1
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Brossard Stoos KA, Ren J, Shields-Cutler RR, Sams KL, Caldwell S, Ho MB, Rivara G, Whistler CA, Jones SH, Wiedmann M, DeMent J, Getchell RG, Marquis H. Coastal water bacteriophages infect various sets of Vibrio parahaemolyticus sequence types. Front Microbiol 2022; 13:1041942. [PMID: 36601403 PMCID: PMC9807174 DOI: 10.3389/fmicb.2022.1041942] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 10/31/2022] [Indexed: 12/23/2022] Open
Abstract
Introduction Gastrointestinal illnesses associated with the consumption of shellfish contaminated with Vibrio parahaemolyticus have a negative impact on the shellfish industry due to recalls and loss of consumer confidence in products. This bacterial pathogen is very diverse and specific sequence types (STs), ST631 and ST36, have emerged as prevalent causes of Vibrio foodborne disease outbreaks in the US, though other STs have been implicated in sporadic cases. We investigated whether bacteriophages could be used as a proxy to monitor for the presence of distinct V. parahaemolyticus STs in coastal waters. Methods For this purpose, bacteriophages infecting V. parahaemolyticus were isolated from water samples collected on the Northeast Atlantic coast. The isolated phages were tested against a collection of 29 V. parahaemolyticus isolates representing 18 STs, including six clonal complexes (CC). Four distinct phages were identified based on their ability to infect different sets of V. parahaemolyticus isolates. Results and Discussion Overall, the 29 bacterial isolates segregated into one of eight patterns of susceptibility, ranging from resistance to all four phages to susceptibility to any number of phages. STs represented by more than one bacterial isolate segregated within the same pattern of susceptibility except for one V. parahaemolyticus ST. Other patterns of susceptibility included exclusively clinical isolates represented by distinct STs. Overall, this study suggests that phages populating coastal waters could be exploited to monitor for the presence of V. parahaemolyticus STs known to cause foodborne outbreaks.
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Affiliation(s)
- Kari A. Brossard Stoos
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, United States,Department of Health Promotion and Physical Education, Ithaca College, Ithaca, NY, United States,*Correspondence: Kari A. Brossard Stoos,
| | - Jennifer Ren
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, United States
| | | | - Kelly L. Sams
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, United States
| | - Shannon Caldwell
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, United States
| | - Marvin B. Ho
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, United States
| | - Gregg Rivara
- Cornell Cooperative Extension of Suffolk County, Southold, NY, United States
| | - Cheryl A. Whistler
- Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, NH, United States,Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Stephen H. Jones
- Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, NH, United States,Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, United States
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Jamie DeMent
- Florida Department of Health, Tallahassee, FL, United States
| | - Rodman G. Getchell
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, United States
| | - Hélène Marquis
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, United States
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2
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Khuat LT, Le CT, Pai CCS, Shields-Cutler RR, Holtan SG, Rashidi A, Parker SL, Knights D, Luna JI, Dunai C, Wang Z, Sturgill IR, Stoffel KM, Merleev AA, More SK, Maverakis E, Raybould HE, Chen M, Canter RJ, Monjazeb AM, Dave M, Ferrara JLM, Levine JE, Longo DL, Abedi M, Blazar BR, Murphy WJ. Obesity induces gut microbiota alterations and augments acute graft-versus-host disease after allogeneic stem cell transplantation. Sci Transl Med 2021; 12:12/571/eaay7713. [PMID: 33239390 DOI: 10.1126/scitranslmed.aay7713] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 01/22/2020] [Accepted: 06/02/2020] [Indexed: 12/22/2022]
Abstract
The efficacy of allogeneic hematopoietic stem cell transplantation (allo-HSCT) is limited by acute and chronic graft-versus-host disease (GVHD). The impact of obesity on allo-HSCT outcomes is poorly understood. Here, we report that obesity had a negative and selective impact on acute gut GVHD after allo-HSCT in mice with diet-induced obesity (DIO). These animals exhibited increased gut permeability, endotoxin translocation across the gut, and radiation-induced gastrointestinal damage after allo-HSCT. After allo-HSCT, both male and female DIO mouse recipients showed increased proinflammatory cytokine production and expression of the GVHD marker ST2 (IL-33R) and MHC class II molecules; they also exhibited decreased survival associated with acute severe gut GVHD. This rapid-onset, obesity-associated gut GVHD depended on donor CD4+ T cells and occurred even with a minor MHC mismatch between donor and recipient animals. Retrospective analysis of clinical cohorts receiving allo-HSCT transplants from unrelated donors revealed that recipients with a high body mass index (BMI, >30) had reduced survival and higher serum ST2 concentrations compared with nonobese transplant recipients. Assessment of both DIO mice and allo-HSCT recipients with a high BMI revealed reduced gut microbiota diversity and decreased Clostridiaceae abundance. Prophylactic antibiotic treatment protected DIO mouse recipients from endotoxin translocation across the gut and increased inflammatory cytokine production, as well as gut pathology and mortality, but did not protect against later development of chronic skin GVHD. These results suggest that obesity-induced alterations of the gut microbiota may affect GVHD after allo-HSCT in DIO mice, which could be ameliorated by prophylactic antibiotic treatment.
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Affiliation(s)
- Lam T Khuat
- Department of Dermatology, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Catherine T Le
- Department of Dermatology, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Chien-Chun Steven Pai
- Department of Dermatology, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | | | - Shernan G Holtan
- Blood and Marrow Transplant Program, University of Minnesota, Minneapolis, MN 55455, USA
| | - Armin Rashidi
- Blood and Marrow Transplant Program, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sarah L Parker
- Department of Internal Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | - Dan Knights
- Department of Computer Science and Engineering, Biotechnology Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jesus I Luna
- Department of Dermatology, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Cordelia Dunai
- Department of Dermatology, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Ziming Wang
- Department of Dermatology, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Ian R Sturgill
- Department of Dermatology, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Kevin M Stoffel
- Department of Dermatology, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Alexander A Merleev
- Department of Dermatology, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Shyam K More
- Division of Gastroenterology, Department of Internal Medicine, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Emanual Maverakis
- Department of Dermatology, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Helen E Raybould
- Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Mingyi Chen
- Department of Pathology and Laboratory Medicine, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Robert J Canter
- Division of Surgical Oncology, Department of Surgery, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Arta M Monjazeb
- Department of Radiation Oncology, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Maneesh Dave
- Division of Gastroenterology, Department of Internal Medicine, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - James L M Ferrara
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - John E Levine
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dan L Longo
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Mehrdad Abedi
- Department of Internal Medicine, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Bruce R Blazar
- Masonic Cancer Center and Division of Blood and Marrow Transplantation, Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - William J Murphy
- Department of Dermatology, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA. .,Department of Internal Medicine, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
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3
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Hillmann B, Al-Ghalith GA, Shields-Cutler RR, Zhu Q, Knight R, Knights D. SHOGUN: a modular, accurate and scalable framework for microbiome quantification. Bioinformatics 2020; 36:4088-4090. [PMID: 32365167 DOI: 10.1093/bioinformatics/btaa277] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/24/2020] [Indexed: 11/12/2022] Open
Abstract
SUMMARY The software pipeline SHOGUN profiles known taxonomic and gene abundances of short-read shotgun metagenomics sequencing data. The pipeline is scalable, modular and flexible. Data analysis and transformation steps can be run individually or together in an automated workflow. Users can easily create new reference databases and can select one of three DNA alignment tools, ranging from ultra-fast low-RAM k-mer-based database search to fully exhaustive gapped DNA alignment, to best fit their analysis needs and computational resources. The pipeline includes an implementation of a published method for taxonomy assignment disambiguation with empirical Bayesian redistribution. The software is installable via the conda resource management framework, has plugins for the QIIME2 and QIITA packages and produces both taxonomy and gene abundance profile tables with a single command, thus promoting convenient and reproducible metagenomics research. AVAILABILITY AND IMPLEMENTATION https://github.com/knights-lab/SHOGUN.
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Affiliation(s)
- Benjamin Hillmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, 55455 Minnesota, USA
| | - Gabriel A Al-Ghalith
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, 55455 Minnesota, USA
| | | | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, San Diego, 92161 5 California, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, San Diego, 92161 5 California, USA.,Department of Computer of Science and Engineering, University of California San Diego, San Diego, 92093 California, USA.,Center for Microbiome Innovation, University of California San Diego, San Diego, 92093 California, USA
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, 55455 Minnesota, USA.,Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, 55455 Minnesota, USA.,Biotechnology Institute, University of Minnesota, Minneapolis, 55455 Minnesota, USA
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4
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Turner G, Smith M, Hoeschen AL, Wilson JA, Kennedy J, Abramson M, Cao Q, El Jurdi N, MacMillan ML, Weisdorf DJ, Blazar BR, Khoruts A, Shields-Cutler RR, Knights D, Holtan SG, Rashidi A. Shotgun sequencing of the faecal microbiome to predict response to steroids in patients with lower gastrointestinal acute graft-versus-host disease: An exploratory analysis. Br J Haematol 2020; 192:e69-e73. [PMID: 33222185 DOI: 10.1111/bjh.17238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/22/2020] [Accepted: 10/25/2020] [Indexed: 11/30/2022]
Affiliation(s)
- Gavin Turner
- College of Biological Sciences, BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Madeline Smith
- College of Biological Sciences, BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Andrea L Hoeschen
- Clinical Trials Office, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | | | - Jessica Kennedy
- College of Biological Sciences, BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Max Abramson
- Department of Biology, Macalester College, St. Paul, MN, USA
| | - Qing Cao
- Biostatistics and Informatics, Clinical and Translational Science Institute, University of Minnesota, Minneapolis, MN, USA
| | - Najla El Jurdi
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Margaret L MacMillan
- Blood and Marrow Transplant Program, Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Daniel J Weisdorf
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Bruce R Blazar
- Blood and Marrow Transplant Program, Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Alexander Khoruts
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | | | - Dan Knights
- College of Biological Sciences, BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Shernan G Holtan
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Armin Rashidi
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
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5
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Johnson AJ, Vangay P, Al-Ghalith GA, Hillmann BM, Ward TL, Shields-Cutler RR, Kim AD, Shmagel AK, Syed AN, Walter J, Menon R, Koecher K, Knights D. Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans. Cell Host Microbe 2019; 25:789-802.e5. [PMID: 31194939 DOI: 10.1016/j.chom.2019.05.005] [Citation(s) in RCA: 357] [Impact Index Per Article: 71.4] [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: 10/06/2018] [Revised: 01/31/2019] [Accepted: 05/09/2019] [Indexed: 02/06/2023]
Abstract
Diet is a key determinant of human gut microbiome variation. However, the fine-scale relationships between daily food choices and human gut microbiome composition remain unexplored. Here, we used multivariate methods to integrate 24-h food records and fecal shotgun metagenomes from 34 healthy human subjects collected daily over 17 days. Microbiome composition depended on multiple days of dietary history and was more strongly associated with food choices than with conventional nutrient profiles, and daily microbial responses to diet were highly personalized. Data from two subjects consuming only meal replacement beverages suggest that a monotonous diet does not induce microbiome stability in humans, and instead, overall dietary diversity associates with microbiome stability. Our work provides key methodological insights for future diet-microbiome studies and suggests that food-based interventions seeking to modulate the gut microbiota may need to be tailored to the individual microbiome. Trial Registration: ClinicalTrials.gov: NCT03610477.
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Affiliation(s)
- Abigail J Johnson
- BioTechnology Institute, University of Minnesota, Saint Paul, MN 55108, USA
| | - Pajau Vangay
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gabriel A Al-Ghalith
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Benjamin M Hillmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | | | | | - Austin D Kim
- Department of Mathematics, Statistics, and Computer Science, Macalester College, St. Paul, MN 55105, USA
| | - Anna Konstantinovna Shmagel
- Division of Rheumatic and Autoimmune Diseases, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | - Arzang N Syed
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
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- Microbial Engineering Program, Biotechnology Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jens Walter
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Ravi Menon
- Bell Institute of Health & Nutrition, General Mills Inc, Minneapolis, MN 55427, USA
| | - Katie Koecher
- Bell Institute of Health & Nutrition, General Mills Inc, Minneapolis, MN 55427, USA
| | - Dan Knights
- BioTechnology Institute, University of Minnesota, Saint Paul, MN 55108, USA; Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA.
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6
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Rashidi A, Ebadi M, Shields-Cutler RR, Kruziki K, Manias DA, Barnes AMT, DeFor TE, Ferrieri P, Young JAH, Knights D, Blazar BR, Weisdorf DJ, Dunny GM. Early E. casseliflavus gut colonization and outcomes of allogeneic hematopoietic cell transplantation. PLoS One 2019; 14:e0220850. [PMID: 31393924 PMCID: PMC6687141 DOI: 10.1371/journal.pone.0220850] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 03/15/2019] [Accepted: 07/24/2019] [Indexed: 12/25/2022] Open
Abstract
Gut dysbiosis has been associated with worse allogeneic hematopoietic cell transplantation (allo-HCT) outcomes. We reported an association between intrinsically vancomycin-resistant enterococci (iVRE: E. gallinarum and E. casseliflavus) gut colonization and lower post-transplant mortality. In this study, using an expanded cohort, we evaluated whether our previously observed association is species-specific. We included allo-HCT recipients with ≥1 positive rectal swab or stool culture for iVRE between days -14 and +14 of transplant. To investigate whether iVRE modulate the gut microbiota, we performed agar diffusion assays. To investigate whether iVRE differ in their ability to activate the aryl hydrocarbon receptor, we analyzed iVRE genomes for enzymes in the shikimate and tryptophan pathways. Sixty six (23 E. casseliflavus and 43 E. gallinarum) of the 908 allograft recipients (2011-2017) met our inclusion criteria. Overall survival was significantly higher in patients with E. casseliflavus (91% vs. 62% at 3 years, P = 0.04). In multivariable analysis, E. casseliflavus gut colonization was significantly associated with reduced all-cause mortality (hazard ratio 0.20, 95% confidence interval 0.04-0.91, P = 0.04). While agar assays were largely unremarkable, genome mining predicted that E. casseliflavus encodes a larger number of enzymes in the tryptophan metabolism pathway. In conclusion, E. casseliflavus gut colonization is associated with reduced post-HCT morality. Further research is needed to understand the mechanisms for this association.
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Affiliation(s)
- Armin Rashidi
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, United States of America
| | - Maryam Ebadi
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States of America
| | - Robin R. Shields-Cutler
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, MN, United States of America
- Department of Biology, Macalester College, Saint Paul, MN, United States of America
| | - Kathryn Kruziki
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, United States of America
| | - Dawn A. Manias
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, United States of America
| | - Aaron M. T. Barnes
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, United States of America
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, United States of America
| | - Todd E. DeFor
- Biostatistics Core, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
| | - Patricia Ferrieri
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, United States of America
| | - Jo-Anne H. Young
- Division of Infectious Disease and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, United States of America
| | - Dan Knights
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, MN, United States of America
| | - Bruce R. Blazar
- Division of Blood and Marrow Transplantation, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States of America
| | - Daniel J. Weisdorf
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, United States of America
| | - Gary M. Dunny
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, United States of America
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7
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Vangay P, Johnson AJ, Ward TL, Al-Ghalith GA, Shields-Cutler RR, Hillmann BM, Lucas SK, Beura LK, Thompson EA, Till LM, Batres R, Paw B, Pergament SL, Saenyakul P, Xiong M, Kim AD, Kim G, Masopust D, Martens EC, Angkurawaranon C, McGready R, Kashyap PC, Culhane-Pera KA, Knights D. US Immigration Westernizes the Human Gut Microbiome. Cell 2019; 175:962-972.e10. [PMID: 30388453 DOI: 10.1016/j.cell.2018.10.029] [Citation(s) in RCA: 404] [Impact Index Per Article: 80.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 09/10/2018] [Accepted: 10/12/2018] [Indexed: 12/26/2022]
Abstract
Many US immigrant populations develop metabolic diseases post immigration, but the causes are not well understood. Although the microbiome plays a role in metabolic disease, there have been no studies measuring the effects of US immigration on the gut microbiome. We collected stool, dietary recalls, and anthropometrics from 514 Hmong and Karen individuals living in Thailand and the United States, including first- and second-generation immigrants and 19 Karen individuals sampled before and after immigration, as well as from 36 US-born European American individuals. Using 16S and deep shotgun metagenomic DNA sequencing, we found that migration from a non-Western country to the United States is associated with immediate loss of gut microbiome diversity and function in which US-associated strains and functions displace native strains and functions. These effects increase with duration of US residence and are compounded by obesity and across generations.
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Affiliation(s)
- Pajau Vangay
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN 55455, USA
| | - Abigail J Johnson
- Biotechnology Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Tonya L Ward
- Biotechnology Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gabriel A Al-Ghalith
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Benjamin M Hillmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sarah K Lucas
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Lalit K Beura
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Emily A Thompson
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Lisa M Till
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN 55902, USA
| | - Rodolfo Batres
- Somali, Latino, and Hmong Partnership for Health and Wellness, West Side Community Health Services, St. Paul, MN 55106, USA
| | - Bwei Paw
- Somali, Latino, and Hmong Partnership for Health and Wellness, West Side Community Health Services, St. Paul, MN 55106, USA
| | - Shannon L Pergament
- Somali, Latino, and Hmong Partnership for Health and Wellness, West Side Community Health Services, St. Paul, MN 55106, USA
| | - Pimpanitta Saenyakul
- Somali, Latino, and Hmong Partnership for Health and Wellness, West Side Community Health Services, St. Paul, MN 55106, USA
| | - Mary Xiong
- Somali, Latino, and Hmong Partnership for Health and Wellness, West Side Community Health Services, St. Paul, MN 55106, USA
| | - Austin D Kim
- Department of Mathematics, Statistics, and Computer Science, Macalester College, St. Paul, MN 55105, USA
| | - Grant Kim
- College of Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - David Masopust
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Eric C Martens
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chaisiri Angkurawaranon
- Department of Family Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Rose McGready
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot 63110, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN 55902, USA
| | - Kathleen A Culhane-Pera
- Somali, Latino, and Hmong Partnership for Health and Wellness, West Side Community Health Services, St. Paul, MN 55106, USA
| | - Dan Knights
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN 55455, USA; Biotechnology Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA.
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8
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Saffouri GB, Shields-Cutler RR, Chen J, Yang Y, Lekatz HR, Hale VL, Cho JM, Battaglioli EJ, Bhattarai Y, Thompson KJ, Kalari KK, Behera G, Berry JC, Peters SA, Patel R, Schuetz AN, Faith JJ, Camilleri M, Sonnenburg JL, Farrugia G, Swann JR, Grover M, Knights D, Kashyap PC. Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders. Nat Commun 2019; 10:2012. [PMID: 31043597 PMCID: PMC6494866 DOI: 10.1038/s41467-019-09964-7] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [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: 10/04/2018] [Accepted: 04/03/2019] [Indexed: 12/18/2022] Open
Abstract
Small intestinal bacterial overgrowth (SIBO) has been implicated in symptoms associated with functional gastrointestinal disorders (FGIDs), though mechanisms remain poorly defined and treatment involves non-specific antibiotics. Here we show that SIBO based on duodenal aspirate culture reflects an overgrowth of anaerobes, does not correspond with patient symptoms, and may be a result of dietary preferences. Small intestinal microbial composition, on the other hand, is significantly altered in symptomatic patients and does not correspond with aspirate culture results. In a pilot interventional study we found that switching from a high fiber diet to a low fiber, high simple sugar diet triggered FGID-related symptoms and decreased small intestinal microbial diversity while increasing small intestinal permeability. Our findings demonstrate that characterizing small intestinal microbiomes in patients with gastrointestinal symptoms may allow a more targeted antibacterial or a diet-based approach to treatment.
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Affiliation(s)
- George B Saffouri
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55902, USA
| | - Robin R Shields-Cutler
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, 55455, USA
- Department of Biology, Macalester College, Saint Paul, MN, 55105, USA
| | - Jun Chen
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55902, USA
| | - Yi Yang
- Computational and Systems Medicine Section of the Department of Surgery and Cancer, Imperial College, (London), UK
| | - Heather R Lekatz
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55902, USA
| | - Vanessa L Hale
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Janice M Cho
- Division of Internal Medicine, Mayo Clinic, Rochester, MN, 55902, USA
| | - Eric J Battaglioli
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55902, USA
| | - Yogesh Bhattarai
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55902, USA
| | - Kevin J Thompson
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55902, USA
| | - Krishna K Kalari
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55902, USA
| | - Gaurav Behera
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55902, USA
| | - Jonathan C Berry
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55902, USA
| | - Stephanie A Peters
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55902, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55902, USA
| | - Audrey N Schuetz
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55902, USA
| | - Jeremiah J Faith
- Department of Genetics and Genomic Sciences, Medicine, and Clinical Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Michael Camilleri
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55902, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, 55902, USA
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, 94305, USA
| | - Gianrico Farrugia
- Division of Gastroenterology, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Jonathan R Swann
- Computational and Systems Medicine Section of the Department of Surgery and Cancer, Imperial College, (London), UK
| | - Madhusudan Grover
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55902, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, 55902, USA
| | - Dan Knights
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, 55455, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55902, USA.
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, 55902, USA.
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9
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Clayton JB, Shields-Cutler RR, Hoops SL, Al-Ghalith GA, Sha JCM, Johnson TJ, Knights D. Bacterial community structure and function distinguish gut sites in captive red-shanked doucs (Pygathrix nemaeus). Am J Primatol 2019; 81:e22977. [PMID: 30997937 DOI: 10.1002/ajp.22977] [Citation(s) in RCA: 7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 03/22/2019] [Accepted: 04/01/2019] [Indexed: 12/12/2022]
Abstract
The mammalian order primates contains wide species diversity. Members of the subfamily Colobinae are unique amongst extant primates in that their gastrointestinal systems more closely resemble those of ruminants than other members of the primate order. In the growing literature surrounding nonhuman primate microbiomes, analysis of microbial communities has been limited to the hindgut, since few studies have captured data on other gut sites, including the foregut of colobine primates. In this study, we used the red-shanked douc (Pygathrix nemaeus) as a model for colobine primates to study the relationship between gastrointestinal bacterial community structure and gut site within and between subjects. We analyzed fecal and pregastric stomach content samples, representative of the hindgut and foregut respectively, using 16S recombinant DNA (rDNA) sequencing and identified microbiota using closed-reference operational taxonomic unit (OTU) picking against the GreenGenes database. Our results show divergent bacterial communities clearly distinguish the foregut and hindgut microbiomes. We found higher bacterial biodiversity and a higher Firmicutes:Bacteroides ratio in the hindgut as opposed to the foregut. These gut sites showed strong associations with bacterial function. Specifically, energy metabolism was upregulated in the hindgut, whereas detoxification was increased in the foregut. Our results suggest a red-shanked douc's foregut microbiome is no more concordant with its own hindgut than it is with any other red-shanked douc's hindgut microbiome, thus reinforcing the notion that the bacterial communities of the foregut and hindgut are distinctly unique. OPEN PRACTICES: This article has been awarded Open Materials and Open Data badges. All materials and data are publicly accessible via the IRIS Repository at https://www.iris-database.org/iris/app/home/detail?id=york:934328. Learn more about the Open Practices badges from the Center for Open Science: https://osf.io/tvyxz/wiki.
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Affiliation(s)
- Jonathan B Clayton
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota.,GreenViet Biodiversity Conservation Center, Danang, Vietnam.,Primate Microbiome Project, University of Minnesota, Minneapolis, Minnesota.,Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota
| | - Robin R Shields-Cutler
- Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota.,Department of Biology, Macalester College, St. Paul, Minnesota
| | - Susan L Hoops
- Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota
| | - Gabriel A Al-Ghalith
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota
| | - John C M Sha
- School of Sociology and Anthropology, Sun Yat-Sen University, Guangzhou, China
| | - Timothy J Johnson
- Primate Microbiome Project, University of Minnesota, Minneapolis, Minnesota.,Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Mennisota.,Mid-Central Research and Outreach Center, University of Minnesota, Willmar, Minnesota
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota.,Primate Microbiome Project, University of Minnesota, Minneapolis, Minnesota.,Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota
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10
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Hillmann B, Al-Ghalith GA, Shields-Cutler RR, Zhu Q, Gohl DM, Beckman KB, Knight R, Knights D. Evaluating the Information Content of Shallow Shotgun Metagenomics. mSystems 2018; 3:e00069-18. [PMID: 30443602 PMCID: PMC6234283 DOI: 10.1128/msystems.00069-18] [Citation(s) in RCA: 228] [Impact Index Per Article: 38.0] [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: 05/09/2018] [Accepted: 09/10/2018] [Indexed: 01/26/2023] Open
Abstract
Although microbial communities are associated with human, environmental, plant, and animal health, there exists no cost-effective method for precisely characterizing species and genes in such communities. While deep whole-metagenome shotgun (WMS) sequencing provides high taxonomic and functional resolution, it is often prohibitively expensive for large-scale studies. The prevailing alternative, 16S rRNA gene amplicon (16S) sequencing, often does not resolve taxonomy past the genus level and provides only moderately accurate predictions of the functional profile; thus, there is currently no widely accepted approach to affordable, high-resolution, taxonomic, and functional microbiome analysis. To address this technology gap, we evaluated the information content of shallow shotgun sequencing with as low as 0.5 million sequences per sample as an alternative to 16S sequencing for large human microbiome studies. We describe a library preparation protocol enabling shallow shotgun sequencing at approximately the same per-sample cost as 16S sequencing. We analyzed multiple real and simulated biological data sets, including two novel human stool samples with ultradeep sequencing of 2.5 billion sequences per sample, and found that shallow shotgun sequencing recovers more-accurate species-level taxonomic and functional profiles of the human microbiome than 16S sequencing. We discuss the inherent limitations of shallow shotgun sequencing and note that 16S sequencing remains a valuable and important method for taxonomic profiling of novel environments. Although deep WMS sequencing remains the gold standard for high-resolution microbiome analysis, we recommend that researchers consider shallow shotgun sequencing as a useful alternative to 16S sequencing for large-scale human microbiome research studies where WMS sequencing may be cost-prohibitive. IMPORTANCE A common refrain in recent microbiome-related academic meetings is that the field needs to move away from broad taxonomic surveys using 16S sequencing and toward more powerful longitudinal studies using shotgun sequencing. However, performing deep shotgun sequencing in large longitudinal studies remains prohibitively expensive for all but the most well-funded research labs and consortia, which leads many researchers to choose 16S sequencing for large studies, followed by deep shotgun sequencing on a subset of targeted samples. Here, we show that shallow- or moderate-depth shotgun sequencing may be used by researchers to obtain species-level taxonomic and functional data at approximately the same cost as amplicon sequencing. While shallow shotgun sequencing is not intended to replace deep shotgun sequencing for strain-level characterization, we recommend that microbiome scientists consider using shallow shotgun sequencing instead of 16S sequencing for large-scale human microbiome studies.
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Affiliation(s)
- Benjamin Hillmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Gabriel A. Al-Ghalith
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota, USA
| | | | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, San Diego, California, USA
| | - Daryl M. Gohl
- University of Minnesota Genomics Center, Minneapolis, Minnesota, USA
| | | | - Rob Knight
- Department of Pediatrics, University of California San Diego, San Diego, California, USA
- Department of Computer of Science and Engineering, University of California San Diego, San Diego, California, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, California, USA
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, USA
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota, USA
- Biotechnology Institute, University of Minnesota, Minneapolis, Minnesota, USA
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11
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Zhang XS, Li J, Krautkramer KA, Badri M, Battaglia T, Borbet TC, Koh H, Ng S, Sibley RA, Li Y, Pathmasiri W, Jindal S, Shields-Cutler RR, Hillmann B, Al-Ghalith GA, Ruiz VE, Livanos A, van 't Wout AB, Nagalingam N, Rogers AB, Sumner SJ, Knights D, Denu JM, Li H, Ruggles KV, Bonneau R, Williamson RA, Rauch M, Blaser MJ. Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity. eLife 2018; 7:37816. [PMID: 30039798 PMCID: PMC6085123 DOI: 10.7554/elife.37816] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/12/2018] [Indexed: 12/18/2022] Open
Abstract
The early-life intestinal microbiota plays a key role in shaping host immune system development. We found that a single early-life antibiotic course (1PAT) accelerated type 1 diabetes (T1D) development in male NOD mice. The single course had deep and persistent effects on the intestinal microbiome, leading to altered cecal, hepatic, and serum metabolites. The exposure elicited sex-specific effects on chromatin states in the ileum and liver and perturbed ileal gene expression, altering normal maturational patterns. The global signature changes included specific genes controlling both innate and adaptive immunity. Microbiome analysis revealed four taxa each that potentially protect against or accelerate T1D onset, that were linked in a network model to specific differences in ileal gene expression. This simplified animal model reveals multiple potential pathways to understand pathogenesis by which early-life gut microbiome perturbations alter a global suite of intestinal responses, contributing to the accelerated and enhanced T1D development.
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Affiliation(s)
- Xue-Song Zhang
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Jackie Li
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Kimberly A Krautkramer
- Department of Biomolecular Chemistry, Wisconsin Institute for Discovery, University of Wisconsin School of Medicine and Public Health, Madison, United States
| | - Michelle Badri
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States.,Center for Data Science, New York University, New York, United States
| | - Thomas Battaglia
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Timothy C Borbet
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Hyunwook Koh
- Department of Population Health, New York University Langone Medical Center, New York, United States
| | - Sandy Ng
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Rachel A Sibley
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Yuanyuan Li
- Nutrition Research Institute, University of North Carolina at Chapel Hill School of Public Health, Kannapolis, United States
| | - Wimal Pathmasiri
- Nutrition Research Institute, University of North Carolina at Chapel Hill School of Public Health, Kannapolis, United States
| | - Shawn Jindal
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Robin R Shields-Cutler
- Computer Science and Engineering, BioTechnology Institute, University of Minnesota, St. Paul, United States
| | - Ben Hillmann
- Computer Science and Engineering, BioTechnology Institute, University of Minnesota, St. Paul, United States
| | - Gabriel A Al-Ghalith
- Computer Science and Engineering, BioTechnology Institute, University of Minnesota, St. Paul, United States
| | - Victoria E Ruiz
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Alexandra Livanos
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Angélique B van 't Wout
- Janssen Prevention Center London, Janssen Pharmaceutical Companies of Johnson and Johnson, London, United Kingdom
| | - Nabeetha Nagalingam
- Janssen Prevention Center London, Janssen Pharmaceutical Companies of Johnson and Johnson, London, United Kingdom
| | - Arlin B Rogers
- Department of Biomedical Sciences, Cummings School of Veterinary Medicine, Tufts University, North Grafton, United States
| | - Susan Jenkins Sumner
- Nutrition Research Institute, University of North Carolina at Chapel Hill School of Public Health, Kannapolis, United States
| | - Dan Knights
- Computer Science and Engineering, BioTechnology Institute, University of Minnesota, St. Paul, United States
| | - John M Denu
- Department of Biomolecular Chemistry, Wisconsin Institute for Discovery, University of Wisconsin School of Medicine and Public Health, Madison, United States
| | - Huilin Li
- Department of Population Health, New York University Langone Medical Center, New York, United States
| | - Kelly V Ruggles
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Richard Bonneau
- Center for Data Science, New York University, New York, United States
| | - R Anthony Williamson
- Janssen Prevention Center London, Janssen Pharmaceutical Companies of Johnson and Johnson, London, United Kingdom
| | - Marcus Rauch
- Janssen Prevention Center London, Janssen Pharmaceutical Companies of Johnson and Johnson, London, United Kingdom
| | - Martin J Blaser
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States.,Department of Microbiology, New York Uniersity Langone Medical Center, New York, United States
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12
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Shields-Cutler RR, Al-Ghalith GA, Yassour M, Knights D. SplinectomeR Enables Group Comparisons in Longitudinal Microbiome Studies. Front Microbiol 2018; 9:785. [PMID: 29740416 PMCID: PMC5924793 DOI: 10.3389/fmicb.2018.00785] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [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: 11/15/2017] [Accepted: 04/06/2018] [Indexed: 12/17/2022] Open
Abstract
Longitudinal, prospective studies often rely on multi-omics approaches, wherein various specimens are analyzed for genomic, metabolomic, and/or transcriptomic profiles. In practice, longitudinal studies in humans and other animals routinely suffer from subject dropout, irregular sampling, and biological variation that may not be normally distributed. As a result, testing hypotheses about observations over time can be statistically challenging without performing transformations and dramatic simplifications to the dataset, causing a loss of longitudinal power in the process. Here, we introduce splinectomeR, an R package that uses smoothing splines to summarize data for straightforward hypothesis testing in longitudinal studies. The package is open-source, and can be used interactively within R or run from the command line as a standalone tool. We present a novel in-depth analysis of a published large-scale microbiome study as an example of its utility in straightforward testing of key hypotheses. We expect that splinectomeR will be a useful tool for hypothesis testing in longitudinal microbiome studies.
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Affiliation(s)
- Robin R Shields-Cutler
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, United States
| | - Gabe A Al-Ghalith
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN, United States
| | - Moran Yassour
- Broad Institute of Massachusetts Institute of Technology, Harvard University, Cambridge, MA, United States.,Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Dan Knights
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, United States.,Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, United States
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13
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Rashidi A, Ebadi M, Shields-Cutler RR, DeFor TE, Al-Ghalith GA, Ferrieri P, Young JAH, Dunny GM, Knights D, Weisdorf DJ. Pretransplant Gut Colonization with Intrinsically Vancomycin-Resistant Enterococci (E. gallinarum and E. casseliflavus) and Outcomes of Allogeneic Hematopoietic Cell Transplantation. Biol Blood Marrow Transplant 2018; 24:1260-1263. [PMID: 29407252 DOI: 10.1016/j.bbmt.2018.01.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 11/22/2017] [Accepted: 01/19/2018] [Indexed: 10/18/2022]
Abstract
Pretransplant gut colonization with intrinsically vancomycin-resistant enterococci (iVRE) (Enterococcus gallinarum and Enterococcus casseliflavus) is uncommon and with unknown clinical impact. In a matched-pairs analysis of patients with versus without iVRE colonization (n = 18 in each group), we demonstrated significantly higher 2-year overall survival (86% [95% confidence interval, 52% to 96%] versus 35% [95% confidence interval, 8% to 65]; P <.01) and lower nonrelapse mortality (P <.01) among colonized patients. Putative metabolomes differentiated iVRE from E. faecalis/faecium and may contribute to a healthier gut microbiome in iVRE-colonized patients.
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Affiliation(s)
- Armin Rashidi
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota.
| | - Maryam Ebadi
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota
| | - Robin R Shields-Cutler
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minnesota
| | - Todd E DeFor
- Biostatistics Core, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Gabriel A Al-Ghalith
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minnesota
| | - Patricia Ferrieri
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
| | - Jo-Anne H Young
- Division of Infectious Disease and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Gary M Dunny
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota
| | - Dan Knights
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minnesota
| | - Daniel J Weisdorf
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
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14
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Shields-Cutler RR, Crowley JR, Miller CD, Stapleton AE, Cui W, Henderson JP. Human Metabolome-derived Cofactors Are Required for the Antibacterial Activity of Siderocalin in Urine. J Biol Chem 2016; 291:25901-25910. [PMID: 27780864 PMCID: PMC5207064 DOI: 10.1074/jbc.m116.759183] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [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: 09/16/2016] [Revised: 10/18/2016] [Indexed: 01/07/2023] Open
Abstract
In human urinary tract infections, host cells release the antimicrobial protein siderocalin (SCN; also known as lipocalin-2, neutrophil gelatinase-associated lipocalin, or 24p3) into the urinary tract. By binding to ferric catechol complexes, SCN can sequester iron, a growth-limiting nutrient for most bacterial pathogens. Recent evidence links the antibacterial activity of SCN in human urine to iron sequestration and metabolomic variation between individuals. To determine whether these metabolomic associations correspond to functional Fe(III)-binding SCN ligands, we devised a biophysical protein binding screen to identify SCN ligands through direct analysis of human urine. This screen revealed a series of physiologic unconjugated urinary catechols that were able to function as SCN ligands of which pyrogallol in particular was positively associated with high urinary SCN activity. In a purified, defined culture system, these physiologic SCN ligands were sufficient to activate SCN antibacterial activity against Escherichia coli. In the presence of multiple SCN ligands, native mass spectrometry demonstrated that SCN may preferentially combine different ligands to coordinate iron, suggesting that availability of specific ligand combinations affects in vivo SCN antibacterial activity. These results support a mechanistic link between the human urinary metabolome and innate immune function.
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Affiliation(s)
- Robin R Shields-Cutler
- From the Division of Infectious Diseases, Department of Medicine.,the Center for Women's Infectious Diseases Research, and
| | - Jan R Crowley
- the Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Connelly D Miller
- From the Division of Infectious Diseases, Department of Medicine.,the Center for Women's Infectious Diseases Research, and
| | - Ann E Stapleton
- the Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington 98195, and
| | - Weidong Cui
- the Department of Chemistry, Washington University, St. Louis, Missouri 63130
| | - Jeffrey P Henderson
- From the Division of Infectious Diseases, Department of Medicine, .,the Center for Women's Infectious Diseases Research, and
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15
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Shields-Cutler RR, Crowley JR, Hung CS, Stapleton AE, Aldrich CC, Marschall J, Henderson JP. Human Urinary Composition Controls Antibacterial Activity of Siderocalin. J Biol Chem 2015; 290:15949-60. [PMID: 25861985 DOI: 10.1074/jbc.m115.645812] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [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: 02/13/2015] [Indexed: 11/06/2022] Open
Abstract
During Escherichia coli urinary tract infections, cells in the human urinary tract release the antimicrobial protein siderocalin (SCN; also known as lipocalin 2, neutrophil gelatinase-associated lipocalin/NGAL, or 24p3). SCN can interfere with E. coli iron acquisition by sequestering ferric iron complexes with enterobactin, the conserved E. coli siderophore. Here, we find that human urinary constituents can reverse this relationship, instead making enterobactin critical for overcoming SCN-mediated growth restriction. Urinary control of SCN activity exhibits wide ranging individual differences. We used these differences to identify elevated urinary pH and aryl metabolites as key biochemical host factors controlling urinary SCN activity. These aryl metabolites are well known products of intestinal microbial metabolism. Together, these results identify an innate antibacterial immune interaction that is critically dependent upon individualistic chemical features of human urine.
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Affiliation(s)
- Robin R Shields-Cutler
- From the Division of Infectious Diseases, Department of Medicine, Center for Women's Infectious Disease Research, and
| | - Jan R Crowley
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Chia S Hung
- From the Division of Infectious Diseases, Department of Medicine, Center for Women's Infectious Disease Research, and
| | - Ann E Stapleton
- the Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington 98195
| | - Courtney C Aldrich
- the Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, and
| | - Jonas Marschall
- From the Division of Infectious Diseases, Department of Medicine, the Department of Infectious Diseases, Bern University Hospital and University of Bern, 3010 Bern, Switzerland
| | - Jeffrey P Henderson
- From the Division of Infectious Diseases, Department of Medicine, Center for Women's Infectious Disease Research, and
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