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Shahar S, Sant KE, Allsing N, Kelley ST. Metagenomic analysis of microbial communities and antibiotic resistant genes in the Tijuana river, and potential sources. Environ Pollut 2024; 342:123067. [PMID: 38043772 DOI: 10.1016/j.envpol.2023.123067] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 11/02/2023] [Accepted: 11/27/2023] [Indexed: 12/05/2023]
Abstract
The Tijuana River is a transborder river that flows northwest across the border from Baja California in Mexico into Southern California before discharging into the Pacific Ocean. The river is frequently contaminated with raw sewage due to inadequate sanitary infrastructure in Tijuana. To assess the type and degree of microbial contamination, water samples were collected monthly from a near-border and an estuarine site from August 2020 until May 2021. A portion of each sample was used for epifluorescent microscopy and DNA was extracted directly from the rest for shotgun metagenomic sequencing. After sequence quality checking and processing, we used the rapid taxonomic identifier tool Kaiju to characterize the microbial diversity of the metagenomes and matched the sequences against the Comprehensive Antibiotic Resistance Database (CARD) to examine antimicrobial resistance genes (ARGs). Bacterial and viral-like particle (VLP) abundance was consistently higher in the near-border samples than in the estuarine samples, while alpha diversity (within sample biodiversity) was higher in estuarine samples. Beta-diversity analysis found clear compositional separation between samples from the two sites, and the near-border samples were more dissimilar to one another than were the estuarine sites. Near-border samples were dominated by fecal-associated bacteria and bacteria associated with sewage sludge, while estuarine sites were dominated by marine bacteria. ARGs were more abundant at the near-border site, but were also readily detectable in the estuarine samples, and the most abundant ARGs had multi-resistance to beta-lactam antibiotics. SourceTracker analysis identified human feces and sewage sludge to be the largest contributors to the near-border samples, while marine waters dominated estuarine samples except for two sewage overflow dates with high fecal contamination. Overall, our research determined human sewage microbes to be common in the Tijuana River, and the prevalence of ARGs confirms the importance of planned infrastructure treatment upgrades for environmental health.
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Affiliation(s)
- Shayla Shahar
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Karilyn E Sant
- School of Public Health, San Diego State University, San Diego, CA 92182, USA
| | - Nicholas Allsing
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA 92182, USA.
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Ortiz-Velez AN, Sukumaran J, Rouzbehani R, Kelley ST. AutoPhy: Automated phylogenetic identification of novel protein subfamilies. PLoS One 2024; 19:e0291801. [PMID: 38206953 PMCID: PMC10783759 DOI: 10.1371/journal.pone.0291801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 09/06/2023] [Indexed: 01/13/2024] Open
Abstract
Phylogenetic analysis of protein sequences provides a powerful means of identifying novel protein functions and subfamilies, and for identifying and resolving annotation errors. However, automation of functional clustering based on phylogenetic trees has been challenging and most of it is done manually. Clustering phylogenetic trees usually requires the delineation of tree-based thresholds (e.g., distances), leading to an ad hoc problem. We propose a new phylogenetic clustering approach that identifies clusters without using ad hoc distances or other pre-defined values. Our workflow combines uniform manifold approximation and projection (UMAP) with Gaussian mixture models as a k-means like procedure to automatically group sequences into clusters. We then apply a "second pass" clade identification algorithm to resolve non-monophyletic groups. We tested our approach with several well-curated protein families (outer membrane porins, acyltransferase, and nuclear receptors) and showed our automated methods recapitulated known subfamilies. We also applied our methods to a broad range of different protein families from multiple databases, including Pfam, PANTHER, and UniProt, and to alignments of RNA viral genomes. Our results showed that AutoPhy rapidly generated monophyletic clusters (subfamilies) within phylogenetic trees evolving at very different rates both within and among phylogenies. The phylogenetic clusters generated by AutoPhy resolved misannotations and identified new protein functional groups and novel viral strains.
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Affiliation(s)
- Adrian N Ortiz-Velez
- Bioinformatics and Medical Informatics Program, San Diego State University, San Diego, CA, United States of America
- Department of Biology, San Diego State University, San Diego, CA, United States of America
| | - Jeet Sukumaran
- Bioinformatics and Medical Informatics Program, San Diego State University, San Diego, CA, United States of America
- Department of Biology, San Diego State University, San Diego, CA, United States of America
| | - Ryin Rouzbehani
- Bioinformatics and Medical Informatics Program, San Diego State University, San Diego, CA, United States of America
| | - Scott T Kelley
- Bioinformatics and Medical Informatics Program, San Diego State University, San Diego, CA, United States of America
- Department of Biology, San Diego State University, San Diego, CA, United States of America
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Chen A, Handzel A, Sau L, Cui L, Kelley ST, Thackray VG. Metabolic dysregulation and gut dysbiosis linked to hyperandrogenism in female mice. Endocrinol Diabetes Metab 2024; 7:e443. [PMID: 37872876 PMCID: PMC10782063 DOI: 10.1002/edm2.443] [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: 02/06/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 10/25/2023] Open
Abstract
INTRODUCTION Polycystic ovary syndrome (PCOS) is a common endocrine pathology in women. In addition to infertility, women with PCOS have metabolic dysregulation which predisposes them to Type 2 diabetes, cardiovascular disease and non-alcoholic fatty liver disease. Moreover, women with PCOS have changes in their gut microbial community that may be indicative of dysbiosis. While hyperandrogenism is associated with both the development of metabolic dysfunction and gut dysbiosis in females, the mechanisms involved are not well understood. METHODS We used dihydrotestosterone (DHT) and ovariectomy (OVX) mouse models coupled with metabolic assessments and 16S rRNA gene sequencing to explore the contributions of hyperandrogenism and oestrogen deficiency to the development of insulin resistance and gut microbial dysbiosis in pubertal female mice. RESULTS We demonstrated that, while DHT treatment or OVX alone were insufficient to induce insulin resistance during the pubertal-to-adult transition, combining OVX with DHT resulted in insulin resistance similar to that observed in letrozole-treated mice with elevated testosterone and decreased oestrogen levels. In addition, our results showed that OVX and DHT in combination resulted in a distinct shift in the gut microbiome compared to DHT or OVX alone, suggesting that the substantial metabolic dysregulation occurring in the OVX + DHT model was accompanied by unique changes in the abundances of gut bacteria including S24-7, Rikenellaceae and Mucispirillum schaedleri. CONCLUSIONS While hyperandrogenism plays an important role in the development of metabolic dysregulation in female mice, our results indicate that investigation into additional factors influencing insulin resistance and the gut microbiome during the pubertal-to-adult transition could provide additional insight into the pathophysiology of PCOS.
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Affiliation(s)
- Annie Chen
- Department of Obstetrics, Gynecology and Reproductive SciencesUniversity of CaliforniaSan Diego, La JollaCaliforniaUSA
| | - Alex Handzel
- Bioinformatics and Medical Informatics ProgramSan Diego State UniversitySan DiegoCaliforniaUSA
| | - Lillian Sau
- Department of Obstetrics, Gynecology and Reproductive SciencesUniversity of CaliforniaSan Diego, La JollaCaliforniaUSA
| | - Laura Cui
- Department of Obstetrics, Gynecology and Reproductive SciencesUniversity of CaliforniaSan Diego, La JollaCaliforniaUSA
| | - Scott T. Kelley
- Bioinformatics and Medical Informatics ProgramSan Diego State UniversitySan DiegoCaliforniaUSA
- Department of BiologySan Diego State UniversitySan DiegoCaliforniaUSA
| | - Varykina G. Thackray
- Department of Obstetrics, Gynecology and Reproductive SciencesUniversity of CaliforniaSan Diego, La JollaCaliforniaUSA
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Sisk-Hackworth L, Brown J, Sau L, Levine AA, Tam LYI, Ramesh A, Shah RS, Kelley-Thackray ET, Wang S, Nguyen A, Kelley ST, Thackray VG. Genetic hypogonadal mouse model reveals niche-specific influence of reproductive axis and sex on intestinal microbial communities. Biol Sex Differ 2023; 14:79. [PMID: 37932822 PMCID: PMC10626657 DOI: 10.1186/s13293-023-00564-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/23/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND The gut microbiome has been linked to many diseases with sex bias including autoimmune, metabolic, neurological, and reproductive disorders. While numerous studies report sex differences in fecal microbial communities, the role of the reproductive axis in this differentiation is unclear and it is unknown how sex differentiation affects microbial diversity in specific regions of the small and large intestine. METHODS We used a genetic hypogonadal mouse model that does not produce sex steroids or go through puberty to investigate how sex and the reproductive axis impact bacterial diversity within the intestine. Using 16S rRNA gene sequencing, we analyzed alpha and beta diversity and taxonomic composition of fecal and intestinal communities from the lumen and mucosa of the duodenum, ileum, and cecum from adult female (n = 20) and male (n = 20) wild-type mice and female (n = 17) and male (n = 20) hypogonadal mice. RESULTS Both sex and reproductive axis inactivation altered bacterial composition in an intestinal section and niche-specific manner. Hypogonadism was significantly associated with bacteria from the Bacteroidaceae, Eggerthellaceae, Muribaculaceae, and Rikenellaceae families, which have genes for bile acid metabolism and mucin degradation. Microbial balances between males and females and between hypogonadal and wild-type mice were also intestinal section-specific. In addition, we identified 3 bacterial genera (Escherichia Shigella, Lachnoclostridium, and Eggerthellaceae genus) with higher abundance in wild-type female mice throughout the intestinal tract compared to both wild-type male and hypogonadal female mice, indicating that activation of the reproductive axis leads to female-specific differentiation of the gut microbiome. Our results also implicated factors independent of the reproductive axis (i.e., sex chromosomes) in shaping sex differences in intestinal communities. Additionally, our detailed profile of intestinal communities showed that fecal samples do not reflect bacterial diversity in the small intestine. CONCLUSIONS Our results indicate that sex differences in the gut microbiome are intestinal niche-specific and that sampling feces or the large intestine may miss significant sex effects in the small intestine. These results strongly support the need to consider both sex and reproductive status when studying the gut microbiome and while developing microbial-based therapies.
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Affiliation(s)
- Laura Sisk-Hackworth
- University of California San Diego, La Jolla, CA, USA
- San Diego State University, San Diego, CA, USA
| | - Jada Brown
- University of California San Diego, La Jolla, CA, USA
| | - Lillian Sau
- University of California San Diego, La Jolla, CA, USA
| | | | | | | | - Reeya S Shah
- University of California San Diego, La Jolla, CA, USA
| | | | - Sophia Wang
- University of California San Diego, La Jolla, CA, USA
| | - Anita Nguyen
- University of California San Diego, La Jolla, CA, USA
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Mason CN, Shahar S, Beals KK, Kelley ST, Lipson DA, Swingley WD, Barber NA. Taxonomic and functional restoration of tallgrass prairie soil microbial communities in comparison to remnant and agricultural soils. FEMS Microbiol Ecol 2023; 99:fiad120. [PMID: 37791391 DOI: 10.1093/femsec/fiad120] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/28/2023] [Accepted: 10/02/2023] [Indexed: 10/05/2023] Open
Abstract
Restoring ecosystems requires the re-establishment of diverse soil microbial communities that drive critical ecosystem functions. In grasslands, restoration and management require the application of disturbances like fire and grazing. Disturbances can shape microbial taxonomic composition and potentially functional composition as well. We characterized taxonomic and functional gene composition of soil communities using whole genome shotgun metagenomic sequencing to determine how restored soil communities differed from pre-restoration agricultural soils and original remnant soils, how management affects soil microbes, and whether restoration and management affect the number of microbial genes associated with carbohydrate degradation. We found distinct differences in both taxonomic and functional diversity and composition among restored, remnant, and agricultural soils. Remnant soils had low taxonomic and functional richness and diversity, as well as distinct composition, indicating that restoration of agricultural soils does not re-create soil microbial communities that match remnants. Prescribed fire management increased functional diversity, which also was higher in more recently planted restorations. Finally, restored and post-fire soils included high abundances of genes encoding cellulose-degrading enzymes, so restorations and their ongoing management can potentially support functions important in carbon cycling.
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Affiliation(s)
- Cayla N Mason
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Shayla Shahar
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Kendall K Beals
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - David A Lipson
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Wesley D Swingley
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115, USA
| | - Nicholas A Barber
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
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Abstract
In brief Sex differences in the gut microbiome may impact multiple aspects of human health and disease. In this study, we review the evidence for microbial sex differences in puberty and adulthood and discuss potential mechanisms driving differentiation of the sex-specific gut microbiome. Abstract In humans, the gut microbiome is strongly implicated in numerous sex-specific physiological processes and diseases. Given this, it is important to understand how sex differentiation of the gut microbiome occurs and how these differences contribute to host health and disease. While it is commonly believed that the gut microbiome stabilizes after 3 years of age, our review of the literature found considerable evidence that the gut microbiome continues to mature during and after puberty in a sex-dependent manner. We also review the intriguing, though sparse, literature on potential mechanisms by which host sex may influence the gut microbiome, and vice versa, via sex steroids, bile acids, and the immune system. We conclude that the evidence for the existence of a sex-specific gut microbiome is strong but that there is a dearth of research on how host-microbe interactions lead to this differentiation. Finally, we discuss the types of future studies needed to understand the processes driving the maturation of sex-specific microbial communities and the interplay between gut microbiota, host sex, and human health.
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Affiliation(s)
| | - Scott T. Kelley
- Department of Biology, San Diego State University, San Diego, California 92182
| | - Varykina G. Thackray
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, California 92093
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Allsing N, Kelley ST, Fox AN, Sant KE. Metagenomic Analysis of Microbial Contamination in the U.S. Portion of the Tijuana River Watershed. Int J Environ Res Public Health 2022; 20:ijerph20010600. [PMID: 36612923 PMCID: PMC9819409 DOI: 10.3390/ijerph20010600] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/22/2022] [Accepted: 12/24/2022] [Indexed: 06/02/2023]
Abstract
The Tijuana River watershed is binational, flowing from Tijuana, Mexico into San Diego and Imperial Beach, USA. Aging sewage and stormwater infrastructure in Tijuana has not kept pace with population growth, causing overflows into this watershed during major rainfall or equipment failures. The public health consequences of this impaired watershed on the surrounding communities remain unknown. Here, we performed untargeted metagenomic sequencing to better characterize the sewage contamination in the Tijuana River, identifying potential pathogens and molecular indicators of antibiotic resistance in surface waters. In 2019-2020, water samples were collected within 48 h of major rainfall events at five transborder flow sites and at the mouth of the river in the US portion of the Tijuana River and estuary. After filtration, DNA was extracted and sequenced, and sequences were run through the Kaiju taxonomic classification program. A pathogen profile of the most abundant disease-causing microbes and viruses present in each of the samples was constructed, and specific markers of fecal contamination were identified and linked to each site. Results from diversity analysis between the sites showed clear distinction as well as similarities between sites and dates, and antibiotic-resistant genes were found at each site. This serves as a baseline characterization of microbial exposures to these local communities.
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Affiliation(s)
- Nicholas Allsing
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Scott T. Kelley
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
- Bioinformatics and Medical Informatics Program, San Diego State University, San Diego, CA 92182, USA
| | - Alexandra N. Fox
- School of Public Health, San Diego State University, San Diego, CA 92182, USA
| | - Karilyn E. Sant
- School of Public Health, San Diego State University, San Diego, CA 92182, USA
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Bendik J, Kalia R, Sukumaran J, Richardot WH, Hoh E, Kelley ST. Automated high confidence compound identification of electron ionization mass spectra for nontargeted analysis. J Chromatogr A 2021; 1660:462656. [PMID: 34798444 DOI: 10.1016/j.chroma.2021.462656] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 10/19/2022]
Abstract
Nontargeted analysis based on mass spectrometry is a rising practice in environmental monitoring for identifying contaminants of emerging concern. Nontargeted analysis performed using comprehensive two-dimensional gas chromatography coupled with time-of-flight mass spectrometry (GC×GC/TOF-MS) generates large numbers of possible analytes. Moreover, the default spectral library similarity score-based search algorithm used by LECO® ChromaTOF® does not ensure that high similarity scores result in correct library matches. Therefore, an additional manual screening is necessary, but leads to human errors especially when dealing with large amounts of data. To improve the speed and accuracy of the chemical identification, we developed CINeMA.py (Classification Is Never Manual Again). This programming suite automates GC×GC/TOF-MS data interpretation by determining the confidence of a match between the observed analyte mass spectrum and the LECO® ChromaTOF® software generated library hit from the NIST Electron Ionization Mass Spectral (NIST EI-MS) library. Our script allows the user to evaluate the confidence of the match using an algorithmic method that mimics the manual curation process and two different machine learning approaches (neural networks and random forest). The script allows the user to adjust various parameters (e.g., similarity threshold) and study their effects on prediction accuracy. To test CINeMA.py, we used data from two different environmental contaminant studies: an EPA study on household dust and a study on stormwater runoff. Using a reference set based on the analysis performed by highly trained users of the ChromaTOF and GC×GC/TOF-MS systems, the random forest model had the highest prediction accuracies of 86% and 83% on the EPA and Stormwater data sets, respectively. The algorithmic approach had the second-best prediction accuracy (82% and 79%), while the neural network accuracy had the lowest (63% and 67%). All the approaches required less than 1 min to classify 986 observed analytes, whereas manual data analysis required hours or days to complete. Our methods were also able to detect high confidence matches missed during the manual review. Overall, CINeMA.py provides users with a powerful suite of tools that should significantly speed-up data analysis while reducing the possibilities of manual errors and discrepancies among users, and can be applicable to other GC/EI-MS instrument based nontargeted analysis.
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Affiliation(s)
- Joseph Bendik
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Richa Kalia
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Jeet Sukumaran
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92104, USA
| | - William H Richardot
- San Diego State University Research Foundation, San Diego, CA, USA; School of Public Health, San Diego State University, San Diego, CA, USA
| | - Eunha Hoh
- School of Public Health, San Diego State University, San Diego, CA, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, USA; Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92104, USA.
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Kelley ST, Liu W, Quintana PJ, Hoh E, Dodder NG, Mahabee-Gittens EM, Padilla S, Ogden S, Frenzel S, Sisk-Hackworth L, Matt GE. Altered microbiomes in thirdhand smoke-exposed children and their home environments. Pediatr Res 2021; 90:1153-1160. [PMID: 33654287 PMCID: PMC8410873 DOI: 10.1038/s41390-021-01400-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/29/2020] [Accepted: 01/06/2021] [Indexed: 12/30/2022]
Abstract
INTRODUCTION Tobacco smoke contains numerous toxic chemicals that accumulate in indoor environments creating thirdhand smoke (THS). We investigated if THS-polluted homes differed in children's human and built-environment microbiomes as compared to THS-free homes. METHODS Participants were n = 19 THS-exposed children and n = 10 unexposed children (≤5 years) and their caregivers. Environmental and biological samples were analyzed for THS pollutants and exposure. Swab samples were collected from the built-environment (floor, table, armrest, bed frame) and child (finger, nose, mouth, and ear canal), and 16S ribosomal RNA genes were analyzed for bacterial taxa using high-throughput DNA sequencing. RESULTS Phylogenetic α-diversity was significantly higher for the built-environment microbiomes in THS-polluted homes compared to THS-free homes (p < 0.014). Log2-fold comparison found differences between THS-polluted and THS-free homes for specific genera in samples from the built-environment (e.g., Acinetobacter, Bradyrhizobium, Corynebacterium, Gemella, Neisseria, Staphylococcus, Streptococcus, and Veillonella) and in samples from children (esp. Corynebacterium, Gemella, Lautropia, Neisseria, Rothia, Staphylococcus, and Veillonella). CONCLUSION When exposed to THS, indoor and children microbiomes are altered in an environment-specific manner. Changes are similar to those reported in previous studies for smokers and secondhand smoke-exposed persons. THS-induced changes in child and built-environmental microbiomes may play a role in clinical outcomes in children. IMPACT Despite smoking bans, children can be exposed to tobacco smoke residue (i.e., thirdhand smoke) that lingers on surfaces and in settled house dust. Thirdhand smoke exposure is associated with changes in the microbiomes of the home environment and of the children living in these homes. Thirdhand smoke is associated with increased phylogenetic diversity of the home environment and changes in the abundances of several genera of the child microbiome known to be affected by active smoking and secondhand smoke (e.g., Corynebacterium, Staphylococcus, Streptococcus). Thirdhand smoke exposure by itself may induce alterations in the microbiome that play a role in childhood pathologies.
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Affiliation(s)
| | - William Liu
- San Diego State University, San Diego CA, USA
| | | | - Eunha Hoh
- San Diego State University, San Diego CA, USA
| | | | - E. Melinda Mahabee-Gittens
- Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, U.S.A
| | | | - Shawn Ogden
- San Diego State University, San Diego CA, USA
| | - Sia Frenzel
- San Diego State University, San Diego CA, USA
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Sisk-Hackworth L, Ortiz-Velez A, Reed MB, Kelley ST. Compositional Data Analysis of Periodontal Disease Microbial Communities. Front Microbiol 2021; 12:617949. [PMID: 34079525 PMCID: PMC8165185 DOI: 10.3389/fmicb.2021.617949] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 03/23/2021] [Indexed: 12/21/2022] Open
Abstract
Periodontal disease (PD) is a chronic, progressive polymicrobial disease that induces a strong host immune response. Culture-independent methods, such as next-generation sequencing (NGS) of bacteria 16S amplicon and shotgun metagenomic libraries, have greatly expanded our understanding of PD biodiversity, identified novel PD microbial associations, and shown that PD biodiversity increases with pocket depth. NGS studies have also found PD communities to be highly host-specific in terms of both biodiversity and the response of microbial communities to periodontal treatment. As with most microbiome work, the majority of PD microbiome studies use standard data normalization procedures that do not account for the compositional nature of NGS microbiome data. Here, we apply recently developed compositional data analysis (CoDA) approaches and software tools to reanalyze multiomics (16S, metagenomics, and metabolomics) data generated from previously published periodontal disease studies. CoDA methods, such as centered log-ratio (clr) transformation, compensate for the compositional nature of these data, which can not only remove spurious correlations but also allows for the identification of novel associations between microbial features and disease conditions. We validated many of the studies’ original findings, but also identified new features associated with periodontal disease, including the genera Schwartzia and Aerococcus and the cytokine C-reactive protein (CRP). Furthermore, our network analysis revealed a lower connectivity among taxa in deeper periodontal pockets, potentially indicative of a more “random” microbiome. Our findings illustrate the utility of CoDA techniques in multiomics compositional data analysis of the oral microbiome.
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Affiliation(s)
| | - Adrian Ortiz-Velez
- Department of Biology, San Diego State University, San Diego, CA, United States
| | - Micheal B Reed
- Department of Nanoengineering, Joint School of Nanoscience and Nanoengineering, North Carolina Agricultural and Technical State University, Greensboro, NC, United States
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, United States
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Yanagihara R, Berry MJ, Carson MJ, Chang SP, Corliss H, Cox MB, Haddad G, Hohmann C, Kelley ST, Lee ESY, Link BG, Noel RJ, Pickrel J, Porter JT, Quirk GJ, Samuel T, Stiles JK, Sy AU, Taira DA, Trepka MJ, Villalta F, Wiese TE. Building a Diverse Workforce and Thinkforce to Reduce Health Disparities. Int J Environ Res Public Health 2021; 18:1569. [PMID: 33562262 PMCID: PMC7915161 DOI: 10.3390/ijerph18041569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/20/2021] [Accepted: 02/03/2021] [Indexed: 02/03/2023]
Abstract
The Research Centers in Minority Institutions (RCMI) Program was congressionally mandated in 1985 to build research capacity at institutions that currently and historically recruit, train, and award doctorate degrees in the health professions and health-related sciences, primarily to individuals from underrepresented and minority populations. RCMI grantees share similar infrastructure needs and institutional goals. Of particular importance is the professional development of multidisciplinary teams of academic and community scholars (the "workforce") and the harnessing of the heterogeneity of thought (the "thinkforce") to reduce health disparities. The purpose of this report is to summarize the presentations and discussion at the RCMI Investigator Development Core (IDC) Workshop, held in conjunction with the RCMI Program National Conference in Bethesda, Maryland, in December 2019. The RCMI IDC Directors provided information about their professional development activities and Pilot Projects Programs and discussed barriers identified by new and early-stage investigators that limit effective career development, as well as potential solutions to overcome such obstacles. This report also proposes potential alignments of professional development activities, targeted goals and common metrics to track productivity and success.
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Affiliation(s)
- Richard Yanagihara
- University of Hawaii at Manoa, Honolulu, HI 96813, USA; (M.J.B.); (S.P.C.); (A.U.S.); (D.A.T.)
| | - Marla J. Berry
- University of Hawaii at Manoa, Honolulu, HI 96813, USA; (M.J.B.); (S.P.C.); (A.U.S.); (D.A.T.)
| | - Monica J. Carson
- University of California, Riverside, Riverside, CA 92521, USA; (M.J.C.); (B.G.L.)
| | - Sandra P. Chang
- University of Hawaii at Manoa, Honolulu, HI 96813, USA; (M.J.B.); (S.P.C.); (A.U.S.); (D.A.T.)
| | - Heather Corliss
- San Diego State University, San Diego, CA 92182, USA; (H.C.); (S.T.K.); (J.P.)
| | - Marc B. Cox
- University of Texas at El Paso, El Paso, TX 79968, USA;
| | | | | | - Scott T. Kelley
- San Diego State University, San Diego, CA 92182, USA; (H.C.); (S.T.K.); (J.P.)
| | - Eun Sook Yu Lee
- Florida Agricultural and Mechanical University, Tallahassee, FL 32307, USA;
| | - Bruce G. Link
- University of California, Riverside, Riverside, CA 92521, USA; (M.J.C.); (B.G.L.)
| | - Richard J. Noel
- Ponce Health Sciences University, Ponce, PR 00716, USA; (R.J.N.J.); (J.T.P.)
| | - Julie Pickrel
- San Diego State University, San Diego, CA 92182, USA; (H.C.); (S.T.K.); (J.P.)
| | - James T. Porter
- Ponce Health Sciences University, Ponce, PR 00716, USA; (R.J.N.J.); (J.T.P.)
| | - Gregory J. Quirk
- University of Puerto Rico Medical Sciences Campus, San Juan, PR 00936, USA;
| | | | | | - Angela U. Sy
- University of Hawaii at Manoa, Honolulu, HI 96813, USA; (M.J.B.); (S.P.C.); (A.U.S.); (D.A.T.)
| | - Deborah A. Taira
- University of Hawaii at Manoa, Honolulu, HI 96813, USA; (M.J.B.); (S.P.C.); (A.U.S.); (D.A.T.)
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12
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Xu Y, Tandon R, Ancheta C, Arroyo P, Gilbert JA, Stephens B, Kelley ST. Quantitative profiling of built environment bacterial and fungal communities reveals dynamic material dependent growth patterns and microbial interactions. Indoor Air 2021; 31:188-205. [PMID: 32757488 DOI: 10.1111/ina.12727] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 07/01/2020] [Accepted: 07/29/2020] [Indexed: 06/11/2023]
Abstract
Indoor microbial communities vary in composition and diversity depending on material type, moisture levels, and occupancy. In this study, we integrated bacterial cell counting, fungal biomass estimation, and fluorescence-assisted cell sorting (FACS) with amplicon sequencing of bacterial (16S rRNA) and fungal (ITS) communities to investigate the influence of wetting on medium density fiberboard (MDF) and gypsum wallboard. Surface samples were collected longitudinally from wetted materials maintained at high relative humidity (~95%). Bacterial and fungal growth patterns were strongly time-dependent and material-specific. Fungal growth phenotypes differed between materials: spores dominated MDF surfaces while fungi transitioned from spores to hyphae on gypsum. FACS confirmed that most of the bacterial cells were intact (viable) on both materials over the course of the study. Integrated cell count and biomass data (quantitative profiling) revealed that small changes in relative abundance often resulted from large changes in absolute abundance, while negative correlations in relative abundances were explained by rapid growth of only one group of bacteria or fungi. Comparisons of bacterial-bacterial and fungal-bacterial networks suggested a top-down control of fungi on bacterial growth, possibly via antibiotic production. In conclusion, quantitative profiling provides novel insights into microbial growth dynamics on building materials with potential implications for human health.
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Affiliation(s)
- Ying Xu
- Graduate Program in Bioinformatics and Medical Informatics, San Diego State University, San Diego, CA, USA
| | - Ruby Tandon
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Chrislyn Ancheta
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Pablo Arroyo
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Jack A Gilbert
- Department of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Brent Stephens
- Department of Civil, Architectural, and Environmental Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - Scott T Kelley
- Graduate Program in Bioinformatics and Medical Informatics, San Diego State University, San Diego, CA, USA
- Department of Biology, San Diego State University, San Diego, CA, USA
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13
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Sau L, Olmstead CM, Cui LJ, Chen A, Shah RS, Kelley ST, Thackray VG. Alterations in Gut Microbiota Do Not Play a Causal Role in Diet-independent Weight Gain Caused by Ovariectomy. J Endocr Soc 2020; 5:bvaa173. [PMID: 33324864 PMCID: PMC7724750 DOI: 10.1210/jendso/bvaa173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 09/18/2020] [Indexed: 01/03/2023] Open
Abstract
Acute estrogen deficiency in women can occur due to many conditions including hyperprolactinemia, chemotherapy, GnRH agonist treatment, and removal of hormone replacement therapy. Ovariectomized (OVX) rodent models, often combined with a high-fat diet (HFD), have been used to investigate the effects of decreased estrogen production on metabolism. Since evidence suggests that gut microbes may facilitate the protective effect of estrogen on metabolic dysregulation in an OVX + HFD model, we investigated whether the gut microbiome plays a role in the diet-independent weight gain that occurs after OVX in adult female mice. 16S rRNA gene sequence analysis demonstrated that OVX was not associated with changes in overall gut bacterial biodiversity but was correlated with a shift in beta diversity. Using differential abundance analysis, we observed a difference in the relative abundance of a few bacterial taxa, such as Turicibacter, 3 to 5 weeks after OVX, which was subsequent to the weight gain that occurred 2 weeks postsurgery. A cohousing study was performed to determine whether exposure to a healthy gut microbiome was protective against the development of the metabolic phenotype associated with OVX. Unlike mouse models of obesity, HFD maternal-induced metabolic dysregulation, or polycystic ovary syndrome, cohousing OVX mice with healthy mice did not improve the metabolic phenotype of OVX mice. Altogether, these results indicate that changes in the gut microbiome are unlikely to play a causal role in diet-independent, OVX-induced weight gain (since they occurred after the weight gain) and cohousing with healthy mice did not have a protective effect.
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Affiliation(s)
- Lillian Sau
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, California, USA
| | | | - Laura J Cui
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, California, USA
| | - Annie Chen
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, California, USA
| | - Reeya S Shah
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, California, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Varykina G Thackray
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, California, USA
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14
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Sisk-Hackworth L, Kelley ST. An application of compositional data analysis to multiomic time-series data. NAR Genom Bioinform 2020; 2:lqaa079. [PMID: 33575625 PMCID: PMC7671389 DOI: 10.1093/nargab/lqaa079] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 08/07/2020] [Accepted: 09/07/2020] [Indexed: 12/18/2022] Open
Abstract
Compositional data analysis (CoDA) methods have increased in popularity as a new framework for analyzing next-generation sequencing (NGS) data. CoDA methods, such as the centered log-ratio (clr) transformation, adjust for the compositional nature of NGS counts, which is not addressed by traditional normalization methods. CoDA has only been sparsely applied to NGS data generated from microbial communities or to multiple ‘omics’ datasets. In this study, we applied CoDA methods to analyze NGS and untargeted metabolomic datasets obtained from bacterial and fungal communities. Specifically, we used clr transformation to reanalyze NGS amplicon and metabolomics data from a study investigating the effects of building material type, moisture and time on microbial and metabolomic diversity. Compared to analysis of untransformed data, analysis of clr-transformed data revealed novel relationships and stronger associations between sample conditions and microbial and metabolic community profiles.
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Affiliation(s)
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
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15
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Zhao D, Cardona C, Gottel N, Winton VJ, Thomas PM, Raba DA, Kelley ST, Henry C, Gilbert JA, Stephens B. Chemical composition of material extractives influences microbial growth and dynamics on wetted wood materials. Sci Rep 2020; 10:14500. [PMID: 32879425 PMCID: PMC7467922 DOI: 10.1038/s41598-020-71560-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 11/23/2019] [Accepted: 08/18/2020] [Indexed: 11/12/2022] Open
Abstract
The impact of material chemical composition on microbial growth on building materials remains relatively poorly understood. We investigate the influence of the chemical composition of material extractives on microbial growth and community dynamics on 30 different wood species that were naturally inoculated, wetted, and held at high humidity for several weeks. Microbial growth was assessed by visual assessment and molecular sequencing. Unwetted material powders and microbial swab samples were analyzed using reverse phase liquid chromatography with tandem mass spectrometry. Different wood species demonstrated varying susceptibility to microbial growth after 3 weeks and visible coverage and fungal qPCR concentrations were correlated (R2 = 0.55). Aspergillaceae was most abundant across all samples; Meruliaceae was more prevalent on 8 materials with the highest visible microbial growth. A larger and more diverse set of compounds was detected from the wood shavings compared to the microbial swabs, indicating a complex and heterogeneous chemical composition within wood types. Several individual compounds putatively identified in wood samples showed statistically significant, near-monotonic associations with microbial growth, including C11H16O4, C18H34O4, and C6H15NO. A pilot experiment confirmed the inhibitory effects of dosing a sample of wood materials with varying concentrations of liquid C6H15NO (assuming it presented as Diethylethanolamine).
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Affiliation(s)
- Dan Zhao
- Department of Civil, Architectural, and Environmental Engineering, Illinois Institute of Technology, Alumni Memorial Hall 228E, 3201 South Dearborn Street, Chicago, IL, 60616, USA
| | - Cesar Cardona
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL, USA
- Department of Surgery, The University of Chicago, Chicago, IL, USA
| | - Neil Gottel
- Department of Pediatrics, University of California San Diego School of Medicine, San Diego, CA, USA
| | - Valerie J Winton
- Proteomics Center of Excellence and Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Paul M Thomas
- Proteomics Center of Excellence and Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Daniel A Raba
- Department of Biology, Illinois Institute of Technology, Chicago, IL, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Christopher Henry
- Mathematics and Computer Science, Argonne National Laboratory, Lemont, IL, USA
| | - Jack A Gilbert
- Department of Pediatrics, University of California San Diego School of Medicine, San Diego, CA, USA
| | - Brent Stephens
- Department of Civil, Architectural, and Environmental Engineering, Illinois Institute of Technology, Alumni Memorial Hall 228E, 3201 South Dearborn Street, Chicago, IL, 60616, USA.
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16
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Chopyk J, Akrami K, Bavly T, Shin JH, Schwanemann LK, Ly M, Kalia R, Xu Y, Kelley ST, Malhotra A, Torriani FJ, Sweeney DA, Pride DT. Temporal variations in bacterial community diversity and composition throughout intensive care unit renovations. Microbiome 2020; 8:86. [PMID: 32513256 PMCID: PMC7278141 DOI: 10.1186/s40168-020-00852-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 05/01/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Inanimate surfaces within a hospital serve as a reservoir of microbial life that may colonize patients and ultimately result in healthcare associated infections (HAIs). Critically ill patients in intensive care units (ICUs) are particularly vulnerable to HAIs. Little is known about how the microbiome of the ICU is established or what factors influence its evolution over time. A unique opportunity to bridge the knowledge gap into how the ICU microbiome evolves emerged in our health system, where we were able to characterize microbial communities in an established hospital ICU prior to closing for renovations, during renovations, and then after re-opening. RESULTS We collected swab specimens from ICU bedrails, computer keyboards, and sinks longitudinally at each renovation stage, and analyzed the bacterial compositions on these surfaces by 16S rRNA gene sequencing. Specimens collected before ICU closure had the greatest alpha diversity, while specimens collected after the ICU had been closed for over 300 days had the least. We sampled the ICU during the 45 days after re-opening; however, within that time frame, the alpha diversity never reached pre-closure levels. There were clear and significant differences in microbiota compositions at each renovation stage, which was driven by environmental bacteria after closure and human-associated bacteria after re-opening and before closure. CONCLUSIONS Overall, we identified significant differences in microbiota diversity and community composition at each renovation stage. These data help to decipher the evolution of the microbiome in the most critical part of the hospital and demonstrate the significant impacts that microbiota from patients and staff have on the evolution of ICU surfaces. Video Abstract.
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Affiliation(s)
- Jessica Chopyk
- Department of Pathology, University of California, San Diego, USA
| | - Kevan Akrami
- Department of Medicine, University of California, San Diego, USA
| | - Tovia Bavly
- Department of Pathology, University of California, San Diego, USA
| | - Ji H Shin
- Department of Pathology, University of California, San Diego, USA
| | | | - Melissa Ly
- Department of Pathology, University of California, San Diego, USA
| | - Richa Kalia
- Department of Biology, San Diego State University, San Diego, USA
| | - Ying Xu
- Department of Biology, San Diego State University, San Diego, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, USA
| | - Atul Malhotra
- Department of Medicine, University of California, San Diego, USA
| | | | - Daniel A Sweeney
- Department of Medicine, University of California, San Diego, USA
| | - David T Pride
- Department of Pathology, University of California, San Diego, USA.
- Department of Medicine, University of California, San Diego, USA.
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17
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McGhee JJ, Rawson N, Bailey BA, Fernandez-Guerra A, Sisk-Hackworth L, Kelley ST. Meta-SourceTracker: application of Bayesian source tracking to shotgun metagenomics. PeerJ 2020; 8:e8783. [PMID: 32231882 PMCID: PMC7100590 DOI: 10.7717/peerj.8783] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 02/21/2020] [Indexed: 11/20/2022] Open
Abstract
Background Microbial source tracking methods are used to determine the origin of contaminating bacteria and other microorganisms, particularly in contaminated water systems. The Bayesian SourceTracker approach uses deep-sequencing marker gene libraries (16S ribosomal RNA) to determine the proportional contributions of bacteria from many potential source environments to a given sink environment simultaneously. Since its development, SourceTracker has been applied to an extensive diversity of studies, from beach contamination to human behavior. Methods Here, we demonstrate a novel application of SourceTracker to work with metagenomic datasets and tested this approach using sink samples from a study of coastal marine environments. Source environment metagenomes were obtained from metagenomics studies of gut, freshwater, marine, sand and soil environments. As part of this effort, we implemented features for determining the stability of source proportion estimates, including precision visualizations for performance optimization, and performed domain-specific source-tracking analyses (i.e., Bacteria, Archaea, Eukaryota and viruses). We also applied SourceTracker to metagenomic libraries generated from samples collected from the International Space Station (ISS). Results SourceTracker proved highly effective at predicting the composition of known sources using shotgun metagenomic libraries. In addition, we showed that different taxonomic domains sometimes presented highly divergent pictures of environmental source origins for both the coastal marine and ISS samples. These findings indicated that applying SourceTracker to separate domains may provide a deeper understanding of the microbial origins of complex, mixed-source environments, and further suggested that certain domains may be preferable for tracking specific sources of contamination.
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Affiliation(s)
- Jordan J McGhee
- Bioinformatics and Medical Informatics Program, San Diego State University, San Diego, CA, United States of America
| | - Nick Rawson
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA, United States of America
| | - Barbara A Bailey
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA, United States of America
| | - Antonio Fernandez-Guerra
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.,Current affiliation: Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Laura Sisk-Hackworth
- Department of Biology, San Diego State University, San Diego, CA, United States of America
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, United States of America
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18
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Prussin AJ, Belser JA, Bischoff W, Kelley ST, Lin K, Lindsley WG, Nshimyimana JP, Schuit M, Wu Z, Bibby K, Marr LC. Viruses in the Built Environment (VIBE) meeting report. Microbiome 2020; 8:1. [PMID: 31901242 PMCID: PMC6942371 DOI: 10.1186/s40168-019-0777-4] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 12/18/2019] [Indexed: 05/04/2023]
Abstract
BACKGROUND During a period of rapid growth in our understanding of the microbiology of the built environment in recent years, the majority of research has focused on bacteria and fungi. Viruses, while probably as numerous, have received less attention. In response, the Alfred P. Sloan Foundation supported a workshop entitled "Viruses in the Built Environment (VIBE)," at which experts in environmental engineering, environmental microbiology, epidemiology, infection prevention, fluid dynamics, occupational health, metagenomics, and virology convened to synthesize recent advances and identify key research questions and knowledge gaps regarding viruses in the built environment. RESULTS Four primary research areas and funding priorities were identified. First, a better understanding of viral communities in the built environment is needed, specifically which viruses are present and their sources, spatial and temporal dynamics, and interactions with bacteria. Second, more information is needed about viruses and health, including viral transmission in the built environment, the relationship between virus detection and exposure, and the definition of a healthy virome. The third research priority is to identify and evaluate interventions for controlling viruses and the virome in the built environment. This encompasses interactions among viruses, buildings, and occupants. Finally, to overcome the challenge of working with viruses, workshop participants emphasized that improved sampling methods, laboratory techniques, and bioinformatics approaches are needed to advance understanding of viruses in the built environment. CONCLUSIONS We hope that identifying these key questions and knowledge gaps will engage other investigators and funding agencies to spur future research on the highly interdisciplinary topic of viruses in the built environment. There are numerous opportunities to advance knowledge, as many topics remain underexplored compared to our understanding of bacteria and fungi. Video abstract.
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Affiliation(s)
- Aaron J. Prussin
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061 USA
| | - Jessica A. Belser
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333 USA
| | - Werner Bischoff
- Section on Infectious Diseases, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - Scott T. Kelley
- Department of Biology, San Diego State University, San Diego, CA 92182 USA
| | - Kaisen Lin
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061 USA
| | - William G. Lindsley
- Health Effects Laboratory Division (HELD), National Institute for Occupational Safety and Health, Morgantown, WV 26505 USA
| | | | - Michael Schuit
- National Biodefense Analysis and Countermeasures Center, Frederick, MD 21702 USA
| | - Zhenyu Wu
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Kyle Bibby
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Linsey C. Marr
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061 USA
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19
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Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 2019; 37:852-857. [PMID: 31341288 DOI: 10.1038/s41587-019-0209-9] [Citation(s) in RCA: 8045] [Impact Index Per Article: 1609.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Evan Bolyen
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Jai Ram Rideout
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Matthew R Dillon
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Nicholas A Bokulich
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Christian C Abnet
- Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA
| | - Gabriel A Al-Ghalith
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Harriet Alexander
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.,Department of Population Health and Reproduction, University of California, Davis, Davis, CA, USA
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Manimozhiyan Arumugam
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.,Centre of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences & John Innes Centre, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jordan E Bisanz
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Kyle Bittinger
- Division of Gastroenterology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Hepatology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Asker Brejnrod
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Colin J Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - C Titus Brown
- Department of Population Health and Reproduction, University of California, Davis, Davis, CA, USA
| | - Benjamin J Callahan
- Department of Population Health & Pathobiology, North Carolina State University, Raleigh, NC, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Andrés Mauricio Caraballo-Rodríguez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - John Chase
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Emily K Cope
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Ricardo Da Silva
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | | | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Gavin M Douglas
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Daniel M Durall
- Irving K. Barber School of Arts and Sciences, University of British Columbia, Kelowna, British Columbia, Canada
| | - Claire Duvallet
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Christian F Edwardson
- A. Watson Armour III Center for Animal Health and Welfare, Aquarium Microbiome Project, John G. Shedd Aquarium, Chicago, IL, USA
| | - Madeleine Ernst
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.,Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Mehrbod Estaki
- Department of Biology, University of British Columbia Okanagan, Okanagan, British Columbia, Canada
| | - Jennifer Fouquier
- Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Julia M Gauglitz
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Sean M Gibbons
- Institute for Systems Biology, Seattle, WA, USA.,eScience Institute, University of Washington, Seattle, WA, USA
| | - Deanna L Gibson
- Irving K. Barber School of Arts and Sciences, Department of Biology, University of British Columbia, Kelowna, British Columbia, Canada.,Department of Medicine, University of British Columbia, Kelowna, British Columbia, Canada
| | - Antonio Gonzalez
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Kestrel Gorlick
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Jiarong Guo
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Benjamin Hillmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Susan Holmes
- Statistics Department, Stanford University, Palo Alto, CA, USA
| | - Hannes Holste
- 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
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gavin A Huttley
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Stefan Janssen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Dusseldorf, Dusseldorf, Germany
| | - Alan K Jarmusch
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Lingjing Jiang
- Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | - Benjamin D Kaehler
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia.,School of Science, University of New South Wales, Canberra, Australian Capital Territory, Australia
| | - Kyo Bin Kang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.,College of Pharmacy, Sookmyung Women's University, Seoul, Republic of Korea
| | - Christopher R Keefe
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Paul Keim
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA.,Biotechnology Institute, University of Minnesota, Saint Paul, MN, USA
| | - Irina Koester
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.,Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Tomasz Kosciolek
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Jorden Kreps
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Morgan G I Langille
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Joslynn Lee
- Science Education, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Ruth Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Yong-Xin Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.,Centre of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences & John Innes Centre, Beijing, China
| | - Erikka Loftfield
- Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA
| | - Catherine Lozupone
- Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Massoud Maher
- Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA
| | - Clarisse Marotz
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Bryan D Martin
- Department of Statistics, University of Washington, Seattle, WA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Lauren J McIver
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Jessica L Metcalf
- Department of Animal Science, Colorado State University, Fort Collins, CO, USA
| | - Sydney C Morgan
- Irving K. Barber School of Arts and Sciences, Unit 2 (Biology), University of British Columbia, Kelowna, British Columbia, Canada
| | - Jamie T Morton
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA
| | - Ahmad Turan Naimey
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Jose A Navas-Molina
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA.,Google LLC, Mountain View, CA, USA
| | - Louis Felix Nothias
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Stephanie B Orchanian
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Talima Pearson
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Samuel L Peoples
- School of Information Studies, Syracuse University, Syracuse, NY, USA.,School of STEM, University of Washington Bothell, Bothell, WA, USA
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Mary Lai Preuss
- Department of Biological Sciences, Webster University, St. Louis, MO, USA
| | - Elmar Pruesse
- Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Lasse Buur Rasmussen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Adam Rivers
- Agricultural Research Service, Genomics and Bioinformatics Research Unit, United States Department of Agriculture, Gainesville, FL, USA
| | - Michael S Robeson
- College of Medicine, Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Patrick Rosenthal
- Department of Biological Sciences, Webster University, St. Louis, MO, USA
| | - Nicola Segata
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Michael Shaffer
- Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Arron Shiffer
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Rashmi Sinha
- Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA
| | - Se Jin Song
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - John R Spear
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Luke R Thompson
- Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, MS, USA.,Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, La Jolla, CA, USA
| | - Pedro J Torres
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Pauline Trinh
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Anupriya Tripathi
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.,Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Division of Biological Sciences, University of California San Diego, San Diego, CA, USA
| | - Peter J Turnbaugh
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Sabah Ul-Hasan
- Quantitative and Systems Biology Graduate Program, University of California Merced, Merced, CA, USA
| | | | - Fernando Vargas
- Division of Biological Sciences, University of California San Diego, San Diego, CA, USA
| | | | - Emily Vogtmann
- Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA
| | - Max von Hippel
- Department of Mathematics, University of Arizona, Tucson, AZ, USA
| | - William Walters
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Yunhu Wan
- Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Jonathan Warren
- National Laboratory Service, Environment Agency, Starcross, UK
| | - Kyle C Weber
- Agricultural Research Service, Genomics and Bioinformatics Research Unit, United States Department of Agriculture, Gainesville, FL, USA.,College of Agriculture and Life Sciences, University of Florida, Gainesville, FL, USA
| | | | - Amy D Willis
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Zhenjiang Zech Xu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Jesse R Zaneveld
- School of STEM, Division of Biological Sciences, University of Washington Bothell, Bothell, WA, USA
| | | | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- 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
| | - J Gregory Caporaso
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA. .,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
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20
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Edwards RA, Vega AA, Norman HM, Ohaeri M, Levi K, Dinsdale EA, Cinek O, Aziz RK, McNair K, Barr JJ, Bibby K, Brouns SJJ, Cazares A, de Jonge PA, Desnues C, Díaz Muñoz SL, Fineran PC, Kurilshikov A, Lavigne R, Mazankova K, McCarthy DT, Nobrega FL, Reyes Muñoz A, Tapia G, Trefault N, Tyakht AV, Vinuesa P, Wagemans J, Zhernakova A, Aarestrup FM, Ahmadov G, Alassaf A, Anton J, Asangba A, Billings EK, Cantu VA, Carlton JM, Cazares D, Cho GS, Condeff T, Cortés P, Cranfield M, Cuevas DA, De la Iglesia R, Decewicz P, Doane MP, Dominy NJ, Dziewit L, Elwasila BM, Eren AM, Franz C, Fu J, Garcia-Aljaro C, Ghedin E, Gulino KM, Haggerty JM, Head SR, Hendriksen RS, Hill C, Hyöty H, Ilina EN, Irwin MT, Jeffries TC, Jofre J, Junge RE, Kelley ST, Khan Mirzaei M, Kowalewski M, Kumaresan D, Leigh SR, Lipson D, Lisitsyna ES, Llagostera M, Maritz JM, Marr LC, McCann A, Molshanski-Mor S, Monteiro S, Moreira-Grez B, Morris M, Mugisha L, Muniesa M, Neve H, Nguyen NP, Nigro OD, Nilsson AS, O'Connell T, Odeh R, Oliver A, Piuri M, Prussin Ii AJ, Qimron U, Quan ZX, Rainetova P, Ramírez-Rojas A, Raya R, Reasor K, Rice GAO, Rossi A, Santos R, Shimashita J, Stachler EN, Stene LC, Strain R, Stumpf R, Torres PJ, Twaddle A, Ugochi Ibekwe M, Villagra N, Wandro S, White B, Whiteley A, Whiteson KL, Wijmenga C, Zambrano MM, Zschach H, Dutilh BE. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nat Microbiol 2019. [PMID: 31285584 DOI: 10.1038/s41564-019-04904-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
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Affiliation(s)
- Robert A Edwards
- Department of Biology, San Diego State University, San Diego, CA, USA.
- The Viral Information Institute, San Diego State University, San Diego, CA, USA.
| | - Alejandro A Vega
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Holly M Norman
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Maria Ohaeri
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Kyle Levi
- Department of Computer Science, San Diego State University, San Diego, CA, USA
| | | | - Ondrej Cinek
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Katelyn McNair
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Kyle Bibby
- Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Stan J J Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Adrian Cazares
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Patrick A de Jonge
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Christelle Desnues
- MEPHI, Aix-Marseille Université, IRD, AP-HM, CNRS, IHU Méditerranée Infection, Marseille, France
- Mediterranean Institute of Oceanography, Aix-Marseille Université, Université de Toulon, CNRS, IRD, UM 110, Marseille, France
| | - Samuel L Díaz Muñoz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Alexander Kurilshikov
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Karla Mazankova
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - David T McCarthy
- EPHM Lab, Civil Engineering Department, Monash University, Clayton, Victoria, Australia
| | - Franklin L Nobrega
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Alejandro Reyes Muñoz
- Max Planck Tandem Group in Computational Biology, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - German Tapia
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Huechuraba, Chile
| | - Alexander V Tyakht
- Laboratory of Bioinformatics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
- Department of Informational Technologies, ITMO University, Saint Petersburg, Russia
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Frank M Aarestrup
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Abeer Alassaf
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Josefa Anton
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Abigail Asangba
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Emma K Billings
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Vito Adrian Cantu
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jane M Carlton
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Daniel Cazares
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Tess Condeff
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Mike Cranfield
- Wildlife Health Center, University of California, Davis, Davis, CA, USA
| | - Daniel A Cuevas
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Rodrigo De la Iglesia
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Przemyslaw Decewicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Michael P Doane
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Bashir Mukhtar Elwasila
- Department of Pediatrics and Child Health, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Charles Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Jingyuan Fu
- Department of Pediatrics, University Medical Center Groningen, Groningen, The Netherlands
| | - Cristina Garcia-Aljaro
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Elodie Ghedin
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Kristen M Gulino
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - John M Haggerty
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Steven R Head
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA, USA
| | - Rene S Hendriksen
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Colin Hill
- School of Microbiology, University College Cork, Cork, Ireland
| | - Heikki Hyöty
- Department of Virology, School of Medicine, University of Tampere, Tampere, Finland
| | - Elena N Ilina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Mitchell T Irwin
- Department of Anthropology, Northern Illinois University, DeKalb, IL, USA
| | - Thomas C Jeffries
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia
| | - Juan Jofre
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Randall E Junge
- Department of Animal Health, Columbus Zoo and Aquarium, Powell, OH, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Martin Kowalewski
- Department Estacion Biologica Corrientes, Institution Museo Arg. Cs. Naturales-CONICET, Corrientes, Argentina
| | - Deepak Kumaresan
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Steven R Leigh
- Department of Anthropology, University of Colorado, Boulder, CO, USA
| | - David Lipson
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Montserrat Llagostera
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Julia M Maritz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Linsey C Marr
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Angela McCann
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Shahar Molshanski-Mor
- Clinical Microbiology & Immunology, Sackler school of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Silvia Monteiro
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - Benjamin Moreira-Grez
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Megan Morris
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Lawrence Mugisha
- CEHA, Kampala, Uganda
- COVAB, Makerere University, Kampala, Uganda
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Nam-Phuong Nguyen
- Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Olivia D Nigro
- College of Natural and Computational Sciences, Hawai'i Pacific University, Kaneohe, HI, USA
| | - Anders S Nilsson
- Department of Molecular Biosciences, Stockholm University, Stockholm, Sweden
| | - Taylor O'Connell
- Biological and Medical Informatics Program, San Diego State University, San Diego, CA, USA
| | - Rasha Odeh
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Andrew Oliver
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Mariana Piuri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Aaron J Prussin Ii
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Petra Rainetova
- Centre of Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | | | | | - Kim Reasor
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Alessandro Rossi
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
- Department of Biology, University of Padova, Padova, Italy
| | - Ricardo Santos
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - John Shimashita
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Elyse N Stachler
- Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lars C Stene
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ronan Strain
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Rebecca Stumpf
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Pedro J Torres
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Alan Twaddle
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - MaryAnn Ugochi Ibekwe
- Department of Pediatrics, Federal Teaching Hospital Abakaliki, Ebonyi State University, Abakaliki, Nigeria
| | - Nicolás Villagra
- Escuela de Tecnología Médica, Universidad Andres Bello, Santiago, Chile
| | - Stephen Wandro
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Bryan White
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andy Whiteley
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Katrine L Whiteson
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Henrike Zschach
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands.
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.
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21
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Edwards RA, Vega AA, Norman HM, Ohaeri M, Levi K, Dinsdale EA, Cinek O, Aziz RK, McNair K, Barr JJ, Bibby K, Brouns SJJ, Cazares A, de Jonge PA, Desnues C, Díaz Muñoz SL, Fineran PC, Kurilshikov A, Lavigne R, Mazankova K, McCarthy DT, Nobrega FL, Reyes Muñoz A, Tapia G, Trefault N, Tyakht AV, Vinuesa P, Wagemans J, Zhernakova A, Aarestrup FM, Ahmadov G, Alassaf A, Anton J, Asangba A, Billings EK, Cantu VA, Carlton JM, Cazares D, Cho GS, Condeff T, Cortés P, Cranfield M, Cuevas DA, De la Iglesia R, Decewicz P, Doane MP, Dominy NJ, Dziewit L, Elwasila BM, Eren AM, Franz C, Fu J, Garcia-Aljaro C, Ghedin E, Gulino KM, Haggerty JM, Head SR, Hendriksen RS, Hill C, Hyöty H, Ilina EN, Irwin MT, Jeffries TC, Jofre J, Junge RE, Kelley ST, Khan Mirzaei M, Kowalewski M, Kumaresan D, Leigh SR, Lipson D, Lisitsyna ES, Llagostera M, Maritz JM, Marr LC, McCann A, Molshanski-Mor S, Monteiro S, Moreira-Grez B, Morris M, Mugisha L, Muniesa M, Neve H, Nguyen NP, Nigro OD, Nilsson AS, O'Connell T, Odeh R, Oliver A, Piuri M, Prussin Ii AJ, Qimron U, Quan ZX, Rainetova P, Ramírez-Rojas A, Raya R, Reasor K, Rice GAO, Rossi A, Santos R, Shimashita J, Stachler EN, Stene LC, Strain R, Stumpf R, Torres PJ, Twaddle A, Ugochi Ibekwe M, Villagra N, Wandro S, White B, Whiteley A, Whiteson KL, Wijmenga C, Zambrano MM, Zschach H, Dutilh BE. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nat Microbiol 2019; 4:1727-1736. [PMID: 31285584 DOI: 10.1101/527796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 10/14/2018] [Accepted: 05/22/2019] [Indexed: 05/26/2023]
Abstract
Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
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Affiliation(s)
- Robert A Edwards
- Department of Biology, San Diego State University, San Diego, CA, USA.
- The Viral Information Institute, San Diego State University, San Diego, CA, USA.
| | - Alejandro A Vega
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Holly M Norman
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Maria Ohaeri
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Kyle Levi
- Department of Computer Science, San Diego State University, San Diego, CA, USA
| | | | - Ondrej Cinek
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Katelyn McNair
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Kyle Bibby
- Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Stan J J Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Adrian Cazares
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Patrick A de Jonge
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Christelle Desnues
- MEPHI, Aix-Marseille Université, IRD, AP-HM, CNRS, IHU Méditerranée Infection, Marseille, France
- Mediterranean Institute of Oceanography, Aix-Marseille Université, Université de Toulon, CNRS, IRD, UM 110, Marseille, France
| | - Samuel L Díaz Muñoz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Alexander Kurilshikov
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Karla Mazankova
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - David T McCarthy
- EPHM Lab, Civil Engineering Department, Monash University, Clayton, Victoria, Australia
| | - Franklin L Nobrega
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Alejandro Reyes Muñoz
- Max Planck Tandem Group in Computational Biology, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - German Tapia
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Huechuraba, Chile
| | - Alexander V Tyakht
- Laboratory of Bioinformatics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
- Department of Informational Technologies, ITMO University, Saint Petersburg, Russia
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Frank M Aarestrup
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Abeer Alassaf
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Josefa Anton
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Abigail Asangba
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Emma K Billings
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Vito Adrian Cantu
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jane M Carlton
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Daniel Cazares
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Tess Condeff
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Mike Cranfield
- Wildlife Health Center, University of California, Davis, Davis, CA, USA
| | - Daniel A Cuevas
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Rodrigo De la Iglesia
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Przemyslaw Decewicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Michael P Doane
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Bashir Mukhtar Elwasila
- Department of Pediatrics and Child Health, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Charles Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Jingyuan Fu
- Department of Pediatrics, University Medical Center Groningen, Groningen, The Netherlands
| | - Cristina Garcia-Aljaro
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Elodie Ghedin
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Kristen M Gulino
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - John M Haggerty
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Steven R Head
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA, USA
| | - Rene S Hendriksen
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Colin Hill
- School of Microbiology, University College Cork, Cork, Ireland
| | - Heikki Hyöty
- Department of Virology, School of Medicine, University of Tampere, Tampere, Finland
| | - Elena N Ilina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Mitchell T Irwin
- Department of Anthropology, Northern Illinois University, DeKalb, IL, USA
| | - Thomas C Jeffries
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia
| | - Juan Jofre
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Randall E Junge
- Department of Animal Health, Columbus Zoo and Aquarium, Powell, OH, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Martin Kowalewski
- Department Estacion Biologica Corrientes, Institution Museo Arg. Cs. Naturales-CONICET, Corrientes, Argentina
| | - Deepak Kumaresan
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Steven R Leigh
- Department of Anthropology, University of Colorado, Boulder, CO, USA
| | - David Lipson
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Montserrat Llagostera
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Julia M Maritz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Linsey C Marr
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Angela McCann
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Shahar Molshanski-Mor
- Clinical Microbiology & Immunology, Sackler school of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Silvia Monteiro
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - Benjamin Moreira-Grez
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Megan Morris
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Lawrence Mugisha
- CEHA, Kampala, Uganda
- COVAB, Makerere University, Kampala, Uganda
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Nam-Phuong Nguyen
- Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Olivia D Nigro
- College of Natural and Computational Sciences, Hawai'i Pacific University, Kaneohe, HI, USA
| | - Anders S Nilsson
- Department of Molecular Biosciences, Stockholm University, Stockholm, Sweden
| | - Taylor O'Connell
- Biological and Medical Informatics Program, San Diego State University, San Diego, CA, USA
| | - Rasha Odeh
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Andrew Oliver
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Mariana Piuri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Aaron J Prussin Ii
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Petra Rainetova
- Centre of Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | | | | | - Kim Reasor
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Alessandro Rossi
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
- Department of Biology, University of Padova, Padova, Italy
| | - Ricardo Santos
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - John Shimashita
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Elyse N Stachler
- Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lars C Stene
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ronan Strain
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Rebecca Stumpf
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Pedro J Torres
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Alan Twaddle
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - MaryAnn Ugochi Ibekwe
- Department of Pediatrics, Federal Teaching Hospital Abakaliki, Ebonyi State University, Abakaliki, Nigeria
| | - Nicolás Villagra
- Escuela de Tecnología Médica, Universidad Andres Bello, Santiago, Chile
| | - Stephen Wandro
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Bryan White
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andy Whiteley
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Katrine L Whiteson
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Henrike Zschach
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands.
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.
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22
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Arroyo P, Ho BS, Sau L, Kelley ST, Thackray VG. Letrozole treatment of pubertal female mice results in activational effects on reproduction, metabolism and the gut microbiome. PLoS One 2019; 14:e0223274. [PMID: 31568518 PMCID: PMC6768472 DOI: 10.1371/journal.pone.0223274] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [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: 04/05/2019] [Accepted: 09/17/2019] [Indexed: 12/23/2022] Open
Abstract
Polycystic ovary syndrome (PCOS) is a common endocrine disorder in reproductive-aged women that is comprised of two out of the following three features: hyperandrogenism, oligo- or amenorrhea, or polycystic ovaries. In addition to infertility, many women with PCOS have metabolic dysregulation that increases the risk of developing type 2 diabetes, hypertension, and non-alcoholic fatty liver disease. Changes in the gut microbiome are associated with PCOS and gut microbes may be involved in the pathology of this disorder. Since PCOS often manifests in the early reproductive years, puberty is considered to be a critical time period for the development of PCOS. Exposure to sex steroid hormones during development results in permanent, organizational effects, while activational effects are transient and require the continued presence of the hormone. Androgens exert organizational effects during prenatal or early post-natal development, but it is unclear whether androgen excess results in organizational or activational effects during puberty. We recently developed a letrozole-induced PCOS mouse model that recapitulates both reproductive and metabolic phenotypes of PCOS. In this study, we investigated whether letrozole treatment of pubertal female mice exerts organizational or activational effects on host physiology and the gut microbiome. Two months after letrozole removal, we observed recovery of reproductive and metabolic parameters, as well as diversity and composition of the gut microbiome, indicating that letrozole treatment of female mice during puberty resulted in predominantly activational effects. These results suggest that if exposure to excess androgens during puberty leads to the development of PCOS, reduction of androgen levels during this time may improve reproductive and metabolic phenotypes in women with PCOS. These results also imply that continuous letrozole exposure is required to model PCOS in pubertal female mice since letrozole exerts activational rather than organizational effects during puberty.
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Affiliation(s)
- Pablo Arroyo
- Department of Biology, San Diego State University, San Diego, CA, United States of America
| | - Bryan S. Ho
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, United States of America
| | - Lillian Sau
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, United States of America
| | - Scott T. Kelley
- Department of Biology, San Diego State University, San Diego, CA, United States of America
| | - Varykina G. Thackray
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, United States of America
- * E-mail:
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23
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Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG. Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 2019; 37:1091. [PMID: 31399723 DOI: 10.1038/s41587-019-0252-6] [Citation(s) in RCA: 281] [Impact Index Per Article: 56.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Evan Bolyen
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Jai Ram Rideout
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Matthew R Dillon
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Nicholas A Bokulich
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Christian C Abnet
- Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA
| | - Gabriel A Al-Ghalith
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Harriet Alexander
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.,Department of Population Health and Reproduction, University of California, Davis, Davis, CA, USA
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Manimozhiyan Arumugam
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.,Centre of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences & John Innes Centre, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jordan E Bisanz
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Kyle Bittinger
- Division of Gastroenterology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Hepatology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Asker Brejnrod
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Colin J Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - C Titus Brown
- Department of Population Health and Reproduction, University of California, Davis, Davis, CA, USA
| | - Benjamin J Callahan
- Department of Population Health & Pathobiology, North Carolina State University, Raleigh, NC, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Andrés Mauricio Caraballo-Rodríguez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - John Chase
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Emily K Cope
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Ricardo Da Silva
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | | | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Gavin M Douglas
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Daniel M Durall
- Irving K. Barber School of Arts and Sciences, University of British Columbia, Kelowna, British Columbia, Canada
| | - Claire Duvallet
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Christian F Edwardson
- A. Watson Armour III Center for Animal Health and Welfare, Aquarium Microbiome Project, John G. Shedd Aquarium, Chicago, IL, USA
| | - Madeleine Ernst
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.,Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Mehrbod Estaki
- Department of Biology, University of British Columbia Okanagan, Okanagan, British Columbia, Canada
| | - Jennifer Fouquier
- Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Julia M Gauglitz
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Sean M Gibbons
- Institute for Systems Biology, Seattle, WA, USA.,eScience Institute, University of Washington, Seattle, WA, USA
| | - Deanna L Gibson
- Irving K. Barber School of Arts and Sciences, Department of Biology, University of British Columbia, Kelowna, British Columbia, Canada.,Department of Medicine, University of British Columbia, Kelowna, British Columbia, Canada
| | - Antonio Gonzalez
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Kestrel Gorlick
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Jiarong Guo
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Benjamin Hillmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Susan Holmes
- Statistics Department, Stanford University, Palo Alto, CA, USA
| | - Hannes Holste
- 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
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gavin A Huttley
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Stefan Janssen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Dusseldorf, Dusseldorf, Germany
| | - Alan K Jarmusch
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Lingjing Jiang
- Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | - Benjamin D Kaehler
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia.,School of Science, University of New South Wales, Canberra, Australian Capital Territory, Australia
| | - Kyo Bin Kang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.,College of Pharmacy, Sookmyung Women's University, Seoul, Republic of Korea
| | - Christopher R Keefe
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Paul Keim
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA.,Biotechnology Institute, University of Minnesota, Saint Paul, MN, USA
| | - Irina Koester
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.,Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Tomasz Kosciolek
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Jorden Kreps
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Morgan G I Langille
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Joslynn Lee
- Science Education, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Ruth Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Yong-Xin Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.,Centre of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences & John Innes Centre, Beijing, China
| | - Erikka Loftfield
- Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA
| | - Catherine Lozupone
- Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Massoud Maher
- Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA
| | - Clarisse Marotz
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Bryan D Martin
- Department of Statistics, University of Washington, Seattle, WA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Lauren J McIver
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Jessica L Metcalf
- Department of Animal Science, Colorado State University, Fort Collins, CO, USA
| | - Sydney C Morgan
- Irving K. Barber School of Arts and Sciences, Unit 2 (Biology), University of British Columbia, Kelowna, British Columbia, Canada
| | - Jamie T Morton
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA
| | - Ahmad Turan Naimey
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Jose A Navas-Molina
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA.,Google LLC, Mountain View, CA, USA
| | - Louis Felix Nothias
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Stephanie B Orchanian
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Talima Pearson
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Samuel L Peoples
- School of Information Studies, Syracuse University, Syracuse, NY, USA.,School of STEM, University of Washington Bothell, Bothell, WA, USA
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Mary Lai Preuss
- Department of Biological Sciences, Webster University, St. Louis, MO, USA
| | - Elmar Pruesse
- Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Lasse Buur Rasmussen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Adam Rivers
- Agricultural Research Service, Genomics and Bioinformatics Research Unit, United States Department of Agriculture, Gainesville, FL, USA
| | - Michael S Robeson
- College of Medicine, Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Patrick Rosenthal
- Department of Biological Sciences, Webster University, St. Louis, MO, USA
| | - Nicola Segata
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Michael Shaffer
- Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Arron Shiffer
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Rashmi Sinha
- Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA
| | - Se Jin Song
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - John R Spear
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Luke R Thompson
- Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, MS, USA.,Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, La Jolla, CA, USA
| | - Pedro J Torres
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Pauline Trinh
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Anupriya Tripathi
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.,Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Division of Biological Sciences, University of California San Diego, San Diego, CA, USA
| | - Peter J Turnbaugh
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Sabah Ul-Hasan
- Quantitative and Systems Biology Graduate Program, University of California Merced, Merced, CA, USA
| | | | - Fernando Vargas
- Division of Biological Sciences, University of California San Diego, San Diego, CA, USA
| | | | - Emily Vogtmann
- Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA
| | - Max von Hippel
- Department of Mathematics, University of Arizona, Tucson, AZ, USA
| | - William Walters
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Yunhu Wan
- Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Jonathan Warren
- National Laboratory Service, Environment Agency, Starcross, UK
| | - Kyle C Weber
- Agricultural Research Service, Genomics and Bioinformatics Research Unit, United States Department of Agriculture, Gainesville, FL, USA.,College of Agriculture and Life Sciences, University of Florida, Gainesville, FL, USA
| | | | - Amy D Willis
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Zhenjiang Zech Xu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Jesse R Zaneveld
- School of STEM, Division of Biological Sciences, University of Washington Bothell, Bothell, WA, USA
| | | | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- 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
| | - J Gregory Caporaso
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA. .,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
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24
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de la Cuesta-Zuluaga J, Kelley ST, Chen Y, Escobar JS, Mueller NT, Ley RE, McDonald D, Huang S, Swafford AD, Knight R, Thackray VG. Age- and Sex-Dependent Patterns of Gut Microbial Diversity in Human Adults. mSystems 2019; 4:e00261-19. [PMID: 31098397 PMCID: PMC6517691 DOI: 10.1128/msystems.00261-19] [Citation(s) in RCA: 182] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 04/30/2019] [Indexed: 11/22/2022] Open
Abstract
Gut microbial diversity changes throughout the human life span and is known to be associated with host sex. We investigated the association of age, sex, and gut bacterial alpha diversity in three large cohorts of adults from four geographical regions: subjects from the United States and United Kingdom in the American Gut Project (AGP) citizen-science initiative and two independent cohorts of Colombians and Chinese. In three of the four cohorts, we observed a strong positive association between age and alpha diversity in young adults that plateaued after age 40 years. We also found sex-dependent differences that were more pronounced in younger adults than in middle-aged adults, with women having higher alpha diversity than men. In contrast to the other three cohorts, no association of alpha diversity with age or sex was observed in the Chinese cohort. The association of alpha diversity with age and sex remained after adjusting for cardiometabolic parameters in the Colombian cohort and antibiotic usage in the AGP cohort. We further attempted to predict the microbiota age in individuals using a machine-learning approach for the men and women in each cohort. Consistent with our alpha-diversity-based findings, U.S. and U.K. women had a significantly higher predicted microbiota age than men, with a reduced difference being seen above age 40 years. This difference was not observed in the Colombian cohort and was observed only in middle-aged Chinese adults. Together, our results provide new insights into the influence of age and sex on the biodiversity of the human gut microbiota during adulthood while highlighting similarities and differences across diverse cohorts. IMPORTANCE Microorganisms in the human gut play a role in health and disease, and in adults higher gut biodiversity has been linked to better health. Since gut microorganisms may be pivotal in the development of microbial therapies, understanding the factors that shape gut biodiversity is of utmost interest. We performed large-scale analyses of the relationship of age and sex to gut bacterial diversity in adult cohorts from four geographic regions: the United States, the United Kingdom, Colombia, and China. In the U.S., U.K., and Colombian cohorts, bacterial biodiversity correlated positively with age in young adults but plateaued at about age 40 years, with no positive association being found in middle-aged adults. Young, but not middle-aged, adult women had higher gut bacterial diversity than men, a pattern confirmed via supervised machine learning. Interestingly, in the Chinese cohort, minimal associations were observed between gut biodiversity and age or sex. Our results highlight the patterns of adult gut biodiversity and provide a framework for future research.
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Affiliation(s)
| | - Scott T. Kelley
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Yingfeng Chen
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Juan S. Escobar
- Vidarium—Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia
| | - Noel T. Mueller
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Welch Center for Epidemiology, Prevention and Clinical Research, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Ruth E. Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Daniel McDonald
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Shi Huang
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Austin D. Swafford
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
- Department of Computer Science, University of California, San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Varykina G. Thackray
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, California, USA
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25
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Kosnicki KL, Penprase JC, Cintora P, Torres PJ, Harris GL, Brasser SM, Kelley ST. Effects of moderate, voluntary ethanol consumption on the rat and human gut microbiome. Addict Biol 2019; 24:617-630. [PMID: 29750384 PMCID: PMC6230504 DOI: 10.1111/adb.12626] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [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: 11/30/2017] [Revised: 04/03/2018] [Accepted: 04/04/2018] [Indexed: 12/13/2022]
Abstract
Many alcohol-induced health complications are directly attributable to the toxicity of alcohol or its metabolites, but another potential health impact of alcohol may be on the microbial communities of the human gut. Clear distinctions between healthy and diseased-state gut microbiota have been observed in subjects with metabolic diseases, and recent studies suggest that chronic alcoholism is linked to gut microbiome dysbiosis. Here, we investigated the effects of moderate levels of alcohol consumption on the gut microbiome in both rats and humans. The gut microbiota of rats voluntarily consuming a 20 percent ethanol solution, on alternate days, were compared with a non-exposed control group to identify differential taxonomic and functional profiles. Gut microbial diversity profiles were determined using culture-independent amplification, next-generation sequencing and bioinformatic analysis of bacterial 16S ribosomal RNA gene sequence libraries. Our results showed that, compared with controls, ethanol-consuming rats experienced a significant decline in the biodiversity of their gut microbiomes, a state generally associated with dysbiosis. We also observed significant shifts in the overall diversity of the gut microbial communities and a dramatic change in the relative abundance of particular microbes, such as the Lactobacilli. We also compared our results to human fecal microbiome data collected as part of the citizen science American Gut Project. In contrast to the rat data, human drinkers had significantly higher gut microbial biodiversity than non-drinkers. However, we also observed that microbes that differed among the human subjects displayed similar trends in the rat model, including bacteria implicated in metabolic disease.
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Affiliation(s)
- Kassi L. Kosnicki
- Department of Biology, San Diego State University, San Diego, CA, 92104 USA
| | - Jerrold C. Penprase
- Department of Psychology, San Diego State University, San Diego, CA, 92182 USA
| | - Patricia Cintora
- Department of Psychology, San Diego State University, San Diego, CA, 92182 USA
| | - Pedro J. Torres
- Department of Biology, San Diego State University, San Diego, CA, 92104 USA
| | - Greg L. Harris
- Department of Biology, San Diego State University, San Diego, CA, 92104 USA
| | - Susan M. Brasser
- Department of Psychology, San Diego State University, San Diego, CA, 92182 USA
| | - Scott T. Kelley
- Department of Biology, San Diego State University, San Diego, CA, 92104 USA
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26
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Torres PJ, Ho BS, Arroyo P, Sau L, Chen A, Kelley ST, Thackray VG. Exposure to a Healthy Gut Microbiome Protects Against Reproductive and Metabolic Dysregulation in a PCOS Mouse Model. Endocrinology 2019; 160:1193-1204. [PMID: 30924862 PMCID: PMC6482036 DOI: 10.1210/en.2019-00050] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 03/24/2019] [Indexed: 12/17/2022]
Abstract
Polycystic ovary syndrome (PCOS) is a common endocrine disorder affecting ∼10% to 15% of reproductive-aged women worldwide. Diagnosis requires two of the following: hyperandrogenism, oligo-ovulation or anovulation, and polycystic ovaries. In addition to reproductive dysfunction, many women with PCOS display metabolic abnormalities associated with hyperandrogenism. Recent studies have reported that the gut microbiome is altered in women with PCOS and rodent models of the disorder. However, it is unknown whether the gut microbiome plays a causal role in the development and pathology of PCOS. Given its potential role, we hypothesized that exposure to a healthy gut microbiome would protect against development of PCOS. A cohousing study was performed using a letrozole-induced PCOS mouse model that recapitulates many reproductive and metabolic characteristics of PCOS. Because mice are coprophagic, cohousing results in repeated, noninvasive inoculation of gut microbes in cohoused mice via the fecal-oral route. In contrast to letrozole-treated mice housed together, letrozole mice cohoused with placebo mice showed significant improvement in both reproductive and metabolic PCOS phenotypes. Using 16S rRNA gene sequencing, we also observed that the overall composition of the gut microbiome and the relative abundance of Coprobacillus and Lactobacillus differed in letrozole-treated mice cohoused with placebo mice compared with letrozole mice housed together. These results suggest that dysbiosis of the gut microbiome may play a causal role in PCOS and that modulation of the gut microbiome may be a potential treatment option for PCOS.
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Affiliation(s)
- Pedro J Torres
- Department of Biology, San Diego State University, San Diego, California
| | - Bryan S Ho
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, California
| | - Pablo Arroyo
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, California
| | - Lillian Sau
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, California
| | - Annie Chen
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, California
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, California
| | - Varykina G Thackray
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, California
- Correspondence: Varykina G. Thackray, PhD, Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, California 92093. E-mail:
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27
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Prussin AJ, Torres PJ, Shimashita J, Head SR, Bibby KJ, Kelley ST, Marr LC. Seasonal dynamics of DNA and RNA viral bioaerosol communities in a daycare center. Microbiome 2019; 7:53. [PMID: 30935423 PMCID: PMC6444849 DOI: 10.1186/s40168-019-0672-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 03/22/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Viruses play an important role in ecosystems, including the built environment (BE). While numerous studies have characterized bacterial and fungal microbiomes in the BE, few have focused on the viral microbiome (virome). Longitudinal microbiome studies provide insight into the stability and dynamics of microbial communities; however, few such studies exist for the microbiome of the BE, and most have focused on bacteria. Here, we present a longitudinal, metagenomic-based analysis of the airborne DNA and RNA virome of a children's daycare center. Specifically, we investigate how the airborne virome varies as a function of season and human occupancy, and we identify possible sources of the viruses and their hosts, mainly humans, animals, plants, and insects. RESULTS Season strongly influenced the airborne viral community composition, and a single sample collected when the daycare center was unoccupied suggested that occupancy also influenced the community. The pattern of influence differed between DNA and RNA viromes. Human-associated viruses were much more diverse and dominant in the winter, while the summertime virome contained a high relative proportion and diversity of plant-associated viruses. CONCLUSIONS This airborne microbiome in this building exhibited seasonality in its viral community but not its bacterial community. Human occupancy influenced both types of communities. By adding new data about the viral microbiome to complement burgeoning information about the bacterial and fungal microbiomes, this study contributes to a more complete understanding of the airborne microbiome.
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Affiliation(s)
- Aaron J. Prussin
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061 USA
| | - Pedro J. Torres
- Department of Biology, San Diego State University, San Diego, CA 92182 USA
| | - John Shimashita
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Steven R. Head
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Kyle J. Bibby
- Department of Civil and Environmental Engineering, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Scott T. Kelley
- Department of Biology, San Diego State University, San Diego, CA 92182 USA
| | - Linsey C. Marr
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061 USA
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28
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Torres PJ, Skarra DV, Ho BS, Sau L, Anvar AR, Kelley ST, Thackray VG. Letrozole treatment of adult female mice results in a similar reproductive phenotype but distinct changes in metabolism and the gut microbiome compared to pubertal mice. BMC Microbiol 2019; 19:57. [PMID: 30871463 PMCID: PMC6419356 DOI: 10.1186/s12866-019-1425-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 04/27/2018] [Accepted: 02/22/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND A majority of women with polycystic ovary syndrome (PCOS) have metabolic dysfunction that results in an increased risk of type 2 diabetes. We previously developed a pubertal mouse model using the aromatase inhibitor, letrozole, which recapitulates many of the reproductive and metabolic features of PCOS. To further our understanding of the effects of androgen excess, we compared the effects of letrozole treatment initiated in puberty versus adulthood on reproductive and metabolic phenotypes as well as on the gut microbiome. RESULTS Letrozole treatment of both pubertal and adult female mice resulted in reproductive hallmarks of PCOS, including hyperandrogenemia, anovulation and polycystic ovaries. However, unlike pubertal mice, treatment of adult female mice resulted in modest weight gain and abdominal adiposity, minimal elevation in fasting blood glucose and insulin levels, and no detectable insulin resistance. In addition, letrozole treatment of adult mice was associated with a distinct shift in gut microbial diversity compared to letrozole treatment of pubertal mice. CONCLUSIONS Our results indicate that dysregulation of metabolism and the gut microbiome in PCOS may be influenced by the timing of androgen exposure. In addition, the minimal weight gain and lack of insulin resistance in adult female mice after letrozole treatment indicates that this model may be useful for investigating the effects of hyperandrogenemia on the hypothalamic-pituitary-gonadal axis and the periphery without the influence of substantial metabolic dysregulation.
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Affiliation(s)
- Pedro J. Torres
- Department of Biology, San Diego State University, San Diego, CA USA
| | - Danalea V. Skarra
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92093 USA
| | - Bryan S. Ho
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92093 USA
| | - Lillian Sau
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92093 USA
| | - Arya R. Anvar
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92093 USA
| | - Scott T. Kelley
- Department of Biology, San Diego State University, San Diego, CA USA
| | - Varykina G. Thackray
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92093 USA
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29
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Torres PJ, Thompson J, McLean JS, Kelley ST, Edlund A. Discovery of a Novel Periodontal Disease-Associated Bacterium. Microb Ecol 2019; 77:267-276. [PMID: 29860637 PMCID: PMC6275135 DOI: 10.1007/s00248-018-1200-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 04/30/2018] [Indexed: 06/08/2023]
Abstract
One of the world's most common infectious disease, periodontitis (PD), derives from largely uncharacterized communities of oral bacteria growing as biofilms (a.k.a. plaque) on teeth and gum surfaces in periodontal pockets. Bacteria associated with periodontal disease trigger inflammatory responses in immune cells, which in later stages of the disease cause loss of both soft and hard tissue structures supporting teeth. Thus far, only a handful of bacteria have been characterized as infectious agents of PD. Although deep sequencing technologies, such as whole community shotgun sequencing have the potential to capture a detailed picture of highly complex bacterial communities in any given environment, we still lack major reference genomes for the oral microbiome associated with PD and other diseases. In recent work, by using a combination of supervised machine learning and genome assembly, we identified a genome from a novel member of the Bacteroidetes phylum in periodontal samples. Here, by applying a comparative metagenomics read-classification approach, including 272 metagenomes from various human body sites, and our previously assembled draft genome of the uncultivated Candidatus Bacteroides periocalifornicus (CBP) bacterium, we show CBP's ubiquitous distribution in dental plaque, as well as its strong association with the well-known pathogenic "red complex" that resides in deep periodontal pockets.
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Affiliation(s)
- Pedro J Torres
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | - John Thompson
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | - Jeffrey S McLean
- Department of Periodontics, University of Washington School of Dentistry, Seattle, WA, 98195, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | - Anna Edlund
- J. Craig Venter Institute, Genomic Medicine Group, La Jolla, CA, 92037, USA.
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30
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Torres PJ, Siakowska M, Banaszewska B, Pawelczyk L, Duleba AJ, Kelley ST, Thackray VG. Gut Microbial Diversity in Women With Polycystic Ovary Syndrome Correlates With Hyperandrogenism. J Clin Endocrinol Metab 2018; 103:1502-1511. [PMID: 29370410 PMCID: PMC6276580 DOI: 10.1210/jc.2017-02153] [Citation(s) in RCA: 178] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/28/2017] [Indexed: 12/12/2022]
Abstract
CONTEXT A majority of women with polycystic ovary syndrome (PCOS) have metabolic abnormalities that result in an increased risk of developing type 2 diabetes and heart disease. Correlative studies have shown an association between changes in the gut microbiome and metabolic disorders. Two recent studies reported a decrease in α diversity of the gut microbiome in women with PCOS compared with healthy women. OBJECTIVE We investigated whether changes in the gut microbiome correlated with specific clinical parameters in women with PCOS compared with healthy women. We also investigated whether there were changes in the gut microbiome in women with polycystic ovarian morphology (PCOM) who lacked the other diagnostic criteria of PCOS. PARTICIPANTS Subjects were recruited at the Poznan University of Medical Sciences. Fecal microbial diversity profiles of healthy women (n = 48), women with PCOM (n = 42), and women diagnosed with PCOS using the Rotterdam criteria (n = 73) were analyzed using 16S ribosomal RNA gene sequencing. RESULTS Lower α diversity was observed in women with PCOS compared with healthy women. Women with PCOM had a change in α diversity that was intermediate between that of the other two groups. Regression analyses showed that hyperandrogenism, total testosterone, and hirsutism were negatively correlated with α diversity. Permutational multivariate analysis of variance in UniFrac distances showed that hyperandrogenism was also correlated with β diversity. A random forest identified bacteria that discriminated between healthy women and women with PCOS. CONCLUSION These results suggest that hyperandrogenism may play a critical role in altering the gut microbiome in women with PCOS.
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Affiliation(s)
- Pedro J Torres
- Department of Biology, San Diego State University, San Diego, California
| | - Martyna Siakowska
- Department of Gynecology, Obstetrics and Gynecological Oncology, Poznan
University of Medical Sciences, Poznan, Poland
| | - Beata Banaszewska
- Department of Gynecology, Obstetrics and Gynecological Oncology, Poznan
University of Medical Sciences, Poznan, Poland
| | - Leszek Pawelczyk
- Department of Gynecology, Obstetrics and Gynecological Oncology, Poznan
University of Medical Sciences, Poznan, Poland
| | - Antoni J Duleba
- Department of Reproductive Medicine, University of California, San Diego, La
Jolla, California
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, California
| | - Varykina G Thackray
- Department of Reproductive Medicine, University of California, San Diego, La
Jolla, California
- Correspondence and Reprint Requests: Varykina G. Thackray, PhD, Department of Reproductive Medicine, MC:0674, 9500
Gilman Drive, University of California, San Diego, La Jolla, California 92093. E-mail:
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Pinkowski NJ, Kosnicki KL, Penprase JC, Cintora P, Torres PJ, Harris GL, Brasser SM, Kelley ST. Effects of Moderate Voluntary Ethanol Consumption on the Rat and Human Gut Microbiome. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.534.21] [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: 11/11/2022]
Affiliation(s)
- Natalie J. Pinkowski
- BiologySan Diego State UniversitySan DiegoCA
- PsychologySan Diego State UniversitySan DiegoCA
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Delange N, Lindsay S, Lemus H, Finlayson TL, Kelley ST, Gottlieb RA. Periodontal disease and its connection to systemic biomarkers of cardiovascular disease in young American Indian/Alaskan natives. J Periodontol 2018; 89:219-227. [PMID: 29520828 PMCID: PMC6242269 DOI: 10.1002/jper.17-0319] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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: 05/19/2017] [Revised: 07/29/2017] [Accepted: 08/20/2017] [Indexed: 12/14/2022]
Abstract
BACKGROUND Periodontal disease has been shown to be associated with cardiovascular disease (CVD). No known studies evaluate the relationship between periodontal disease status and biomarkers of CVD risk in the American Indian/Alaskan Native (AI/AN) population despite their disproportionately high rates of poor oral health and cardiovascular disease-related outcomes. This study compared levels of interleukin (IL)-6 and C-reactive protein (CRP) across increasing severity of periodontal disease status among younger adults between the ages of 21 and 43 years. METHODS Plasma levels of IL-6 and CRP were measured in adult participants (ages 21 to 43 years) as part of a study of periodontal disease and CVD risk among an AI/AN population in southern California (n = 59). Periodontal evaluations were performed and disease status was classified into three categories based on highest probing depth (none/mild: < 3 mm; moderate: 4 to 5 mm; severe: ≥6 mm). Participants with known systemic disease or active infection were excluded. RESULTS Severe periodontitis was significantly associated with increased levels of IL-6 compared with those with none or mild periodontitis before controlling for other variables (P = 0.02), but lacked significance after controlling for sex, BMI, smoking status, and high-density lipoprotein (P = 0.09). Moderate periodontal disease was positively associated with IL-6 levels after controlling for potential confounders (P = 0.01). Periodontal status was not associated with CRP, before or after adjusting for covariates. CONCLUSIONS In this otherwise healthy AI/AN adult sample, moderate periodontal disease compared with none or mild periodontal disease was associated with increased levels of IL-6. High levels of CRP found in this population warrant further research.
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Affiliation(s)
- Nicole Delange
- San Diego State University, Graduate School of Public Health, Division of Epidemiology and Biostatistics, San Diego, CA
| | - Suzanne Lindsay
- San Diego State University, Graduate School of Public Health, Division of Epidemiology and Biostatistics, San Diego, CA
- Institute for Public Health, San Diego, CA
| | - Hector Lemus
- San Diego State University, Graduate School of Public Health, Division of Epidemiology and Biostatistics, San Diego, CA
| | - Tracy L Finlayson
- San Diego State University, Graduate School of Public Health, Division of Health Management and Policy, San Diego, CA
| | - Scott T Kelley
- San Diego State University, Department of Biology, San Diego, CA
| | - Roberta A Gottlieb
- Cedars-Sinai Heart Institute and Barbra Streisand Women's Heart Center, Los Angeles, CA
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Torres PJ, Kelley ST. Sampling, Extraction, and High-Throughput Sequencing Methods for Environmental Microbial and Viral Communities. Methods Mol Biol 2017; 1712:163-173. [PMID: 29224074 DOI: 10.1007/978-1-4939-7514-3_11] [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] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The emergence of high-throughput sequencing technologies has deepened our understanding of complex microbial communities and greatly facilitated the study of as-yet uncultured microbes and viruses. Studies of complex microbial communities require high-quality data to generate valid results. Here, we detail current methods of microbial and viral community sample acquisition, DNA extraction, sample preparation, and sequencing on Illumina high-throughput platforms. While using appropriate analytical tools is important, it must not overshadow the need for establishing a proper experimental design and obtaining sufficient numbers of samples for statistical purposes. Researchers must also take care to sample biologically relevant sites and control for potential confounding factors (e.g., contamination).
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Affiliation(s)
- Pedro J Torres
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, USA.
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Kelley ST, Farrell BD. IS SPECIALIZATION A DEAD END? THE PHYLOGENY OF HOST USE INDENDROCTONUSBARK BEETLES (SCOLYTIDAE). Evolution 2017; 52:1731-1743. [DOI: 10.1111/j.1558-5646.1998.tb02253.x] [Citation(s) in RCA: 156] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/1997] [Accepted: 07/14/1998] [Indexed: 12/01/2022]
Affiliation(s)
- Scott T. Kelley
- Department of Environmental, Population and Organismic Biology; University of Colorado; Boulder Colorado 80309-0334
| | - Brian D. Farrell
- Museum of Comparative Zoology; Harvard University; Cambridge Massachusetts 02138
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Gurfield N, Grewal S, Cua LS, Torres PJ, Kelley ST. Endosymbiont interference and microbial diversity of the Pacific coast tick, Dermacentor occidentalis, in San Diego County, California. PeerJ 2017; 5:e3202. [PMID: 28503372 PMCID: PMC5426561 DOI: 10.7717/peerj.3202] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 03/19/2017] [Indexed: 01/13/2023] Open
Abstract
The Pacific coast tick, Dermacentor occidentalis Marx, is found throughout California and can harbor agents that cause human diseases such as anaplasmosis, ehrlichiosis, tularemia, Rocky Mountain spotted fever and rickettsiosis 364D. Previous studies have demonstrated that nonpathogenic endosymbiotic bacteria can interfere with Rickettsia co-infections in other tick species. We hypothesized that within D. occidentalis ticks, interference may exist between different nonpathogenic endosymbiotic or nonendosymbiotic bacteria and Spotted Fever group Rickettsia (SFGR). Using PCR amplification and sequencing of the rompA gene and intergenic region we identified a cohort of SFGR-infected and non-infected D. occidentalis ticks collected from San Diego County. We then amplified a partial segment of the 16S rRNA gene and used next-generation sequencing to elucidate the microbiomes and levels of co-infection in the ticks. The SFGR R. philipii str. 364D and R. rhipicephali were detected in 2.3% and 8.2% of the ticks, respectively, via rompA sequencing. Interestingly, next generation sequencing revealed an inverse relationship between the number of Francisella-like endosymbiont (FLE) 16S rRNA sequences and Rickettsia 16S rRNA sequences within individual ticks that is consistent with partial interference between FLE and SFGR infecting ticks. After excluding the Rickettsia and FLE endosymbionts from the analysis, there was a small but significant difference in microbial community diversity and a pattern of geographic isolation by distance between collection locales. In addition, male ticks had a greater diversity of bacteria than female ticks and ticks that weren’t infected with SFGR had similar microbiomes to canine skin microbiomes. Although experimental studies are required for confirmation, our findings are consistent with the hypothesis that FLEs and, to a lesser extent, other bacteria, interfere with the ability of D. occidentalis to be infected with certain SFGR. The results also raise interesting possibilities about the effects of putative vertebrate hosts on the tick microbiome.
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Affiliation(s)
- Nikos Gurfield
- Department of Environmental Health-Vector Control Program, County of San Diego, San Diego, CA, United States of America
| | - Saran Grewal
- Department of Environmental Health-Vector Control Program, County of San Diego, San Diego, CA, United States of America
| | - Lynnie S Cua
- Department of Environmental Health-Vector Control Program, County of San Diego, San Diego, CA, United States of America
| | - Pedro J Torres
- Department of Biology, San Diego State University, San Diego, CA, United States of America
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, United States of America
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Fouquier J, Schwartz T, Kelley ST. Rapid assemblage of diverse environmental fungal communities on public restroom floors. Indoor Air 2016; 26:869-879. [PMID: 26717555 DOI: 10.1111/ina.12279] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 12/23/2015] [Indexed: 05/25/2023]
Abstract
An increasing proportion of humanity lives in urban environments where they spend most of their lives indoors. Recent molecular studies have shown that bacterial assemblages in built environments (BEs) are extremely diverse, but BE fungal diversity remains poorly understood. We applied culture-independent methods based on next-generation sequencing (NGS) of the fungal internal transcribed spacer to investigate the diversity and temporal dynamics of fungi in restrooms. Swab samples were collected weekly from three different surfaces in two public restrooms (male and female) in San Diego, CA, USA, over an 8-week period. DNA amplification and culturing methods both found that the floor samples had significantly higher fungal loads than other surfaces. NGS sequencing of floor fungal assemblages identified a total of 2550 unique phylotypes (~800 per sample), less than half of which were identifiable. Of the known fungi, the majority came from environmental sources and we found little evidence of known human skin fungi. Fungal assemblages reformed rapidly in a highly consistent manner, and the variance in the species diversity among samples was low. Overall, our study contributes to a better understanding of public restroom floor fungal communities.
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Affiliation(s)
- J Fouquier
- Graduate Program in Bioinformatics and Medical Informatics, San Diego State University, San Diego, CA, USA
| | - T Schwartz
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - S T Kelley
- Graduate Program in Bioinformatics and Medical Informatics, San Diego State University, San Diego, CA, USA
- Department of Biology, San Diego State University, San Diego, CA, USA
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Fouquier J, Rideout JR, Bolyen E, Chase J, Shiffer A, McDonald D, Knight R, Caporaso JG, Kelley ST. Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses. Microbiome 2016; 4:11. [PMID: 26905735 PMCID: PMC4765138 DOI: 10.1186/s40168-016-0153-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 02/05/2016] [Indexed: 05/11/2023]
Abstract
BACKGROUND Fungi play critical roles in many ecosystems, cause serious diseases in plants and animals, and pose significant threats to human health and structural integrity problems in built environments. While most fungal diversity remains unknown, the development of PCR primers for the internal transcribed spacer (ITS) combined with next-generation sequencing has substantially improved our ability to profile fungal microbial diversity. Although the high sequence variability in the ITS region facilitates more accurate species identification, it also makes multiple sequence alignment and phylogenetic analysis unreliable across evolutionarily distant fungi because the sequences are hard to align accurately. To address this issue, we created ghost-tree, a bioinformatics tool that integrates sequence data from two genetic markers into a single phylogenetic tree that can be used for diversity analyses. Our approach starts with a "foundation" phylogeny based on one genetic marker whose sequences can be aligned across organisms spanning divergent taxonomic groups (e.g., fungal families). Then, "extension" phylogenies are built for more closely related organisms (e.g., fungal species or strains) using a second more rapidly evolving genetic marker. These smaller phylogenies are then grafted onto the foundation tree by mapping taxonomic names such that each corresponding foundation-tree tip would branch into its new "extension tree" child. RESULTS We applied ghost-tree to graft fungal extension phylogenies derived from ITS sequences onto a foundation phylogeny derived from fungal 18S sequences. Our analysis of simulated and real fungal ITS data sets found that phylogenetic distances between fungal communities computed using ghost-tree phylogenies explained significantly more variance than non-phylogenetic distances. The phylogenetic metrics also improved our ability to distinguish small differences (effect sizes) between microbial communities, though results were similar to non-phylogenetic methods for larger effect sizes. CONCLUSIONS The Silva/UNITE-based ghost tree presented here can be easily integrated into existing fungal analysis pipelines to enhance the resolution of fungal community differences and improve understanding of these communities in built environments. The ghost-tree software package can also be used to develop phylogenetic trees for other marker gene sets that afford different taxonomic resolution, or for bridging genome trees with amplicon trees. AVAILABILITY ghost-tree is pip-installable. All source code, documentation, and test code are available under the BSD license at https://github.com/JTFouquier/ghost-tree .
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Affiliation(s)
- Jennifer Fouquier
- Graduate Program in Bioinformatics and Medical Informatics, San Diego State University, San Diego, CA, USA.
| | - Jai Ram Rideout
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA.
| | - Evan Bolyen
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA.
| | - John Chase
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA.
| | - Arron Shiffer
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA.
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
| | | | - Rob Knight
- Department of Pediatrics, and Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA.
| | - J Gregory Caporaso
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA.
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
| | - Scott T Kelley
- Graduate Program in Bioinformatics and Medical Informatics, San Diego State University, San Diego, CA, USA.
- Department of Biology, San Diego State University, San Diego, CA, USA.
- San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182-4614, USA.
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Kelley ST, Skarra DV, Rivera AJ, Thackray VG. The Gut Microbiome Is Altered in a Letrozole-Induced Mouse Model of Polycystic Ovary Syndrome. PLoS One 2016; 11:e0146509. [PMID: 26731268 PMCID: PMC4701222 DOI: 10.1371/journal.pone.0146509] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [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: 08/13/2015] [Accepted: 12/19/2015] [Indexed: 01/12/2023] Open
Abstract
Women with polycystic ovary syndrome (PCOS) have reproductive and metabolic abnormalities that result in an increased risk of infertility, diabetes and cardiovascular disease. The large intestine contains a complex community of microorganisms (the gut microbiome) that is dysregulated in humans with obesity and type 2 diabetes. Using a letrozole-induced PCOS mouse model, we demonstrated significant diet-independent changes in the gut microbial community, suggesting that gut microbiome dysbiosis may also occur in PCOS women. Letrozole treatment was associated with a time-dependent shift in the gut microbiome and a substantial reduction in overall species and phylogenetic richness. Letrozole treatment also correlated with significant changes in the abundance of specific Bacteroidetes and Firmicutes previously implicated in other mouse models of metabolic disease in a time-dependent manner. Our results suggest that the hyperandrogenemia observed in PCOS may significantly alter the gut microbiome independently of diet.
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Affiliation(s)
- Scott T. Kelley
- Department of Biology, San Diego State University, San Diego, CA, United States of America
| | - Danalea V. Skarra
- Department of Reproductive Medicine, University of California San Diego, La Jolla, CA, United States of America
| | - Alissa J. Rivera
- Department of Reproductive Medicine, University of California San Diego, La Jolla, CA, United States of America
| | - Varykina G. Thackray
- Department of Reproductive Medicine, University of California San Diego, La Jolla, CA, United States of America
- Center for Reproductive Science and Medicine, University of California San Diego, La Jolla, CA, United States of America
- * E-mail:
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Torres PJ, Fletcher EM, Gibbons SM, Bouvet M, Doran KS, Kelley ST. Characterization of the salivary microbiome in patients with pancreatic cancer. PeerJ 2015; 3:e1373. [PMID: 26587342 PMCID: PMC4647550 DOI: 10.7717/peerj.1373] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 10/13/2015] [Indexed: 12/15/2022] Open
Abstract
Clinical manifestations of pancreatic cancer often do not occur until the cancer has undergone metastasis, resulting in a very low survival rate. In this study, we investigated whether salivary bacterial profiles might provide useful biomarkers for early detection of pancreatic cancer. Using high-throughput sequencing of bacterial small subunit ribosomal RNA (16S rRNA) gene, we characterized the salivary microbiota of patients with pancreatic cancer and compared them to healthy patients and patients with other diseases, including pancreatic disease, non-pancreatic digestive disease/cancer and non-digestive disease/cancer. A total of 146 patients were enrolled at the UCSD Moores Cancer Center where saliva and demographic data were collected from each patient. Of these, we analyzed the salivary microbiome of 108 patients: 8 had been diagnosed with pancreatic cancer, 78 with other diseases and 22 were classified as non-diseased (healthy) controls. Bacterial 16S rRNA sequences were amplified directly from salivary DNA extractions and subjected to high-throughput sequencing (HTS). Several bacterial genera differed in abundance in patients with pancreatic cancer. We found a significantly higher ratio of Leptotrichia to Porphyromonas in the saliva of patients with pancreatic cancer than in the saliva of healthy patients or those with other disease (Kruskal–Wallis Test; P < 0.001). Leptotrichia abundances were confirmed using real-time qPCR with Leptotrichia specific primers. Similar to previous studies, we found lower relative abundances of Neisseria and Aggregatibacter in the saliva of pancreatic cancer patients, though these results were not significant at the P < 0.05 level (K–W Test; P = 0.07 and P = 0.09 respectively). However, the relative abundances of other previously identified bacterial biomarkers, e.g., Streptococcus mitis and Granulicatella adiacens, were not significantly different in the saliva of pancreatic cancer patients. Overall, this study supports the hypothesis that bacteria abundance profiles in saliva are useful biomarkers for pancreatic cancer though much larger patient studies are needed to verify their predictive utility.
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Affiliation(s)
- Pedro J Torres
- Department of Biology, San Diego State University , San Diego, CA , United States
| | - Erin M Fletcher
- Department of Medical Sciences, Harvard University , Boston, MA , United States
| | - Sean M Gibbons
- Graduate Program in Biophysical Sciences, University of Chicago , Chicago, IL , United States ; Institute for Genomics and Systems Biology, Argonne National Laboratory , Lemont, IL , United States
| | - Michael Bouvet
- Department of Surgery, University of California, San Diego , La Jolla, CA , United States
| | - Kelly S Doran
- Department of Biology, San Diego State University , San Diego, CA , United States ; Department of Pediatrics, University of California San Diego School of Medicine , La Jolla, CA , United States
| | - Scott T Kelley
- Department of Biology, San Diego State University , San Diego, CA , United States
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Lipson DA, Raab TK, Parker M, Kelley ST, Brislawn CJ, Jansson J. Changes in microbial communities along redox gradients in polygonized Arctic wet tundra soils. Environ Microbiol Rep 2015; 7:649-657. [PMID: 26034016 DOI: 10.1111/1758-2229.12301] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 05/19/2015] [Indexed: 06/04/2023]
Abstract
This study investigated how microbial community structure and diversity varied with depth and topography in ice wedge polygons of wet tundra of the Arctic Coastal Plain in northern Alaska and what soil variables explain these patterns. We observed strong changes in community structure and diversity with depth, and more subtle changes between areas of high and low topography, with the largest differences apparent near the soil surface. These patterns are most strongly correlated with redox gradients (measured using the ratio of reduced Fe to total Fe in acid extracts as a proxy): conditions grew more reducing with depth and were most oxidized in shallow regions of polygon rims. Organic matter and pH also changed with depth and topography but were less effective predictors of the microbial community structure and relative abundance of specific taxa. Of all other measured variables, lactic acid concentration was the best, in combination with redox, for describing the microbial community. We conclude that redox conditions are the dominant force in shaping microbial communities in this landscape. Oxygen and other electron acceptors allowed for the greatest diversity of microbes: at depth the community was reduced to a simpler core of anaerobes, dominated by fermenters (Bacteroidetes and Firmicutes).
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Affiliation(s)
- David A Lipson
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Theodore K Raab
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Melanie Parker
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Janet Jansson
- Pacific Northwest National Laboratory, Richland, WA, USA
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Huttenhower C, Knight R, Brown CT, Caporaso JG, Clemente JC, Gevers D, Franzosa EA, Kelley ST, Knights D, Ley RE, Mahurkar A, Ravel J, White O. Advancing the microbiome research community. Cell 2015; 159:227-30. [PMID: 25303518 DOI: 10.1016/j.cell.2014.09.022] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The human microbiome has become a recognized factor in promoting and maintaining health. We outline opportunities in interdisciplinary research, analytical rigor, standardization, and policy development for this relatively new and rapidly developing field. Advances in these aspects of the research community may in turn advance our understanding of human microbiome biology.
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Affiliation(s)
- Curtis Huttenhower
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rob Knight
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA; BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA; HHMI, University of Colorado, Boulder, CO 80309, USA
| | - C Titus Brown
- Department of Microbiology and Molecular Genetics and Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - J Gregory Caporaso
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86001, USA; Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Jose C Clemente
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dirk Gevers
- BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Eric A Franzosa
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA; Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108, USA
| | - Ruth E Ley
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Anup Mahurkar
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | | | - Owen White
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Center for Health-Related Informatics and Bioimaging, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
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Wall K, Cornell J, Bizzoco RW, Kelley ST. Biodiversity hot spot on a hot spot: novel extremophile diversity in Hawaiian fumaroles. Microbiologyopen 2015; 4:267-281. [PMID: 25565172 PMCID: PMC4398508 DOI: 10.1002/mbo3.236] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 11/18/2014] [Accepted: 11/24/2014] [Indexed: 02/01/2023] Open
Abstract
Fumaroles (steam vents) are the most common, yet least understood, microbial habitat in terrestrial geothermal settings. Long believed too extreme for life, recent advances in sample collection and DNA extraction methods have found that fumarole deposits and subsurface waters harbor a considerable diversity of viable microbes. In this study, we applied culture-independent molecular methods to explore fumarole deposit microbial assemblages in 15 different fumaroles in four geographic locations on the Big Island of Hawai'i. Just over half of the vents yielded sufficient high-quality DNA for the construction of 16S ribosomal RNA gene sequence clone libraries. The bacterial clone libraries contained sequences belonging to 11 recognized bacterial divisions and seven other division-level phylogenetic groups. Archaeal sequences were less numerous, but similarly diverse. The taxonomic composition among fumarole deposits was highly heterogeneous. Phylogenetic analysis found cloned fumarole sequences were related to microbes identified from a broad array of globally distributed ecotypes, including hot springs, terrestrial soils, and industrial waste sites. Our results suggest that fumarole deposits function as an “extremophile collector” and may be a hot spot of novel extremophile biodiversity.
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Affiliation(s)
- Kate Wall
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California
| | - Jennifer Cornell
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California
| | - Richard W Bizzoco
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California
| | - Scott T Kelley
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California
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Schwarzberg K, Le R, Bharti B, Lindsay S, Casaburi G, Salvatore F, Saber MH, Alonaizan F, Slots J, Gottlieb RA, Caporaso JG, Kelley ST. The personal human oral microbiome obscures the effects of treatment on periodontal disease. PLoS One 2014; 9:e86708. [PMID: 24489772 PMCID: PMC3906071 DOI: 10.1371/journal.pone.0086708] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [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: 09/25/2013] [Accepted: 12/12/2013] [Indexed: 02/05/2023] Open
Abstract
Periodontitis is a progressive disease of the periodontium with a complex, polymicrobial etiology. Recent Next-Generation Sequencing (NGS) studies of the microbial diversity associated with periodontitis have revealed strong, community-level differences in bacterial assemblages associated with healthy or diseased periodontal sites. In this study, we used NGS approaches to characterize changes in periodontal pocket bacterial diversity after standard periodontal treatment. Despite consistent changes in the abundance of certain taxa in individuals whose condition improved with treatment, post-treatment samples retained the highest similarity to pre-treatment samples from the same individual. Deeper phylogenetic analysis of periodontal pathogen-containing genera Prevotella and Fusobacterium found both unexpected diversity and differential treatment response among species. Our results highlight how understanding interpersonal variability among microbiomes is necessary for determining how polymicrobial diseases respond to treatment and disturbance.
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Affiliation(s)
- Karen Schwarzberg
- Department of Biology, San Diego State University, San Diego, California, United States of America
| | - Rosalin Le
- Department of Biology, San Diego State University, San Diego, California, United States of America
| | - Balambal Bharti
- Graduate School of Public Health, San Diego State University, San Diego, California, United States of America
| | - Suzanne Lindsay
- Graduate School of Public Health, San Diego State University, San Diego, California, United States of America
| | - Giorgio Casaburi
- CEINGE-Biotecnologie Avanzate, Napoli, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Napoli, Italy
| | - Francesco Salvatore
- CEINGE-Biotecnologie Avanzate, Napoli, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Napoli, Italy
| | - Mohamed H. Saber
- Section of Endodontics, Herman Ostrow School of Dentistry of USC, Los Angeles, California, United States of America
| | - Faisal Alonaizan
- Section of Endodontics, Herman Ostrow School of Dentistry of USC, Los Angeles, California, United States of America
| | - Jørgen Slots
- Professor of Dentistry and Microbiology, Herman Ostrow School of Dentistry of USC, Los Angeles, California, United States of America
| | - Roberta A. Gottlieb
- BioScience Center, San Diego State University, San Diego, California, United States of America
| | - J. Gregory Caporaso
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
- Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, Illinois, United States of America
| | - Scott T. Kelley
- Department of Biology, San Diego State University, San Diego, California, United States of America
- * E-mail:
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Sherman MP, Minnerly J, Curtiss W, Rangwala S, Kelley ST. Research on neonatal microbiomes: what neonatologists need to know. Neonatology 2014; 105:14-24. [PMID: 24193200 PMCID: PMC3903415 DOI: 10.1159/000354944] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 08/06/2013] [Indexed: 01/08/2023]
Abstract
The aim of this article is to educate neonatal caregivers about metagenomics. This scientific field uses novel and ever changing molecular methods to identify how infants become colonized with microbes after birth. Publications using metagenomics appear infrequently in the neonatal literature because clinicians are unaccustomed to the analytical techniques, data interpretation, and illustration of the results. This review covers those areas. After a brief introduction of neonatal citations forthcoming from metagenomic studies, the following topics are covered: (1) the history of metagenomics, (2) a description of current and emerging instruments used to define microbial populations in human organs, and (3) how extensive databases generated by genome analyzers are examined and presented to readers. Clinicians may feel like they are learning a new language; however, they will appreciate this task is essential to understanding and practicing neonatal medicine in the future.
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Affiliation(s)
- Michael P Sherman
- Department of Child Health, University of Missouri, Columbia, Mo., USA
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Shogan BD, Smith DP, Packman AI, Kelley ST, Landon EM, Bhangar S, Vora GJ, Jones RM, Keegan K, Stephens B, Ramos T, Kirkup BC, Levin H, Rosenthal M, Foxman B, Chang EB, Siegel J, Cobey S, An G, Alverdy JC, Olsiewski PJ, Martin MO, Marrs R, Hernandez M, Christley S, Morowitz M, Weber S, Gilbert J. The Hospital Microbiome Project: Meeting report for the 2nd Hospital Microbiome Project, Chicago, USA, January 15(th), 2013. Stand Genomic Sci 2013; 8:571-9. [PMID: 24501640 PMCID: PMC3910697 DOI: 10.4056/sigs.4187859] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Benjamin D Shogan
- Department of Surgery, University of Chicago Medicine, Chicago, IL, 60637, USA
| | | | - Aaron I Packman
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | - Emily M Landon
- Department of Medicine, Section of Infectious Diseases & Global Health, University of Chicago Medicine, Chicago, IL 60637, USA
| | - Seema Bhangar
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA 94720, USA
| | - Gary J Vora
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington DC, 20375, USA
| | - Rachael M Jones
- Division of Environmental and Occupational Health Sciences, School of Public Health, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Kevin Keegan
- Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Brent Stephens
- Department of Civil, Architectural and Environmental Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Tiffanie Ramos
- Department of Civil, Architectural and Environmental Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Benjamin C Kirkup
- Department of Wound Infections, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA ; Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Hal Levin
- Building Ecology Research Group, Santa Cruz, California, 95060, USA
| | - Mariana Rosenthal
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI 48109
| | - Betsy Foxman
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI 48109
| | - Eugene B Chang
- Department of Medicine, University of Chicago Medicine, Chicago, IL, 60637, USA
| | - Jeffrey Siegel
- Department of Civil Engineering, University of Toronto, Ontario, Canada
| | - Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA
| | - Gary An
- Department of Surgery, University of Chicago Medicine, Chicago, IL, 60637, USA
| | - John C Alverdy
- Department of Surgery, University of Chicago Medicine, Chicago, IL, 60637, USA
| | | | - Mark O Martin
- Department of Biology, University of Puget Sound, Tacoma, Washington, 98416, USA
| | - Rachel Marrs
- Department of Medicine, Section of Infectious Diseases & Global Health, University of Chicago Medicine, Chicago, IL 60637, USA
| | - Mark Hernandez
- Department of Civil, Environmental and Architectural Engineering, University of Colorado, Boulder, CO, 80309, USA
| | - Scott Christley
- Department of Surgery, University of Chicago Medicine, Chicago, IL, 60637, USA
| | - Michael Morowitz
- University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh of UPMC, 4401 Penn Avenue, Pittsburgh, PA 15224
| | - Stephen Weber
- Department of Medicine, Section of Infectious Diseases & Global Health, University of Chicago Medicine, Chicago, IL 60637, USA
| | - Jack Gilbert
- Argonne National Laboratory, Argonne, IL, 60439, USA ; Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA
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Smith D, Alverdy J, An G, Coleman M, Garcia-Houchins S, Green J, Keegan K, Kelley ST, Kirkup BC, Kociolek L, Levin H, Landon E, Olsiewski P, Knight R, Siegel J, Weber S, Gilbert J. The Hospital Microbiome Project: Meeting Report for the 1st Hospital Microbiome Project Workshop on sampling design and building science measurements, Chicago, USA, June 7th-8th 2012. Stand Genomic Sci 2013; 8:112-7. [PMID: 23961316 PMCID: PMC3739179 DOI: 10.4056/sigs.3717348] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This report details the outcome of the 1st Hospital Microbiome Project workshop held on June 7th-8th, 2012 at the University of Chicago, USA. The workshop was arranged to determine the most appropriate sampling strategy and approach to building science measurement to characterize the development of a microbial community within a new hospital pavilion being built at the University of Chicago Medical Center. The workshop made several recommendations and led to the development of a full proposal to the Alfred P. Sloan Foundation as well as to the creation of the Hospital Microbiome Consortium.
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Affiliation(s)
- Daniel Smith
- Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
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Abstract
The majority of people in the developed world spend more than 90% of their lives indoors. Here, we examine our understanding of the bacteria that co-inhabit our artificial world and how they might influence human health.
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Saber MH, Schwarzberg K, Alonaizan FA, Kelley ST, Sedghizadeh PP, Furlan M, Levy TA, Simon JH, Slots J. Bacterial Flora of Dental Periradicular Lesions Analyzed by the 454-Pyrosequencing Technology. J Endod 2012; 38:1484-8. [DOI: 10.1016/j.joen.2012.06.037] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 06/24/2012] [Accepted: 06/30/2012] [Indexed: 12/25/2022]
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Abubucker S, Segata N, Goll J, Schubert AM, Izard J, Cantarel BL, Rodriguez-Mueller B, Zucker J, Thiagarajan M, Henrissat B, White O, Kelley ST, Methé B, Schloss PD, Gevers D, Mitreva M, Huttenhower C. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol 2012; 8:e1002358. [PMID: 22719234 PMCID: PMC3374609 DOI: 10.1371/journal.pcbi.1002358] [Citation(s) in RCA: 714] [Impact Index Per Article: 59.5] [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: 08/06/2011] [Accepted: 12/07/2011] [Indexed: 12/18/2022] Open
Abstract
Microbial communities carry out the majority of the biochemical activity on the planet, and they play integral roles in processes including metabolism and immune homeostasis in the human microbiome. Shotgun sequencing of such communities' metagenomes provides information complementary to organismal abundances from taxonomic markers, but the resulting data typically comprise short reads from hundreds of different organisms and are at best challenging to assemble comparably to single-organism genomes. Here, we describe an alternative approach to infer the functional and metabolic potential of a microbial community metagenome. We determined the gene families and pathways present or absent within a community, as well as their relative abundances, directly from short sequence reads. We validated this methodology using a collection of synthetic metagenomes, recovering the presence and abundance both of large pathways and of small functional modules with high accuracy. We subsequently applied this method, HUMAnN, to the microbial communities of 649 metagenomes drawn from seven primary body sites on 102 individuals as part of the Human Microbiome Project (HMP). This provided a means to compare functional diversity and organismal ecology in the human microbiome, and we determined a core of 24 ubiquitously present modules. Core pathways were often implemented by different enzyme families within different body sites, and 168 functional modules and 196 metabolic pathways varied in metagenomic abundance specifically to one or more niches within the microbiome. These included glycosaminoglycan degradation in the gut, as well as phosphate and amino acid transport linked to host phenotype (vaginal pH) in the posterior fornix. An implementation of our methodology is available at http://huttenhower.sph.harvard.edu/humann. This provides a means to accurately and efficiently characterize microbial metabolic pathways and functional modules directly from high-throughput sequencing reads, enabling the determination of community roles in the HMP cohort and in future metagenomic studies.
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Affiliation(s)
- Sahar Abubucker
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
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Reeve JD, Anderson FE, Kelley ST. Ancestral state reconstruction for Dendroctonus bark beetles: evolution of a tree killer. Environ Entomol 2012; 41:723-730. [PMID: 22732632 DOI: 10.1603/en11281] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
While most bark beetles attack only dead or weakened trees, many species in the genus Dendroctonus have the ability to kill healthy conifers through mass attack of the host tree, and can exhibit devastating outbreaks. Other species in this group are able to successfully colonize trees in small numbers without killing the host. We reconstruct the evolution of these ecological and life history traits, first classifying the extant Dendroctonus species by attack type (mass or few), outbreaks (yes or no), host genus (Pinus and others), location of attacks on the tree (bole, base, etc.), whether the host is killed (yes or no), and if the larvae are gregarious or have individual galleries (yes or no). We then estimated a molecular phylogeny for a data set of cytochrome oxidase I sequences sampled from nearly all Dendroctonus species, and used this phylogeny to reconstruct the ancestral state at various nodes on the tree, employing maximum parsimony, maximum likelihood, and Bayesian methods. Our reconstructions suggest that extant Dendroctonus species likely evolved from an ancestor that killed host pines through mass attack of the bole, had individual larvae, and exhibited outbreaks. The ability to colonize a host tree in small numbers (as well as gregarious larvae and attacks at the tree base) apparently evolved later, possibly as two separate events in different clades. It is likely that tree mortality and outbreaks have been continuing features of the interaction between conifers and Dendroctonus bark beetles.
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Affiliation(s)
- John D Reeve
- Department of Zoology, Southern Illinois University, Carbondale, IL 62901, USA.
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