1
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Gellman RH, Olm MR, Terrapon N, Enam F, Higginbottom SK, Sonnenburg JL, Sonnenburg ED. Hadza Prevotella require diet-derived microbiota-accessible carbohydrates to persist in mice. Cell Rep 2023; 42:113233. [PMID: 38510311 PMCID: PMC10954246 DOI: 10.1016/j.celrep.2023.113233] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024] Open
Abstract
Industrialization has transformed the gut microbiota, reducing the prevalence of Prevotella relative to Bacteroides. Here, we isolate Bacteroides and Prevotella strains from the microbiota of Hadza hunter-gatherers in Tanzania, a population with high levels of Prevotella. We demonstrate that plant-derived microbiota-accessible carbohydrates (MACs) are required for persistence of Prevotella copri but not Bacteroides thetaiotaomicron in vivo. Differences in carbohydrate metabolism gene content, expression, and in vitro growth reveal that Hadza Prevotella strains specialize in degrading plant carbohydrates, while Hadza Bacteroides isolates use both plant and host-derived carbohydrates, a difference mirrored in Bacteroides from non-Hadza populations. When competing directly, P. copri requires plant-derived MACs to maintain colonization in the presence of B. thetaiotaomicron, as a no-MAC diet eliminates P. copri colonization. Prevotella's reliance on plant-derived MACs and Bacteroides' ability to use host mucus carbohydrates could explain the reduced prevalence of Prevotella in populations consuming a low-MAC, industrialized diet.
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Affiliation(s)
- Rebecca H. Gellman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew R. Olm
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolé cules Biologiques, INRAE, CNRS, Aix-Marseille Université, Marseille, France
| | - Fatima Enam
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Steven K. Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Justin L. Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Center for Human Microbiome Studies, Stanford University School of Medicine, Stanford, CA, USA
| | - Erica D. Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Center for Human Microbiome Studies, Stanford University School of Medicine, Stanford, CA, USA
- Lead contact
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2
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Landry MJ, Ward CP, Cunanan KM, Durand LR, Perelman D, Robinson JL, Hennings T, Koh L, Dant C, Zeitlin A, Ebel ER, Sonnenburg ED, Sonnenburg JL, Gardner CD. Cardiometabolic Effects of Omnivorous vs Vegan Diets in Identical Twins: A Randomized Clinical Trial. JAMA Netw Open 2023; 6:e2344457. [PMID: 38032644 PMCID: PMC10690456 DOI: 10.1001/jamanetworkopen.2023.44457] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 10/12/2023] [Indexed: 12/01/2023] Open
Abstract
Importance Increasing evidence suggests that, compared with an omnivorous diet, a vegan diet confers potential cardiovascular benefits from improved diet quality (ie, higher consumption of vegetables, legumes, fruits, whole grains, nuts, and seeds). Objective To compare the effects of a healthy vegan vs healthy omnivorous diet on cardiometabolic measures during an 8-week intervention. Design, Setting, and Participants This single-center, population-based randomized clinical trial of 22 pairs of twins (N = 44) randomized participants to a vegan or omnivorous diet (1 twin per diet). Participant enrollment began March 28, 2022, and continued through May 5, 2022. The date of final follow-up data collection was July 20, 2022. This 8-week, open-label, parallel, dietary randomized clinical trial compared the health impact of a vegan diet vs an omnivorous diet in identical twins. Primary analysis included all available data. Intervention Twin pairs were randomized to follow a healthy vegan diet or a healthy omnivorous diet for 8 weeks. Diet-specific meals were provided via a meal delivery service from baseline through week 4, and from weeks 5 to 8 participants prepared their own diet-appropriate meals and snacks. Main Outcomes and Measures The primary outcome was difference in low-density lipoprotein cholesterol concentration from baseline to end point (week 8). Secondary outcome measures were changes in cardiometabolic factors (plasma lipids, glucose, and insulin levels and serum trimethylamine N-oxide level), plasma vitamin B12 level, and body weight. Exploratory measures were adherence to study diets, ease or difficulty in following the diets, participant energy levels, and sense of well-being. Results A total of 22 pairs (N = 44) of twins (34 [77.3%] female; mean [SD] age, 39.6 [12.7] years; mean [SD] body mass index, 25.9 [4.7]) were enrolled in the study. After 8 weeks, compared with twins randomized to an omnivorous diet, the twins randomized to the vegan diet experienced significant mean (SD) decreases in low-density lipoprotein cholesterol concentration (-13.9 [5.8] mg/dL; 95% CI, -25.3 to -2.4 mg/dL), fasting insulin level (-2.9 [1.3] μIU/mL; 95% CI, -5.3 to -0.4 μIU/mL), and body weight (-1.9 [0.7] kg; 95% CI, -3.3 to -0.6 kg). Conclusions and Relevance In this randomized clinical trial of the cardiometabolic effects of omnivorous vs vegan diets in identical twins, the healthy vegan diet led to improved cardiometabolic outcomes compared with a healthy omnivorous diet. Clinicians can consider this dietary approach as a healthy alternative for their patients. Trial Registration ClinicalTrials.gov Identifier: NCT05297825.
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Affiliation(s)
- Matthew J. Landry
- Stanford Prevention Research Center, Department of Medicine, School of Medicine, Stanford University, Palo Alto, California
- Department of Population Health and Disease Prevention, Program in Public Health, University of California, Irvine
| | - Catherine P. Ward
- Stanford Prevention Research Center, Department of Medicine, School of Medicine, Stanford University, Palo Alto, California
| | - Kristen M. Cunanan
- Quantitative Sciences Unit, Department of Medicine, Stanford University, Palo Alto, California
| | - Lindsay R. Durand
- Stanford Prevention Research Center, Department of Medicine, School of Medicine, Stanford University, Palo Alto, California
| | - Dalia Perelman
- Stanford Prevention Research Center, Department of Medicine, School of Medicine, Stanford University, Palo Alto, California
| | - Jennifer L. Robinson
- Stanford Prevention Research Center, Department of Medicine, School of Medicine, Stanford University, Palo Alto, California
| | - Tayler Hennings
- Stanford Prevention Research Center, Department of Medicine, School of Medicine, Stanford University, Palo Alto, California
| | - Linda Koh
- Stanford Prevention Research Center, Department of Medicine, School of Medicine, Stanford University, Palo Alto, California
| | - Christopher Dant
- Stanford Prevention Research Center, Department of Medicine, School of Medicine, Stanford University, Palo Alto, California
| | - Amanda Zeitlin
- Stanford Prevention Research Center, Department of Medicine, School of Medicine, Stanford University, Palo Alto, California
| | - Emily R. Ebel
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford University, Palo Alto, California
| | - Erica D. Sonnenburg
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford University, Palo Alto, California
| | - Justin L. Sonnenburg
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford University, Palo Alto, California
- Chan Zuckerberg Biohub, San Francisco, California
- Center for Human Microbiome Studies, Stanford University School of Medicine, Stanford, California
| | - Christopher D. Gardner
- Stanford Prevention Research Center, Department of Medicine, School of Medicine, Stanford University, Palo Alto, California
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3
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Carter MM, Olm MR, Merrill BD, Dahan D, Tripathi S, Spencer SP, Yu FB, Jain S, Neff N, Jha AR, Sonnenburg ED, Sonnenburg JL. Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes. Cell 2023; 186:3111-3124.e13. [PMID: 37348505 PMCID: PMC10330870 DOI: 10.1016/j.cell.2023.05.046] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [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: 08/08/2022] [Revised: 02/12/2023] [Accepted: 05/26/2023] [Indexed: 06/24/2023]
Abstract
The gut microbiome modulates immune and metabolic health. Human microbiome data are biased toward industrialized populations, limiting our understanding of non-industrialized microbiomes. Here, we performed ultra-deep metagenomic sequencing on 351 fecal samples from the Hadza hunter-gatherers of Tanzania and comparative populations in Nepal and California. We recovered 91,662 genomes of bacteria, archaea, bacteriophages, and eukaryotes, 44% of which are absent from existing unified datasets. We identified 124 gut-resident species vanishing in industrialized populations and highlighted distinct aspects of the Hadza gut microbiome related to in situ replication rates, signatures of selection, and strain sharing. Industrialized gut microbes were found to be enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes. This unparalleled view of the Hadza gut microbiome provides a valuable resource, expands our understanding of microbes capable of colonizing the human gut, and clarifies the extensive perturbation induced by the industrialized lifestyle.
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Affiliation(s)
- Matthew M Carter
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Matthew R Olm
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Bryan D Merrill
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Dylan Dahan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Surya Tripathi
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Sean P Spencer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Feiqiao B Yu
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Sunit Jain
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Aashish R Jha
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Erica D Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA.
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Center for Human Microbiome Studies, Stanford University School of Medicine, Stanford, CA 94304, USA.
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4
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Gellman RH, Olm MR, Terrapon N, Enam F, Higginbottom SK, Sonnenburg JL, Sonnenburg ED. Hadza Prevotella Require Diet-derived Microbiota Accessible Carbohydrates to Persist in Mice. bioRxiv 2023:2023.03.08.531063. [PMID: 36945614 PMCID: PMC10028851 DOI: 10.1101/2023.03.08.531063] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Industrialization has transformed the gut microbiota, reducing the prevalence of Prevotella relative to Bacteroides. Here, we isolate Bacteroides and Prevotella strains from the microbiota of Hadza hunter-gatherers of Tanzania, a population with high levels of Prevotella. We demonstrate that plant-derived microbiota-accessible carbohydrates (MACs) are required for persistence of Prevotella copri but not Bacteroides thetaiotaomicron in vivo. Differences in carbohydrate metabolism gene content, expression, and in vitro growth reveal that Hadza Prevotella strains specialize in degrading plant carbohydrates, while Hadza Bacteroides isolates use both plant and host-derived carbohydrates, a difference mirrored in Bacteroides from non-Hadza populations. When competing directly, P. copri requires plant-derived MACs to maintain colonization in the presence of B. thetaiotaomicron, as a no MAC diet eliminates P. copri colonization. Prevotella's reliance on plant-derived MACs and Bacteroides' ability to use host mucus carbohydrates could explain the reduced prevalence of Prevotella in populations consuming a low-MAC, industrialized diet.
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Affiliation(s)
- Rebecca H Gellman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew R Olm
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, INRAE, CNRS, Aix-Marseille Université, Marseille, France
| | - Fatima Enam
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Steven K Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Center for Human Microbiome Studies, Stanford University School of Medicine, Stanford, CA, USA
| | - Erica D Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
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5
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Wastyk HC, Perelman D, Topf M, Fragiadakis GK, Robinson JL, Sonnenburg JL, Gardner CD, Sonnenburg ED. Randomized controlled trial demonstrates response to a probiotic intervention for metabolic syndrome that may correspond to diet. Gut Microbes 2023; 15:2178794. [PMID: 36803658 PMCID: PMC9980610 DOI: 10.1080/19490976.2023.2178794] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
An individual's immune and metabolic status is coupled to their microbiome. Probiotics offer a promising, safe route to influence host health, possibly via the microbiome. Here, we report an 18-week, randomized prospective study that explores the effects of a probiotic vs. placebo supplement on 39 adults with elevated parameters of metabolic syndrome. We performed longitudinal sampling of stool and blood to profile the human microbiome and immune system. While we did not see changes in metabolic syndrome markers in response to the probiotic across the entire cohort, there were significant improvements in triglycerides and diastolic blood pressure in a subset of probiotic arm participants. Conversely, the non-responders had increased blood glucose and insulin levels over time. The responders had a distinct microbiome profile at the end of the intervention relative to the non-responders and placebo arm. Importantly, diet was a key differentiating factor between responders and non-responders. Our results show participant-specific effects of a probiotic supplement on improving parameters of metabolic syndrome and suggest that dietary factors may enhance stability and efficacy of the supplement.
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Affiliation(s)
- Hannah C. Wastyk
- Department of Bioengineering, Stanford School of Medicine, Stanford, CA, USA
| | - Dalia Perelman
- Stanford Prevention Research Center, Department of Medicine, Stanford School of 4Medicine, Stanford, CA, USA
| | - Madeline Topf
- Microbiology & Immunology, Stanford School of Medicine, Stanford, CA, USA
| | | | - Jennifer L. Robinson
- Stanford Prevention Research Center, Department of Medicine, Stanford School of 4Medicine, Stanford, CA, USA
| | - Justin L. Sonnenburg
- Microbiology & Immunology, Stanford School of Medicine, Stanford, CA, USA,Center for Human Microbiome Studies, Stanford School of Medicine, Stanford University, Stanford, CA, USA,Chan Zuckerberg Biohub, San Francisco, CA, USA,CONTACT Justin L. Sonnenburg Microbiology & Immunology, Stanford School of Medicine, Stanford, CA94305, USA
| | - Christopher D. Gardner
- Stanford Prevention Research Center, Department of Medicine, Stanford School of 4Medicine, Stanford, CA, USA,Christopher D. Gardner Stanford Prevention Research Center, Department of Medicine, Stanford School of Medicine, Stanford, CA94305, USA
| | - Erica D. Sonnenburg
- Microbiology & Immunology, Stanford School of Medicine, Stanford, CA, USA,Center for Human Microbiome Studies, Stanford School of Medicine, Stanford University, Stanford, CA, USA,Erica D. Sonnenburg Microbiology & Immunology, Stanford School of Medicine, Stanford, CA, 94305, USA
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6
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Olm MR, Dahan D, Carter MM, Merrill BD, Yu FB, Jain S, Meng XD, Tripathi S, Wastyk H, Neff N, Holmes S, Sonnenburg ED, Jha AR, Sonnenburg JL. Robust variation in infant gut microbiome assembly across a spectrum of lifestyles. Science 2022; 376:1220-1223. [PMID: 35679413 PMCID: PMC9894631 DOI: 10.1126/science.abj2972] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Infant microbiome assembly has been intensely studied in infants from industrialized nations, but little is known about this process in nonindustrialized populations. We deeply sequenced infant stool samples from the Hadza hunter-gatherers of Tanzania and analyzed them in a global meta-analysis. Infant microbiomes develop along lifestyle-associated trajectories, with more than 20% of genomes detected in the Hadza infant gut representing novel species. Industrialized infants-even those who are breastfed-have microbiomes characterized by a paucity of Bifidobacterium infantis and gene cassettes involved in human milk utilization. Strains within lifestyle-associated taxonomic groups are shared between mother-infant dyads, consistent with early life inheritance of lifestyle-shaped microbiomes. The population-specific differences in infant microbiome composition and function underscore the importance of studying microbiomes from people outside of wealthy, industrialized nations.
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Affiliation(s)
- Matthew R. Olm
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Dylan Dahan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew M. Carter
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bryan D. Merrill
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Sunit Jain
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Surya Tripathi
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Hannah Wastyk
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Susan Holmes
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Statistics, Stanford University, Stanford, CA, USA
| | - Erica D. Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Aashish R. Jha
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Justin L. Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA.,Corresponding author:
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7
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Guthrie L, Spencer SP, Perelman D, Van Treuren W, Han S, Yu FB, Sonnenburg ED, Fischbach MA, Meyer TW, Sonnenburg JL. Impact of a 7-day homogeneous diet on interpersonal variation in human gut microbiomes and metabolomes. Cell Host Microbe 2022; 30:863-874.e4. [PMID: 35643079 PMCID: PMC9296065 DOI: 10.1016/j.chom.2022.05.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [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: 10/29/2021] [Revised: 02/17/2022] [Accepted: 05/04/2022] [Indexed: 02/06/2023]
Abstract
Gut microbiota metabolism of dietary compounds generates a vast array of microbiome-dependent metabolites (MDMs), which are highly variable between individuals. The uremic MDMs (uMDMs) phenylacetylglutamine (PAG), p-cresol sulfate (PCS), and indoxyl sulfate (IS) accumulate during renal failure and are associated with poor outcomes. Targeted dietary interventions may reduce toxic MDM generation; however, it is unclear if inter-individual differences in diet or gut microbiome dominantly contribute to MDM variance. Here, we use a 7-day homogeneous average American diet to standardize dietary precursor availability in 21 healthy individuals. During dietary homogeneity, the coefficient of variation in PAG, PCS, and IS (primary outcome) did not decrease, nor did inter-individual variation in most identified metabolites; other microbiome metrics showed no or modest responses to the intervention. Host identity and age are dominant contributors to variability in MDMs. These results highlight the potential need to pair dietary modification with microbial therapies to control MDM profiles.
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Affiliation(s)
- Leah Guthrie
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sean Paul Spencer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Dalia Perelman
- Stanford Prevention Research Center, Department of Medicine, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Will Van Treuren
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shuo Han
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Erica D Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael A Fischbach
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; ChEM-H, Stanford University, Stanford, CA 94305, USA; Chan-Zuckerburg Biohub, San Francisco, CA 94158, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Timothy W Meyer
- Department of Medicine, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan-Zuckerburg Biohub, San Francisco, CA 94158, USA; Center for Human Microbiome Studies, Stanford, CA 94305, USA.
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8
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Merrill BD, Carter MM, Olm MR, Dahan D, Tripathi S, Spencer SP, Yu B, Jain S, Neff N, Jha AR, Sonnenburg ED, Sonnenburg JL. Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Microbes.. [PMID: 36238714 PMCID: PMC9558438 DOI: 10.1101/2022.03.30.486478] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The gut microbiome is a key modulator of immune and metabolic health. Human microbiome data is biased towards industrialized populations, providing limited understanding of the distinct and diverse non-industrialized microbiomes. Here, we performed ultra-deep metagenomic sequencing and strain cultivation on 351 fecal samples from the Hadza, hunter-gatherers in Tanzania, and comparative populations in Nepal and California. We recover 94,971 total genomes of bacteria, archaea, bacteriophages, and eukaryotes, 43% of which are absent from existing unified datasets. Analysis of in situ growth rates, genetic pN/pS signatures, high-resolution strain tracking, and 124 gut-resident species vanishing in industrialized populations reveals differentiating dynamics of the Hadza gut microbiome. Industrialized gut microbes are enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes. This unparalleled view of the Hadza gut microbiome provides a valuable resource that expands our understanding of microbes capable of colonizing the human gut and clarifies the extensive perturbation brought on by the industrialized lifestyle.
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9
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Wastyk HC, Fragiadakis GK, Perelman D, Dahan D, Merrill BD, Yu FB, Topf M, Gonzalez CG, Van Treuren W, Han S, Robinson JL, Elias JE, Sonnenburg ED, Gardner CD, Sonnenburg JL. Gut-microbiota-targeted diets modulate human immune status. Cell 2021; 184:4137-4153.e14. [PMID: 34256014 DOI: 10.1016/j.cell.2021.06.019] [Citation(s) in RCA: 390] [Impact Index Per Article: 130.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 04/13/2021] [Accepted: 06/11/2021] [Indexed: 12/21/2022]
Abstract
Diet modulates the gut microbiome, which in turn can impact the immune system. Here, we determined how two microbiota-targeted dietary interventions, plant-based fiber and fermented foods, influence the human microbiome and immune system in healthy adults. Using a 17-week randomized, prospective study (n = 18/arm) combined with -omics measurements of microbiome and host, including extensive immune profiling, we found diet-specific effects. The high-fiber diet increased microbiome-encoded glycan-degrading carbohydrate active enzymes (CAZymes) despite stable microbial community diversity. Although cytokine response score (primary outcome) was unchanged, three distinct immunological trajectories in high-fiber consumers corresponded to baseline microbiota diversity. Alternatively, the high-fermented-food diet steadily increased microbiota diversity and decreased inflammatory markers. The data highlight how coupling dietary interventions to deep and longitudinal immune and microbiome profiling can provide individualized and population-wide insight. Fermented foods may be valuable in countering the decreased microbiome diversity and increased inflammation pervasive in industrialized society.
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Affiliation(s)
- Hannah C Wastyk
- Department of Bioengineering, Stanford School of Medicine, Stanford, CA 94305, USA
| | | | - Dalia Perelman
- Stanford Prevention Research Center, Department of Medicine, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Dylan Dahan
- Microbiology & Immunology, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Bryan D Merrill
- Microbiology & Immunology, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Feiqiao B Yu
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Madeline Topf
- Microbiology & Immunology, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Carlos G Gonzalez
- Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - William Van Treuren
- Microbiology & Immunology, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Shuo Han
- Microbiology & Immunology, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Jennifer L Robinson
- Stanford Prevention Research Center, Department of Medicine, Stanford School of Medicine, Stanford, CA 94305, USA
| | | | - Erica D Sonnenburg
- Microbiology & Immunology, Stanford School of Medicine, Stanford, CA 94305, USA; Center for Human Microbiome Studies, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA.
| | - Christopher D Gardner
- Stanford Prevention Research Center, Department of Medicine, Stanford School of Medicine, Stanford, CA 94305, USA.
| | - Justin L Sonnenburg
- Microbiology & Immunology, Stanford School of Medicine, Stanford, CA 94305, USA; Center for Human Microbiome Studies, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA.
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10
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Pruss KM, Marcobal A, Southwick AM, Dahan D, Smits SA, Ferreyra JA, Higginbottom SK, Sonnenburg ED, Kashyap PC, Choudhury B, Bode L, Sonnenburg JL. Mucin-derived O-glycans supplemented to diet mitigate diverse microbiota perturbations. ISME J 2021; 15:577-591. [PMID: 33087860 PMCID: PMC8027378 DOI: 10.1038/s41396-020-00798-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [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] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 09/19/2020] [Accepted: 09/25/2020] [Indexed: 12/17/2022]
Abstract
Microbiota-accessible carbohydrates (MACs) are powerful modulators of microbiota composition and function. These substrates are often derived from diet, such as complex polysaccharides from plants or human milk oligosaccharides (HMOs) during breastfeeding. Host-derived mucus glycans on gut-secreted mucin proteins serve as a continuous endogenous source of MACs for resident microbes; here we investigate the potential role of purified, orally administered mucus glycans in maintaining a healthy microbial community. In this study, we liberated and purified O-linked glycans from porcine gastric mucin and assessed their efficacy in shaping the recovery of a perturbed microbiota in a mouse model. We found that porcine mucin glycans (PMGs) and HMOs enrich for taxonomically similar resident microbes. We demonstrate that PMGs aid recovery of the microbiota after antibiotic treatment, suppress Clostridium difficile abundance, delay the onset of diet-induced obesity, and increase the relative abundance of resident Akkermansia muciniphila. In silico analysis revealed that genes associated with mucus utilization are abundant and diverse in prevalent gut commensals and rare in enteric pathogens, consistent with these glycan-degrading capabilities being selected for during host development and throughout the evolution of the host-microbe relationship. Importantly, we identify mucus glycans as a novel class of prebiotic compounds that can be used to mitigate perturbations to the microbiota and provide benefits to host physiology.
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Affiliation(s)
- K M Pruss
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - A Marcobal
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - A M Southwick
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - D Dahan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - S A Smits
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - J A Ferreyra
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - S K Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - E D Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - P C Kashyap
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - B Choudhury
- GlycoAnalytics Core, University of California, San Diego, CA, USA
| | - L Bode
- Division of Neonatology and Division of Gastroenterology and Nutrition, Department of Pediatrics, University of California, San Diego, CA, USA
| | - J L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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11
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Crimarco A, Springfield S, Petlura C, Streaty T, Cunanan K, Lee J, Fielding-Singh P, Carter MM, Topf MA, Wastyk HC, Sonnenburg ED, Sonnenburg JL, Gardner CD. A randomized crossover trial on the effect of plant-based compared with animal-based meat on trimethylamine-N-oxide and cardiovascular disease risk factors in generally healthy adults: Study With Appetizing Plantfood-Meat Eating Alternative Trial (SWAP-MEAT). Am J Clin Nutr 2020; 112:1188-1199. [PMID: 32780794 PMCID: PMC7657338 DOI: 10.1093/ajcn/nqaa203] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/29/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Despite the rising popularity of plant-based alternative meats, there is limited evidence of the health effects of these products. OBJECTIVES We aimed to compare the effect of consuming plant-based alternative meat (Plant) as opposed to animal meat (Animal) on health factors. The primary outcome was fasting serum trimethylamine-N-oxide (TMAO). Secondary outcomes included fasting insulin-like growth factor 1, lipids, glucose, insulin, blood pressure, and weight. METHODS SWAP-MEAT (The Study With Appetizing Plantfood-Meat Eating Alternatives Trial) was a single-site, randomized crossover trial with no washout period. Participants received Plant and Animal products, dietary counseling, lab assessments, microbiome assessments (16S), and anthropometric measurements. Participants were instructed to consume ≥2 servings/d of Plant compared with Animal for 8 wk each, while keeping all other foods and beverages as similar as possible between the 2 phases. RESULTS The 36 participants who provided complete data for both crossover phases included 67% women, were 69% Caucasian, had a mean ± SD age 50 ± 14 y, and BMI 28 ± 5 kg/m2. Mean ± SD servings per day were not different by intervention sequence: 2.5 ± 0.6 compared with 2.6 ± 0.7 for Plant and Animal, respectively (P = 0.76). Mean ± SEM TMAO concentrations were significantly lower overall for Plant (2.7 ± 0.3) than for Animal (4.7 ± 0.9) (P = 0.012), but a significant order effect was observed (P = 0.023). TMAO concentrations were significantly lower for Plant among the n = 18 who received Plant second (2.9 ± 0.4 compared with 6.4 ± 1.5, Plant compared with Animal, P = 0.007), but not for the n = 18 who received Plant first (2.5 ± 0.4 compared with 3.0 ± 0.6, Plant compared with Animal, P = 0.23). Exploratory analyses of the microbiome failed to reveal possible responder compared with nonresponder factors. Mean ± SEM LDL-cholesterol concentrations (109.9 ± 4.5 compared with 120.7 ± 4.5 mg/dL, P = 0.002) and weight (78.7 ± 3.0 compared with 79.6 ± 3.0 kg, P < 0.001) were lower during the Plant phase. CONCLUSIONS Among generally healthy adults, contrasting Plant with Animal intake, while keeping all other dietary components similar, the Plant products improved several cardiovascular disease risk factors, including TMAO; there were no adverse effects on risk factors from the Plant products.This trial was registered at clinicaltrials.gov as NCT03718988.
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Affiliation(s)
- Anthony Crimarco
- Stanford Prevention Research Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Sparkle Springfield
- Stanford Prevention Research Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Christina Petlura
- Stanford Prevention Research Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Taylor Streaty
- Stanford Prevention Research Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Kristen Cunanan
- Quantitative Sciences Unit, Stanford University School of Medicine, Stanford, CA, USA
| | - Justin Lee
- Quantitative Sciences Unit, Stanford University School of Medicine, Stanford, CA, USA
| | - Priya Fielding-Singh
- Stanford Prevention Research Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew M Carter
- Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Madeline A Topf
- Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Hannah C Wastyk
- Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Bioengineering, Stanford University School of Medicine, Stanford, CA, USA
| | - Erica D Sonnenburg
- Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Center for Human Microbiome Studies, Stanford University, Stanford, CA, USA
| | - Justin L Sonnenburg
- Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Center for Human Microbiome Studies, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Christopher D Gardner
- Stanford Prevention Research Center, Stanford University School of Medicine, Stanford, CA, USA
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12
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Fragiadakis GK, Wastyk HC, Robinson JL, Sonnenburg ED, Sonnenburg JL, Gardner CD. Long-term dietary intervention reveals resilience of the gut microbiota despite changes in diet and weight. Am J Clin Nutr 2020; 111:1127-1136. [PMID: 32186326 PMCID: PMC7266695 DOI: 10.1093/ajcn/nqaa046] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [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: 04/24/2019] [Accepted: 02/24/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND With the rising rates of obesity and associated metabolic disorders, there is a growing need for effective long-term weight-loss strategies, coupled with an understanding of how they interface with human physiology. Interest is growing in the potential role of gut microbes as they pertain to responses to different weight-loss diets; however, the ways that diet, the gut microbiota, and long-term weight loss influence one another is not well understood. OBJECTIVES Our primary objective was to determine if baseline microbiota composition or diversity was associated with weight-loss success. A secondary objective was to track the longitudinal associations of changes to lower-carbohydrate or lower-fat diets and concomitant weight loss with the composition and diversity of the gut microbiota. METHODS We used 16S ribosomal RNA gene amplicon sequencing to profile microbiota composition over a 12-mo period in 49 participants as part of a larger randomized dietary intervention study of participants consuming either a healthy low-carbohydrate or a healthy low-fat diet. RESULTS While baseline microbiota composition was not predictive of weight loss, each diet resulted in substantial changes in the microbiota 3-mo after the start of the intervention; some of these changes were diet specific (14 taxonomic changes specific to the healthy low-carbohydrate diet, 12 taxonomic changes specific to the healthy low-fat diet) and others tracked with weight loss (7 taxonomic changes in both diets). After these initial shifts, the microbiota returned near its original baseline state for the remainder of the intervention, despite participants maintaining their diet and weight loss for the entire study. CONCLUSIONS These results suggest a resilience to perturbation of the microbiota's starting profile. When considering the established contribution of obesity-associated microbiotas to weight gain in animal models, microbiota resilience may need to be overcome for long-term alterations to human physiology. This trial was registered at clinicaltrials.gov as NCT01826591.
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Affiliation(s)
| | - Hannah C Wastyk
- Department of Bioengineering, Stanford School of Medicine, Stanford, CA, USA
| | - Jennifer L Robinson
- Stanford Prevention Research Center, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Erica D Sonnenburg
- Microbiology and Immunology, Stanford School of Medicine, Stanford, CA, USA,Center for Human Microbiome Studies, Stanford University, Stanford, CA, USA
| | - Justin L Sonnenburg
- Microbiology and Immunology, Stanford School of Medicine, Stanford, CA, USA,Center for Human Microbiome Studies, Stanford University, Stanford, CA, USA,Chan Zuckerberg Biohub, San Francisco, CA, USA,Address correspondence to JLS (e-mail: )
| | - Christopher D Gardner
- Stanford Prevention Research Center, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA,Address correspondence to CDG (e-mail: )
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Abstract
The human body is an ecosystem that is home to a complex array of microbes known as the microbiome or microbiota. This ecosystem plays an important role in human health, but as a result of recent lifestyle changes occurring around the planet, whole populations are seeing a major shift in their gut microbiota. Measures meant to kill or limit exposure to pathogenic microbes, such as antibiotics and sanitation, combined with other factors such as processed food, have had unintended consequences for the human microbial ecosystem, including changes that may be difficult to reverse. Microbiota alteration and the accompanying loss of certain functional attributes might result in the microbial communities of people living in industrialized societies being suboptimal for human health. As macroecologists, conservationists, and climate scientists race to document, understand, predict, and delay global changes in our wider environment, microbiota scientists may benefit by using analogous approaches to study and protect our intimate microbial ecosystems.
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Affiliation(s)
- Justin L Sonnenburg
- Department of Microbiology and Immunology and Center for Human Microbiome Studies, Stanford University, Stanford, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Erica D Sonnenburg
- Department of Microbiology and Immunology and Center for Human Microbiome Studies, Stanford University, Stanford, CA, USA.
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14
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15
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Fragiadakis GK, Smits SA, Sonnenburg ED, Van Treuren W, Reid G, Knight R, Manjurano A, Changalucha J, Dominguez-Bello MG, Leach J, Sonnenburg JL. Links between environment, diet, and the hunter-gatherer microbiome. Gut Microbes 2018; 10:216-227. [PMID: 30118385 PMCID: PMC6546328 DOI: 10.1080/19490976.2018.1494103] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [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: 02/07/2023] Open
Abstract
The study of traditional populations provides a view of human-associated microbes unperturbed by industrialization, as well as a window into the microbiota that co-evolved with humans. Here we discuss our recent work characterizing the microbiota from the Hadza hunter-gatherers of Tanzania. We found seasonal shifts in bacterial taxa, diversity, and carbohydrate utilization by the microbiota. When compared to the microbiota composition from other populations around the world, the Hadza microbiota shares bacterial families with other traditional societies that are rare or absent from microbiotas of industrialized nations. We present additional observations from the Hadza microbiota and their lifestyle and environment, including microbes detected on hands, water, and animal sources, how the microbiota varies with sex and age, and the short-term effects of introducing agricultural products into the diet. In the context of our previously published findings and of these additional observations, we discuss a path forward for future work.
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Affiliation(s)
- Gabriela K. Fragiadakis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Samuel A. Smits
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Erica D. Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - William Van Treuren
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Gregor Reid
- Department of Microbiology & Immunology, Department of Surgery, Western University, Lawson Health Research Institute, London, Ontario, Canada
| | - Rob Knight
- Departments of Pediatrics and Computer Science & Engineering and Center for Microbiome Innovation, University of California, San Diego, CA, USA
| | - Alphaxard Manjurano
- Parasitic Diseases Programme and Laboratory Sciences Programme, National Institute for Medical Research, Mwanza Centre, Mwanza, Tanzania
| | - John Changalucha
- Sexual and Reproductive Health Programme and Laboratory Sciences Programme, National Institute for Medical Research, Mwanza Centre, Mwanza, Tanzania
| | - Maria Gloria Dominguez-Bello
- Department of Biochemistry and Microbiology, Department of AnthropologyRutgers, The State University of New Jersey, New Brunswick, NJUSA
| | - Jeff Leach
- Human Food Project, Terlingua, Texas, USA,The Department of Twin Research and Genetic EpidemiologyKing’s College London, St Thomas’ Hospital, London, UK
| | - Justin L. Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA,Chan Zuckerberg Biohub, San Francisco, CA, USA,CONTACT Justin L. Sonnenburg
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16
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Smits SA, Leach J, Sonnenburg ED, Gonzalez CG, Lichtman JS, Reid G, Knight R, Manjurano A, Changalucha J, Elias JE, Dominguez-Bello MG, Sonnenburg JL. Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania. Science 2017; 357:802-806. [PMID: 28839072 DOI: 10.1126/science.aan4834] [Citation(s) in RCA: 493] [Impact Index Per Article: 70.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 07/24/2017] [Indexed: 12/14/2022]
Abstract
Although humans have cospeciated with their gut-resident microbes, it is difficult to infer features of our ancestral microbiome. Here, we examine the microbiome profile of 350 stool samples collected longitudinally for more than a year from the Hadza hunter-gatherers of Tanzania. The data reveal annual cyclic reconfiguration of the microbiome, in which some taxa become undetectable only to reappear in a subsequent season. Comparison of the Hadza data set with data collected from 18 populations in 16 countries with varying lifestyles reveals that gut community membership corresponds to modernization: Notably, the taxa within the Hadza that are the most seasonally volatile similarly differentiate industrialized and traditional populations. These data indicate that some dynamic lineages of microbes have decreased in prevalence and abundance in modernized populations.
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Affiliation(s)
- Samuel A Smits
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jeff Leach
- Human Food Project, 53600 Highway 118, Terlingua, TX 79852, USA.,The Department of Twin Research and Genetic Epidemiology, King's College London, St. Thomas' Hospital, Lambeth Palace Road, London SE1 7EH, UK
| | - Erica D Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Carlos G Gonzalez
- Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford University, Stanford, CA 94025, USA
| | - Joshua S Lichtman
- Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford University, Stanford, CA 94025, USA
| | - Gregor Reid
- Lawson Health Research Institute and Western University, London, Ontario N6A 4V2, Canada
| | - Rob Knight
- Departments of Pediatrics and Computer Science and Engineering and Center for Microbiome Innovation, University of California, San Diego, CA 92093, USA
| | | | | | - Joshua E Elias
- Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford University, Stanford, CA 94025, USA
| | | | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
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17
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Abstract
The gut microbiota of a healthy person may not be equivalent to a healthy microbiota. It is possible that the Western microbiota is actually dysbiotic and predisposes individuals to a variety of diseases. The asymmetric plasticity between the relatively stable human genome and the more malleable gut microbiome suggests that incompatibilities between the two could rapidly arise. The Western lifestyle, which includes a diet low in microbiota-accessible carbohydrates (MACs), has selected for a microbiota with altered membership and functionality compared to those of groups living traditional lifestyles. Interactions between resident microbes and host leading to immune dysregulation may explain several diseases that share inflammation as a common basis. The low-MAC Western diet results in poor production of gut microbiota-generated short-chain fatty acids (SCFAs), which attenuate inflammation through a variety of mechanisms in mouse models. Studies focused on modern and traditional societies, combined with animal models, are needed to characterize the connection between diet, microbiota composition, and function. Differentiating between an optimal microbiota, one that increases disease risk, and one that is causative or potentiates disease will be required to further understand both the etiology and possible treatments for health problems related to microbiota dysbiosis.
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Affiliation(s)
- Erica D Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, 259 Campus Drive, Stanford, CA 94305, USA
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, 259 Campus Drive, Stanford, CA 94305, USA.
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18
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Kashyap PC, Marcobal A, Ursell LK, Smits SA, Sonnenburg ED, Costello EK, Higginbottom SK, Domino SE, Holmes SP, Relman DA, Knight R, Gordon JI, Sonnenburg JL. Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiota. Proc Natl Acad Sci U S A 2013; 110:17059-64. [PMID: 24062455 PMCID: PMC3800993 DOI: 10.1073/pnas.1306070110] [Citation(s) in RCA: 199] [Impact Index Per Article: 18.1] [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] [Indexed: 12/13/2022] Open
Abstract
We investigate how host mucus glycan composition interacts with dietary carbohydrate content to influence the composition and expressed functions of a human gut community. The humanized gnotobiotic mice mimic humans with a nonsecretor phenotype due to knockout of their α1-2 fucosyltransferase (Fut2) gene. The fecal microbiota of Fut2(-) mice that lack fucosylated host glycans show decreased alpha diversity relative to Fut2(+) mice and exhibit significant differences in community composition. A glucose-rich plant polysaccharide-deficient (PD) diet exerted a strong effect on the microbiota membership but eliminated the effect of Fut2 genotype. Additionally fecal metabolites predicted host genotype in mice on a polysaccharide-rich standard diet but not on a PD diet. A more detailed mechanistic analysis of these interactions involved colonization of gnotobiotic Fut2(+) and Fut2(-) mice with Bacteroides thetaiotaomicron, a prominent member of the human gut microbiota known to adaptively forage host mucosal glycans when dietary polysaccharides are absent. Within Fut2(-) mice, the B. thetaiotaomicron fucose catabolic pathway was markedly down-regulated, whereas BT4241-4247, an operon responsive to terminal β-galactose, the precursor that accumulates in the Fut2(-) mice, was significantly up-regulated. These changes in B. thetaiotaomicron gene expression were only evident in mice fed a PD diet, wherein B. thetaiotaomicron relies on host mucus consumption. Furthermore, up-regulation of the BT4241-4247 operon was also seen in humanized Fut2(-) mice. Together, these data demonstrate that differences in host genotype that affect the carbohydrate landscape of the distal gut interact with diet to alter the composition and function of resident microbes in a diet-dependent manner.
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Affiliation(s)
- Purna C. Kashyap
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905
| | - Angela Marcobal
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Luke K. Ursell
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309
| | - Samuel A. Smits
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Erica D. Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Elizabeth K. Costello
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Steven K. Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Steven E. Domino
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI 48109
| | - Susan P. Holmes
- Department of Statistics, Stanford University, Stanford, CA 94305
| | - David A. Relman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305
- Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304; and
| | - Rob Knight
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309
| | - Jeffrey I. Gordon
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108
| | - Justin L. Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
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19
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Kashyap PC, Marcobal A, Ursell LK, Larauche M, Duboc H, Earle KA, Sonnenburg ED, Ferreyra JA, Higginbottom SK, Million M, Tache Y, Pasricha PJ, Knight R, Farrugia G, Sonnenburg JL. Complex interactions among diet, gastrointestinal transit, and gut microbiota in humanized mice. Gastroenterology 2013; 144:967-77. [PMID: 23380084 PMCID: PMC3890323 DOI: 10.1053/j.gastro.2013.01.047] [Citation(s) in RCA: 311] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 01/16/2013] [Accepted: 01/22/2013] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS Diet has major effects on the intestinal microbiota, but the exact mechanisms that alter complex microbial communities have been difficult to elucidate. In addition to the direct influence that diet exerts on microbes, changes in microbiota composition and function can alter host functions such as gastrointestinal (GI) transit time, which in turn can further affect the microbiota. METHODS We investigated the relationships among diet, GI motility, and the intestinal microbiota using mice that are germ-free (GF) or humanized (ex-GF mice colonized with human fecal microbiota). RESULTS Analysis of gut motility revealed that humanized mice fed a standard polysaccharide-rich diet had faster GI transit and increased colonic contractility compared with GF mice. Humanized mice with faster transit due to administration of polyethylene glycol or a nonfermentable cellulose-based diet had similar changes in gut microbiota composition, indicating that diet can modify GI transit, which then affects the composition of the microbial community. However, altered transit in mice fed a diet of fermentable fructooligosaccharide indicates that diet can change gut microbial function, which can affect GI transit. CONCLUSIONS Based on studies in humanized mice, diet can affect GI transit through microbiota-dependent or microbiota-independent pathways, depending on the type of dietary change. The effect of the microbiota on transit largely depends on the amount and type (fermentable vs nonfermentable) of polysaccharides present in the diet. These results have implications for disorders that affect GI transit and gut microbial communities, including irritable bowel syndrome and inflammatory bowel disease.
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Affiliation(s)
- Purna C. Kashyap
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California,Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Angela Marcobal
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California
| | - Luke K. Ursell
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado
| | - Muriel Larauche
- Department of Medicine, CURE/Digestive Diseases Research Center and Center for Neurobiology of Stress, Digestive Diseases Division, University of California at Los Angeles, and Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, California
| | - Henri Duboc
- Department of Medicine, CURE/Digestive Diseases Research Center and Center for Neurobiology of Stress, Digestive Diseases Division, University of California at Los Angeles, and Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, California
| | - Kristen A. Earle
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California
| | - Erica D. Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California
| | - Jessica A. Ferreyra
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California
| | - Steven K. Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California
| | - Mulugeta Million
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado
| | - Yvette Tache
- Department of Medicine, CURE/Digestive Diseases Research Center and Center for Neurobiology of Stress, Digestive Diseases Division, University of California at Los Angeles, and Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, California
| | - Pankaj J. Pasricha
- Department of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, California
| | - Rob Knight
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado,Howard Hughes Medical Institute, Boulder, Colorado
| | - Gianrico Farrugia
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Jusin l. Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California
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20
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Marcobal A, Barboza M, Sonnenburg ED, Pudlo N, Martens EC, Desai P, Lebrilla CB, Weimer BC, Mills DA, German JB, Sonnenburg JL. Bacteroides in the infant gut consume milk oligosaccharides via mucus-utilization pathways. Cell Host Microbe 2011; 10:507-14. [PMID: 22036470 DOI: 10.1016/j.chom.2011.10.007] [Citation(s) in RCA: 378] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 08/18/2011] [Accepted: 09/26/2011] [Indexed: 02/07/2023]
Abstract
Newborns are colonized with an intestinal microbiota shortly after birth, but the factors governing the retention and abundance of specific microbial lineages are unknown. Nursing infants consume human milk oligosaccharides (HMOs) that pass undigested to the distal gut, where they may be digested by microbes. We determined that the prominent neonate gut residents, Bacteroides thetaiotaomicron and Bacteroides fragilis, induce the same genes during HMO consumption that are used to harvest host mucus glycans, which are structurally similar to HMOs. Lacto-N-neotetraose, a specific HMO component, selects for HMO-adapted species such as Bifidobacterium infantis, which cannot use mucus, and provides a selective advantage to B. infantis in vivo when biassociated with B. thetaiotaomicron in the gnotobiotic mouse gut. This indicates that the complex oligosaccharide mixture within HMOs attracts both mutualistic mucus-adapted species and HMO-adapted bifidobacteria to the infant intestine that likely facilitate both milk and future solid food digestion.
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Affiliation(s)
- Angela Marcobal
- Department of Microbiology and Immunology, Stanford School of Medicine, CA 94305, USA
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Sonnenburg ED, Zheng H, Joglekar P, Higginbottom SK, Firbank SJ, Bolam DN, Sonnenburg JL. Specificity of polysaccharide use in intestinal bacteroides species determines diet-induced microbiota alterations. Cell 2010; 141:1241-52. [PMID: 20603004 DOI: 10.1016/j.cell.2010.05.005] [Citation(s) in RCA: 509] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Revised: 01/20/2010] [Accepted: 04/27/2010] [Indexed: 12/18/2022]
Abstract
The intestinal microbiota impacts many facets of human health and is associated with human diseases. Diet impacts microbiota composition, yet mechanisms that link dietary changes to microbiota alterations remain ill-defined. Here we elucidate the basis of Bacteroides proliferation in response to fructans, a class of fructose-based dietary polysaccharides. Structural and genetic analysis disclosed a fructose-binding, hybrid two-component signaling sensor that controls the fructan utilization locus in Bacteroides thetaiotaomicron. Gene content of this locus differs among Bacteroides species and dictates the specificity and breadth of utilizable fructans. BT1760, an extracellular beta2-6 endo-fructanase, distinguishes B. thetaiotaomicron genetically and functionally, and enables the use of the beta2-6-linked fructan levan. The genetic and functional differences between Bacteroides species are predictive of in vivo competitiveness in the presence of dietary fructans. Gene sequences that distinguish species' metabolic capacity serve as potential biomarkers in microbiomic datasets to enable rational manipulation of the microbiota via diet.
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Affiliation(s)
- Erica D Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
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Sonnenburg ED, Sonnenburg JL, Manchester JK, Hansen EE, Chiang HC, Gordon JI. A hybrid two-component system protein of a prominent human gut symbiont couples glycan sensing in vivo to carbohydrate metabolism. Proc Natl Acad Sci U S A 2006; 103:8834-9. [PMID: 16735464 PMCID: PMC1472243 DOI: 10.1073/pnas.0603249103] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacteroides thetaiotaomicron is a prominent member of our normal adult intestinal microbial community and a useful model for studying the foundations of human-bacterial mutualism in our densely populated distal gut microbiota. A central question is how members of this microbiota sense nutrients and implement an appropriate metabolic response. B. thetaiotaomicron contains a large number of glycoside hydrolases not represented in our own proteome, plus a markedly expanded collection of hybrid two-component system (HTCS) proteins that incorporate all domains found in classical two-component environmental sensors into one polypeptide. To understand the role of HTCS in nutrient sensing, we used B. thetaiotaomicron GeneChips to characterize their expression in gnotobiotic mice consuming polysaccharide-rich or -deficient diets. One HTCS, BT3172, was selected for further analysis because it is induced in vivo by polysaccharides, and its absence reduces B. thetaiotaomicron fitness in polysaccharide-rich diet-fed mice. Functional genomic and biochemical analyses of WT and BT3172-deficient strains in vivo and in vitro disclosed that alpha-mannosides induce BT3172 expression, which in turn induces expression of secreted alpha-mannosidases. Yeast two-hybrid screens revealed that the cytoplasmic portion of BT3172's sensor domain serves as a scaffold for recruiting glucose-6-phosphate isomerase and dehydrogenase. These interactions are a unique feature of BT3172 and specific for the cytoplasmic face of its sensor domain. Loss of BT3172 reduces glycolytic pathway activity in vitro and in vivo. Thus, this HTCS functions as a metabolic reaction center, coupling nutrient sensing to dynamic regulation of monosaccharide metabolism. An expanded repertoire of HTCS proteins with diversified sensor domains may be one reason for B. thetaiotaomicron's success in our intestinal ecosystem.
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Affiliation(s)
- Erica D. Sonnenburg
- Center for Genome Sciences, Washington University School of Medicine, St. Louis, MO 63108
| | - Justin L. Sonnenburg
- Center for Genome Sciences, Washington University School of Medicine, St. Louis, MO 63108
| | - Jill K. Manchester
- Center for Genome Sciences, Washington University School of Medicine, St. Louis, MO 63108
| | - Elizabeth E. Hansen
- Center for Genome Sciences, Washington University School of Medicine, St. Louis, MO 63108
| | - Herbert C. Chiang
- Center for Genome Sciences, Washington University School of Medicine, St. Louis, MO 63108
| | - Jeffrey I. Gordon
- Center for Genome Sciences, Washington University School of Medicine, St. Louis, MO 63108
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23
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Abstract
The activity and intracellular localization of protein kinase C (PKC) family members are controlled by phosphorylation at three highly conserved sites in the catalytic kinase domain. In the case of the novel PKCepsilon isoform, these are Thr(566) in the activation loop, Thr(710) in the turn motif and Ser(729) in the C-terminal hydrophobic motif. In the present study, we analysed the contribution of the phosphoinositide-dependent kinase 1 (PDK-1) and PKCepsilon kinase activity in controlling the phosphorylation of Thr(566) and Ser(729). In NIH 3T3 fibroblasts, PKCepsilon migrated as a single band, and stimulation with platelet-derived growth factor resulted in the appearance of a second band with a slower electrophoretic mobility, concomitant with an increase in phosphorylation of Thr(566) and Ser(729). Cells transfected with an active PDK-1 allele also resulted in increased PKCepsilon Thr(566) and Ser(729) phosphorylation, whereas an active myristoylated PKCepsilon mutant was constitutively phosphorylated at these sites. Protein kinase-inactive mutants of PKCepsilon were not phosphorylated at Ser(729) in cells, and phosphorylation of this site leads to dephosphorylation of the activation-loop Thr(566), an effect which can be reversed with either okadaic acid or co-transfection with active PDK-1. In vitro, PDK-1 catalysed the phosphorylation of purified PKCepsilon in the presence of mixed micelles containing either diacylglycerol or PtdIns(3,4,5)P(3), concomitant with an increase in Ser(729) phosphorylation. These studies reveal that the mechanism of phosphorylation of a novel PKC is the same as that for conventional PKCs: PDK-1 phosphorylation of the activation loop triggers autophosphorylation of the hydrophobic motif. However, the regulation of this phosphorylation is different for novel and conventional PKCs. Specifically, the phosphorylation of novel PKCs is regulated rather than constitutive.
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Affiliation(s)
- Vittoria Cenni
- Boston Biomedical Research Institute, Watertown, MA 02472, USA
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Sonnenburg ED, Gao T, Newton AC. The phosphoinositide-dependent kinase, PDK-1, phosphorylates conventional protein kinase C isozymes by a mechanism that is independent of phosphoinositide 3-kinase. J Biol Chem 2001; 276:45289-97. [PMID: 11579098 DOI: 10.1074/jbc.m107416200] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phosphorylation by the phosphoinositide-dependent kinase, PDK-1, is required for the activation of diverse members of the AGC family of protein kinases, including the protein kinase C (PKC) isozymes. Here we explore the subcellular location of the PDK-1-mediated phosphorylation of conventional PKCs, and we address whether this phosphorylation is regulated by phosphoinositide 3-kinase. Pulse-chase experiments reveal that newly synthesized endogenous PKC alpha is primarily phosphorylated in the membrane fraction of COS-7 cells, where it is processed to a species that is phosphorylated at the activation loop and at two carboxyl-terminal positions. This "mature" species is then released into the cytosol. Deletion of the plekstrin homology domain of PDK-1 results in a 4-fold increase in the rate of processing of PKC indicating an autoinhibitory role for this domain. Autoinhibition by the plekstrin homology domain is not relieved by binding 3'-phosphoinositides; PKC is phosphorylated at a similar rate in serum-treated cells and serum-starved cells treated with the phosphoinositide 3-kinase inhibitors, LY294002 and wortmannin. Under the same conditions, the PDK-1-catalyzed phosphorylation of another substrate, Akt/protein kinase B, is abolished by these inhibitors. Our data are consistent with a model in which PDK-1 phosphorylates newly synthesized PKC by a mechanism that is independent of 3'-phosphoinositides.
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Affiliation(s)
- E D Sonnenburg
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093-0640, USA
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