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Li M, Kopylova E, Mao J, Namkoong J, Sanders J, Wu J. Microbiome and lipidomic analysis reveal the interplay between skin bacteria and lipids in a cohort study. Front Microbiol 2024; 15:1383656. [PMID: 38666261 PMCID: PMC11043602 DOI: 10.3389/fmicb.2024.1383656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Human skin acts as a protective barrier between the body and the external environment. Skin microbiome and intercellular lipids in the stratum corneum (SC) are essential for maintaining skin barrier function. However, the interplay between skin bacteria and the lipids is not fully understood. In this study, we characterized the skin microbiome and SC lipid profiles from the forearm and face in a cohort of 57 healthy participants. 16S rRNA gene sequencing showed the skin microbial composition is significantly different between body locations and genders. Female forearm samples have the highest microbial diversity. The relative abundance of Staphylococcus hominis, Micrococcus luteus, Corynebacterium tuberculostearicum, Finegoldia magna, and Moraxellaceae sp. are significantly higher in the forearm than the face. The predictive functional analysis of 16S rRNA gene sequencing by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) and ANCOM-BC showed different bacterial metabolic pathway profiles between body locations or genders, and identified 271 differential pathways, including arginine and polyamine biosynthesis, chorismate biosynthesis pathways, which are more abundant in the female forearm, and sulfur oxidation pathway, which is more abundant in the male face. The SC lipid profiles differ between the body locations as well. Total free fatty acids (FFA), cholesterol sulfate and sphingosine are more abundant in the face. Dihydro-/6-hydroxy/phyto-ceramides are more abundant in the forearm. The correlation analysis of 16S rRNA gene sequencing and lipids revealed novel interplay between the bacteria and skin lipids. Shannon entropy and S. hominis negatively correlated with FFA, cholesterol sulfate and sphingosine; while positively correlated with dihydro-/6-hydroxy/phyto-ceramides. The correlation of predictive pathway profiles and lipids identified pathways involved in amino acids metabolism, carbohydrates degradation, aromatic compounds metabolism and fatty acid degradation metabolism are positively correlated with dihydro-/6-hydroxy/phyto-ceramides and negatively correlated with FFA, cholesterol sulfate and sphingosine. This study provides insights on the potential correlation between skin microbiome and lipids.
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Affiliation(s)
- Min Li
- Colgate-Palmolive Company, Global Technology Center, Piscataway, NJ, United States
| | | | - Junhong Mao
- Colgate-Palmolive Company, Global Technology Center, Piscataway, NJ, United States
| | - Jin Namkoong
- Colgate-Palmolive Company, Global Technology Center, Piscataway, NJ, United States
| | - Jon Sanders
- Clarity Genomics, San Diego, CA, United States
| | - Joanna Wu
- Colgate-Palmolive Company, Global Technology Center, Piscataway, NJ, United States
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Sepich-Poore GD, McDonald D, Kopylova E, Guccione C, Zhu Q, Austin G, Carpenter C, Fraraccio S, Wandro S, Kosciolek T, Janssen S, Metcalf JL, Song SJ, Kanbar J, Miller-Montgomery S, Heaton R, Mckay R, Patel SP, Swafford AD, Korem T, Knight R. Correction: Robustness of cancer microbiome signals over a broad range of methodological variation. Oncogene 2024:10.1038/s41388-024-03018-z. [PMID: 38580705 DOI: 10.1038/s41388-024-03018-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024]
Affiliation(s)
- Gregory D Sepich-Poore
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Micronoma, San Diego, CA, USA
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Evguenia Kopylova
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Clarity Genomics, Antwerp, Belgium
| | - Caitlin Guccione
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - George Austin
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Carolina Carpenter
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Serena Fraraccio
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Micronoma, San Diego, CA, USA
| | - Stephen Wandro
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Micronoma, San Diego, CA, USA
| | - Tomasz Kosciolek
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Malopolska Centre of Biotechnology, Jagiellonian University in Kraków, Kraków, Poland
| | - Stefan Janssen
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Algorithmic Bioinformatics, Department of Biology and Chemistry, Justus Liebig University Gießen, Gießen, Germany
| | - Jessica L Metcalf
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - Se Jin Song
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Jad Kanbar
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sandrine Miller-Montgomery
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Micronoma, San Diego, CA, USA
| | - Robert Heaton
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Rana Mckay
- Moores Cancer Center, University of California San Diego Health, La Jolla, CA, USA
| | - Sandip Pravin Patel
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego Health, La Jolla, CA, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Tal Korem
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA
| | - Rob Knight
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
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3
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Sepich-Poore GD, McDonald D, Kopylova E, Guccione C, Zhu Q, Austin G, Carpenter C, Fraraccio S, Wandro S, Kosciolek T, Janssen S, Metcalf JL, Song SJ, Kanbar J, Miller-Montgomery S, Heaton R, Mckay R, Patel SP, Swafford AD, Korem T, Knight R. Robustness of cancer microbiome signals over a broad range of methodological variation. Oncogene 2024; 43:1127-1148. [PMID: 38396294 PMCID: PMC10997506 DOI: 10.1038/s41388-024-02974-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/03/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024]
Abstract
In 2020, we identified cancer-specific microbial signals in The Cancer Genome Atlas (TCGA) [1]. Multiple peer-reviewed papers independently verified or extended our findings [2-12]. Given this impact, we carefully considered concerns by Gihawi et al. [13] that batch correction and database contamination with host sequences artificially created the appearance of cancer type-specific microbiomes. (1) We tested batch correction by comparing raw and Voom-SNM-corrected data per-batch, finding predictive equivalence and significantly similar features. We found consistent results with a modern microbiome-specific method (ConQuR [14]), and when restricting to taxa found in an independent, highly-decontaminated cohort. (2) Using Conterminator [15], we found low levels of human contamination in our original databases (~1% of genomes). We demonstrated that the increased detection of human reads in Gihawi et al. [13] was due to using a newer human genome reference. (3) We developed Exhaustive, a method twice as sensitive as Conterminator, to clean RefSeq. We comprehensively host-deplete TCGA with many human (pan)genome references. We repeated all analyses with this and the Gihawi et al. [13] pipeline, and found cancer type-specific microbiomes. These extensive re-analyses and updated methods validate our original conclusion that cancer type-specific microbial signatures exist in TCGA, and show they are robust to methodology.
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Affiliation(s)
- Gregory D Sepich-Poore
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Micronoma, San Diego, CA, USA
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Evguenia Kopylova
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Clarity Genomics, Antwerp, Belgium
| | - Caitlin Guccione
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - George Austin
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Carolina Carpenter
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Serena Fraraccio
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Micronoma, San Diego, CA, USA
| | - Stephen Wandro
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Micronoma, San Diego, CA, USA
| | - Tomasz Kosciolek
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Malopolska Centre of Biotechnology, Jagiellonian University in Kraków, Kraków, Poland
| | - Stefan Janssen
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Algorithmic Bioinformatics, Department of Biology and Chemistry, Justus Liebig University Gießen, Gießen, Germany
| | - Jessica L Metcalf
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - Se Jin Song
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Jad Kanbar
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sandrine Miller-Montgomery
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Micronoma, San Diego, CA, USA
| | - Robert Heaton
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Rana Mckay
- Moores Cancer Center, University of California San Diego Health, La Jolla, CA, USA
| | - Sandip Pravin Patel
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego Health, La Jolla, CA, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Tal Korem
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA
| | - Rob Knight
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
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4
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Li M, Mao J, Diaz I, Kopylova E, Melnik AV, Aksenov AA, Tipton CD, Soliman N, Morgan AM, Boyd T. Multi-omic approach to decipher the impact of skincare products with pre/postbiotics on skin microbiome and metabolome. Front Med (Lausanne) 2023; 10:1165980. [PMID: 37534320 PMCID: PMC10392128 DOI: 10.3389/fmed.2023.1165980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 07/03/2023] [Indexed: 08/04/2023] Open
Abstract
Introduction Although pre/pro/postbiotics have become more prevalent in dermatologic and cosmetic fields, the mode of action when topically applied is largely unknown. A multi-omic approach was applied to decipher the impact of the skincare products with pre/postbiotics on skin microbiome and metabolome. Methods Subjects with dry skin applied a body wash and body lotion with or without pre/postbiotics for 6 weeks. Skin hydration was measured at baseline, 3 and 6 weeks. Skin swabs were collected for 16S rRNA gene sequencing, metagenomics and metabolomics analysis. Results Skin hydration significantly increased in both groups. The prebiotic group significantly reduced opportunistic pathogens, e.g., Pseudomonas stutzeri and Sphingomonas anadarae, and increased the commensals, e.g., Staphylococcus equorum, Streptococcus mitis, Halomonas desiderata. Bacterial sugar degradation pathways were enriched in the prebiotic group, while fatty acid biosynthesis pathways were reduced in control. The changes on skin metabolome profiles by the products were more prominent. The prebiotic group performed greater modulation on many clinically-relevant metabolites compared to control. Correlation analysis showed H. desiderata and S. mitis positively correlated with skin hydration, P. stutzeri and S. anadarae negatively correlated with the metabolites that are positively associated with skin hydration improvement. Conclusion This holistic study supported a hypothesis that the pre/postbiotics increased skin hydration through the modulation of skin microbiome, metabolic pathways and metabolome.
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Affiliation(s)
- Min Li
- Colgate−Palmolive Company, Piscataway, NJ, United States
| | - Junhong Mao
- Colgate−Palmolive Company, Piscataway, NJ, United States
| | - Isabel Diaz
- Colgate−Palmolive Company, Piscataway, NJ, United States
| | - Evguenia Kopylova
- Clarity Genomics Inc., San Diego, CA, United States
- Arome Science Inc., Farmington, CT, United States
| | - Alexey V. Melnik
- Clarity Genomics Inc., San Diego, CA, United States
- Arome Science Inc., Farmington, CT, United States
| | - Alexander A. Aksenov
- Clarity Genomics Inc., San Diego, CA, United States
- Arome Science Inc., Farmington, CT, United States
| | | | - Nadia Soliman
- Colgate−Palmolive Company, Piscataway, NJ, United States
| | | | - Thomas Boyd
- Colgate−Palmolive Company, Piscataway, NJ, United States
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5
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Bajorek S, Duar RM, Corrigan M, Matrone C, Winn KA, Norman S, Mitchell RD, Cagney O, Aksenov AA, Melnik AV, Kopylova E, Perez J. B. infantis EVC001 Is Well-Tolerated and Improves Human Milk Oligosaccharide Utilization in Preterm Infants in the Neonatal Intensive Care Unit. Front Pediatr 2021; 9:795970. [PMID: 35071138 PMCID: PMC8767116 DOI: 10.3389/fped.2021.795970] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/07/2021] [Indexed: 12/30/2022] Open
Abstract
Not all infants carry specialized gut microbes, meaning they cannot digest human milk oligosaccharides and therefore do not receive complete benefits from human milk. B. infantis EVC001 is equipped to convert the full array of complex oligosaccharides into compounds usable by the infant, making it an ideal candidate to stabilize gut function and improve nutrition in preterm infants. A prospective, open-label study design was used to evaluate the tolerability of B. infantis EVC001 and its effects on the fecal microbiota in preterm infants in a Neonatal Intensive Care Unit. Thirty preterm infants <1,500 g and/or <33 weeks gestation at birth were divided into two matched groups, and control infants were enrolled and discharged prior to enrolling EVC001 infants to prevent cross-colonization of B. infantis: (1) fifteen control infants received no EVC001, and (2) fifteen infants received once-daily feedings of B. infantis EVC001 (8.0 x 109 CFU) in MCT oil. Clinical information regarding medications, growth, nutrition, gastrointestinal events, diagnoses, and procedures was collected throughout admission. Infant stool samples were collected at baseline, Study Days 14 and 28, and 34-, 36-, and 38-weeks of gestation. Taxonomic composition of the fecal microbiota, functional microbiota analysis, B. infantis, and human milk oligosaccharides (HMOs) in the stool were determined or quantified using 16S rRNA gene sequencing, metagenomic sequencing, qPCR, and mass spectrometry, respectively. No adverse events or tolerability issues related to EVC001 were reported. Control infants had no detectable levels of B. infantis. EVC001 infants achieved high levels of B. infantis (mean = 9.7 Log10 CFU/μg fecal DNA) by Study Day 14, correlating with less fecal HMOs (ρ = -0.83, P < 0.0001), indicating better HMO utilization in the gut. In this study, B. infantis EVC001 was shown to be safe, well-tolerated, and efficient in colonizing the preterm infant gut and able to increase the abundance of bifidobacteria capable of metabolizing HMOs, resulting in significantly improved utilization of human milk. Clinical Trial Registration: https://clinicaltrials.gov/ct2/show/NCT03939546, identifier: NCT03939546.
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Affiliation(s)
- Sarah Bajorek
- St. Mary's Hospital, Grand Junction, CO, United States.,Orlando Health Winnie Palmer Hospital for Women and Babies, Orlando, FL, United States
| | | | - Maxwell Corrigan
- Orlando Health Winnie Palmer Hospital for Women and Babies, Orlando, FL, United States
| | - Christa Matrone
- Orlando Health Winnie Palmer Hospital for Women and Babies, Orlando, FL, United States
| | - Kathryn A Winn
- Orlando Health Winnie Palmer Hospital for Women and Babies, Orlando, FL, United States
| | - Susan Norman
- Orlando Health Winnie Palmer Hospital for Women and Babies, Orlando, FL, United States
| | | | - Orla Cagney
- Evolve BioSystems Inc., Davis, CA, United States
| | - Alexander A Aksenov
- Department of Chemistry, University of Connecticut, Storrs, CT, United States.,Arome Science Inc., Farmington, CT, United States.,Clarity Genomics Inc., San Diego, CA, United States
| | - Alexey V Melnik
- Department of Chemistry, University of Connecticut, Storrs, CT, United States.,Arome Science Inc., Farmington, CT, United States.,Clarity Genomics Inc., San Diego, CA, United States
| | - Evguenia Kopylova
- Arome Science Inc., Farmington, CT, United States.,Clarity Genomics Inc., San Diego, CA, United States
| | - Jose Perez
- Orlando Health Winnie Palmer Hospital for Women and Babies, Orlando, FL, United States.,Seattle Children's Hospital, University of Washington, Seattle, WA, United States
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Asnicar F, Thomas AM, Beghini F, Mengoni C, Manara S, Manghi P, Zhu Q, Bolzan M, Cumbo F, May U, Sanders JG, Zolfo M, Kopylova E, Pasolli E, Knight R, Mirarab S, Huttenhower C, Segata N. Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nat Commun 2020; 11:2500. [PMID: 32427907 PMCID: PMC7237447 DOI: 10.1038/s41467-020-16366-7] [Citation(s) in RCA: 293] [Impact Index Per Article: 73.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 04/27/2020] [Indexed: 01/10/2023] Open
Abstract
Microbial genomes are available at an ever-increasing pace, as cultivation and sequencing become cheaper and obtaining metagenome-assembled genomes (MAGs) becomes more effective. Phylogenetic placement methods to contextualize hundreds of thousands of genomes must thus be efficiently scalable and sensitive from closely related strains to divergent phyla. We present PhyloPhlAn 3.0, an accurate, rapid, and easy-to-use method for large-scale microbial genome characterization and phylogenetic analysis at multiple levels of resolution. PhyloPhlAn 3.0 can assign genomes from isolate sequencing or MAGs to species-level genome bins built from >230,000 publically available sequences. For individual clades of interest, it reconstructs strain-level phylogenies from among the closest species using clade-specific maximally informative markers. At the other extreme of resolution, it scales to large phylogenies comprising >17,000 microbial species. Examples including Staphylococcus aureus isolates, gut metagenomes, and meta-analyses demonstrate the ability of PhyloPhlAn 3.0 to support genomic and metagenomic analyses.
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Affiliation(s)
| | | | | | | | - Serena Manara
- Department CIBIO, University of Trento, Trento, Italy
| | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Mattia Bolzan
- Department CIBIO, University of Trento, Trento, Italy
- PreBiomics s.r.l, Trento, Italy
| | - Fabio Cumbo
- Department CIBIO, University of Trento, Trento, Italy
| | - Uyen May
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA
| | - Jon G Sanders
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Cornell Institute for Host-Microbe Interaction and Disease, Cornell University, Ithaca, NY, USA
| | - Moreno Zolfo
- Department CIBIO, University of Trento, Trento, Italy
| | - Evguenia Kopylova
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Clarity Genomics BVBA, Sint-Michielskaai 34, 2000, Antwerpen, Belgium
| | - Edoardo Pasolli
- Department CIBIO, University of Trento, Trento, Italy
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy.
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7
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Poore GD, Kopylova E, Zhu Q, Carpenter C, Fraraccio S, Wandro S, Kosciolek T, Janssen S, Metcalf J, Song SJ, Kanbar J, Miller-Montgomery S, Heaton R, Mckay R, Patel SP, Swafford AD, Knight R. Microbiome analyses of blood and tissues suggest cancer diagnostic approach. Nature 2020; 579:567-574. [PMID: 32214244 PMCID: PMC7500457 DOI: 10.1038/s41586-020-2095-1] [Citation(s) in RCA: 575] [Impact Index Per Article: 143.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 02/06/2020] [Indexed: 01/05/2023]
Abstract
Systematic characterization of the cancer microbiome provides the opportunity to develop techniques that exploit non-human, microorganism-derived molecules in the diagnosis of a major human disease. Following recent demonstrations that some types of cancer show substantial microbial contributions1-10, we re-examined whole-genome and whole-transcriptome sequencing studies in The Cancer Genome Atlas11 (TCGA) of 33 types of cancer from treatment-naive patients (a total of 18,116 samples) for microbial reads, and found unique microbial signatures in tissue and blood within and between most major types of cancer. These TCGA blood signatures remained predictive when applied to patients with stage Ia-IIc cancer and cancers lacking any genomic alterations currently measured on two commercial-grade cell-free tumour DNA platforms, despite the use of very stringent decontamination analyses that discarded up to 92.3% of total sequence data. In addition, we could discriminate among samples from healthy, cancer-free individuals (n = 69) and those from patients with multiple types of cancer (prostate, lung, and melanoma; 100 samples in total) solely using plasma-derived, cell-free microbial nucleic acids. This potential microbiome-based oncology diagnostic tool warrants further exploration.
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Affiliation(s)
- Gregory D Poore
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Evguenia Kopylova
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Clarity Genomics, Beerse, Belgium
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Carolina Carpenter
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Serena Fraraccio
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Stephen Wandro
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Tomasz Kosciolek
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Malopolska Centre of Biotechnology, Jagiellonian University in Krakow, Krakow, Poland
| | - Stefan Janssen
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Algorithmic Bioinformatics, Department of Biology and Chemistry, Justus Liebig University Gießen, Gießen, Germany
| | - Jessica Metcalf
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - Se Jin Song
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Jad Kanbar
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sandrine Miller-Montgomery
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Robert Heaton
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Rana Mckay
- Moores Cancer Center, University of California San Diego Health, La Jolla, CA, USA
| | - Sandip Pravin Patel
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego Health, La Jolla, CA, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
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8
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Zhu Q, Mai U, Pfeiffer W, Janssen S, Asnicar F, Sanders JG, Belda-Ferre P, Al-Ghalith GA, Kopylova E, McDonald D, Kosciolek T, Yin JB, Huang S, Salam N, Jiao JY, Wu Z, Xu ZZ, Cantrell K, Yang Y, Sayyari E, Rabiee M, Morton JT, Podell S, Knights D, Li WJ, Huttenhower C, Segata N, Smarr L, Mirarab S, Knight R. Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea. Nat Commun 2019; 10:5477. [PMID: 31792218 PMCID: PMC6889312 DOI: 10.1038/s41467-019-13443-4] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 11/06/2019] [Indexed: 11/10/2022] Open
Abstract
Rapid growth of genome data provides opportunities for updating microbial evolutionary relationships, but this is challenged by the discordant evolution of individual genes. Here we build a reference phylogeny of 10,575 evenly-sampled bacterial and archaeal genomes, based on a comprehensive set of 381 markers, using multiple strategies. Our trees indicate remarkably closer evolutionary proximity between Archaea and Bacteria than previous estimates that were limited to fewer "core" genes, such as the ribosomal proteins. The robustness of the results was tested with respect to several variables, including taxon and site sampling, amino acid substitution heterogeneity and saturation, non-vertical evolution, and the impact of exclusion of candidate phyla radiation (CPR) taxa. Our results provide an updated view of domain-level relationships.
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Affiliation(s)
- Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Uyen Mai
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Wayne Pfeiffer
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA
| | - Stefan Janssen
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Algorithmic Bioinformatics, Department of Biology and Chemistry, Justus Liebig University Gießen, Giessen, Germany
| | | | - Jon G Sanders
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Gabriel A Al-Ghalith
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Evguenia Kopylova
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tomasz Kosciolek
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - John B Yin
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Mathematics, University of California San Diego, La Jolla, CA, USA
| | - Shi Huang
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Single-Cell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Nimaichand Salam
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zijun Wu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Zhenjiang Z Xu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Kalen Cantrell
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Yimeng Yang
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Erfan Sayyari
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA
| | - Maryam Rabiee
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - James T Morton
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Sheila Podell
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
| | - Larry Smarr
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- California Institute for Telecommunications and Information Technology, University of California San Diego, La Jolla, CA, USA
| | - Siavash Mirarab
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
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9
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Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, Navas-Molina JA, Janssen S, Kopylova E, Vázquez-Baeza Y, González A, Morton JT, Mirarab S, Zech Xu Z, Jiang L, Haroon MF, Kanbar J, Zhu Q, Jin Song S, Kosciolek T, Bokulich NA, Lefler J, Brislawn CJ, Humphrey G, Owens SM, Hampton-Marcell J, Berg-Lyons D, McKenzie V, Fierer N, Fuhrman JA, Clauset A, Stevens RL, Shade A, Pollard KS, Goodwin KD, Jansson JK, Gilbert JA, Knight R. A communal catalogue reveals Earth's multiscale microbial diversity. Nature 2017; 551:457-463. [PMID: 29088705 PMCID: PMC6192678 DOI: 10.1038/nature24621] [Citation(s) in RCA: 1219] [Impact Index Per Article: 174.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 10/10/2017] [Indexed: 02/07/2023]
Abstract
Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.
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Affiliation(s)
- Luke R Thompson
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, Mississippi, USA.,Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, stationed at Southwest Fisheries Science Center, La Jolla, California, USA
| | - Jon G Sanders
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Amnon Amir
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Joshua Ladau
- The Gladstone Institutes and University of California San Francisco, San Francisco, California, USA
| | - Kenneth J Locey
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Robert J Prill
- Industrial and Applied Genomics, IBM Almaden Research Center, San Jose, California, USA
| | - Anupriya Tripathi
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Division of Biological Sciences, University of California San Diego, La Jolla, California, USA.,Skaggs School of Pharmacy, University of California San Diego, La Jolla, California, USA
| | - Sean M Gibbons
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Jose A Navas-Molina
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Stefan Janssen
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Evguenia Kopylova
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Yoshiki Vázquez-Baeza
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Antonio González
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - James T Morton
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, California, USA
| | - Zhenjiang Zech Xu
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Lingjing Jiang
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Family Medicine and Public Health, University of California San Diego, La Jolla, California, USA
| | - Mohamed F Haroon
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Jad Kanbar
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Se Jin Song
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Tomasz Kosciolek
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Nicholas A Bokulich
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Joshua Lefler
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Colin J Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Gregory Humphrey
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Sarah M Owens
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Jarrad Hampton-Marcell
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA.,Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Donna Berg-Lyons
- BioFrontiers Institute, University of Colorado, Boulder, Colorado, USA
| | - Valerie McKenzie
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA.,Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Aaron Clauset
- BioFrontiers Institute, University of Colorado, Boulder, Colorado, USA.,Department of Computer Science, University of Colorado, Boulder, Colorado, USA
| | - Rick L Stevens
- Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, Illinois, USA.,Department of Computer Science, University of Chicago, Chicago, Illinois, USA
| | - Ashley Shade
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA.,Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA.,Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, Michigan, USA
| | - Katherine S Pollard
- The Gladstone Institutes and University of California San Francisco, San Francisco, California, USA
| | - Kelly D Goodwin
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, stationed at Southwest Fisheries Science Center, La Jolla, California, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jack A Gilbert
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA.,Department of Surgery, University of Chicago, Chicago, Illinois, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
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10
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Amir A, McDonald D, Navas-Molina JA, Kopylova E, Morton JT, Zech Xu Z, Kightley EP, Thompson LR, Hyde ER, Gonzalez A, Knight R. Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns. mSystems 2017; 2:e00191-16. [PMID: 28289731 PMCID: PMC5340863 DOI: 10.1128/msystems.00191-00116 10.1128/msystems.00191-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 12/14/2016] [Indexed: 11/23/2023] Open
Abstract
High-throughput sequencing of 16S ribosomal RNA gene amplicons has facilitated understanding of complex microbial communities, but the inherent noise in PCR and DNA sequencing limits differentiation of closely related bacteria. Although many scientific questions can be addressed with broad taxonomic profiles, clinical, food safety, and some ecological applications require higher specificity. Here we introduce a novel sub-operational-taxonomic-unit (sOTU) approach, Deblur, that uses error profiles to obtain putative error-free sequences from Illumina MiSeq and HiSeq sequencing platforms. Deblur substantially reduces computational demands relative to similar sOTU methods and does so with similar or better sensitivity and specificity. Using simulations, mock mixtures, and real data sets, we detected closely related bacterial sequences with single nucleotide differences while removing false positives and maintaining stability in detection, suggesting that Deblur is limited only by read length and diversity within the amplicon sequences. Because Deblur operates on a per-sample level, it scales to modern data sets and meta-analyses. To highlight Deblur's ability to integrate data sets, we include an interactive exploration of its application to multiple distinct sequencing rounds of the American Gut Project. Deblur is open source under the Berkeley Software Distribution (BSD) license, easily installable, and downloadable from https://github.com/biocore/deblur. IMPORTANCE Deblur provides a rapid and sensitive means to assess ecological patterns driven by differentiation of closely related taxa. This algorithm provides a solution to the problem of identifying real ecological differences between taxa whose amplicons differ by a single base pair, is applicable in an automated fashion to large-scale sequencing data sets, and can integrate sequencing runs collected over time.
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Affiliation(s)
- Amnon Amir
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Jose A. Navas-Molina
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Evguenia Kopylova
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - James T. Morton
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Zhenjiang Zech Xu
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Eric P. Kightley
- Department of Applied Mathematics, and Interdisciplinary Quantitative Biology Graduate Program, University of Colorado Boulder, Boulder, Colorado, USA
| | - Luke R. Thompson
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Embriette R. Hyde
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Antonio Gonzalez
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, California, USA
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11
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Komech A, Kopylova E. On the Linear Stability of Crystals in the Schrödinger-Poisson Model. J Stat Phys 2016; 165:246-273. [PMID: 27773944 PMCID: PMC5050255 DOI: 10.1007/s10955-016-1613-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 09/02/2016] [Indexed: 06/06/2023]
Abstract
We consider the Schrödinger-Poisson-Newton equations for crystals with one ion per cell. We linearize this dynamics at the periodic minimizers of energy per cell and introduce a novel class of the ion charge densities that ensures the stability of the linearized dynamics. Our main result is the energy positivity for the Bloch generators of the linearized dynamics under a Wiener-type condition on the ion charge density. We also adopt an additional 'Jellium' condition which cancels the negative contribution caused by the electrostatic instability and provides the 'Jellium' periodic minimizers and the optimality of the lattice: the energy per cell of the periodic minimizer attains the global minimum among all possible lattices. We show that the energy positivity can fail if the Jellium condition is violated, while the Wiener condition holds. The proof of the energy positivity relies on a novel factorization of the corresponding Hamilton functional. The Bloch generators are nonselfadjoint (and even nonsymmetric) Hamilton operators. We diagonalize these generators using our theory of spectral resolution of the Hamilton operators with positive definite energy (Komech and Kopylova in, J Stat Phys 154(1-2):503-521, 2014, J Spectral Theory 5(2):331-361, 2015). The stability of the linearized crystal dynamics is established using this spectral resolution.
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Affiliation(s)
- A. Komech
- Faculty of Mathematics, Vienna University, Vienna, Austria
- Institute for Information Transmission Problems, RAS, Moscow, Russia
| | - E. Kopylova
- Faculty of Mathematics, Vienna University, Vienna, Austria
- Institute for Information Transmission Problems, RAS, Moscow, Russia
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12
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He Y, Caporaso JG, Jiang XT, Sheng HF, Huse SM, Rideout JR, Edgar RC, Kopylova E, Walters WA, Knight R, Zhou HW. Erratum to: Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity. Microbiome 2015; 3:34. [PMID: 26229598 PMCID: PMC4520016 DOI: 10.1186/s40168-015-0098-1] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 07/22/2015] [Indexed: 06/04/2023]
Abstract
[This corrects the article DOI: 10.1186/s40168-015-0081-x.].
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Affiliation(s)
- Yan He
- />State Key Laboratory of Organ Failure Research, Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, 510515 China
| | - J. Gregory Caporaso
- />Department of Biological Sciences, Northern Arizona University, PO Box 5640, Flagstaff, AZ 86011-5640 USA
- />Center for Microbial Genetics and Genomics, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011-4073 USA
| | - Xiao-Tao Jiang
- />State Key Laboratory of Organ Failure Research, Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, 510515 China
| | - Hua-Fang Sheng
- />State Key Laboratory of Organ Failure Research, Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, 510515 China
| | - Susan M. Huse
- />Department of Pathology and Laboratory Science, Warren Alpert Medical School, Brown University, 70 Ship Street, Providence, RI 02912 USA
| | - Jai Ram Rideout
- />Center for Microbial Genetics and Genomics, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011-4073 USA
| | | | - Evguenia Kopylova
- />Department of Pediatrics, University of California at San Diego, 9500 Gilman Drive MC0763, La Jolla, CA 92093-0763 USA
| | - William A. Walters
- />Department of Molecular Biology and Genetics, Cornell University, 526 Campus Road, Ithaca, NY 14853 USA
| | - Rob Knight
- />Department of Pediatrics, University of California at San Diego, 9500 Gilman Drive MC0763, La Jolla, CA 92093-0763 USA
- />Department of Computer Science and Engineering, University of California at San Diego, 9500 Gilman Drive MC0763, La Jolla, CA 92093-0763 USA
| | - Hong-Wei Zhou
- />State Key Laboratory of Organ Failure Research, Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, 510515 China
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13
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Bokulich NA, Rideout JR, Kopylova E, Bolyen E, Patnode J, Ellett Z, Mcdonald D, Wolfe B, Maurice CF, Dutton RJ, Turnbaugh PJ, Knight R, Caporaso JG. A standardized, extensible framework for optimizing classification improves marker-gene taxonomic assignments.. [PMID: 0 DOI: 10.7287/peerj.preprints.934v2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Background: Taxonomic classification of marker-gene (i.e., amplicon) sequences represents an important step for molecular identification of microorganisms.
Results: We present three advances in our ability to assign and interpret taxonomic classifications of short marker gene sequences: two new methods for taxonomy assignment, which reduce runtime up to two-fold and achieve high-precision genus-level assignments; an evaluation of classification methods that highlights differences in performance with different marker genes and at different levels of taxonomic resolution; and an extensible framework for evaluating and optimizing new classification methods, which we hope will serve as a model for standardized and reproducible bioinformatics methods evaluations.
Conclusions: Our new methods are accessible in QIIME 1.9.0, and our evaluation framework will support ongoing optimization of classification methods to complement rapidly evolving short-amplicon sequencing and bioinformatics technologies. Static versions of all of the analysis notebooks generated with this framework, which contain all code and analysis results, can be viewed at http://bit.ly/srta-012 .
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Affiliation(s)
- Nicholas A Bokulich
- Department of Medicine, New York University Langone Medical Center, New York, NY, USA
| | - Jai Ram Rideout
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011
| | - Evguenia Kopylova
- Department of Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Evan Bolyen
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011
| | - Jessica Patnode
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, United States
| | - Zach Ellett
- Department of Computer Science, Northern Arizona University, Flagstaff, AZ, USA
| | - Daniel McDonald
- Department of Computer Science, University of Colorado at Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado at Boulder, Boulder, CO, United States
| | - Benjamin Wolfe
- FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA
| | - Corinne F Maurice
- Department of Microbiology and Immunology, Microbiome and Disease Tolerance Centre, McGill University, Montreal, QC, Canada
| | - Rachel J Dutton
- FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA
| | - Peter J Turnbaugh
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - J Gregory Caporaso
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, United States
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14
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Abstract
Metatranscriptomic data contributes another piece of the puzzle to understanding the phylogenetic structure and function of a community of organisms. High-quality total RNA is a bountiful mixture of ribosomal, transfer, messenger and other noncoding RNAs, where each family of RNA is vital to answering questions concerning the hidden microbial world. Software tools designed for deciphering metatranscriptomic data fall under two main categories: the first is to reassemble millions of short nucleotide fragments produced by high-throughput sequencing technologies into the original full-length transcriptomes for all organisms within a sample, and the second is to taxonomically classify the organisms and determine their individual functional roles within a community. Species identification is mainly established using the ribosomal RNA genes, whereas the behavior and functionality of a community is revealed by the messenger RNA of the expressed genes. Numerous chemical and computational methods exist to separate families of RNA prior to conducting further downstream analyses, primarily suitable for isolating mRNA or rRNA from a total RNA sample. In this chapter, we demonstrate a computational technique for filtering rRNA from total RNA using the software SortMeRNA. Additionally, we propose a post-processing pipeline using the latest software tools to conduct further studies on the filtered data, including the reconstruction of mRNA transcripts for functional analyses and phylogenetic classification of a community using the ribosomal RNA.
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15
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He Y, Caporaso JG, Jiang XT, Sheng HF, Huse SM, Rideout JR, Edgar RC, Kopylova E, Walters WA, Knight R, Zhou HW. Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity. Microbiome 2015; 3:20. [PMID: 25995836 PMCID: PMC4438525 DOI: 10.1186/s40168-015-0081-x] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 04/03/2015] [Indexed: 05/11/2023]
Abstract
BACKGROUND The operational taxonomic unit (OTU) is widely used in microbial ecology. Reproducibility in microbial ecology research depends on the reliability of OTU-based 16S ribosomal subunit RNA (rRNA) analyses. RESULTS Here, we report that many hierarchical and greedy clustering methods produce unstable OTUs, with membership that depends on the number of sequences clustered. If OTUs are regenerated with additional sequences or samples, sequences originally assigned to a given OTU can be split into different OTUs. Alternatively, sequences assigned to different OTUs can be merged into a single OTU. This OTU instability affects alpha-diversity analyses such as rarefaction curves, beta-diversity analyses such as distance-based ordination (for example, Principal Coordinate Analysis (PCoA)), and the identification of differentially represented OTUs. Our results show that the proportion of unstable OTUs varies for different clustering methods. We found that the closed-reference method is the only one that produces completely stable OTUs, with the caveat that sequences that do not match a pre-existing reference sequence collection are discarded. CONCLUSIONS As a compromise to the factors listed above, we propose using an open-reference method to enhance OTU stability. This type of method clusters sequences against a database and includes unmatched sequences by clustering them via a relatively stable de novo clustering method. OTU stability is an important consideration when analyzing microbial diversity and is a feature that should be taken into account during the development of novel OTU clustering methods.
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Affiliation(s)
- Yan He
- />State Key Laboratory of Organ Failure Research, Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, 510515 China
| | - J Gregory Caporaso
- />Department of Biological Sciences, Northern Arizona University, PO Box 5640, Flagstaff, AZ 86011-5640 USA
- />Center for Microbial Genetics and Genomics, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011-4073 USA
| | - Xiao-Tao Jiang
- />State Key Laboratory of Organ Failure Research, Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, 510515 China
| | - Hua-Fang Sheng
- />State Key Laboratory of Organ Failure Research, Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, 510515 China
| | - Susan M Huse
- />Department of Pathology and Laboratory Science, Warren Alpert Medical School, Brown University, 70 Ship Street, Providence, RI 02912 USA
| | - Jai Ram Rideout
- />Center for Microbial Genetics and Genomics, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011-4073 USA
| | | | - Evguenia Kopylova
- />Department of Pediatrics, University of California at San Diego, 9500 Gilman Drive MC0763, La Jolla, CA 92093-0763 USA
| | - William A Walters
- />Department of Molecular Biology and Genetics, Cornell University, 526 Campus Road, Ithaca, NY 14853 USA
| | - Rob Knight
- />Department of Pediatrics, University of California at San Diego, 9500 Gilman Drive MC0763, La Jolla, CA 92093-0763 USA
- />Department of Computer Science and Engineering, University of California at San Diego, 9500 Gilman Drive MC0763, La Jolla, CA 92093-0763 USA
| | - Hong-Wei Zhou
- />State Key Laboratory of Organ Failure Research, Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, 510515 China
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Abstract
MOTIVATION The application of next-generation sequencing (NGS) technologies to RNAs directly extracted from a community of organisms yields a mixture of fragments characterizing both coding and non-coding types of RNAs. The task to distinguish among these and to further categorize the families of messenger RNAs and ribosomal RNAs (rRNAs) is an important step for examining gene expression patterns of an interactive environment and the phylogenetic classification of the constituting species. RESULTS We present SortMeRNA, a new software designed to rapidly filter rRNA fragments from metatranscriptomic data. It is capable of handling large sets of reads and sorting out all fragments matching to the rRNA database with high sensitivity and low running time.
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