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Santiago-Rodriguez TM, Garoutte A, Adams E, Nasser W, Ross MC, La Reau A, Henseler Z, Ward T, Knights D, Petrosino JF, Hollister EB. Metagenomic Information Recovery from Human Stool Samples Is Influenced by Sequencing Depth and Profiling Method. Genes (Basel) 2020; 11:E1380. [PMID: 33233349 PMCID: PMC7700633 DOI: 10.3390/genes11111380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/20/2022] Open
Abstract
Sequencing of the 16S rRNA gene (16S) has long been a go-to method for microbiome characterization due to its accessibility and lower cost compared to shotgun metagenomic sequencing (SMS). However, 16S sequencing rarely provides species-level resolution and cannot provide direct assessment of other taxa (e.g., viruses and fungi) or functional gene content. Shallow shotgun metagenomic sequencing (SSMS) has emerged as an approach to bridge the gap between 16S sequencing and deep metagenomic sequencing. SSMS is cost-competitive with 16S sequencing, while also providing species-level resolution and functional gene content insights. In the present study, we evaluated the effects of sequencing depth on marker gene-mapping- and alignment-based annotation of bacteria in healthy human stool samples. The number of identified taxa decreased with lower sequencing depths, particularly with the marker gene-mapping-based approach. Other annotations, including viruses and pathways, also showed a depth-dependent effect on feature recovery. These results refine the understanding of the suitability and shortcomings of SSMS, as well as annotation tools for metagenomic analyses in human stool samples. Results may also translate to other sample types and may open the opportunity to explore the effect of sequencing depth and annotation method.
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Affiliation(s)
| | - Aaron Garoutte
- Diversigen Inc., Houston, TX 77021, USA; (A.G.); (E.A.); (W.N.); (J.F.P.); (E.B.H.)
| | - Emmase Adams
- Diversigen Inc., Houston, TX 77021, USA; (A.G.); (E.A.); (W.N.); (J.F.P.); (E.B.H.)
| | - Waleed Nasser
- Diversigen Inc., Houston, TX 77021, USA; (A.G.); (E.A.); (W.N.); (J.F.P.); (E.B.H.)
| | - Matthew C. Ross
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX 77030, USA;
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alex La Reau
- Diversigen Inc., Saint Paul, MN 55112, USA; (A.L.R.); (Z.H.); (T.W.); (D.K.)
| | - Zachariah Henseler
- Diversigen Inc., Saint Paul, MN 55112, USA; (A.L.R.); (Z.H.); (T.W.); (D.K.)
| | - Tonya Ward
- Diversigen Inc., Saint Paul, MN 55112, USA; (A.L.R.); (Z.H.); (T.W.); (D.K.)
| | - Dan Knights
- Diversigen Inc., Saint Paul, MN 55112, USA; (A.L.R.); (Z.H.); (T.W.); (D.K.)
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Biotechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Joseph F. Petrosino
- Diversigen Inc., Houston, TX 77021, USA; (A.G.); (E.A.); (W.N.); (J.F.P.); (E.B.H.)
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX 77030, USA;
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Emily B. Hollister
- Diversigen Inc., Houston, TX 77021, USA; (A.G.); (E.A.); (W.N.); (J.F.P.); (E.B.H.)
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Porter SS, Bantay R, Friel CA, Garoutte A, Gdanetz K, Ibarreta K, Moore BM, Shetty P, Siler E, Friesen ML. Beneficial microbes ameliorate abiotic and biotic sources of stress on plants. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13499] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
| | - Roxanne Bantay
- Department of Plant Biology Michigan State University East Lansing MI USA
| | - Colleen A. Friel
- Department of Plant Biology Michigan State University East Lansing MI USA
| | - Aaron Garoutte
- Department of Plant Biology Michigan State University East Lansing MI USA
- Department of Plant Soil & Microbial Sciences Michigan State University East Lansing MI USA
| | - Kristi Gdanetz
- Department of Plant Biology Michigan State University East Lansing MI USA
| | - Kathleen Ibarreta
- School of Biological Sciences Washington State University Vancouver WA USA
| | - Bethany M. Moore
- Department of Plant Biology Michigan State University East Lansing MI USA
| | - Prateek Shetty
- Department of Plant Biology Michigan State University East Lansing MI USA
| | - Eleanor Siler
- Department of Plant Biology Michigan State University East Lansing MI USA
| | - Maren L. Friesen
- Department of Plant Biology Michigan State University East Lansing MI USA
- Department of Plant Pathology Washington State University Pullman WA USA
- Department of Crop & Soil Sciences Washington State University Pullman WA USA
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Helliwell EE, Faber‐Hammond J, Lopez ZC, Garoutte A, Wettberg E, Friesen ML, Porter SS. Rapid establishment of a flowering cline in
Medicago polymorpha
after invasion of North America. Mol Ecol 2018; 27:4758-4774. [DOI: 10.1111/mec.14898] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 10/01/2018] [Accepted: 10/03/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Emily E. Helliwell
- School of Biological Sciences Washington State University Vancouver Washington
| | | | - Zoie C. Lopez
- School of Biological Sciences Washington State University Vancouver Washington
| | - Aaron Garoutte
- Department of Plant Biology Michigan State University East Lansing Michigan
| | - Eric Wettberg
- Department of Plant and Soil Science The University of Vermont Burlington Vermont
| | - Maren L. Friesen
- Department of Plant Biology Michigan State University East Lansing Michigan
- Department of Plant Pathology Washington State University Pullman Washington
- Department of Crop and Soil Sciences Washington State University Pullman Washington
| | - Stephanie S. Porter
- School of Biological Sciences Washington State University Vancouver Washington
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Roley SS, Duncan DS, Liang D, Garoutte A, Jackson RD, Tiedje JM, Robertson GP. Associative nitrogen fixation (ANF) in switchgrass (Panicum virgatum) across a nitrogen input gradient. PLoS One 2018; 13:e0197320. [PMID: 29856843 PMCID: PMC5983442 DOI: 10.1371/journal.pone.0197320] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 04/29/2018] [Indexed: 11/23/2022] Open
Abstract
Associative N fixation (ANF), the process by which dinitrogen gas is converted to ammonia by bacteria in casual association with plants, has not been well-studied in temperate ecosystems. We examined the ANF potential of switchgrass (Panicum virgatum L.), a North American prairie grass whose productivity is often unresponsive to N fertilizer addition, via separate short-term 15N2 incubations of rhizosphere soils and excised roots four times during the growing season. Measurements occurred along N fertilization gradients at two sites with contrasting soil fertility (Wisconsin, USA Mollisols and Michigan, USA Alfisols). In general, we found that ANF potentials declined with long-term N addition, corresponding with increased soil N availability. Although we hypothesized that ANF potential would track plant N demand through the growing season, the highest root fixation rates occurred after plants senesced, suggesting that root diazotrophs exploit carbon (C) released during senescence, as C is translocated from aboveground tissues to roots for wintertime storage. Measured ANF potentials, coupled with mass balance calculations, suggest that ANF appears to be an important source of N to unfertilized switchgrass, and, by extension, to temperate grasslands in general.
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Affiliation(s)
- Sarah S. Roley
- WK Kellogg Biological Station, Michigan State University, Hickory Corners, Michigan, United States of America
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, United States of America
- * E-mail:
| | - David S. Duncan
- Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Di Liang
- WK Kellogg Biological Station, Michigan State University, Hickory Corners, Michigan, United States of America
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, United States of America
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
| | - Aaron Garoutte
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, United States of America
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States of America
| | - Randall D. Jackson
- Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - James M. Tiedje
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, United States of America
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States of America
| | - G. Philip Robertson
- WK Kellogg Biological Station, Michigan State University, Hickory Corners, Michigan, United States of America
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, United States of America
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
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Choi J, Yang F, Stepanauskas R, Cardenas E, Garoutte A, Williams R, Flater J, Tiedje JM, Hofmockel KS, Gelder B, Howe A. Strategies to improve reference databases for soil microbiomes. ISME J 2016; 11:829-834. [PMID: 27935589 PMCID: PMC5364351 DOI: 10.1038/ismej.2016.168] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 10/10/2016] [Accepted: 10/21/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Jinlyung Choi
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA
| | - Fan Yang
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA
| | | | - Erick Cardenas
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Aaron Garoutte
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Ryan Williams
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA
| | - Jared Flater
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Kirsten S Hofmockel
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA.,Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Brian Gelder
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA
| | - Adina Howe
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA
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Garoutte A, Cardenas E, Tiedje J, Howe A. Methodologies for probing the metatranscriptome of grassland soil. J Microbiol Methods 2016; 131:122-129. [PMID: 27793585 DOI: 10.1016/j.mimet.2016.10.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/21/2016] [Accepted: 10/21/2016] [Indexed: 10/20/2022]
Abstract
Metatranscriptomics provides an opportunity to identify active microbes and expressed genes in complex soil communities in response to particular conditions. Currently, there are a limited number of soil metatranscriptome studies to provide guidance for using this approach in this challenging matrix. Hence, we evaluated the technical challenges of applying soil metatranscriptomics to a highly diverse, low activity natural system. We used a non-targeted rRNA removal approach, duplex nuclease specific (DSN) normalization, to generate a metatranscriptomic library from field collected soil supporting a perennial grass, Miscanthus x giganteus (a biofuel crop), and evaluated its ability to provide insight into its active community members and their expressed protein-coding genes. We also evaluated various bioinformatics approaches for analyzing our soil metatranscriptome, including annotation of unassembled transcripts, de novo assembly, and aligning reads to known genomes. Further, we evaluated various databases for their ability to provide annotations for our metatranscriptome. Overall, our results emphasize that low activity, highly genetically diverse and relatively stable microbiomes, like soil, requires very deep sequencing to sample the transcriptome beyond the common core functions. We identified several key areas that metatranscriptomic analyses will benefit from including increased rRNA removal, assembly of short read transcripts, and more relevant reference bases while providing a priority set of expressed genes for functional assessment.
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Affiliation(s)
- Aaron Garoutte
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States.
| | - Erick Cardenas
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - James Tiedje
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States; Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Adina Howe
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States; Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, United States
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Dong Q, Brulc JM, Iovieno A, Bates B, Garoutte A, Miller D, Revanna KV, Gao X, Antonopoulos DA, Slepak VZ, Shestopalov VI. Diversity of bacteria at healthy human conjunctiva. Invest Ophthalmol Vis Sci 2011; 52:5408-13. [PMID: 21571682 DOI: 10.1167/iovs.10-6939] [Citation(s) in RCA: 248] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Ocular surface (OS) microbiota contributes to infectious and autoimmune diseases of the eye. Comprehensive analysis of microbial diversity at the OS has been impossible because of the limitations of conventional cultivation techniques. This pilot study aimed to explore true diversity of human OS microbiota using DNA sequencing-based detection and identification of bacteria. METHODS Composition of the bacterial community was characterized using deep sequencing of the 16S rRNA gene amplicon libraries generated from total conjunctival swab DNA. The DNA sequences were classified and the diversity parameters measured using bioinformatics software ESPRIT and MOTHUR and tools available through the Ribosomal Database Project-II (RDP-II). RESULTS Deep sequencing of conjunctival rDNA from four subjects yielded a total of 115,003 quality DNA reads, corresponding to 221 species-level phylotypes per subject. The combined bacterial community classified into 5 phyla and 59 distinct genera. However, 31% of all DNA reads belonged to unclassified or novel bacteria. The intersubject variability of individual OS microbiomes was very significant. Regardless, 12 genera-Pseudomonas, Propionibacterium, Bradyrhizobium, Corynebacterium, Acinetobacter, Brevundimonas, Staphylococci, Aquabacterium, Sphingomonas, Streptococcus, Streptophyta, and Methylobacterium-were ubiquitous among the analyzed cohort and represented the putative "core" of conjunctival microbiota. The other 47 genera accounted for <4% of the classified portion of this microbiome. Unexpectedly, healthy conjunctiva contained many genera that are commonly identified as ocular surface pathogens. CONCLUSIONS The first DNA sequencing-based survey of bacterial population at the conjunctiva have revealed an unexpectedly diverse microbial community. All analyzed samples contained ubiquitous (core) genera that included commensal, environmental, and opportunistic pathogenic bacteria.
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Affiliation(s)
- Qunfeng Dong
- Department of Biological Sciences, University of North Texas, Denton, Texas, USA
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