucleotide diversity (π) in autistic children. Analysis of the percentage of genomes detected under positive selection was also lower among autistic children, suggesting that higher viral π in neurotypical children may be beneficial because it allows populations to better “bet hedge” in changing environments. Further, comparisons of microdiversity pre- and post-FMT in autistic children revealed that the delivery FMT method (oral versus rectal) may influence viral activity and engraftment of microdiverse viral populations, with children who received their FMT rectally having higher microdiversity post-FMT. Overall, these results show that analyses at the macro level alone can miss important biological differences. Conclusions These findings suggest that standardized population and genetic variation analyses will be invaluable for maximizing biological inference, and MetaPop provides a convenient tool package to explore the dual impact of macro- and microdiversity across microbial communities. Video abstract |
| first_indexed | 2024-12-14T18:48:00Z |
| format | Article |
| id | doaj.art-2de177bf08bc4c999607fa2b2415d4ab |
| institution | Directory Open Access Journal |
| issn | 2049-2618 |
| language | English |
| last_indexed | 2024-12-14T18:48:00Z |
| publishDate | 2022-03-01 |
| publisher | BMC |
| record_format | Article |
| series | Microbiome |
| spelling | doaj.art-2de177bf08bc4c999607fa2b2415d4ab2022-12-21T22:51:20ZengBMCMicrobiome2049-26182022-03-0110111910.1186/s40168-022-01231-0MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populationsAnn C. Gregory0Kenji Gerhardt1Zhi-Ping Zhong2Benjamin Bolduc3Ben Temperton4Konstantinos T. Konstantinidis5Matthew B. Sullivan6Department of Microbiology, Ohio State UniversityDepartment of Microbiology, Ohio State UniversityDepartment of Microbiology, Ohio State UniversityDepartment of Microbiology, Ohio State UniversitySchool of Biosciences, University of ExeterSchool of Biological Sciences, Georgia Institute of TechnologyDepartment of Microbiology, Ohio State UniversityAbstract Background Microbes and their viruses are hidden engines driving Earth’s ecosystems from the oceans and soils to humans and bioreactors. Though gene marker approaches can now be complemented by genome-resolved studies of inter-(macrodiversity) and intra-(microdiversity) population variation, analytical tools to do so remain scattered or under-developed. Results Here, we introduce MetaPop, an open-source bioinformatic pipeline that provides a single interface to analyze and visualize microbial and viral community metagenomes at both the macro- and microdiversity levels. Macrodiversity estimates include population abundances and α- and β-diversity. Microdiversity calculations include identification of single nucleotide polymorphisms, novel codon-constrained linkage of SNPs, nucleotide diversity (π and θ), and selective pressures (pN/pS and Tajima’s D) within and fixation indices (F ST) between populations. MetaPop will also identify genes with distinct codon usage. Following rigorous validation, we applied MetaPop to the gut viromes of autistic children that underwent fecal microbiota transfers and their neurotypical peers. The macrodiversity results confirmed our prior findings for viral populations (microbial shotgun metagenomes were not available) that diversity did not significantly differ between autistic and neurotypical children. However, by also quantifying microdiversity, MetaPop revealed lower average viral nucleotide diversity (π) in autistic children. Analysis of the percentage of genomes detected under positive selection was also lower among autistic children, suggesting that higher viral π in neurotypical children may be beneficial because it allows populations to better “bet hedge” in changing environments. Further, comparisons of microdiversity pre- and post-FMT in autistic children revealed that the delivery FMT method (oral versus rectal) may influence viral activity and engraftment of microdiverse viral populations, with children who received their FMT rectally having higher microdiversity post-FMT. Overall, these results show that analyses at the macro level alone can miss important biological differences. Conclusions These findings suggest that standardized population and genetic variation analyses will be invaluable for maximizing biological inference, and MetaPop provides a convenient tool package to explore the dual impact of macro- and microdiversity across microbial communities. Video abstracthttps://doi.org/10.1186/s40168-022-01231-0MetagenomesVisualizationSNP profilingCommunity ecologyPopulation geneticsMacrodiversity |
| spellingShingle | Ann C. Gregory Kenji Gerhardt Zhi-Ping Zhong Benjamin Bolduc Ben Temperton Konstantinos T. Konstantinidis Matthew B. Sullivan MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations Microbiome Metagenomes Visualization SNP profiling Community ecology Population genetics Macrodiversity |
| title | MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations |
| title_full | MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations |
| title_fullStr | MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations |
| title_full_unstemmed | MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations |
| title_short | MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations |
| title_sort | metapop a pipeline for macro and microdiversity analyses and visualization of microbial and viral metagenome derived populations |
| topic | Metagenomes Visualization SNP profiling Community ecology Population genetics Macrodiversity |
| url | https://doi.org/10.1186/s40168-022-01231-0 |
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