1
|
Chang YH, Yanckello LM, Chlipala GE, Green SJ, Aware C, Runge A, Xing X, Chen A, Wenger K, Flemister A, Wan C, Lin AL. Prebiotic inulin enhances gut microbial metabolism and anti-inflammation in apolipoprotein E4 mice with sex-specific implications. Sci Rep 2023; 13:15116. [PMID: 37704738 PMCID: PMC10499887 DOI: 10.1038/s41598-023-42381-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 09/09/2023] [Indexed: 09/15/2023] Open
Abstract
Gut dysbiosis has been identified as a crucial factor of Alzheimer's disease (AD) development for apolipoprotein E4 (APOE4) carriers. Inulin has shown the potential to mitigate dysbiosis. However, it remains unclear whether the dietary response varies depending on sex. In the study, we fed 4-month-old APOE4 mice with inulin for 16 weeks and performed shotgun metagenomic sequencing to determine changes in microbiome diversity, taxonomy, and functional gene pathways. We also formed the same experiments with APOE3 mice to identify whether there are APOE-genotype dependent responses to inulin. We found that APOE4 female mice fed with inulin had restored alpha diversity, significantly reduced Escherichia coli and inflammation-associated pathway responses. However, compared with APOE4 male mice, they had less metabolic responses, including the levels of short-chain fatty acids-producing bacteria and the associated kinases, especially those related to acetate and Erysipelotrichaceae. These diet- and sex- effects were less pronounced in the APOE3 mice, indicating that different APOE variants also play a significant role. The findings provide insights into the higher susceptibility of APOE4 females to AD, potentially due to inefficient energy production, and imply the importance of considering precision nutrition for mitigating dysbiosis and AD risk in the future.
Collapse
Affiliation(s)
- Ya-Hsuan Chang
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY, 40536, USA
- Sanders Brown Center on Aging, University of Kentucky, Lexington, KY, 40536, USA
- Department of Radiology, University of Missouri, Columbia, MO, 65212, USA
- NextGen Precision Health, University of Missouri, Columbia, MO, 65212, USA
| | - Lucille M Yanckello
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY, 40536, USA
- Sanders Brown Center on Aging, University of Kentucky, Lexington, KY, 40536, USA
| | - George E Chlipala
- Research Informatics Core, University of Illinois Chicago, Chicago, IL, 60612, USA
| | - Stefan J Green
- Genomics and Microbiome Core Facility, Rush University, Chicago, IL, 60612, USA
| | - Chetan Aware
- Department of Radiology, University of Missouri, Columbia, MO, 65212, USA
- NextGen Precision Health, University of Missouri, Columbia, MO, 65212, USA
| | - Amelia Runge
- Department of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Xin Xing
- Department of Radiology, University of Missouri, Columbia, MO, 65212, USA
- NextGen Precision Health, University of Missouri, Columbia, MO, 65212, USA
- Department of Computer Science, University of Kentucky, Lexington, KY, 40506, USA
| | - Anna Chen
- Sanders Brown Center on Aging, University of Kentucky, Lexington, KY, 40536, USA
| | - Kathryn Wenger
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Abeoseh Flemister
- Department of Radiology, University of Missouri, Columbia, MO, 65212, USA
- NextGen Precision Health, University of Missouri, Columbia, MO, 65212, USA
| | - Caixia Wan
- Department of Biological and Biomedical Engineering, University of Missouri, Columbia, MO, 65211, USA
| | - Ai-Ling Lin
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY, 40536, USA.
- Sanders Brown Center on Aging, University of Kentucky, Lexington, KY, 40536, USA.
- Department of Radiology, University of Missouri, Columbia, MO, 65212, USA.
- NextGen Precision Health, University of Missouri, Columbia, MO, 65212, USA.
- Department of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA.
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, 65211, USA.
| |
Collapse
|
2
|
Hammond TC, Green SJ, Jacobs Y, Chlipala GE, Xing X, Heil S, Chen A, Aware C, Flemister A, Stromberg A, Balchandani P, Lin AL. Gut microbiome association with brain imaging markers, APOE genotype, calcium and vegetable intakes, and obesity in healthy aging adults. Front Aging Neurosci 2023; 15:1227203. [PMID: 37736325 PMCID: PMC10510313 DOI: 10.3389/fnagi.2023.1227203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/17/2023] [Indexed: 09/23/2023] Open
Abstract
Introduction Advanced age is a significant factor in changes to brain physiology and cognitive functions. Recent research has highlighted the critical role of the gut microbiome in modulating brain functions during aging, which can be influenced by various factors such as apolipoprotein E (APOE) genetic variance, body mass index (BMI), diabetes, and dietary intake. However, the associations between the gut microbiome and these factors, as well as brain structural, vascular, and metabolic imaging markers, have not been well explored. Methods We recruited 30 community dwelling older adults between age 55-85 in Kentucky. We collected the medical history from the electronic health record as well as the Dietary Screener Questionnaire. We performed APOE genotyping with an oral swab, gut microbiome analysis using metagenomics sequencing, and brain structural, vascular, and metabolic imaging using MRI. Results Individuals with APOE e2 and APOE e4 genotypes had distinct microbiota composition, and higher level of pro-inflammatory microbiota were associated higher BMI and diabetes. In contrast, calcium- and vegetable-rich diets were associated with microbiota that produced short chain fatty acids leading to an anti-inflammatory state. We also found that important gut microbial butyrate producers were correlated with the volume of the thalamus and corpus callosum, which are regions of the brain responsible for relaying and processing information. Additionally, putative proinflammatory species were negatively correlated with GABA production, an inhibitory neurotransmitter. Furthermore, we observed that the relative abundance of bacteria from the family Eggerthellaceae, equol producers, was correlated with white matter integrity in tracts connecting the brain regions related to language, memory, and learning. Discussion These findings highlight the importance of gut microbiome association with brain health in aging population and could have important implications aimed at optimizing healthy brain aging through precision prebiotic, probiotic or dietary interventions.
Collapse
Affiliation(s)
- Tyler C. Hammond
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, United States
- Department of Neuroscience, University of Kentucky, Lexington, KY, United States
| | - Stefan J. Green
- Genomics and Microbiome Core Facility, Rush University, Chicago, IL, United States
| | - Yael Jacobs
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - George E. Chlipala
- Research Informatics Core, University of Illinois Chicago, Chicago, IL, United States
| | - Xin Xing
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, United States
- Department of Computer Science, University of Kentucky, Lexington, KY, United States
- Roy Blunt NextGen Precision Health, University of Missouri, Columbia, MO, United States
- Department of Radiology, University of Missouri, Columbia, MO, United States
| | - Sally Heil
- School of Medicine, University of Missouri, Columbia, MO, United States
| | - Anna Chen
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, United States
| | - Chetan Aware
- Roy Blunt NextGen Precision Health, University of Missouri, Columbia, MO, United States
- Department of Radiology, University of Missouri, Columbia, MO, United States
| | - Abeoseh Flemister
- Roy Blunt NextGen Precision Health, University of Missouri, Columbia, MO, United States
- Department of Radiology, University of Missouri, Columbia, MO, United States
| | - Arnold Stromberg
- Dr. Bing Zhang Department of Statistics, University of Kentucky, Lexington, KY, United States
| | - Priti Balchandani
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Ai-Ling Lin
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, United States
- Roy Blunt NextGen Precision Health, University of Missouri, Columbia, MO, United States
- Department of Radiology, University of Missouri, Columbia, MO, United States
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, United States
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| |
Collapse
|
3
|
Lockwood MB, Chlipala GE, Maeinschein-Cline M, DeVon HA, Lichvar AB, Samra MK, Park CG, Campara M, Doorenbos AZ, Tussing-Humphreys LM, Spaggiari M, Bronas UG, Steel JL, Green SS. Pain Interference in End Stage Kidney Disease is Associated with Changes in Gut Microbiome Features Before and After Kidney Transplantation. Pain Manag Nurs 2023; 24:68-77. [PMID: 36184305 PMCID: PMC9925398 DOI: 10.1016/j.pmn.2022.08.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/19/2022] [Accepted: 08/27/2022] [Indexed: 10/14/2022]
Abstract
BACKGROUND Pain, a common debilitating symptom among kidney transplant recipients (KTRs), is among the most common and undertreated symptoms after kidney transplantation. AIMS Characterize associations between gut microbiome features and pain interference before and after kidney transplantation. DESIGN Longitudinal, repeated measures study, collecting fecal specimens and pain interference data pretransplant and 3 months posttransplant. SETTING Participants were recruited at the kidney transplant clinic at the University of Illinois Hospital & Health Sciences System. PARTICIPANTS/SUBJECTS 19 living donor kidney transplant recipients. METHODS We assessed fecal microbial community structure with shotgun metagenomic sequencing; we used pain interference scores derived from the Patient-Reported Outcomes Measurement Information System-57. RESULTS We measured a reduction in the Shannon diversity index in both groups after transplantation but observed no significant differences between groups at either time point. We did observe significant differences in fecal microbial Bray-Curtis similarity index among those reporting pain interference pre- transplant versus no pain interference at 3-months posttransplant (R = .306, p = .022), and between pain interference groups at posttransplant (R = .249, p = .041). Pairwise models showed significant differences between groups posttransplant in relative abundances of several taxa, including a 5-fold reduction.ßin Akkermansia among those with pain interference and a higher relative abundance of taxa associated with chronic inflammation in those with pain interference posttransplant. Functional gene analysis identified two features that were significantly enriched in those with pain interference, including a peptide transport system gene. CONCLUSIONS Gut microbiota community structure differs between groups with and without pain interference at 3 months after kidney transplantation. Several taxa involved in intestinal barrier integrity and chronic inflammation were associated with posttransplant pain.
Collapse
Affiliation(s)
- Mark B Lockwood
- Department of Biobehavioral Health Science, University of Illinois Chicago, College of Nursing, Chicago, Illinois.
| | - George E Chlipala
- Research informatics core, University of Illinois, Chicago, Illinois
| | | | - Holli A DeVon
- Community Health Research, University of California Los Angeles School of Nursing, Los Angeles, California
| | | | - Manpreet K Samra
- Department of Medicine, Edward Hines Jr. VA Transplant Center, Loyola University Medical Center, Chicago, Illinois
| | - Chang G Park
- Department of Population Health Nursing Science, University of Illinois Chicago, College of Nursing, Chicago, Illinois
| | - Maya Campara
- University of Illinois Chicago, College of Medicine/Surgery, Chicago, Illinois
| | - Ardith Z Doorenbos
- Department of Biobehavioral Nursing Science, University of Illinois Chicago, College of Nursing, Chicago, Illinois
| | - Lisa M Tussing-Humphreys
- Department of Kinesiology and Nutrition, University of Illinois Chicago, College of Nursing, Chicago, Illinois
| | - Mario Spaggiari
- College of Medicine, University of Illinois Chicago, College of Nursing, Chicago, Illinois
| | - Ulf G Bronas
- Department of Biobehavioral Nursing Science, University of Illinois Chicago, College of Nursing, Chicago, Illinois
| | - Jennifer L Steel
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania; Center for Excellence in Behavioral Medicine, Pittsburgh, Pennsylvania
| | - Stefan S Green
- Core Laboratory Services and Genomics and Microbiome Core Facility, Rush University Medical Center, Chicago, Illinois; Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois
| |
Collapse
|
4
|
Priyadarshini M, Navarro G, Reiman DJ, Sharma A, Xu K, Lednovich K, Manzella CR, Khan MW, Garcia MS, Allard S, Wicksteed B, Chlipala GE, Szynal B, Bernabe BP, Maki PM, Gill RK, Perdew GH, Gilbert J, Dai Y, Layden BT. Gestational Insulin Resistance Is Mediated by the Gut Microbiome-Indoleamine 2,3-Dioxygenase Axis. Gastroenterology 2022; 162:1675-1689.e11. [PMID: 35032499 PMCID: PMC9040389 DOI: 10.1053/j.gastro.2022.01.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 12/23/2021] [Accepted: 01/03/2022] [Indexed: 01/07/2023]
Abstract
BACKGROUND & AIMS Normal gestation involves a reprogramming of the maternal gut microbiome (GM) that contributes to maternal metabolic changes by unclear mechanisms. This study aimed to understand the mechanistic underpinnings of the GM-maternal metabolism interaction. METHODS The GM and plasma metabolome of CD1, NIH-Swiss, and C57 mice were analyzed with the use of 16S rRNA sequencing and untargeted liquid chromatography-mass spectrometry throughout gestation. Pharmacologic and genetic knockout mouse models were used to identify the role of indoleamine 2,3-dioxygenase (IDO1) in pregnancy-associated insulin resistance (IR). Involvement of gestational GM was studied with the use of fecal microbial transplants (FMTs). RESULTS Significant variation in GM alpha diversity occurred throughout pregnancy. Enrichment in gut bacterial taxa was mouse strain and pregnancy time point specific, with the species enriched at gestation day 15/19 (G15/19), a point of heightened IR, being distinct from those enriched before or after pregnancy. Metabolomics revealed elevated plasma kynurenine at G15/19 in all 3 mouse strains. IDO1, the rate-limiting enzyme for kynurenine production, had increased intestinal expression at G15, which was associated with mild systemic and gut inflammation. Pharmacologic and genetic inhibition of IDO1 inhibited kynurenine levels and reversed pregnancy-associated IR. FMT revealed that IDO1 induction and local kynurenine level effects on IR derive from the GM in both mouse and human pregnancy. CONCLUSIONS GM changes accompanying pregnancy shift IDO1-dependent tryptophan metabolism toward kynurenine production, intestinal inflammation, and gestational IR, a phenotype reversed by genetic deletion or inhibition of IDO1. (Gestational Gut Microbiome-IDO1 Axis Mediates Pregnancy Insulin Resistance; EMBL-ENA ID: PRJEB45047. MetaboLights ID: MTBLS3598).
Collapse
Affiliation(s)
- Medha Priyadarshini
- Division of Endocrinology, Diabetes, and Metabolism and UIC, Chicago-IL, U.S.A
| | - Guadalupe Navarro
- Division of Endocrinology, Diabetes, and Metabolism and UIC, Chicago-IL, U.S.A
| | - Derek J Reiman
- Department of Biomedical Engineering, UIC, Chicago-IL, U.S.A
| | - Anukriti Sharma
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Main Campus, Cleveland-OH, U.S.A
| | - Kai Xu
- Division of Endocrinology, Diabetes, and Metabolism and UIC, Chicago-IL, U.S.A
| | - Kristen Lednovich
- Division of Endocrinology, Diabetes, and Metabolism and UIC, Chicago-IL, U.S.A
| | | | - Md Wasim Khan
- Division of Endocrinology, Diabetes, and Metabolism and UIC, Chicago-IL, U.S.A
| | - Mariana Salas Garcia
- Department of Pediatrics, University of California San Diego (UCSD) School of Medicine, La Jolla-CA, U.S.A
| | - Sarah Allard
- Department of Pediatrics, University of California San Diego (UCSD) School of Medicine, La Jolla-CA, U.S.A
| | - Barton Wicksteed
- Division of Endocrinology, Diabetes, and Metabolism and UIC, Chicago-IL, U.S.A
| | - George E Chlipala
- Research Informatics Core, Research Resources Center, UIC, Chicago-IL, U.S.A
| | - Barbara Szynal
- Division of Endocrinology, Diabetes, and Metabolism and UIC, Chicago-IL, U.S.A
| | | | - Pauline M Maki
- Department of Psychiatry, UIC, Chicago-IL, U.S.A.; Department of Psychology, and UIC, Chicago-IL, U.S.A.; Department of Obstetrics and Gynecology, UIC, Chicago-IL, U.S.A
| | - Ravinder K Gill
- Division of Gastroenterology and Hepatology, UIC, Chicago-IL, U.S.A
| | - Gary H Perdew
- Department of Veterinary and Biomedical Sciences, Center for Molecular Toxicology and Carcinogenesis, The Pennsylvania State University, Pennsylvania, U.S.A
| | - Jack Gilbert
- Department of Pediatrics, University of California San Diego (UCSD) School of Medicine, La Jolla-CA, U.S.A.; Scripps Institution of Oceanography, UCSD, La Jolla-CA, U.S.A
| | - Yang Dai
- Department of Biomedical Engineering, UIC, Chicago-IL, U.S.A
| | - Brian T Layden
- Division of Endocrinology, Diabetes, and Metabolism, University of Illinois, Chicago, Illinois; Jesse Brown Veterans Affair Medical Center, Chicago, Illinois.
| |
Collapse
|
5
|
Hooper MJ, LeWitt TM, Pang Y, Veon FL, Chlipala GE, Feferman L, Green SJ, Sweeney D, Bagnowski KT, Burns MB, Seed PC, Choi J, Guitart J, Zhou XA. Gut dysbiosis in cutaneous T-cell lymphoma is characterized by shifts in relative abundances of specific bacterial taxa and decreased diversity in more advanced disease. J Eur Acad Dermatol Venereol 2022; 36:1552-1563. [PMID: 35366365 PMCID: PMC9391260 DOI: 10.1111/jdv.18125] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 12/03/2021] [Revised: 02/11/2022] [Accepted: 03/14/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Cutaneous T-cell lymphoma (CTCL) patients often suffer from recurrent skin infections and profound immune dysregulation in advanced disease. The gut microbiome has been recognized to influence cancers and cutaneous conditions; however, it has not yet been studied in CTCL. OBJECTIVES To investigate the gut microbiome in patients with CTCL and in healthy controls. METHODS Case-control study conducted between January 2019 and November 2020 at Northwestern's busy multidisciplinary CTCL clinic (Chicago, Illinois, USA) utilizing 16S ribosomal RNA gene amplicon sequencing and bioinformatics analyses to characterize the microbiota present in fecal samples of CTCL patients (n=38) and age-matched healthy controls (n=13) from the same geographical region. RESULTS Gut microbial α-diversity trended lower in patients with CTCL and was significantly lower in patients with advanced CTCL relative to controls (p=0.015). No differences in β-diversity were identified. Specific taxa were significantly reduced in patient samples; significance was determined using adjusted p-values (q-values) that accounted for a false discovery rate threshold of 0.05. Significantly reduced taxa in patient samples included the phylum Actinobacteria (q=0.0002), classes Coriobacteriia (q=0.002) and Actinobacteria (q=0.03), order Coriobacteriales (q=0.003), and genus Anaerotruncus (q=0.01). The families of Eggerthellaceae (q=0.0007) and Lactobacillaceae (q=0.02) were significantly reduced in patients with high skin disease burden. CONCLUSIONS Gut dysbiosis can be seen in patients with CTCL compared to healthy controls and is pronounced in more advanced CTCL. The taxonomic shifts associated with CTCL are similar to those previously reported in atopic dermatitis and opposite those of psoriasis, suggesting microbial parallels to the immune profile and skin barrier differences between these conditions. These findings may suggest new microbial disease biomarkers and reveal a new angle for intervention.
Collapse
Affiliation(s)
- M J Hooper
- Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - T M LeWitt
- Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Y Pang
- Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - F L Veon
- Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - G E Chlipala
- Research Informatics Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL, USA
| | - L Feferman
- Research Informatics Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL, USA
| | - S J Green
- Genomics and Microbiome Core Facility, Rush University Medical Center, Chicago, IL, USA
| | - D Sweeney
- Genome Research Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL, USA
| | - K T Bagnowski
- Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - M B Burns
- Department of Biology, Loyola University Chicago, Chicago, IL, USA
| | - P C Seed
- Division of Pediatric Infectious Diseases, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - J Choi
- Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - J Guitart
- Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - X A Zhou
- Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| |
Collapse
|
6
|
Hooper MJ, LeWitt TM, Veon FL, Pang Y, Chlipala GE, Feferman L, Green SJ, Sweeney D, Bagnowski KT, Burns MB, Seed PC, Guitart J, Zhou XA. Nasal dysbiosis in cutaneous T-cell lymphoma is characterized by shifts in relative abundances of non-Staphylococcus bacteria. JID Innovations 2022; 2:100132. [PMID: 36161104 PMCID: PMC9500465 DOI: 10.1016/j.xjidi.2022.100132] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 01/23/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 12/26/2022] Open
Abstract
The nasal microbiome of patients with cutaneous T-cell lymphoma (CTCL) remains unexplored despite growing evidence connecting nasal bacteria to skin health and disease. Nasal swabs from 45 patients with CTCL (40 with mycosis fungoides, 5 with Sézary syndrome) and 20 healthy controls from the same geographical region (Chicago Metropolitan Area, Chicago, IL) were analyzed using sequencing of 16S ribosomal RNA and tuf2 gene amplicons. Nasal α-diversity did not differ between mycosis fungoides/Sézary syndrome and healthy controls (Shannon index, genus level, P = 0.201), but distinct microbial communities were identified at the class (R2 = 0.104, P = 0.023) and order (R2 = 0.0904, P = 0.038) levels. Increased relative abundance of the genera Catenococcus, Vibrio, Roseomonas, Acinetobacter, and unclassified Clostridiales was associated with increased skin disease burden (P < 0.005, q < 0.05). Performed to accurately resolve nasal Staphylococcus at the species level, tuf2 gene amplicon sequencing revealed no significant differences between mycosis fungoides/Sézary syndrome and healthy controls. Although S. aureus has been shown to worsen CTCL through its toxins, no increase in the relative abundance of this taxon was observed in nasal samples. Despite the lack of differences in Staphylococcus, the CTCL nasal microbiome was characterized by shifts in numerous other bacterial taxa. These data add to our understanding of the greater CTCL microbiome and provide context for comprehending nasal-skin and host‒tumor‒microbial relationships.
Collapse
Affiliation(s)
- Madeline J. Hooper
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Tessa M. LeWitt
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Francesca L. Veon
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Yanzhen Pang
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - George E. Chlipala
- Research Informatics Core, Research Resources Center, University of Illinois Chicago, Chicago, Illinois, USA
| | - Leo Feferman
- Research Informatics Core, Research Resources Center, University of Illinois Chicago, Chicago, Illinois, USA
| | - Stefan J. Green
- Rush Genomics and Microbiome Core Facility, Rush University Medical Center, Chicago, Illinois, USA
| | - Dagmar Sweeney
- Genome Research Core, Genome Research Division, Research Resources Center, University of Illinois Chicago, Chicago, Illinois, USA
| | - Katherine T. Bagnowski
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Michael B. Burns
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Patrick C. Seed
- Division of Pediatric Infectious Diseases, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA
| | - Joan Guitart
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Xiaolong A. Zhou
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Correspondence: Xiaolong A. Zhou, Department of Dermatology, Northwestern University Feinberg School of Medicine, 676 North Street Clair Street, Suite 1600, Chicago, Illinois 60611, USA.
| |
Collapse
|
7
|
Sciurba JD, Chlipala GE, Green SJ, Delaney MA, Fortman JD, Purcell JE. Evaluation of Effects of Laboratory Disinfectants on Mouse Gut Microbiota. Comp Med 2021; 71:492-501. [PMID: 34763749 DOI: 10.30802/aalas-cm-21-000051] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Disturbances in the gut microbiota are known to be associated with numerous human diseases. Mice have proven to be an invaluable tool for investigating the role of the gut microbiota in disease processes. Nonexperimental factors related to maintaining mice in the laboratory environment are increasingly being shown to have inadvertent effects on the gut microbiotaand may function as confounding variables. Microisolation technique is a term used to describe the common biosecuritypractice of spraying gloved hands with disinfectant before handling research mice. This practice prevents contamination with pathogenic microorganisms. To investigate if exposure to disinfectants can affect the mouse gut microbiota, C57BL/6 micewere exposed daily for 27 consecutive days to commonly used laboratory disinfectants through microisolation technique.The effects of 70% ethanol and disinfectant products containing chlorine dioxide, hydrogen peroxide, or potassium peroxymonosulfate were each evaluated. Fecal pellets were collected after 7, 14, 21, and 28 d of disinfectant exposure, and cecal contents were collected at day 28. DNA extractions were performed on all cecal and fecal samples, and microbial community structure was characterized using 16S ribosomal RNA amplicon sequencing. Alpha and β diversity metrics and taxon-level analyses were used to evaluate differences in microbial communities. Disinfectant had a small but significant effect on fecal microbial communities compared with sham-exposed controls, and effects varied by disinfectant type. In general, longerexposure times resulted in greater changes in the fecal microbiota. Effects on the cecal microbiota were less pronounced and only seen with the hydrogen peroxide and potassium peroxymonosulfate disinfectants. These results indicate that laboratory disinfectant use should be considered as a potential factor that can affect the mouse gut microbiota.
Collapse
|
8
|
Kim JY, Lei Z, Maienschein-Cline M, Chlipala GE, Balamurugan A, McDiarmid SV, Azari K, Yang OO. Longitudinal Analysis of the T-cell Receptor Repertoire in Graft-infiltrating Lymphocytes Following Hand Transplantation. Transplantation 2021; 105:1502-1509. [PMID: 33208695 PMCID: PMC8221714 DOI: 10.1097/tp.0000000000003535] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 10/02/2020] [Indexed: 01/23/2023]
Abstract
BACKGROUND T lymphocyte-mediated acute rejection is a significant complication following solid organ transplantation. Standard methods of monitoring for acute rejection rely on assessing histological tissue damage but do not define the immunopathogenesis. Additionally, current therapies for rejection broadly blunt cellular immunity, creating a high risk for opportunistic infections. There is, therefore, a need to better understand the process of acute cellular rejection to help develop improved prognostic tests and narrowly targeted therapies. METHODS Through next-generation sequencing, we characterized and compared the clonal T-cell receptor (TCR) repertoires of graft-infiltrating lymphocytes (GILs) and blood-derived lymphocytes from a hand transplant recipient over 420 days following transplantation. We also tracked the TCR clonal persistence and V beta (BV) gene usage, evaluating overlap between these 2 compartments. RESULTS TCR repertoires of blood and GIL populations remained distinct throughout the sampling period, and differential BV usage was consistently seen between these compartments. GIL TCR clones persisted over time and were seen in only limited frequency in the blood T-lymphocyte populations. CONCLUSIONS We demonstrate that blood monitoring of TCR clones does not reveal the pathogenic process of acute cellular rejection in transplanted tissue. GILs show clonal persistence with biased BV usage, suggesting that tissue TCR clonal monitoring could be useful, although a deeper understanding is necessary to prognosticate rejection based on TCR clonal repertoires. Finally, the distinct TCR BV usage bias in GILs raises the possibility for prevention and therapy of acute cellular rejection based on targeting of specific TCR clones.
Collapse
Affiliation(s)
- Joseph Y. Kim
- Division of Infectious Diseases, Department of Medicine, University of Illinois College of Medicine Peoria, Peoria, IL
| | - Zhengdeng Lei
- Research Informatics Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL
| | - Mark Maienschein-Cline
- Research Informatics Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL
| | - George E. Chlipala
- Research Informatics Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL
| | - Arumugam Balamurugan
- Division of Infectious Diseases, Department of Medicine, Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Sue V. McDiarmid
- Department of Pediatrics, Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
- Department of Surgery, Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Kodi Azari
- Department of Surgery, Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
- Department of Orthopaedic Surgery, Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Otto O. Yang
- Division of Infectious Diseases, Department of Medicine, Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
- Department of Microbiology, Immunology, and Molecular Genetics, Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| |
Collapse
|
9
|
Reutrakul S, Chen H, Chirakalwasan N, Charoensri S, Wanitcharoenkul E, Amnakkittikul S, Saetung S, Layden BT, Chlipala GE. Metabolomic profile associated with obstructive sleep apnoea severity in obese pregnant women with gestational diabetes mellitus: A pilot study. J Sleep Res 2021; 30:e13327. [PMID: 33792106 DOI: 10.1111/jsr.13327] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 02/09/2021] [Accepted: 02/16/2021] [Indexed: 12/16/2022]
Abstract
Obstructive sleep apnoea (OSA) is prevalent in obese women with gestational diabetes mellitus (GDM). The present pilot study explored associations between OSA severity and metabolites in women with GDM. A total of 81 obese women with diet-controlled GDM had OSA assessment (median gestational age [GA] 29 weeks). The metabolic profile was assayed from fasting serum samples via liquid chromatography-mass spectrometry (LC-MS) using an untargeted approach. Metabolites were extracted and subjected to an Agilent 1,290 UPLC coupled to an Agilent 6,545 quadrupole time-of-flight (Q-TOF) MS. Data were acquired using electrospray ionisation in positive and negative ion modes. The raw LC-MS data were processed using the OpenMS toolkit to detect and quantify features, and these features were annotated using the Human Metabolite Database. The feature data were compared with OSA status, apnea-hypopnea index (AHI), body mass index (BMI) and GA using "limma" in R. Correlation analyses of the continuous covariates were performed using Kendall's Tau test. The p values were adjusted for multiple testing using the Benjamini-Hochberg false discovery rate correction. A total of 42 women (51.8%) had OSA, with a median AHI of 9.1 events/hr. There were no significant differences in metabolomics profiles between those with and without OSA. However, differential analyses modelling in GA and BMI found 12 features that significantly associated with the AHI. These features could be annotated to oestradiols, lysophospholipids, and fatty acids, with higher levels related to higher AHI. Metabolites including oestradiols and phospholipids may be involved in pathogenesis of OSA in pregnant women with GDM. A targeted approach may help elucidate our understanding of their role in OSA in this population.
Collapse
Affiliation(s)
- Sirimon Reutrakul
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Hui Chen
- Mass Spectrometry Core, Research Resource Center, Office of Vice Chancellor for Research, University of Illinois at Chicago, Chicago, IL, USA
| | - Naricha Chirakalwasan
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Excellence Center for Sleep Disorders, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Suranut Charoensri
- Division of Endocrinology and Metabolism, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Ekasitt Wanitcharoenkul
- Division of Endocrinology and Metabolism, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Somvang Amnakkittikul
- Division of Endocrinology and Metabolism, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Sunee Saetung
- Division of Endocrinology and Metabolism, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Brian T Layden
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA.,Jesse Brown Veterans Affairs Medical Center, Chicago, IL, USA
| | - George E Chlipala
- Research Informatics Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL, USA
| |
Collapse
|
10
|
Wolf PG, Devendran S, Doden HL, Ly LK, Moore T, Takei H, Nittono H, Murai T, Kurosawa T, Chlipala GE, Green SJ, Kakiyama G, Kashyap P, McCracken VJ, Gaskins HR, Gillevet PM, Ridlon JM. Berberine alters gut microbial function through modulation of bile acids. BMC Microbiol 2021; 21:24. [PMID: 33430766 PMCID: PMC7798349 DOI: 10.1186/s12866-020-02020-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 10/26/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Berberine (BBR) is a plant-based nutraceutical that has been used for millennia to treat diarrheal infections and in contemporary medicine to improve patient lipid profiles. Reduction in lipids, particularly cholesterol, is achieved partly through up-regulation of bile acid synthesis and excretion into the gastrointestinal tract (GI). The efficacy of BBR is also thought to be dependent on structural and functional alterations of the gut microbiome. However, knowledge of the effects of BBR on gut microbiome communities is currently lacking. Distinguishing indirect effects of BBR on bacteria through altered bile acid profiles is particularly important in understanding how dietary nutraceuticals alter the microbiome. RESULTS Germfree mice were colonized with a defined minimal gut bacterial consortium capable of functional bile acid metabolism (Bacteroides vulgatus, Bacteroides uniformis, Parabacteroides distasonis, Bilophila wadsworthia, Clostridium hylemonae, Clostridium hiranonis, Blautia producta; B4PC2). Multi-omics (bile acid metabolomics, 16S rDNA sequencing, cecal metatranscriptomics) were performed in order to provide a simple in vivo model from which to identify network-based correlations between bile acids and bacterial transcripts in the presence and absence of dietary BBR. Significant alterations in network topology and connectivity in function were observed, despite similarity in gut microbial alpha diversity (P = 0.30) and beta-diversity (P = 0.123) between control and BBR treatment. BBR increased cecal bile acid concentrations, (P < 0.05), most notably deoxycholic acid (DCA) (P < 0.001). Overall, analysis of transcriptomes and correlation networks indicates both bacterial species-specific responses to BBR, as well as functional commonalities among species, such as up-regulation of Na+/H+ antiporter, cell wall synthesis/repair, carbohydrate metabolism and amino acid metabolism. Bile acid concentrations in the GI tract increased significantly during BBR treatment and developed extensive correlation networks with expressed genes in the B4PC2 community. CONCLUSIONS This work has important implications for interpreting the effects of BBR on structure and function of the complex gut microbiome, which may lead to targeted pharmaceutical interventions aimed to achieve the positive physiological effects previously observed with BBR supplementation.
Collapse
Affiliation(s)
- Patricia G Wolf
- Institute for Health Research and Policy, University of Illinois Chicago, Chicago, IL, USA
- Cancer Education and Career Development Program, University of Illinois, Chicago, IL, USA
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Saravanan Devendran
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Structural and Computational Biology Research Unit, European Molecular Biology Laboratory, Heidelburg, Germany
| | - Heidi L Doden
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Lindsey K Ly
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Tyler Moore
- Center for Microbiome Analysis, George Mason University, Manassas, VA, USA
| | - Hajime Takei
- Junshin Clinic Bile Acid Institute, Meguro-Ku, Tokyo, 152-0011, Japan
| | - Hiroshi Nittono
- Junshin Clinic Bile Acid Institute, Meguro-Ku, Tokyo, 152-0011, Japan
| | - Tsuyoshi Murai
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Tobetsu, Japan
| | - Takao Kurosawa
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Tobetsu, Japan
| | - George E Chlipala
- University of Illinois Chicago Research Resources Center, University of Illinois Chicago, Chicago, IL, USA
| | - Stefan J Green
- University of Illinois Chicago Research Resources Center, University of Illinois Chicago, Chicago, IL, USA
| | - Genta Kakiyama
- Department of Internal Medicine, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Purna Kashyap
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Vance J McCracken
- Department of Biological Sciences, Southern Illinois University Edwardsville, Edwardsville, IL, USA
| | - H Rex Gaskins
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Pathobiology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Cancer Center of Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Patrick M Gillevet
- Structural and Computational Biology Research Unit, European Molecular Biology Laboratory, Heidelburg, Germany
| | - Jason M Ridlon
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Cancer Center of Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.
| |
Collapse
|
11
|
Teran RA, Ghinai I, Gretsch S, Cable T, Black SR, Green SJ, Perez O, Chlipala GE, Maienschein-Cline M, Kunstman KJ, Bleasdale SC, Fricchione MJ. COVID-19 Outbreak Among a University's Men's and Women's Soccer Teams - Chicago, Illinois, July-August 2020. MMWR Morb Mortal Wkly Rep 2020; 69:1591-1594. [PMID: 34463672 PMCID: PMC7659918 DOI: 10.15585/mmwr.mm6943e5] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
12
|
Ridlon JM, Devendran S, Alves JM, Doden H, Wolf PG, Pereira GV, Ly L, Volland A, Takei H, Nittono H, Murai T, Kurosawa T, Chlipala GE, Green SJ, Hernandez AG, Fields CJ, Wright CL, Kakiyama G, Cann I, Kashyap P, McCracken V, Gaskins HR. The ' in vivo lifestyle' of bile acid 7α-dehydroxylating bacteria: comparative genomics, metatranscriptomic, and bile acid metabolomics analysis of a defined microbial community in gnotobiotic mice. Gut Microbes 2020; 11:381-404. [PMID: 31177942 PMCID: PMC7524365 DOI: 10.1080/19490976.2019.1618173] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The formation of secondary bile acids by gut microbes is a current topic of considerable biomedical interest. However, a detailed understanding of the biology of anaerobic bacteria in the genus Clostridium that are capable of generating secondary bile acids is lacking. We therefore sought to determine the transcriptional responses of two prominent secondary bile acid producing bacteria, Clostridium hylemonae and Clostridium hiranonis to bile salts (in vitro) and the cecal environment of gnotobiotic mice. The genomes of C. hylemonae DSM 15053 and C. hiranonis DSM 13275 were closed, and found to encode 3,647 genes (3,584 protein-coding) and 2,363 predicted genes (of which 2,239 are protein-coding), respectively, and 1,035 orthologs were shared between C. hylemonae and C. hiranonis. RNA-Seq analysis was performed in growth medium alone, and in the presence of cholic acid (CA) and deoxycholic acid (DCA). Growth with CA resulted in differential expression (>0.58 log2FC; FDR < 0.05) of 197 genes in C. hiranonis and 118 genes in C. hylemonae. The bile acid-inducible operons (bai) from each organism were highly upregulated in the presence of CA but not DCA. We then colonized germ-free mice with human gut bacterial isolates capable of metabolizing taurine-conjugated bile acids. This consortium included bile salt hydrolase-expressing Bacteroides uniformis ATCC 8492, Bacteroides vulgatus ATCC 8482, Parabacteroides distasonis DSM 20701, as well as taurine-respiring Bilophila wadsworthia DSM 11045, and deoxycholic/lithocholic acid generating Clostridium hylemonae DSM 15053 and Clostridium hiranonis DSM 13275. Butyrate and iso-bile acid-forming Blautia producta ATCC 27340 was also included. The Bacteroidetes made up 84.71% of 16S rDNA cecal reads, B. wadsworthia, constituted 14.7%, and the clostridia made up <.75% of 16S rDNA cecal reads. Bile acid metabolomics of the cecum, serum, and liver indicate that the synthetic community were capable of functional bile salt deconjugation, oxidation/isomerization, and 7α-dehydroxylation of bile acids. Cecal metatranscriptome analysis revealed expression of genes involved in metabolism of taurine-conjugated bile acids. The in vivo transcriptomes of C. hylemonae and C. hiranonis suggest fermentation of simple sugars and utilization of amino acids glycine and proline as electron acceptors. Genes predicted to be involved in trimethylamine (TMA) formation were also expressed.
Collapse
Affiliation(s)
- Jason M. Ridlon
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA,CONTACT Jason M. Ridlon, Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology
| | - Saravanan Devendran
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - João Mp Alves
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Heidi Doden
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Patricia G. Wolf
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gabriel V. Pereira
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Lindsey Ly
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Alyssa Volland
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hajime Takei
- Junshin Clinic Bile Acid Institute, Meguro-Ku, Tokyo, Japan
| | | | - Tsuyoshi Murai
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Ishikari-Tobetsu, Hokkaido, Japan
| | - Takao Kurosawa
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Ishikari-Tobetsu, Hokkaido, Japan
| | - George E. Chlipala
- UIC Research Resources Center, University of Illinois at Chicago, Chicago, IL, USA
| | - Stefan J. Green
- UIC Research Resources Center, University of Illinois at Chicago, Chicago, IL, USA
| | - Alvaro G. Hernandez
- Keck Center for Biotechnology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Christopher J. Fields
- Keck Center for Biotechnology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Christy L. Wright
- Keck Center for Biotechnology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Genta Kakiyama
- Department of Internal Medicine, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Isaac Cann
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Keck Center for Biotechnology, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Purna Kashyap
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN, USA,Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Vance McCracken
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN, USA,Department of Biological Sciences, Southern Illinois University Edwardsville, Edwardsville, IL, USA
| | - H. Rex Gaskins
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| |
Collapse
|
13
|
Parikh IJ, Estus JL, Zajac DJ, Malik M, Maldonado Weng J, Tai LM, Chlipala GE, LaDu MJ, Green SJ, Estus S. Murine Gut Microbiome Association With APOE Alleles. Front Immunol 2020; 11:200. [PMID: 32117315 PMCID: PMC7034241 DOI: 10.3389/fimmu.2020.00200] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 01/27/2020] [Indexed: 12/19/2022] Open
Abstract
Background: Since APOE alleles represent the most impactful genetic risk factors for Alzheimer's disease (AD), their differential mechanism(s) of action are under intense scrutiny. APOE4 is robustly associated with increased AD risk compared to the neutral APOE3 and protective APOE2. APOE alleles have also been associated with differential inflammation and gastrointestinal recovery after insult in human and murine studies, leading us to hypothesize that APOE alleles impact the gut microbiome. Methods: To assess this hypothesis, we compared 16S ribosomal RNA gene amplicon-based microbiome profiles in a cohort of mice that were homozygous for APOE2, APOE3, or APOE4, and included both males and females as well as carriers and non-carriers of five familial AD (5xFAD) mutations. Fecal samples were analyzed from mice at 4 and 6 months of age. APOE genotype, as well as sex and 5xFAD status, was then tested for influence on alpha diversity (Shannon H index) and beta diversity (principal coordinate analyses and PERMANOVA). A Random Forest analysis was used to identify features that predicted APOE, sex and 5xFAD status. Results: The richness and evenness (alpha diversity) of the fecal microbiome was not robustly associated with APOE genotype, 5xFAD status or sex. In contrast, microbial community composition (beta-diversity) was consistently and strongly associated with APOE genotype. The association between beta-diversity and sex or 5xFAD status was less consistent and more modest. Comparison of the differences underlying APOE effects showed that the relative abundance of multiple bacterial taxa was significantly different as a function of APOE genotype. Conclusions: The structure of the gut microbiome was strongly and significantly associated with APOE alleles in this murine model. Further evaluation of these findings in humans, as well as studies evaluating the impact of the APOE-associated microbiota on AD-relevant phenotypes in murine models, will be necessary to determine if alterations in the gut microbiome represent a novel mechanism whereby APOE genotype impacts AD.
Collapse
Affiliation(s)
- Ishita J. Parikh
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, United States
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, United States
| | - Janice L. Estus
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, United States
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, United States
| | - Diana J. Zajac
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, United States
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, United States
| | - Manasi Malik
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, United States
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, United States
| | - Juan Maldonado Weng
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Leon M. Tai
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - George E. Chlipala
- Research Resources Center, University of Illinois at Chicago, Chicago, IL, United States
| | - Mary Jo LaDu
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Stefan J. Green
- Research Resources Center, University of Illinois at Chicago, Chicago, IL, United States
| | - Steven Estus
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, United States
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, United States
| |
Collapse
|
14
|
Barengolts E, Green SJ, Chlipala GE, Layden BT, Eisenberg Y, Priyadarshini M, Dugas LR. Predictors of Obesity among Gut Microbiota Biomarkers in African American Men with and without Diabetes. Microorganisms 2019; 7:microorganisms7090320. [PMID: 31491976 PMCID: PMC6780321 DOI: 10.3390/microorganisms7090320] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 08/27/2019] [Accepted: 08/30/2019] [Indexed: 02/06/2023] Open
Abstract
Gut microbiota and their biomarkers may be associated with obesity. This study evaluated associations of body mass index (BMI) with circulating microbiota biomarkers in African American men (AAM) (n = 75). The main outcomes included fecal microbial community structure (16S rRNA), gut permeability biomarkers (ELISA), and short-chain fatty acids (SCFAs, metabolome analysis). These outcomes were compared between obese and non-obese men, after adjusting for age. The results showed that lipopolysaccharide-binding protein (LBP), the ratio of LBP to CD14 (LBP/CD14), and SCFAs (propionic, butyric, isovaleric) were higher in obese (n = 41, age 58 years, BMI 36 kg/m2) versus non-obese (n = 34, age 55 years, BMI 26 kg/m2) men. BMI correlated positively with LBP, LBP/CD14 (p < 0.05 for both) and SCFAs (propionic, butyric, isovaleric, p < 0.01 for all). In the regression analysis, LBP, LBP/CD14, propionic and butyric acids were independent determinants of BMI. The study showed for the first time that selected microbiota biomarkers (LBP, LBP/CD14, propionic and butyric acids) together with several other relevant risks explained 39%–47% of BMI variability, emphasizing that factors other than microbiota-related biomarkers could be important. Further research is needed to provide clinical and mechanistic insight into microbiota biomarkers and their utility for diagnostic and therapeutic purposes.
Collapse
Affiliation(s)
- Elena Barengolts
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA.
- Section of Endocrinology, Department of Medicine, Jesse Brown VA Medical Center, Chicago, IL 60612, USA.
| | - Stefan J Green
- Sequencing Core, Research Resources Center, University of Illinois, Chicago, IL 60612, USA
| | - George E Chlipala
- Research Informatics Core, Research Resources Center, University of Illinois, Chicago, IL 60612, USA
| | - Brian T Layden
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
- Section of Endocrinology, Department of Medicine, Jesse Brown VA Medical Center, Chicago, IL 60612, USA
| | - Yuval Eisenberg
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Medha Priyadarshini
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Lara R Dugas
- Department of Public Health Sciences, Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, IL 60153, USA
| |
Collapse
|
15
|
Jiang P, Green SJ, Chlipala GE, Turek FW, Vitaterna MH. Reproducible changes in the gut microbiome suggest a shift in microbial and host metabolism during spaceflight. Microbiome 2019; 7:113. [PMID: 31399081 PMCID: PMC6689164 DOI: 10.1186/s40168-019-0724-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 07/23/2019] [Indexed: 05/11/2023]
Abstract
BACKGROUND Space environment imposes a range of challenges to mammalian physiology and the gut microbiota, and interactions between the two are thought to be important in mammalian health in space. While previous findings have demonstrated a change in the gut microbial community structure during spaceflight, specific environmental factors that alter the gut microbiome and the functional relevance of the microbiome changes during spaceflight remain elusive. METHODS We profiled the microbiome using 16S rRNA gene amplicon sequencing in fecal samples collected from mice after a 37-day spaceflight onboard the International Space Station. We developed an analytical tool, named STARMAPs (Similarity Test for Accordant and Reproducible Microbiome Abundance Patterns), to compare microbiome changes reported here to other relevant datasets. We also integrated the gut microbiome data with the publically available transcriptomic data in the liver of the same animals for a systems-level analysis. RESULTS We report an elevated microbiome alpha diversity and an altered microbial community structure that were associated with spaceflight environment. Using STARMAPs, we found the observed microbiome changes shared similarity with data reported in mice flown in a previous space shuttle mission, suggesting reproducibility of the effects of spaceflight on the gut microbiome. However, such changes were not comparable with those induced by space-type radiation in Earth-based studies. We found spaceflight led to significantly altered taxon abundance in one order, one family, five genera, and six species of microbes. This was accompanied by a change in the inferred microbial gene abundance that suggests an altered capacity in energy metabolism. Finally, we identified host genes whose expression in the liver were concordantly altered with the inferred gut microbial gene content, particularly highlighting a relationship between host genes involved in protein metabolism and microbial genes involved in putrescine degradation. CONCLUSIONS These observations shed light on the specific environmental factors that contributed to a robust effect on the gut microbiome during spaceflight with important implications for mammalian metabolism. Our findings represent a key step toward a better understanding the role of the gut microbiome in mammalian health during spaceflight and provide a basis for future efforts to develop microbiota-based countermeasures that mitigate risks to crew health during long-term human space expeditions.
Collapse
Affiliation(s)
- Peng Jiang
- Center for Sleep and Circadian Biology, Department of Neurobiology, Northwestern University, Evanston, IL USA
| | - Stefan J. Green
- Sequencing Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL USA
| | - George E. Chlipala
- Sequencing Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL USA
| | - Fred W. Turek
- Center for Sleep and Circadian Biology, Department of Neurobiology, Northwestern University, Evanston, IL USA
| | - Martha Hotz Vitaterna
- Center for Sleep and Circadian Biology, Department of Neurobiology, Northwestern University, Evanston, IL USA
| |
Collapse
|
16
|
Sedghi L, Byron C, Jennings R, Chlipala GE, Green SJ, Silo-Suh L. Effect of Dietary Fiber on the Composition of the Murine Dental Microbiome. Dent J (Basel) 2019; 7:dj7020058. [PMID: 31159370 PMCID: PMC6630570 DOI: 10.3390/dj7020058] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/25/2019] [Accepted: 05/13/2019] [Indexed: 11/16/2022] Open
Abstract
The oral cavity houses a diverse consortium of microorganisms, heavily influenced by host diet, that can mediate dental health and disease. While the impact of dietary carbohydrates to the dental microbiome has been well-documented, the effect of fiber as a mechanical influence on the dental microbiome is unexplored. We performed 16S rRNA gene analysis to investigate the response of the dental microbiome to the presence of increased fiber in terms of microbial taxonomic abundance and diversity. Dental microbial community structure was significantly different in mice fed a diet supplemented with increased fiber and/or sugar. Fiber significantly affected measures of beta diversity at the phylum and genus levels, and a strong interactive effect on alpha diversity was observed between sugar and fiber at the phylum level. The addition of fiber also induced significant variation in relative taxonomic abundance. This study demonstrates that fiber can promote significant variations in the mouse dental microbiome.
Collapse
Affiliation(s)
- Lea Sedghi
- Department of BioMedical Sciences, School of Medicine, Mercer University, Macon, GA 31207, USA.
| | - Craig Byron
- Department of Biology, Mercer University, Macon, GA 31207, USA.
| | - Ryan Jennings
- Department of Biology, Frostburg State University, Frostburg, MD 21532-2303, USA.
| | - George E Chlipala
- Research Resources Center, University of Illinois at Chicago, Chicago, IL 60612-3748, USA.
| | - Stefan J Green
- Research Resources Center, University of Illinois at Chicago, Chicago, IL 60612-3748, USA.
| | - Laura Silo-Suh
- Department of BioMedical Sciences, School of Medicine, Mercer University, Macon, GA 31207, USA.
| |
Collapse
|
17
|
Garrett-Bakelman FE, Darshi M, Green SJ, Gur RC, Lin L, Macias BR, McKenna MJ, Meydan C, Mishra T, Nasrini J, Piening BD, Rizzardi LF, Sharma K, Siamwala JH, Taylor L, Vitaterna MH, Afkarian M, Afshinnekoo E, Ahadi S, Ambati A, Arya M, Bezdan D, Callahan CM, Chen S, Choi AMK, Chlipala GE, Contrepois K, Covington M, Crucian BE, De Vivo I, Dinges DF, Ebert DJ, Feinberg JI, Gandara JA, George KA, Goutsias J, Grills GS, Hargens AR, Heer M, Hillary RP, Hoofnagle AN, Hook VYH, Jenkinson G, Jiang P, Keshavarzian A, Laurie SS, Lee-McMullen B, Lumpkins SB, MacKay M, Maienschein-Cline MG, Melnick AM, Moore TM, Nakahira K, Patel HH, Pietrzyk R, Rao V, Saito R, Salins DN, Schilling JM, Sears DD, Sheridan CK, Stenger MB, Tryggvadottir R, Urban AE, Vaisar T, Van Espen B, Zhang J, Ziegler MG, Zwart SR, Charles JB, Kundrot CE, Scott GBI, Bailey SM, Basner M, Feinberg AP, Lee SMC, Mason CE, Mignot E, Rana BK, Smith SM, Snyder MP, Turek FW. The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight. Science 2019; 364:364/6436/eaau8650. [PMID: 30975860 DOI: 10.1126/science.aau8650] [Citation(s) in RCA: 399] [Impact Index Per Article: 79.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 02/28/2019] [Indexed: 12/11/2022]
Abstract
To understand the health impact of long-duration spaceflight, one identical twin astronaut was monitored before, during, and after a 1-year mission onboard the International Space Station; his twin served as a genetically matched ground control. Longitudinal assessments identified spaceflight-specific changes, including decreased body mass, telomere elongation, genome instability, carotid artery distension and increased intima-media thickness, altered ocular structure, transcriptional and metabolic changes, DNA methylation changes in immune and oxidative stress-related pathways, gastrointestinal microbiota alterations, and some cognitive decline postflight. Although average telomere length, global gene expression, and microbiome changes returned to near preflight levels within 6 months after return to Earth, increased numbers of short telomeres were observed and expression of some genes was still disrupted. These multiomic, molecular, physiological, and behavioral datasets provide a valuable roadmap of the putative health risks for future human spaceflight.
Collapse
Affiliation(s)
- Francine E Garrett-Bakelman
- Weill Cornell Medicine, New York, NY, USA.,University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Manjula Darshi
- Center for Renal Precision Medicine, University of Texas Health, San Antonio, TX, USA
| | | | - Ruben C Gur
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ling Lin
- Stanford University School of Medicine, Palo Alto, CA, USA
| | | | | | - Cem Meydan
- Weill Cornell Medicine, New York, NY, USA.,The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | | | - Jad Nasrini
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | | | - Kumar Sharma
- Center for Renal Precision Medicine, University of Texas Health, San Antonio, TX, USA
| | | | - Lynn Taylor
- Colorado State University, Fort Collins, CO, USA
| | | | | | - Ebrahim Afshinnekoo
- Weill Cornell Medicine, New York, NY, USA.,The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Sara Ahadi
- Stanford University School of Medicine, Palo Alto, CA, USA
| | - Aditya Ambati
- Stanford University School of Medicine, Palo Alto, CA, USA
| | | | - Daniela Bezdan
- Weill Cornell Medicine, New York, NY, USA.,The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | | | - Songjie Chen
- Stanford University School of Medicine, Palo Alto, CA, USA
| | | | | | | | - Marisa Covington
- National Aeronautics and Space Administration (NASA), Houston, TX, USA
| | - Brian E Crucian
- National Aeronautics and Space Administration (NASA), Houston, TX, USA
| | | | - David F Dinges
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | | | | | | | | | | | | | | | - Ryan P Hillary
- Stanford University School of Medicine, Palo Alto, CA, USA
| | | | | | | | - Peng Jiang
- Northwestern University, Evanston, IL, USA
| | | | | | | | | | | | | | | | - Tyler M Moore
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Hemal H Patel
- University of California, San Diego, La Jolla, CA, USA
| | | | - Varsha Rao
- Stanford University School of Medicine, Palo Alto, CA, USA
| | - Rintaro Saito
- University of California, San Diego, La Jolla, CA, USA
| | - Denis N Salins
- Stanford University School of Medicine, Palo Alto, CA, USA
| | | | | | | | - Michael B Stenger
- National Aeronautics and Space Administration (NASA), Houston, TX, USA
| | | | | | | | | | - Jing Zhang
- Stanford University School of Medicine, Palo Alto, CA, USA
| | | | - Sara R Zwart
- University of Texas Medical Branch, Galveston, TX, USA
| | - John B Charles
- National Aeronautics and Space Administration (NASA), Houston, TX, USA.
| | - Craig E Kundrot
- Space Life and Physical Sciences Division, NASA Headquarters, Washington, DC, USA.
| | - Graham B I Scott
- National Space Biomedical Research Institute, Baylor College of Medicine, Houston, TX, USA.
| | | | - Mathias Basner
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| | | | | | - Christopher E Mason
- Weill Cornell Medicine, New York, NY, USA. .,The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.,The Feil Family Brain and Mind Research Institute, New York, NY, USA.,The WorldQuant Initiative for Quantitative Prediction, New York, NY, USA
| | | | - Brinda K Rana
- University of California, San Diego, La Jolla, CA, USA.
| | - Scott M Smith
- National Aeronautics and Space Administration (NASA), Houston, TX, USA.
| | | | | |
Collapse
|
18
|
Zhang X, Li Z, Du L, Chlipala GE, Lopez PC, Zhang W, Sherman DH, Li S. Identification of an unexpected shunt pathway product provides new insights into tirandamycin biosynthesis. Tetrahedron Lett 2016; 57:5919-5923. [PMID: 28989201 PMCID: PMC5628624 DOI: 10.1016/j.tetlet.2016.11.080] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Tirandamycin K (7), the first linear 7,13;9,13-diseco-tirandamycin derivative, was isolated from the tamI (encoding the TamI P450 monooxygenase) disruption mutant strain (ΔtamI) of marine Streptomyces sp. 307-9. Its chemical structure with relative and absolute configurations was elucidated by a combination of extensive spectroscopic analyses and biosynthetic inferences. Structural elucidation of this unusual compound provides new insights into tirandamycin biosynthesis. Moreover, examination of the biological activity of 7 confirms the essential function of the bicyclic ketal ring for antibiotic activities of tirandamycins.
Collapse
Affiliation(s)
- Xingwang Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, and CAS Key Laboratory of Biofuels at Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Zhong Li
- Shandong Provincial Key Laboratory of Synthetic Biology, and CAS Key Laboratory of Biofuels at Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Du
- Shandong Provincial Key Laboratory of Synthetic Biology, and CAS Key Laboratory of Biofuels at Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - George E. Chlipala
- Life Sciences Institute, Departments of Medicinal Chemistry, Chemistry, and Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Patricia C. Lopez
- Life Sciences Institute, Departments of Medicinal Chemistry, Chemistry, and Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Wei Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, and CAS Key Laboratory of Biofuels at Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - David H. Sherman
- Life Sciences Institute, Departments of Medicinal Chemistry, Chemistry, and Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shengying Li
- Shandong Provincial Key Laboratory of Synthetic Biology, and CAS Key Laboratory of Biofuels at Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| |
Collapse
|
19
|
Abstract
Microseiramide (1), a cyclic heptapeptide, was isolated from a sample of the freshwater cyanobacterium Microseira sp. UIC 10445 collected in a shallow lake in Northern Indiana. Taxonomic identification of UIC 10445 was performed by a combination of morphological and phylogenetic characterization. Phylogenetic analysis revealed that UIC 10445 was a member of the recently described genus Microseira, which is phylogenetically distinct from the morphologically similar genera. Moorea and Lyngbya. The planar structure of microseiramide (1) was determined by extensive 1D and 2D NMR experiments as well as HRESIMS analysis. The absolute configurations of amino acid residues were determined using acid hydrolysis followed by the advanced Marfey's analysis. microseiramide (1) is the first cyclic peptide reported from a Microseira sp., and the structure of microseiramide (1) is distinct from the previously known metabolites from cyanobacteria of the genera Moorea and Lyngbya.
Collapse
Affiliation(s)
| | | | | | - Jimmy Orjala
- To whom correspondence should be addressed. Tel: +1-312-996-5583. Fax: +1-312-996-7107.
| |
Collapse
|
20
|
Tripathi A, Schofield MM, Chlipala GE, Schultz PJ, Yim I, Newmister SA, Nusca TD, Scaglione JB, Hanna PC, Tamayo-Castillo G, Sherman DH. Correction to “Baulamycins A and B, Broad-Spectrum Antibiotics Identified as Inhibitors of Siderophore Biosynthesis in Staphylococcus aureus and Bacillus anthracis”. J Am Chem Soc 2014. [PMCID: PMC4353028 DOI: 10.1021/ja505297x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
21
|
Tripathi A, Schofield MM, Chlipala GE, Schultz PJ, Yim I, Newmister SA, Nusca TD, Scaglione JB, Hanna PC, Tamayo-Castillo G, Sherman DH. Baulamycins A and B, broad-spectrum antibiotics identified as inhibitors of siderophore biosynthesis in Staphylococcus aureus and Bacillus anthracis. J Am Chem Soc 2014; 136:1579-86. [PMID: 24401083 PMCID: PMC4028973 DOI: 10.1021/ja4115924] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Siderophores are high-affinity iron chelators produced by microorganisms and frequently contribute to the virulence of human pathogens. Targeted inhibition of the biosynthesis of siderophores staphyloferrin B of Staphylococcus aureus and petrobactin of Bacillus anthracis hold considerable potential as a single or combined treatment for methicillin-resistant S. aureus (MRSA) and anthrax infection, respectively. The biosynthetic pathways for both siderophores involve a nonribosomal peptide synthetase independent siderophore (NIS) synthetase, including SbnE in staphyloferrin B and AsbA in petrobactin. In this study, we developed a biochemical assay specific for NIS synthetases to screen for inhibitors of SbnE and AsbA against a library of marine microbial-derived natural product extracts (NPEs). Analysis of the NPE derived from Streptomyces tempisquensis led to the isolation of the novel antibiotics baulamycins A (BmcA, 6) and B (BmcB, 7). BmcA and BmcB displayed in vitro activity with IC50 values of 4.8 μM and 19 μM against SbnE and 180 μM and 200 μM against AsbA, respectively. Kinetic analysis showed that the compounds function as reversible competitive enzyme inhibitors. Liquid culture studies with S. aureus , B. anthracis , E. coli , and several other bacterial pathogens demonstrated the capacity of these natural products to penetrate bacterial barriers and inhibit growth of both Gram-positive and Gram-negative species. These studies provide proof-of-concept that natural product inhibitors targeting siderophore virulence factors can provide access to novel broad-spectrum antibiotics, which may serve as important leads for the development of potent anti-infective agents.
Collapse
Affiliation(s)
- Ashootosh Tripathi
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109
| | - Michael M. Schofield
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - George E. Chlipala
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109
| | - Pamela J. Schultz
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109
| | - Isaiah Yim
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109
| | - Sean A. Newmister
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109
| | - Tyler D. Nusca
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Jamie B. Scaglione
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109
| | - Philip C. Hanna
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Giselle Tamayo-Castillo
- Unidad Estrategica de Bioprospección, Instituto Nacional de Biodiversidad (INBio), Santo Domingo de Heredia, Costa Rica & CIPRONA, Escuela de Química, Universidad de Costa Rica, 2060 San Pedro, Costa Rica
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
- Departments of Medicinal Chemistry and Chemistry, University of Michigan, Ann Arbor, MI 48109
| |
Collapse
|
22
|
Luo S, Kang HS, Krunic A, Chlipala GE, Cai G, Chen WL, Franzblau SG, Swanson SM, Orjala J. Carbamidocyclophanes F and G with Anti- Mycobacterium tuberculosis Activity from the Cultured Freshwater Cyanobacterium Nostoc sp. Tetrahedron Lett 2014; 55:686-689. [PMID: 25225453 PMCID: PMC4161986 DOI: 10.1016/j.tetlet.2013.11.112] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Two new (1 and 2) and three known (3-5) carbamidocyclophanes were isolated from a cultured freshwater cyanobacterium Nostoc sp. (UIC 10274) obtained from a sample collected at Des Plaines, Illinois. Their planar structures and stereoconfigurations were determined by extensive spectroscopic analysis including 1D/2D NMR experiments, HRESIMS as well as CD spectroscopy. Carbamidocyclophane F (1) showed potent anti-Mycobacterium tuberculosis activity in the microplate Alamar blue assay and low-oxygen-recovery assay with MIC values of 0.8 and 5.4 µM, respectively. Carbamidocyclophane F (1) also displayed antimicrobial activities against the gram positive bacteria Staphylococcus aureus and Enterococcus faecalis with MIC values of 0.1 and 0.2 µM, respectively. Carbamidocyclophane F (1) and Carbamidocyclophane G (2) both showed antiproliferative activity against MDA-MB-435 and HT-29 human cancer cell lines with IC50 values in the range from 0.5 to 0.7 µM.
Collapse
Affiliation(s)
- Shangwen Luo
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612
| | - Hahk-Soo Kang
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612
| | - Aleksej Krunic
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612
| | - George E. Chlipala
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612
| | - Geping Cai
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612
| | - Wei-Lun Chen
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612
| | - Scott G. Franzblau
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612
| | - Steven M. Swanson
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612
| | - Jimmy Orjala
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612
| |
Collapse
|
23
|
Chemler JA, Buchholz TJ, Geders TW, Akey DL, Rath CM, Chlipala GE, Smith JL, Sherman DH. Biochemical and structural characterization of germicidin synthase: analysis of a type III polyketide synthase that employs acyl-ACP as a starter unit donor. J Am Chem Soc 2012; 134:7359-66. [PMID: 22480290 DOI: 10.1021/ja2112228] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Germicidin synthase (Gcs) from Streptomyces coelicolor is a type III polyketide synthase (PKS) with broad substrate flexibility for acyl groups linked through a thioester bond to either coenzyme A (CoA) or acyl carrier protein (ACP). Germicidin synthesis was reconstituted in vitro by coupling Gcs with fatty acid biosynthesis. Since Gcs has broad substrate flexibility, we directly compared the kinetic properties of Gcs with both acyl-ACP and acyl-CoA. The catalytic efficiency of Gcs for acyl-ACP was 10-fold higher than for acyl-CoA, suggesting a strong preference toward carrier protein starter unit transfer. The 2.9 Å germicidin synthase crystal structure revealed canonical type III PKS architecture along with an unusual helical bundle of unknown function that appears to extend the dimerization interface. A pair of arginine residues adjacent to the active site affect catalytic activity but not ACP binding. This investigation provides new and surprising information about the interactions between type III PKSs and ACPs that will facilitate the construction of engineered systems for production of novel polyketides.
Collapse
Affiliation(s)
- Joseph A Chemler
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | | | | | | | | | | | | |
Collapse
|
24
|
Chlipala GE, Mo S, Orjala J. Chemodiversity in freshwater and terrestrial cyanobacteria - a source for drug discovery. Curr Drug Targets 2011; 12:1654-73. [PMID: 21561419 PMCID: PMC3244969 DOI: 10.2174/138945011798109455] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Accepted: 03/02/2011] [Indexed: 12/16/2022]
Abstract
Cyanobacteria are considered a promising source for new pharmaceutical lead compounds and a large number of chemically diverse and bioactive metabolites have been obtained from cyanobacteria over the last few decades. This review highlights the structural diversity of natural products from freshwater and terrestrial cyanobacteria. The review is divided into three areas: cytotoxic metabolites, protease inhibitors, and antimicrobial metabolites. The first section discusses the potent cytotoxins cryptophycin and tolytoxin. The second section covers protease inhibitors from freshwater and terrestrial cyanobacteria and is divided in five subsections according to structural class: aeruginosins, cyanopeptolins, microviridins, anabaenopeptins, and microginins. Structure activity relationships are discussed within each protease inhibitor class. The third section, antimicrobial metabolites from freshwater and terrestrial cyanobacteria, is divided by chemical class in three subsections: alkaloids, peptides and terpenoids. These examples emphasize the structural diversity and drug development potential of natural products from freshwater and terrestrial cyanobacteria.
Collapse
Affiliation(s)
- George E. Chlipala
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood St., Chicago, Illinois, 60612
| | - Shunyan Mo
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood St., Chicago, Illinois, 60612
| | - Jimmy Orjala
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood St., Chicago, Illinois, 60612
| |
Collapse
|
25
|
Chlipala GE, Krunic A, Mo S, Sturdy M, Orjala J. CYANOS: a data management system for natural product drug discovery efforts using cultured microorganisms. J Chem Inf Model 2010; 51:171-80. [PMID: 21162567 DOI: 10.1021/ci100280a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A software package, termed "CYANOS", has been developed to facilitate the data management and mining for natural product drug discovery efforts. This system allows for the management of data associated with field collections, culture conditions, harvests, extractions, chemical separations, and biological evaluation. This software utilizes a MySQL database for data storage, which allows for reporting and data mining via third party tools. In addition, a Web-based interface was constructed to allow for multiuser access from a variety of desktop platforms. The code for this system is freely available and has been released under the Illinois Open Source license.
Collapse
Affiliation(s)
- George E Chlipala
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois, United States
| | | | | | | | | |
Collapse
|
26
|
Chlipala GE, Sturdy M, Krunic A, Lantvit DD, Shen Q, Porter K, Swanson SM, Orjala J. Cylindrocyclophanes with proteasome inhibitory activity from the Cyanobacterium Nostoc sp. J Nat Prod 2010; 73:1529-37. [PMID: 20825206 PMCID: PMC2964865 DOI: 10.1021/np100352e] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Material collected from a parkway in the city of Chicago afforded the isolation of a Nostoc species (UIC 10022A). The extract of this strain displayed significant inhibition of the 20S proteasome as well as antiproliferative activity against HT29, MCF7, NCI-H460, and SF268 cancer cell lines. A standardized dereplication protocol allowed for the rapid identification of three known (11-13) and nine new (1-9) chlorinated cylindrocyclophanes from less than 100 mg of organic extract. Scale-up isolation of 1-9 and 11-13 from a larger extract was guided by LC-UV-MS data. In addition, KBr enrichment of the culture media afforded the isolation of a brominated cylindrocyclophane (10). Biological evaluation of 1-5, 9, and 10-13 revealed a large range of activity against the 20S proteasome and allowed the determination of preliminary structure-activity relationships of the cylindrocyclophane pharmacophore.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Jimmy Orjala
- To whom correspondence should be addressed. Tel: 1-312-996-5583. Fax: 1-312-413-4034.
| |
Collapse
|
27
|
Chlipala GE, Tri PH, Van Hung N, Krunic A, Shim SH, Soejarto DD, Orjala J. Nhatrangins A and B, aplysiatoxin-related metabolites from the marine cyanobacterium Lyngbya majuscula from Vietnam. J Nat Prod 2010; 73:784-7. [PMID: 20373744 PMCID: PMC2977956 DOI: 10.1021/np100002q] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Two polyketide metabolites, nhatrangins A (1) and B (2), were isolated from a Vietnamese collection of Lyngbya majuscula. These compounds are related to the aplysiatoxin series of metabolites, which have also been isolated from this species of marine cyanobacterium. The use of 900 MHz cryoprobe NMR allowed the elucidation of the 2D structure of 1 from approximately 0.3 mg of compound. LC-MS analysis was utilized to direct the isolation of additional material as well as the isolation of 2. Conformational analysis was completed using J-based coupling constant analysis and selective NOE experiments.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Jimmy Orjala
- To whom correspondence should be addressed. Tel: 1-312-996-5583. Fax: 1-312-413-4034.
| |
Collapse
|