HTSSIP: An R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments

Youngblut, Nicholas D.; Barnett, Samuel E.; Buckley, Daniel H.; Pan, Chongle

doi:10.1371/journal.pone.0189616

Title: HTSSIP: An R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments

Journal Article · 03 January 2018 · PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0189616 · OSTI ID:1415514

Youngblut, Nicholas D. ^[1]; Barnett, Samuel E. ^[2]; Buckley, Daniel H. ^[2]; Pan, Chongle ^[3]

Cornell Univ., Ithaca, NY (United States). School of Integrative Plant Science; Max Planck Inst. for Developmental Biology, Tubingen (Germany)
Cornell Univ., Ithaca, NY (United States). School of Integrative Plant Science
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

Combining high throughput sequencing with stable isotope probing (HTS-SIP) is a powerful method for mapping in situ metabolic processes to thousands of microbial taxa. However, accurately mapping metabolic processes to taxa is complex and challenging. Multiple HTS-SIP data analysis methods have been developed, including high-resolution stable isotope probing (HR-SIP), multi-window high-resolution stable isotope probing (MW-HR-SIP), quantitative stable isotope probing (qSIP), and ΔBD. Currently, there is no publicly available software designed specifically for analyzing HTS-SIP data. To address this shortfall, we have developed the HTSSIP R package, an open-source, cross-platform toolset for conducting HTS-SIP analyses in a straightforward and easily reproducible manner. The HTSSIP package, along with full documentation and examples, is available from CRAN at https://cran.r-project.org/web/packages/HTSSIP/index.html and Github at https://github.com/buckleylab/HTSSIP.

View Journal Article

Cite

Export

Save

Research Organization:: Cornell Univ., Ithaca, NY (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE

Grant/Contract Number:: SC0004486; SC0010558; SC0016364

OSTI ID:: 1415514

Alternate ID(s):: OSTI ID: 1499888; OSTI ID: 1864328

Journal Information:: PLoS ONE, Vol. 13, Issue 1; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 24 works

Citation information provided by
Web of Science

References (17)

Non-cyanobacterial diazotrophs mediate dinitrogen fixation in biological soil crusts during early crust formation Pepe-Ranney, Charles; Koechli, Chantal; Potrafka, Ruth The ISME Journal, Vol. 10, Issue 2 https://doi.org/10.1038/ismej.2015.106	journal	June 2015
DNA-based stable isotope probing: a link between community structure and function Uhlík, Ondrej; Jecná, Katerina; Leigh, Mary Beth Science of The Total Environment, Vol. 407, Issue 12, p. 3611-3619 https://doi.org/10.1016/j.scitotenv.2008.05.012	journal	June 2009
Identification of Bacterial Micropredators Distinctively Active in a Soil Microbial Food Web Lueders, T.; Kindler, R.; Miltner, A. Applied and Environmental Microbiology, Vol. 72, Issue 8 https://doi.org/10.1128/AEM.00400-06	journal	August 2006
Intra-genomic variation in G + C content and its implications for DNA stable isotope probing: DNA-SIP and intra-genomic variation in G + C content Youngblut, Nicholas D.; Buckley, Daniel H. Environmental Microbiology Reports, Vol. 6, Issue 6 https://doi.org/10.1111/1758-2229.12201	journal	October 2014
RNA stable-isotope probing Whiteley, Andrew S.; Thomson, Bruce; Lueders, Tillmann Nature Protocols, Vol. 2, Issue 4 https://doi.org/10.1038/nprot.2007.115	journal	April 2007
Identification of cellulolytic bacteria in soil by stable isotope probing el Zahar Haichar, Feth; Achouak, Wafa; Christen, Richard Environmental Microbiology, Vol. 9, Issue 3 https://doi.org/10.1111/j.1462-2920.2006.01182.x	journal	March 2007
Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil Pepe-Ranney, Charles; Campbell, Ashley N.; Koechli, Chantal N. Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00703	journal	May 2016
Quantitative Microbial Ecology through Stable Isotope Probing Hungate, Bruce A.; Mau, Rebecca L.; Schwartz, Egbert Applied and Environmental Microbiology, Vol. 81, Issue 21 https://doi.org/10.1128/AEM.02280-15	journal	August 2015
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Love, Michael I.; Huber, Wolfgang; Anders, Simon Genome Biology, Vol. 15, Issue 12 https://doi.org/10.1186/s13059-014-0550-8	journal	December 2014
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data McMurdie, Paul J.; Holmes, Susan PLoS ONE, Vol. 8, Issue 4 https://doi.org/10.1371/journal.pone.0061217	journal	April 2013
Use of Field-Based Stable Isotope Probing To Identify Adapted Populations and Track Carbon Flow through a Phenol-Degrading Soil Microbial Community DeRito, C. M.; Pumphrey, G. M.; Madsen, E. L. Applied and Environmental Microbiology, Vol. 71, Issue 12 https://doi.org/10.1128/AEM.71.12.7858-7865.2005	journal	December 2005
DNA-based stable isotope probing: a link between community structure and function Uhlík, Ondrej; Jecná, Katerina; Leigh, Mary Beth Science of The Total Environment, Vol. 407, Issue 12, p. 3611-3619 https://doi.org/10.1016/j.scitotenv.2008.05.012	journal	June 2009
RNA stable-isotope probing Whiteley, Andrew S.; Thomson, Bruce; Lueders, Tillmann Nature Protocols, Vol. 2, Issue 4 https://doi.org/10.1038/nprot.2007.115	journal	April 2007
Intra-genomic variation in G + C content and its implications for DNA stable isotope probing: DNA-SIP and intra-genomic variation in G + C content Youngblut, Nicholas D.; Buckley, Daniel H. Environmental Microbiology Reports, Vol. 6, Issue 6 https://doi.org/10.1111/1758-2229.12201	journal	October 2014
Identification of cellulolytic bacteria in soil by stable isotope probing el Zahar Haichar, Feth; Achouak, Wafa; Christen, Richard Environmental Microbiology, Vol. 9, Issue 3 https://doi.org/10.1111/j.1462-2920.2006.01182.x	journal	March 2007
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Love, Michael I.; Huber, Wolfgang; Anders, Simon Genome Biology, Vol. 15, Issue 12 https://doi.org/10.1186/s13059-014-0550-8	journal	December 2014
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data McMurdie, Paul J.; Holmes, Susan PLoS ONE, Vol. 8, Issue 4 https://doi.org/10.1371/journal.pone.0061217	journal	April 2013

Cited By (7)

Metabolic activity analyses demonstrate that Lokiarchaeon exhibits homoacetogenesis in sulfidic marine sediments Orsi, William D.; Vuillemin, Aurèle; Rodriguez, Paula Nature Microbiology, Vol. 5, Issue 2 https://doi.org/10.1038/s41564-019-0630-3	journal	December 2019
Evidence for phylogenetically and catabolically diverse active diazotrophs in deep-sea sediment Kapili, Bennett J.; Barnett, Samuel E.; Buckley, Daniel H. The ISME Journal, Vol. 14, Issue 4 https://doi.org/10.1038/s41396-019-0584-8	journal	January 2020
Following the terrestrial tracks of Caulobacter - redefining the ecology of a reputed aquatic oligotroph Wilhelm, Roland C. The ISME Journal, Vol. 12, Issue 12 https://doi.org/10.1038/s41396-018-0257-z	journal	August 2018
Quantifying population-specific growth in benthic bacterial communities under low oxygen using H218O Coskun, Ömer K.; Özen, Volkan; Wankel, Scott D. The ISME Journal, Vol. 13, Issue 6 https://doi.org/10.1038/s41396-019-0373-4	journal	February 2019
Ancylomarina psychrotolerans sp. nov., isolated from sediments of Fildes Peninsula and emended the description of genus Ancylomarina Jia, Chao; Cui, Hong-chang; Han, Yan-qiong Antonie van Leeuwenhoek, Vol. 111, Issue 7 https://doi.org/10.1007/s10482-018-1025-9	journal	February 2018
Quantifying population-specific growth in benthic bacterial communities under low oxygen using H218O Coskun, Ömer K.; Özen, Volkan; Wankel, Scott D. The ISME Journal, Vol. 13, Issue 6 https://doi.org/10.1038/s41396-019-0373-4	journal	February 2019
Evidence for phylogenetically and catabolically diverse active diazotrophs in deep-sea sediment Kapili, Bennett J.; Barnett, Samuel E.; Buckley, Daniel H. The ISME Journal, Vol. 14, Issue 4 https://doi.org/10.1038/s41396-019-0584-8	journal	January 2020