1
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Wright JR, Ly TT, Cromwell KB, Brislawn CJ, Chen See JR, Anderson SLC, Pellegrino J, Peachey L, Walls CY, Lloyd CM, Jones OY, Lawrence MW, Bess JA, Wall AC, Shope AJ, Lamendella R. Assessment of a novel continuous cleaning device using metatranscriptomics in diverse hospital environments. Front Med Technol 2023; 5:1015507. [PMID: 36935775 PMCID: PMC10020724 DOI: 10.3389/fmedt.2023.1015507] [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: 10/27/2022] [Accepted: 02/17/2023] [Indexed: 03/06/2023] Open
Abstract
Introduction Despite routine implementation of cleaning and disinfection practices in clinical healthcare settings, high-touch environmental surfaces and contaminated equipment often serve as reservoirs for the transmission of pathogens associated with healthcare-associated infections (HAIs). Methods The current study involved the analysis of high-touch surface swabs using a metatranscriptomic sequencing workflow (CSI-Dx™) to assess the efficacy of cleanSURFACES® technology in decreasing microbial burden by limiting re-contamination. This is a non-human single center study conducted in the Emergency Department (ED) and on an inpatient Oncology Ward of Walter Reed National Military Medical Center that have followed hygienic practices during the COVID-19 pandemic environment. Results Although there was no difference in observed microbial richness (two-tailed Wilcoxon test with Holm correction, P > 0.05), beta diversity findings identified shifts in microbial community structure between surfaces from baseline and post-intervention timepoints (Day 1, Day 7, Day 14, and Day 28). Biomarker and regression analyses identified significant reductions in annotated transcripts for various clinically relevant microorganisms' post-intervention, coagulase-negative staphylococci and Malassezia restricta, at ED and Oncology ward, respectively. Additionally, post-intervention samples predominantly consisted of Proteobacteria and to a lesser extent skin commensals and endogenous environmental microorganisms in both departments. Discussion Findings support the value of cleanSURFACES®, when coupled with routine disinfection practices, to effectively impact on the composition of active microbial communities found on high-touch surfaces in two different patient care areas of the hospital (one outpatient and one inpatient) with unique demands and patient-centered practices.
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Affiliation(s)
- Justin R Wright
- Contamination Source Identification, LLC., Huntingdon, PA, United States
| | - Truc T Ly
- Contamination Source Identification, LLC., Huntingdon, PA, United States
| | - Karen B Cromwell
- Walter Reed National Military Medical Center, Bethesda, MD, United States
| | - Colin J Brislawn
- Contamination Source Identification, LLC., Huntingdon, PA, United States
| | - Jeremy R Chen See
- Contamination Source Identification, LLC., Huntingdon, PA, United States
| | | | - Jordan Pellegrino
- Contamination Source Identification, LLC., Huntingdon, PA, United States
| | - Logan Peachey
- Contamination Source Identification, LLC., Huntingdon, PA, United States
| | - Christine Y Walls
- Contamination Source Identification, LLC., Huntingdon, PA, United States
| | - Charise M Lloyd
- Walter Reed National Military Medical Center, Bethesda, MD, United States
| | - Olcay Y Jones
- Walter Reed National Military Medical Center, Bethesda, MD, United States
| | - Matthew W Lawrence
- Walter Reed National Military Medical Center, Bethesda, MD, United States
| | | | | | - Alexander J Shope
- Contamination Source Identification, LLC., Huntingdon, PA, United States
- AIONX, Hershey, PA, United States
| | - Regina Lamendella
- Contamination Source Identification, LLC., Huntingdon, PA, United States
- Correspondence: Regina Lamendella
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2
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Wright JR, Ly TT, Brislawn CJ, Chen See JR, Anderson SLC, Pellegrino JT, Peachey L, Walls CY, Bess JA, Bailey AL, Braun KE, Shope AJ, Lamendella R. cleanSURFACES® intervention reduces microbial activity on surfaces in a senior care facility. Front Cell Infect Microbiol 2022; 12:1040047. [PMID: 36439229 PMCID: PMC9682068 DOI: 10.3389/fcimb.2022.1040047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022] Open
Abstract
As one of the top public health challenges outlined by the Centers for Disease Control (CDC), estimates report that hospital acquired infections (HAIs) claim the lives of 99,000 Americans and cost healthcare providers over $28 billion each year. In addition to underlying conditions related to age, elderly patients in long-term care facilities are at an elevated risk of acquiring HAIs. A large percentage of HAIs is attributable to contaminated surfaces and medical devices. To that end, this study utilized a metatranscriptomic sequencing workflow (CSI-Dx™) to profile active microbial communities from surfaces in the HJ Heinz Community Living Center, a long-term care facility in the Veterans Affairs Pittsburgh Health Care System. Swabs were collected from high-touch surfaces (Keyboard, Ledge, Workstation on Wheels, Worksurfaces) before (Baseline) and after cleanSURFACES® were installed at 4 timepoints (Day 1, Day 7, Day 14, and Day 30). Microbial richness was significantly reduced after cleanSURFACES® intervention (Wilcoxon test with Holm correction, p=0.000179). Beta diversity results revealed distinct clustering between Baseline and Post-intervention samples (Adonis, p<0.001). Reduction in bacterial (Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus hominis) and fungal (Malassezia restricta, Candida albicans, Candida glabrata, and Candida orthopsilosis) expression of opportunistic pathogens was observed. Additionally, a subset of taxa (Corynebacterium, Cutibacterium acnes, and Ralstonia pickettii) was present in specific Post-intervention timepoints and surface types. This study revealed decreased microbial activity, highlighting the potential for the combinatorial application of cleanSURFACES® and regular decontamination practices to reduce the prevalence of microbes causing HAIs.
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3
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Chen See J, Ly T, Shope A, Bess J, Wall A, Komanduri S, Goldman J, Anderson S, McLimans CJ, Brislawn CJ, Tokarev V, Wright JR, Lamendella R. A Metatranscriptomics Survey of Microbial Diversity on Surfaces Post-Intervention of cleanSURFACES® Technology in an Intensive Care Unit. Front Cell Infect Microbiol 2021; 11:705593. [PMID: 34354962 PMCID: PMC8330600 DOI: 10.3389/fcimb.2021.705593] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 05/07/2021] [Accepted: 07/05/2021] [Indexed: 12/16/2022] Open
Abstract
Hospital-acquired infections (HAIs) pose a serious threat to patients, and hospitals spend billions of dollars each year to reduce and treat these infections. Many HAIs are due to contamination from workers’ hands and contact with high-touch surfaces. Therefore, we set out to test the efficacy of a new preventative technology, AIONX® Antimicrobial Technologies, Inc’s cleanSURFACES®, which is designed to complement daily chemical cleaning events by continuously preventing re-colonization of surfaces. To that end, we swabbed surfaces before (Baseline) and after (Post) application of the cleanSURFACES® at various time points (Day 1, Day 7, Day 14, and Day 28). To circumvent limitations associated with culture-based and 16S rRNA gene amplicon sequencing methodologies, these surface swabs were processed using metatranscriptomic (RNA) analysis to allow for comprehensive taxonomic resolution and the detection of active microorganisms. Overall, there was a significant (P < 0.05) global reduction of microbial diversity in Post-intervention samples. Additionally, Post sample microbial communities clustered together much more closely than Baseline samples based on pairwise distances calculated with the weighted Jaccard distance metric, suggesting a defined shift after product application. This shift was characterized by a general depletion of several microbes among Post samples, with multiple phyla also being reduced over the duration of the study. Notably, specific clinically relevant microbes, including Staphylococcus aureus, Clostridioides difficile and Streptococcus spp., were depleted Post-intervention. Taken together, these findings suggest that chemical cleaning events used jointly with cleanSURFACES® have the potential to reduce colonization of surfaces by a wide variety of microbes, including many clinically relevant pathogens.
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Affiliation(s)
- Jeremy Chen See
- Contamination Source Identification, Huntingdon, PA, United States
| | - Truc Ly
- Contamination Source Identification, Huntingdon, PA, United States
| | - Alexander Shope
- Contamination Source Identification, Huntingdon, PA, United States.,AIONX, Hershey, PA, United States
| | | | - Art Wall
- Nextflex, San Jose, CA, United States
| | | | | | - Samantha Anderson
- Contamination Source Identification, Huntingdon, PA, United States.,Department of Biology, Juniata College, Huntingdon, PA, United States
| | - Christopher J McLimans
- Contamination Source Identification, Huntingdon, PA, United States.,Department of Biology, Juniata College, Huntingdon, PA, United States
| | - Colin J Brislawn
- Contamination Source Identification, Huntingdon, PA, United States
| | - Vasily Tokarev
- Contamination Source Identification, Huntingdon, PA, United States.,Department of Biology, Juniata College, Huntingdon, PA, United States
| | - Justin R Wright
- Contamination Source Identification, Huntingdon, PA, United States
| | - Regina Lamendella
- Contamination Source Identification, Huntingdon, PA, United States.,Department of Biology, Juniata College, Huntingdon, PA, United States
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Kim YM, Snijders AM, Brislawn CJ, Stratton KG, Zink EM, Fansler SJ, Metz TO, Mao JH, Jansson JK. Corrigendum: Light-Stress Influences the Composition of the Murine Gut Microbiome, Memory Function, and Plasma Metabolome. Front Mol Biosci 2021; 7:619718. [PMID: 33732731 PMCID: PMC7959737 DOI: 10.3389/fmolb.2020.619718] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/23/2020] [Indexed: 11/14/2022] Open
Affiliation(s)
- Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Colin J Brislawn
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Kelly G Stratton
- Computing and Analytics Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Erika M Zink
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Sarah J Fansler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
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Mao JH, Kim YM, Zhou YX, Hu D, Zhong C, Chang H, Brislawn CJ, Fansler S, Langley S, Wang Y, Peisl BYL, Celniker SE, Threadgill DW, Wilmes P, Orr G, Metz TO, Jansson JK, Snijders AM. Correction to: Genetic and metabolic links between the murine microbiome and memory. Microbiome 2020; 8:73. [PMID: 32466793 PMCID: PMC7257159 DOI: 10.1186/s40168-020-00870-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
An amendment to this paper has been published and can be accessed via the original article.
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Affiliation(s)
- Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Young-Mo Kim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yan-Xia Zhou
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Marine College, Shandong University, Weihai, 264209, China
| | - Dehong Hu
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Chenhan Zhong
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Colin J Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Sarah Fansler
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Sasha Langley
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yunshan Wang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, 250033, Shandong, China
| | - B Y Loulou Peisl
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, Avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Susan E Celniker
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - David W Threadgill
- Department of Veterinary Pathobiology, A&M University, College Station, Texas, USA
- Department of Molecular and Cellular Medicine Texas, A&M University, College Station, Texas, USA
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, Avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Galya Orr
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Thomas O Metz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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6
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Mao JH, Kim YM, Zhou YX, Hu D, Zhong C, Chang H, Brislawn CJ, Fansler S, Langley S, Wang Y, Peisl BYL, Celniker SE, Threadgill DW, Wilmes P, Orr G, Metz TO, Jansson JK, Snijders AM. Genetic and metabolic links between the murine microbiome and memory. Microbiome 2020; 8:53. [PMID: 32299497 PMCID: PMC7164142 DOI: 10.1186/s40168-020-00817-w] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [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: 02/03/2020] [Accepted: 03/02/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Recent evidence has linked the gut microbiome to host behavior via the gut-brain axis [1-3]; however, the underlying mechanisms remain unexplored. Here, we determined the links between host genetics, the gut microbiome and memory using the genetically defined Collaborative Cross (CC) mouse cohort, complemented with microbiome and metabolomic analyses in conventional and germ-free (GF) mice. RESULTS A genome-wide association analysis (GWAS) identified 715 of 76,080 single-nucleotide polymorphisms (SNPs) that were significantly associated with short-term memory using the passive avoidance model. The identified SNPs were enriched in genes known to be involved in learning and memory functions. By 16S rRNA gene sequencing of the gut microbial community in the same CC cohort, we identified specific microorganisms that were significantly correlated with longer latencies in our retention test, including a positive correlation with Lactobacillus. Inoculation of GF mice with individual species of Lactobacillus (L. reuteri F275, L. plantarum BDGP2 or L. brevis BDGP6) resulted in significantly improved memory compared to uninoculated or E. coli DH10B inoculated controls. Untargeted metabolomics analysis revealed significantly higher levels of several metabolites, including lactate, in the stools of Lactobacillus-colonized mice, when compared to GF control mice. Moreover, we demonstrate that dietary lactate treatment alone boosted memory in conventional mice. Mechanistically, we show that both inoculation with Lactobacillus or lactate treatment significantly increased the levels of the neurotransmitter, gamma-aminobutyric acid (GABA), in the hippocampus of the mice. CONCLUSION Together, this study provides new evidence for a link between Lactobacillus and memory and our results open possible new avenues for treating memory impairment disorders using specific gut microbial inoculants and/or metabolites. Video Abstract.
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Affiliation(s)
- Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Young-Mo Kim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Yan-Xia Zhou
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Marine College, Shandong University, Weihai, 264209 China
| | - Dehong Hu
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Chenhan Zhong
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Colin J. Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Sarah Fansler
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Sasha Langley
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Yunshan Wang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, 250033 Shandong China
| | - B. Y. Loulou Peisl
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, Avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | - Susan E. Celniker
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - David W. Threadgill
- Department of Veterinary Pathobiology, A&M University, College Station, Texas, USA
- Department of Molecular and Cellular Medicine Texas, A&M University, College Station, Texas, USA
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, Avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | - Galya Orr
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Thomas O. Metz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Janet K. Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Antoine M. Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
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7
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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: 8012] [Impact Index Per Article: 1602.4] [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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8
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Kim YM, Snijders AM, Brislawn CJ, Stratton KG, Zink EM, Fansler SJ, Metz TO, Mao JH, Jansson JK. Light-Stress Influences the Composition of the Murine Gut Microbiome, Memory Function, and Plasma Metabolome. Front Mol Biosci 2019; 6:108. [PMID: 31681796 PMCID: PMC6813214 DOI: 10.3389/fmolb.2019.00108] [Citation(s) in RCA: 18] [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: 05/28/2019] [Accepted: 09/30/2019] [Indexed: 12/12/2022] Open
Abstract
The gut microbiome plays an important role in the mammalian host and when in proper balance helps protect health and prevent disease. Host environmental stress and its influence on the gut microbiome, health, and disease is an emerging area of research. Exposures to unnatural light cycles are becoming increasingly common due to travel and shift work. However, much remains unknown about how these changes influence the microbiome and host health. This information is needed to understand and predict the relationship between the microbiome and host response to altered sleep cycles. In the present study, we exposed three cohorts of mice to different light cycle regimens for 12 consecutive weeks; including continuous light, continuous dark, and a standard light dark regimen consisting of 12 h light followed by 12 h of dark. After exposure, motor and memory behavior, and the composition of the fecal microbiome and plasma metabolome were measured. Memory potential was significantly reduced in mice exposed to continuous light, whereas rotarod performance was minimally affected. The overall composition of the microbiome was relatively constant over time. However, Bacteroidales Rikenellaceae was relatively more abundant in mice exposed to continuous dark, while Bacteroidales S24-7 was relatively more abundant in mice exposed to continuous light. The plasma metabolome after the continuous dark exposure differed from the other exposure conditions. Several plasma metabolites, including glycolic acid, tryptophan, pyruvate, and several unidentified metabolites, were correlated to continuous dark and light exposure conditions. Networking analyses showed that serotonin was positively correlated with three microbial families (Rikenellaceae, Ruminococcaceae, and Turicibacteraceae), while tryptophan was negatively correlated with abundance of Bacteroidales S24-7 based on light exposure. This study provides the foundation for future studies into the mechanisms underlying the role of the gut microbiome on the murine host during light-dark stress.
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Affiliation(s)
- Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Colin J Brislawn
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Kelly G Stratton
- Computing and Analytics Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Erika M Zink
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Sarah J Fansler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
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9
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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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10
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Lloyd-Price J, Arze C, Ananthakrishnan AN, Schirmer M, Avila-Pacheco J, Poon TW, Andrews E, Ajami NJ, Bonham KS, Brislawn CJ, Casero D, Courtney H, Gonzalez A, Graeber TG, Hall AB, Lake K, Landers CJ, Mallick H, Plichta DR, Prasad M, Rahnavard G, Sauk J, Shungin D, Vázquez-Baeza Y, White RA, Braun J, Denson LA, Jansson JK, Knight R, Kugathasan S, McGovern DPB, Petrosino JF, Stappenbeck TS, Winter HS, Clish CB, Franzosa EA, Vlamakis H, Xavier RJ, Huttenhower C. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature 2019; 569:655-662. [PMID: 31142855 PMCID: PMC6650278 DOI: 10.1038/s41586-019-1237-9] [Citation(s) in RCA: 1328] [Impact Index Per Article: 265.6] [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: 02/06/2018] [Accepted: 04/16/2019] [Indexed: 12/11/2022]
Abstract
Inflammatory bowel diseases, which include Crohn’s disease and ulcerative colitis, affect several million individuals worldwide. Crohn’s disease and ulcerative colitis are complex diseases that are heterogeneous at the clinical, immunological, molecular, genetic, and microbial levels. Individual contributing factors have been the focus of extensive research. As part of the Integrative Human Microbiome Project (HMP2 or iHMP), we followed 132 subjects for one year each to generate integrated longitudinal molecular profiles of host and microbial activity during disease (up to 24 time points each; in total 2,965 stool, biopsy, and blood specimens). Here we present the results, which provide a comprehensive view of functional dysbiosis in the gut microbiome during inflammatory bowel disease activity. We demonstrate a characteristic increase in facultative anaerobes at the expense of obligate anaerobes, as well as molecular disruptions in microbial transcription (for example, among clostridia), metabolite pools (acylcarnitines, bile acids, and short-chain fatty acids), and levels of antibodies in host serum. Periods of disease activity were also marked by increases in temporal variability, with characteristic taxonomic, functional, and biochemical shifts. Finally, integrative analysis identified microbial, biochemical, and host factors central to this dysregulation. The study’s infrastructure resources, results, and data, which are available through the Inflammatory Bowel Disease Multi’omics Database (http://ibdmdb.org), provide the most comprehensive description to date of host and microbial activities in inflammatory bowel diseases. The Inflammatory Bowel Disease Multi’omics Database includes longitudinal data encompassing a multitude of analyses of stool, blood and biopsies of more than 100 individuals, and provides a comprehensive description of host and microbial activities in inflammatory bowel diseases.
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Affiliation(s)
- Jason Lloyd-Price
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Cesar Arze
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | | | - Melanie Schirmer
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | | | - Tiffany W Poon
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Nadim J Ajami
- Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Kevin S Bonham
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Colin J Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Lab, Richland, WA, USA
| | - David Casero
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Holly Courtney
- Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Antonio Gonzalez
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Thomas G Graeber
- Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA
| | - A Brantley Hall
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kathleen Lake
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Carol J Landers
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Himel Mallick
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Damian R Plichta
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mahadev Prasad
- Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Gholamali Rahnavard
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Jenny Sauk
- Vatche and Tamar Manoukian Division of Digestive Diseases, University of California Los Angeles, Los Angeles, CA, USA
| | - Dmitry Shungin
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Odontology, Umeå University, Umeå, Sweden
| | - Yoshiki Vázquez-Baeza
- Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Richard A White
- Earth and Biological Sciences Directorate, Pacific Northwest National Lab, Richland, WA, USA
| | | | - Jonathan Braun
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Lee A Denson
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Lab, Richland, WA, 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
| | | | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Joseph F Petrosino
- Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | | | - Harland S Winter
- Department of Pediatrics, MassGeneral Hospital for Children, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Clary B Clish
- Metabolomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eric A Franzosa
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Hera Vlamakis
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ramnik J Xavier
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Gastroenterology, Massachusetts General Hospital, Boston, MA, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Curtis Huttenhower
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
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11
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Gonzalez A, Navas-Molina JA, Kosciolek T, McDonald D, Vázquez-Baeza Y, Ackermann G, DeReus J, Janssen S, Swafford AD, Orchanian SB, Sanders JG, Shorenstein J, Holste H, Petrus S, Robbins-Pianka A, Brislawn CJ, Wang M, Rideout JR, Bolyen E, Dillon M, Caporaso JG, Dorrestein PC, Knight R. Qiita: rapid, web-enabled microbiome meta-analysis. Nat Methods 2018; 15:796-798. [PMID: 30275573 PMCID: PMC6235622 DOI: 10.1038/s41592-018-0141-9] [Citation(s) in RCA: 338] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 08/10/2018] [Indexed: 01/08/2023]
Abstract
Multi-omic insights into microbiome function and composition typically advance one study at a time. However, to understand relationships across studies, they must be aggregated into meta-analyses. This makes it possible to generate new hypotheses by finding features that are reproducible across biospecimens and data layers. Qiita dramatically accelerates such integration tasks in a web-based microbiome comparison platform, which we demonstrate with Human Microbiome Project and iHMP data.
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Affiliation(s)
- Antonio Gonzalez
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jose A Navas-Molina
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA.,Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.,Google LLC, Mountain View, CA, USA
| | - Tomasz Kosciolek
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Yoshiki Vázquez-Baeza
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Gail Ackermann
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jeff DeReus
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Stefan Janssen
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Stephanie B Orchanian
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Jon G Sanders
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Joshua Shorenstein
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA.,Inscripta, Inc., Boulder, CO, USA
| | - Hannes Holste
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA.,Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Semar Petrus
- Department of Biology, University of California, San Diego, La Jolla, CA, USA
| | - Adam Robbins-Pianka
- Department of Computer Science, University of Colorado, Boulder, Boulder, CO, USA
| | - Colin J Brislawn
- Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Jai Ram Rideout
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Evan Bolyen
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Matthew Dillon
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - J Gregory Caporaso
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Pieter C Dorrestein
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA. .,Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA. .,Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
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12
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Noguti J, Chan AA, Bandera B, Brislawn CJ, Protic M, Sim MS, Jansson JK, Bilchik AJ, Lee DJ. Both the intratumoral immune and microbial microenvironment are linked to recurrence in human colon cancer: results from a prospective, multicenter nodal ultrastaging trial. Oncotarget 2018; 9:23564-23576. [PMID: 29805756 PMCID: PMC5955112 DOI: 10.18632/oncotarget.25276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 01/10/2018] [Accepted: 04/08/2018] [Indexed: 12/15/2022] Open
Abstract
Colon cancer (CC) is the third most common cancer diagnosed in the United States and the incidence has been rising among young adults. We and others have shown a relationship between the immune infiltrate and prognosis, with improved disease-free survival (DFS) being associated with a higher expression of CD8+ T cells. We hypothesized that a microbial signature might be associated with intratumoral immune cells as well as DFS. We found that the relative abundance of one Operational Taxonomic Unit (OTU), OTU_104, was significantly associated with recurrence even after applying false discovery correction (HR 1.21, CI 1.08 to 1.36). The final multivariable model showed that DFS was influenced by three parameters: N-stage, CD8+ labeling, as well as this OTU_104 belonging to the order Clostridiales. Not only were CD8+ labeling and OTU_104 significant contributors in the final DFS model, but they were also inversely correlated to each other (p=0.022). Interestingly, CD8+ was also significantly associated with the microbiota composition in the tumor: CD8+ T cells was inversely correlated with alpha diversity (p=0.027) and significantly associated with the beta diversity. This study is the first to demonstrate an association among the intratumoral microbiome, CD8+ T cells, and recurrence in CC. An increased relative abundance of a specific OTU_104 was inversely associated with CD8+ T cells and directly associated with CC recurrence. The link between this microbe, CD8+ T cells, and DFS has not been previously shown.
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Affiliation(s)
- Juliana Noguti
- Dirks/Dougherty Laboratory for Cancer Research, Department of Translational Immunology, John Wayne Cancer Institute, Providence Saint John's Health Center, Santa Monica, CA, USA.,Los Angeles Biomedical Research Institute, Harbor - UCLA Medical Center, Torrance, CA, USA
| | - Alfred A Chan
- Dirks/Dougherty Laboratory for Cancer Research, Department of Translational Immunology, John Wayne Cancer Institute, Providence Saint John's Health Center, Santa Monica, CA, USA.,Los Angeles Biomedical Research Institute, Harbor - UCLA Medical Center, Torrance, CA, USA
| | - Bradley Bandera
- Department of Surgical Oncology. The John Wayne Cancer Institute at Providence St. John's Health Center, Santa Monica, CA, USA
| | - Colin J Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Mladjan Protic
- University of Novi Sad, Faculty of Medicine, Novi Sad, Serbia.,Oncology Institute of Vojvodina, Sremska Kamenica, Serbia
| | - Myung S Sim
- UCLA Department of Medicine, Statistics Core, Los Angeles, CA, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Anton J Bilchik
- Department of Surgical Oncology. The John Wayne Cancer Institute at Providence St. John's Health Center, Santa Monica, CA, USA
| | - Delphine J Lee
- Dirks/Dougherty Laboratory for Cancer Research, Department of Translational Immunology, John Wayne Cancer Institute, Providence Saint John's Health Center, Santa Monica, CA, USA.,Los Angeles Biomedical Research Institute, Harbor - UCLA Medical Center, Torrance, CA, USA.,Division of Dermatology, Department of Medicine, Harbor - UCLA Medical Center, Torrance, CA, USA.,David Geffen School of Medicine, University of California - Los Angeles, Los Angeles, CA, USA
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13
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Bernstein HC, Brislawn CJ, Dana K, Flores-Wentz T, Cory AB, Fansler SJ, Fredrickson JK, Moran JJ. Primary and heterotrophic productivity relate to multikingdom diversity in a hypersaline mat. FEMS Microbiol Ecol 2018; 93:4555378. [PMID: 29045626 PMCID: PMC5812518 DOI: 10.1093/femsec/fix121] [Citation(s) in RCA: 6] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 10/16/2017] [Indexed: 11/13/2022] Open
Abstract
Benthic microbial ecosystems are widespread yet knowledge gaps still remain on the relationships between the diversity of species across kingdoms and productivity. Here, we ask two fundamental questions: (i) How does species diversity relate to the rates of primary and heterotrophic productivity? (ii) How do diel variations in light-energy inputs influence productivity and microbiome diversity? To answer these questions, microbial mats from a magnesium sulfate hypersaline lake were used to establish microcosms. Both the number and relatedness between bacterial and eukaryotic taxa in the microbiome were assayed via amplicon-based sequencing of 16S and 18S rRNA genes over two diel cycles. These results correlated with biomass productivity obtained from substrate-specific 13C stable isotope tracers that enabled comparisons between primary and heterotrophic productivity. Both bacterial and eukaryotic species richness and evenness were related only to the rates of 13C-labeled glucose and acetate biomass incorporation. Interestingly, measures of these heterotrophic relationships changed from positive and negative correlations depending on carbon derived from glucose or acetate, respectively. The bacterial and eukaryotic diversity of this ecosystem is also controlled, in part, from energy constraints imposed by changing irradiance over a diel cycle.
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Affiliation(s)
- Hans C Bernstein
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.,The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99164, USA
| | - Colin J Brislawn
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Karl Dana
- Signature Science and Technology Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Tobias Flores-Wentz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Alexandra B Cory
- Signature Science and Technology Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Sarah J Fansler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - James K Fredrickson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - James J Moran
- Signature Science and Technology Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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14
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Espínola F, Dionisi HM, Borglin S, Brislawn CJ, Jansson JK, Mac Cormack WP, Carroll J, Sjöling S, Lozada M. Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes. Microb Ecol 2018; 75:123-139. [PMID: 28702706 DOI: 10.1007/s00248-017-1028-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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: 05/06/2017] [Accepted: 06/27/2017] [Indexed: 06/07/2023]
Abstract
In this work, we analyzed the community structure and metabolic potential of sediment microbial communities in high-latitude coastal environments subjected to low to moderate levels of chronic pollution. Subtidal sediments from four low-energy inlets located in polar and subpolar regions from both Hemispheres were analyzed using large-scale 16S rRNA gene and metagenomic sequencing. Communities showed high diversity (Shannon's index 6.8 to 10.2), with distinct phylogenetic structures (<40% shared taxa at the Phylum level among regions) but similar metabolic potential in terms of sequences assigned to KOs. Environmental factors (mainly salinity, temperature, and in less extent organic pollution) were drivers of both phylogenetic and functional traits. Bacterial taxa correlating with hydrocarbon pollution included families of anaerobic or facultative anaerobic lifestyle, such as Desulfuromonadaceae, Geobacteraceae, and Rhodocyclaceae. In accordance, biomarker genes for anaerobic hydrocarbon degradation (bamA, ebdA, bcrA, and bssA) were prevalent, only outnumbered by alkB, and their sequences were taxonomically binned to the same bacterial groups. BssA-assigned metagenomic sequences showed an extremely wide diversity distributed all along the phylogeny known for this gene, including bssA sensu stricto, nmsA, assA, and other clusters from poorly or not yet described variants. This work increases our understanding of microbial community patterns in cold coastal sediments, and highlights the relevance of anaerobic hydrocarbon degradation processes in subtidal environments.
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Affiliation(s)
- Fernando Espínola
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Centro Nacional Patagónico, Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina
| | - Hebe M Dionisi
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Centro Nacional Patagónico, Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina
| | - Sharon Borglin
- Energy Geosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Colin J Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Walter P Mac Cormack
- Instituto Nanobiotec, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina
- Instituto Antártico Argentino, Buenos Aires, Argentina
| | - JoLynn Carroll
- Akvaplan-niva, Fram-High North Research Centre for Climate and the Environment, and ARCEx-Research Centre for Arctic Petroleum Exploration, Department of Geosciences, UiT The Arctic University of Norway, N-9037, Tromsø, Norway
| | - Sara Sjöling
- School of Natural Sciences and Environmental Studies, Södertörn University, Huddinge, Sweden
| | - Mariana Lozada
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Centro Nacional Patagónico, Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina.
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15
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Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, Navas-Molina JA, Janssen S, Kopylova E, Vázquez-Baeza Y, González A, Morton JT, Mirarab S, Zech Xu Z, Jiang L, Haroon MF, Kanbar J, Zhu Q, Jin Song S, Kosciolek T, Bokulich NA, Lefler J, Brislawn CJ, Humphrey G, Owens SM, Hampton-Marcell J, Berg-Lyons D, McKenzie V, Fierer N, Fuhrman JA, Clauset A, Stevens RL, Shade A, Pollard KS, Goodwin KD, Jansson JK, Gilbert JA, Knight R. A communal catalogue reveals Earth's multiscale microbial diversity. Nature 2017; 551:457-463. [PMID: 29088705 PMCID: PMC6192678 DOI: 10.1038/nature24621] [Citation(s) in RCA: 1219] [Impact Index Per Article: 174.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 10/10/2017] [Indexed: 02/07/2023]
Abstract
Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.
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Affiliation(s)
- Luke R Thompson
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, Mississippi, USA.,Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, stationed at Southwest Fisheries Science Center, La Jolla, California, USA
| | - Jon G Sanders
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Amnon Amir
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Joshua Ladau
- The Gladstone Institutes and University of California San Francisco, San Francisco, California, USA
| | - Kenneth J Locey
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Robert J Prill
- Industrial and Applied Genomics, IBM Almaden Research Center, San Jose, California, USA
| | - Anupriya Tripathi
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Division of Biological Sciences, University of California San Diego, La Jolla, California, USA.,Skaggs School of Pharmacy, University of California San Diego, La Jolla, California, USA
| | - Sean M Gibbons
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Jose A Navas-Molina
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Stefan Janssen
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Evguenia Kopylova
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Yoshiki Vázquez-Baeza
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Antonio González
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - James T Morton
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, California, USA
| | - Zhenjiang Zech Xu
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Lingjing Jiang
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Family Medicine and Public Health, University of California San Diego, La Jolla, California, USA
| | - Mohamed F Haroon
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Jad Kanbar
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Se Jin Song
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Tomasz Kosciolek
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Nicholas A Bokulich
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Joshua Lefler
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Colin J Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Gregory Humphrey
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Sarah M Owens
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Jarrad Hampton-Marcell
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA.,Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Donna Berg-Lyons
- BioFrontiers Institute, University of Colorado, Boulder, Colorado, USA
| | - Valerie McKenzie
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA.,Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Aaron Clauset
- BioFrontiers Institute, University of Colorado, Boulder, Colorado, USA.,Department of Computer Science, University of Colorado, Boulder, Colorado, USA
| | - Rick L Stevens
- Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, Illinois, USA.,Department of Computer Science, University of Chicago, Chicago, Illinois, USA
| | - Ashley Shade
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA.,Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA.,Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, Michigan, USA
| | - Katherine S Pollard
- The Gladstone Institutes and University of California San Francisco, San Francisco, California, USA
| | - Kelly D Goodwin
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, stationed at Southwest Fisheries Science Center, La Jolla, California, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jack A Gilbert
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA.,Department of Surgery, University of Chicago, Chicago, Illinois, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
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16
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Toole DR, Cannon GH, Brislawn CJ, Graves JM, Lamendella R, Muth TR, Muth NZ. Differences in soil fungal assemblages associated with native and non-native tree species of varying weediness. Biol Invasions 2017. [DOI: 10.1007/s10530-017-1580-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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Nakamura YK, Metea C, Karstens L, Asquith M, Gruner H, Moscibrocki C, Lee I, Brislawn CJ, Jansson JK, Rosenbaum JT, Lin P. Gut Microbial Alterations Associated With Protection From Autoimmune Uveitis. Invest Ophthalmol Vis Sci 2017; 57:3747-58. [PMID: 27415793 PMCID: PMC4960998 DOI: 10.1167/iovs.16-19733] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [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] [Indexed: 12/31/2022] Open
Abstract
Purpose To investigate the contribution of the gut microbiota to the pathogenesis of uveitis. Methods Experimental autoimmune uveitis (EAU) in B10.RIII mice was induced using interphotoreceptor binding protein peptide. Mice were treated with oral or intraperitoneal (IP) antibiotics. Effector (Teff) and regulatory (Treg) T lymphocytes were identified using flow cytometry; 16S rRNA gene sequencing and qPCR were performed on gastrointestinal (GI) contents. Results Broad-spectrum (four antibiotics given simultaneously) oral, but not IP, antibiotics reduced mean uveitis clinical scores significantly compared with water-treated animals (0.5 vs. 3.0, P < 0.0001 for oral; 3.4 vs. 3.4, P > 0.99 for IP). Both oral metronidazole (P = 0.02) and vancomycin (P < 0.0001) alone decreased inflammation, whereas neomycin (P = 0.7) and ampicillin (P = 0.4) did not change mean uveitis scores. Oral broad-spectrum antibiotics increased Tregs in the GI lamina propria of EAU animals at 1 week, and in extraintestinal lymphoid tissues later, whereas Teff and inflammatory cytokines were reduced. 16S sequencing of GI contents revealed altered microbiota in immunized mice compared with nonimmunized mice, and microbial diversity clustering in EAU mice treated with uveitis-protective antibiotics. Experimental autoimmune uveitis mice also demonstrated gut microbial diversity clustering associated with clinical score severity. Conclusions Oral antibiotics modulate the severity of inducible EAU by increasing Tregs in the gut and extraintestinal tissues, as well as decreasing effector T cells and cytokines. 16S sequencing suggests that there may be protective and, conversely, potentially uveitogenic, gut microbiota. These findings may lead to a better understanding of how uveitis can be treated or prevented by modulating the gut microbiome.
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Affiliation(s)
- Yukiko K Nakamura
- Casey Eye Institute Oregon Health and Science University, Portland, Oregon, United States
| | - Christina Metea
- Casey Eye Institute Oregon Health and Science University, Portland, Oregon, United States
| | - Lisa Karstens
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, Oregon, United States
| | - Mark Asquith
- Division of Rheumatology, Department of Medicine, Oregon Health and Science University, Portland, Oregon, United States
| | - Henry Gruner
- Casey Eye Institute Oregon Health and Science University, Portland, Oregon, United States
| | - Cathleen Moscibrocki
- Casey Eye Institute Oregon Health and Science University, Portland, Oregon, United States
| | - Iris Lee
- Casey Eye Institute Oregon Health and Science University, Portland, Oregon, United States
| | - Colin J Brislawn
- Pacific Northwest National Laboratory, Richland, Washington, United States
| | - Janet K Jansson
- Pacific Northwest National Laboratory, Richland, Washington, United States
| | - James T Rosenbaum
- Casey Eye Institute Oregon Health and Science University, Portland, Oregon, United States 3Division of Rheumatology, Department of Medicine, Oregon Health and Science University, Portland, Oregon, United States 5Devers Eye Institute, Portland, Oregon, Uni
| | - Phoebe Lin
- Casey Eye Institute Oregon Health and Science University, Portland, Oregon, United States
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18
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Halfvarson J, Brislawn CJ, Lamendella R, Vázquez-Baeza Y, Walters WA, Bramer LM, D'Amato M, Bonfiglio F, McDonald D, Gonzalez A, McClure EE, Dunklebarger MF, Knight R, Jansson JK. Dynamics of the human gut microbiome in inflammatory bowel disease. Nat Microbiol 2017; 2:17004. [PMID: 28191884 PMCID: PMC5319707 DOI: 10.1038/nmicrobiol.2017.4] [Citation(s) in RCA: 676] [Impact Index Per Article: 96.6] [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: 09/12/2016] [Accepted: 01/05/2017] [Indexed: 12/16/2022]
Abstract
Inflammatory bowel disease (IBD) is characterized by flares of inflammation with a periodic need for increased medication and sometimes even surgery. The aetiology of IBD is partly attributed to a deregulated immune response to gut microbiome dysbiosis. Cross-sectional studies have revealed microbial signatures for different IBD subtypes, including ulcerative colitis, colonic Crohn's disease and ileal Crohn's disease. Although IBD is dynamic, microbiome studies have primarily focused on single time points or a few individuals. Here, we dissect the long-term dynamic behaviour of the gut microbiome in IBD and differentiate this from normal variation. Microbiomes of IBD subjects fluctuate more than those of healthy individuals, based on deviation from a newly defined healthy plane (HP). Ileal Crohn's disease subjects deviated most from the HP, especially subjects with surgical resection. Intriguingly, the microbiomes of some IBD subjects periodically visited the HP then deviated away from it. Inflammation was not directly correlated with distance to the healthy plane, but there was some correlation between observed dramatic fluctuations in the gut microbiome and intensified medication due to a flare of the disease. These results will help guide therapies that will redirect the gut microbiome towards a healthy state and maintain remission in IBD.
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Affiliation(s)
- Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro SE-701 82, Sweden
| | - Colin J Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | | | - Yoshiki Vázquez-Baeza
- Department of Computer Science and Engineering, University of California, San Diego, California 92093, USA
| | | | - Lisa M Bramer
- National Security Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Mauro D'Amato
- Clinical Epidemiology Unit, Department of Medicine Solna, Karolinska Institutet, SE-171 76 Stockholm, Sweden.,BioDonostia Health Research Institute San Sebastian, and IKERBASQUE Basque Foundation for Science Bilbao 48011, Spain
| | - Ferdinando Bonfiglio
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-171 77, Stockholm Sweden
| | - Daniel McDonald
- Department of Pediatrics, University of California, San Diego, California 92093, USA
| | - Antonio Gonzalez
- Center for Microbiome Innovation, University of California, San Diego, California 92093, USA
| | | | | | - Rob Knight
- Department of Computer Science and Engineering, University of California, San Diego, California 92093, USA.,Department of Pediatrics, University of California, San Diego, California 92093, USA.,Center for Microbiome Innovation, University of California, San Diego, California 92093, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
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19
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Snijders AM, Langley SA, Kim YM, Brislawn CJ, Noecker C, Zink EM, Fansler SJ, Casey CP, Miller DR, Huang Y, Karpen GH, Celniker SE, Brown JB, Borenstein E, Jansson JK, Metz TO, Mao JH. Influence of early life exposure, host genetics and diet on the mouse gut microbiome and metabolome. Nat Microbiol 2016; 2:16221. [PMID: 27892936 DOI: 10.1038/nmicrobiol.2016.221] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 10/07/2016] [Indexed: 12/22/2022]
Abstract
Although the gut microbiome plays important roles in host physiology, health and disease1, we lack understanding of the complex interplay between host genetics and early life environment on the microbial and metabolic composition of the gut. We used the genetically diverse Collaborative Cross mouse system2 to discover that early life history impacts the microbiome composition, whereas dietary changes have only a moderate effect. By contrast, the gut metabolome was shaped mostly by diet, with specific non-dietary metabolites explained by microbial metabolism. Quantitative trait analysis identified mouse genetic trait loci (QTL) that impact the abundances of specific microbes. Human orthologues of genes in the mouse QTL are implicated in gastrointestinal cancer. Additionally, genes located in mouse QTL for Lactobacillales abundance are implicated in arthritis, rheumatic disease and diabetes. Furthermore, Lactobacillales abundance was predictive of higher host T-helper cell counts, suggesting an important link between Lactobacillales and host adaptive immunity.
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Affiliation(s)
- Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Sasha A Langley
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Young-Mo Kim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Colin J Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Cecilia Noecker
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, USA
| | - Erika M Zink
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Sarah J Fansler
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Cameron P Casey
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Darla R Miller
- Systems Genetics Core Facility, Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Yurong Huang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Gary H Karpen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Susan E Celniker
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - James B Brown
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Elhanan Borenstein
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, USA.,Department of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, USA.,Santa Fe Institute, Santa Fe, New Mexico 87501, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Thomas O Metz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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20
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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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21
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Trexler R, Solomon C, Brislawn CJ, Wright JR, Rosenberger A, McClure EE, Grube AM, Peterson MP, Keddache M, Mason OU, Hazen TC, Grant CJ, Lamendella R. Assessing impacts of unconventional natural gas extraction on microbial communities in headwater stream ecosystems in Northwestern Pennsylvania. Front Microbiol 2014; 5:522. [PMID: 25408683 PMCID: PMC4219493 DOI: 10.3389/fmicb.2014.00522] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [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: 07/15/2014] [Accepted: 09/19/2014] [Indexed: 12/17/2022] Open
Abstract
Hydraulic fracturing and horizontal drilling have increased dramatically in Pennsylvania Marcellus shale formations, however the potential for major environmental impacts are still incompletely understood. High-throughput sequencing of the 16S rRNA gene was performed to characterize the microbial community structure of water, sediment, bryophyte, and biofilm samples from 26 headwater stream sites in northwestern Pennsylvania with different histories of fracking activity within Marcellus shale formations. Further, we describe the relationship between microbial community structure and environmental parameters measured. Approximately 3.2 million 16S rRNA gene sequences were retrieved from a total of 58 samples. Microbial community analyses showed significant reductions in species richness as well as evenness in sites with Marcellus shale activity. Beta diversity analyses revealed distinct microbial community structure between sites with and without Marcellus shale activity. For example, operational taxonomic units (OTUs) within the Acetobacteracea, Methylocystaceae, Acidobacteriaceae, and Phenylobacterium were greater than three log-fold more abundant in MSA+ sites as compared to MSA- sites. Further, several of these OTUs were strongly negatively correlated with pH and positively correlated with the number of wellpads in a watershed. It should be noted that many of the OTUs enriched in MSA+ sites are putative acidophilic and/or methanotrophic populations. This study revealed apparent shifts in the autochthonous microbial communities and highlighted potential members that could be responding to changing stream conditions as a result of nascent industrial activity in these aquatic ecosystems.
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Affiliation(s)
- Ryan Trexler
- Juniata College, Department of Biology Huntingdon, PA, USA
| | | | | | | | | | - Erin E McClure
- Juniata College, Department of Biology Huntingdon, PA, USA
| | - Alyssa M Grube
- Juniata College, Department of Biology Huntingdon, PA, USA
| | - Mark P Peterson
- Juniata College, Department of Biology Huntingdon, PA, USA ; Department of Biology and Huck Institutes of Life Sciences, Pennsylvania State University University Park, PA, USA
| | - Mehdi Keddache
- DNA Sequencing and Genotyping Facility, Cincinnati Children's Hospital Medical Center Cincinnati, OH, USA
| | - Olivia U Mason
- Department of Earth, Ocean, and Atmospheric Science, Florida State University Tallahassee, FL, USA
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, University of Tennessee Knoxville Knoxville, TN, USA ; Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
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