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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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2
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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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3
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Wong EOY, Brownlie EJE, Ng KM, Kathirgamanathan S, Yu FB, Merrill BD, Huang KC, Martin A, Tropini C, Navarre WW. The CIAMIB: a Large and Metabolically Diverse Collection of Inflammation-Associated Bacteria from the Murine Gut. mBio 2022; 13:e0294921. [PMID: 35266814 PMCID: PMC9040815 DOI: 10.1128/mbio.02949-21] [Citation(s) in RCA: 4] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 02/09/2022] [Indexed: 02/07/2023] Open
Abstract
Gut inflammation directly impacts the growth and stability of commensal gut microbes and can lead to long-lasting changes in microbiota composition that can prolong or exacerbate disease states. While mouse models are used extensively to investigate the interplay between microbes and the inflamed state, the paucity of cultured mouse gut microbes has hindered efforts to determine causal relationships. To address this issue, we are assembling the Collection of Inflammation-Associated Mouse Intestinal Bacteria (CIAMIB). The initial release of this collection comprises 41 isolates of 39 unique bacterial species, covering 4 phyla and containing 10 previously uncultivated isolates, including 1 novel family and 7 novel genera. The collection significantly expands the number of available Muribaculaceae, Lachnospiraceae, and Coriobacteriaceae isolates and includes microbes from genera associated with inflammation, such as Prevotella and Klebsiella. We characterized the growth of CIAMIB isolates across a diverse range of nutritional conditions and predicted their metabolic potential and anaerobic fermentation capacity based on the genomes of these isolates. We also provide the first metabolic analysis of species within the genus Adlercreutzia, revealing these representatives to be nitrate-reducing and severely restricted in their ability to grow on carbohydrates. CIAMIB isolates are fully sequenced and available to the scientific community as a powerful tool to study host-microbiota interactions. IMPORTANCE Attempts to explore the role of the microbiota in animal physiology have resulted in large-scale efforts to cultivate the thousands of microbes that are associated with humans. In contrast, relatively few lab mouse-associated bacteria have been isolated, despite the fact that the overwhelming number of studies on the microbiota use laboratory mice that are colonized with microbes that are quite distinct from those in humans. Here, we report the results of a large-scale isolation of bacteria from the intestines of laboratory mice either prone to or suffering from gut inflammation. This collection comprises dozens of novel isolates, many of which represent the only cultured representatives of their genus or species. We report their basic growth characteristics and genomes and are making them widely available to the greater research community.
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Affiliation(s)
- Erin Oi-Yan Wong
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Katharine Michelle Ng
- School of Biomedical Engineering, University of British Columbia, Vancouver, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | | | | | - Bryan D. Merrill
- Department of Microbiology and Immunology, Stanford University of School of Medicine, Stanford, California, USA
| | - Kerwyn Casey Huang
- Chan Zuckerberg Biohub, San Francisco, California, USA
- Department of Microbiology and Immunology, Stanford University of School of Medicine, Stanford, California, USA
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Alberto Martin
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Carolina Tropini
- School of Biomedical Engineering, University of British Columbia, Vancouver, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Canada
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4
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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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5
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Lynch JB, Bennett BD, Merrill BD, Ruby EG, Hryckowian AJ. Independent host- and bacterium-based determinants protect a model symbiosis from phage predation. Cell Rep 2022; 38:110376. [PMID: 35172163 PMCID: PMC8983117 DOI: 10.1016/j.celrep.2022.110376] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 11/08/2021] [Accepted: 01/20/2022] [Indexed: 01/21/2023] Open
Abstract
Bacteriophages (phages) are diverse and abundant constituents of microbial communities worldwide, capable of modulating bacterial populations in diverse ways. Here, we describe the phage HNL01, which infects the marine bacterium Vibrio fischeri. We use culture-based approaches to demonstrate that mutations in the exopolysaccharide locus of V. fischeri render this bacterium resistant to infection by HNL01, highlighting the extracellular matrix as a key determinant of HNL01 infection. Additionally, using the natural symbiosis between V. fischeri and the squid Euprymna scolopes, we show that, during colonization, V. fischeri is protected from phages present in the ambient seawater. Taken together, these findings shed light on independent yet synergistic host- and bacterium-based strategies for resisting symbiosis-disrupting phage predation, and we present important implications for understanding these strategies in the context of diverse host-associated microbial ecosystems.
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Affiliation(s)
- Jonathan B Lynch
- Pacific Biosciences Research Center, University of Hawai'i at Manoa, Honolulu, HI 96822, USA; Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Brittany D Bennett
- Pacific Biosciences Research Center, University of Hawai'i at Manoa, Honolulu, HI 96822, USA; Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Bryan D Merrill
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Edward G Ruby
- Pacific Biosciences Research Center, University of Hawai'i at Manoa, Honolulu, HI 96822, USA
| | - Andrew J Hryckowian
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA; Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA.
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6
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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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7
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Han S, Van Treuren W, Fischer CR, Merrill BD, DeFelice BC, Sanchez JM, Higginbottom SK, Guthrie L, Fall LA, Dodd D, Fischbach MA, Sonnenburg JL. A metabolomics pipeline for the mechanistic interrogation of the gut microbiome. Nature 2021; 595:415-420. [PMID: 34262212 PMCID: PMC8939302 DOI: 10.1038/s41586-021-03707-9] [Citation(s) in RCA: 156] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 06/08/2021] [Indexed: 02/06/2023]
Abstract
Gut microorganisms modulate host phenotypes and are associated with numerous health effects in humans, ranging from host responses to cancer immunotherapy to metabolic disease and obesity. However, difficulty in accurate and high-throughput functional analysis of human gut microorganisms has hindered efforts to define mechanistic connections between individual microbial strains and host phenotypes. One key way in which the gut microbiome influences host physiology is through the production of small molecules1-3, yet progress in elucidating this chemical interplay has been hindered by limited tools calibrated to detect the products of anaerobic biochemistry in the gut. Here we construct a microbiome-focused, integrated mass-spectrometry pipeline to accelerate the identification of microbiota-dependent metabolites in diverse sample types. We report the metabolic profiles of 178 gut microorganism strains using our library of 833 metabolites. Using this metabolomics resource, we establish deviations in the relationships between phylogeny and metabolism, use machine learning to discover a previously undescribed type of metabolism in Bacteroides, and reveal candidate biochemical pathways using comparative genomics. Microbiota-dependent metabolites can be detected in diverse biological fluids from gnotobiotic and conventionally colonized mice and traced back to the corresponding metabolomic profiles of cultured bacteria. Collectively, our microbiome-focused metabolomics pipeline and interactive metabolomics profile explorer are a powerful tool for characterizing microorganisms and interactions between microorganisms and their host.
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Affiliation(s)
- Shuo Han
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Will Van Treuren
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA,Microbiology and Immunology Graduate Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Curt R. Fischer
- ChEM-H, Stanford University, Stanford, CA, USA,Chan-Zuckerburg Biohub, San Francisco, CA, USA
| | - Bryan D. Merrill
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA,Microbiology and Immunology Graduate Program, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Steven K. Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Leah Guthrie
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lalla A. Fall
- ChEM-H, Stanford University, Stanford, CA, USA,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Dylan Dodd
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA,Address correspondence to: , ,
| | - Michael A. Fischbach
- Chan-Zuckerburg Biohub, San Francisco, CA, USA,Department of Bioengineering, Stanford University, Stanford, CA, USA,Address correspondence to: , ,
| | - Justin L. Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA,Chan-Zuckerburg Biohub, San Francisco, CA, USA,Center for Human Microbiome Studies, Stanford, CA, USA,Address correspondence to: , ,
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8
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Hryckowian AJ, Merrill BD, Porter NT, Van Treuren W, Nelson EJ, Garlena RA, Russell DA, Martens EC, Sonnenburg JL. Bacteroides thetaiotaomicron-Infecting Bacteriophage Isolates Inform Sequence-Based Host Range Predictions. Cell Host Microbe 2020; 28:371-379.e5. [PMID: 32652063 PMCID: PMC8045012 DOI: 10.1016/j.chom.2020.06.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [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: 03/04/2020] [Revised: 04/22/2020] [Accepted: 06/12/2020] [Indexed: 12/21/2022]
Abstract
Our emerging view of the gut microbiome largely focuses on bacteria, while less is known about other microbial components, such as bacteriophages (phages). Though phages are abundant in the gut, very few phages have been isolated from this ecosystem. Here, we report the genomes of 27 phages from the United States and Bangladesh that infect the prevalent human gut bacterium Bacteroides thetaiotaomicron. These phages are mostly distinct from previously sequenced phages with the exception of two, which are crAss-like phages. We compare these isolates to existing human gut metagenomes, revealing similarities to previously inferred phages and additional unexplored phage diversity. Finally, we use host tropisms of these phages to identify alleles of phage structural genes associated with infectivity. This work provides a detailed view of the gut's "viral dark matter" and a framework for future efforts to further integrate isolation- and sequencing-focused efforts to understand gut-resident phages.
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Affiliation(s)
- Andrew J Hryckowian
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Bryan D Merrill
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nathan T Porter
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - William Van Treuren
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Eric J Nelson
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA
| | - Rebecca A Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Daniel A Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Eric C Martens
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Justin L Sonnenburg
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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9
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Porter NT, Hryckowian AJ, Merrill BD, Fuentes JJ, Gardner JO, Glowacki RWP, Singh S, Crawford RD, Snitkin ES, Sonnenburg JL, Martens EC. Phase-variable capsular polysaccharides and lipoproteins modify bacteriophage susceptibility in Bacteroides thetaiotaomicron. Nat Microbiol 2020; 5:1170-1181. [PMID: 32601452 PMCID: PMC7482406 DOI: 10.1038/s41564-020-0746-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/27/2020] [Indexed: 12/22/2022]
Abstract
A variety of cell surface structures dictate interactions between bacteria and their environment, including their viruses (bacteriophages). Members of the human gut Bacteroidetes characteristically produce several phase-variable capsular polysaccharides (CPSs), but their contributions to bacteriophage interactions are unknown. To begin to understand how CPSs have an impact on Bacteroides-phage interactions, we isolated 71 Bacteroides thetaiotaomicron-infecting bacteriophages from two locations in the United States. Using B. thetaiotaomicron strains that express defined subsets of CPSs, we show that CPSs dictate host tropism for these phages and that expression of non-permissive CPS variants is selected under phage predation, enabling survival. In the absence of CPSs, B. thetaiotaomicron escapes bacteriophage predation by altering expression of eight distinct phase-variable lipoproteins. When constitutively expressed, one of these lipoproteins promotes resistance to multiple bacteriophages. Our results reveal important roles for Bacteroides CPSs and other cell surface structures that allow these bacteria to persist under bacteriophage predation, and hold important implications for using bacteriophages therapeutically to target gut symbionts.
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Affiliation(s)
- Nathan T Porter
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Andrew J Hryckowian
- 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
| | - Jaime J Fuentes
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Jackson O Gardner
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Robert W P Glowacki
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Shaleni Singh
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Ryan D Crawford
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Evan S Snitkin
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.
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10
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Brady TS, Fajardo CP, Merrill BD, Hilton JA, Graves KA, Eggett DL, Hope S. Bystander Phage Therapy: Inducing Host-Associated Bacteria to Produce Antimicrobial Toxins against the Pathogen Using Phages. Antibiotics (Basel) 2018; 7:E105. [PMID: 30518109 PMCID: PMC6315864 DOI: 10.3390/antibiotics7040105] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 11/08/2018] [Revised: 11/30/2018] [Accepted: 12/03/2018] [Indexed: 01/31/2023] Open
Abstract
Brevibacillus laterosporus is often present in beehives, including presence in hives infected with the causative agent of American Foulbrood (AFB), Paenibacillus larvae. In this work, 12 B. laterosporus bacteriophages induced bactericidal products in their host. Results demonstrate that P. larvae is susceptible to antimicrobials induced from field isolates of the bystander, B. laterosporus. Bystander antimicrobial activity was specific against the pathogen and not other bacterial species, indicating that the production was likely due to natural competition between the two bacteria. Three B. laterosporus phages were combined in a cocktail to treat AFB. Healthy hives treated with B. laterosporus phages experienced no difference in brood generation compared to control hives over 8 weeks. Phage presence in bee larvae after treatment rose to 60.8 ± 3.6% and dropped to 0 ± 0.8% after 72 h. In infected hives the recovery rate was 75% when treated, however AFB spores were not susceptible to the antimicrobials as evidenced by recurrence of AFB. We posit that the effectiveness of this treatment is due to the production of the bactericidal products of B. laterosporus when infected with phages resulting in bystander-killing of P. larvae. Bystander phage therapy may provide a new avenue for antibacterial production and treatment of disease.
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Affiliation(s)
- T Scott Brady
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA.
| | - Christopher P Fajardo
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA.
| | - Bryan D Merrill
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA.
| | - Jared A Hilton
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA.
| | - Kiel A Graves
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA.
| | - Dennis L Eggett
- Department of Statistics, Brigham Young University, Provo, UT 84602, USA.
| | - Sandra Hope
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA.
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11
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Berg JA, Merrill BD, Breakwell DP, Hope S, Grose JH. A PCR-Based Method for Distinguishing between Two Common Beehive Bacteria, Paenibacillus larvae and Brevibacillus laterosporus. Appl Environ Microbiol 2018; 84:e01886-18. [PMID: 30217838 PMCID: PMC6210111 DOI: 10.1128/aem.01886-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/01/2018] [Indexed: 12/18/2022] Open
Abstract
Paenibacillus larvae and Brevibacillus laterosporus are two bacteria that are members of the Paenibacillaceae family. Both are commonly found in beehives and have historically been difficult to distinguish from each other due to related genetic and phenotypic characteristics and a shared ecological niche. Here, we discuss the likely mischaracterization of three 16S rRNA sequences previously published as P. larvae and provide the phylogenetic evidence that supported the GenBank reassignment of the sequences as B. laterosporus We explore the issues that arise by using only 16S rRNA or other single-gene analyses to distinguish between these bacteria. We also present three sets of molecular markers, two sets that distinguish P. larvae from B. laterosporus and other closely related species within the Paenibacillus genus and a third set that distinguishes B. laterosporus from P. larvae and other closely related species within the Brevibacillus genus. These molecular markers provide a tool for proper identification of these oft-mistaken species.IMPORTANCE 16S rRNA gene sequencing in bacteria has long been held as the gold standard for typing bacteria and, for the most part, is an excellent method of taxonomically identifying different bacterial species. However, the high level of 16S rRNA sequence similarity of some published strains of P. larvae and B. laterosporus, as well as possible horizontal gene transfer events within their shared ecological niche, complicates the use of 16S rRNA sequence as an effective molecular marker for differentiating these two species. Additionally, shared characteristics of these bacteria limit the effectiveness of using traditional phenotypic identification assays, such as the catalase test. The results from this study provide PCR methods to quickly differentiate between these two genera and will be useful when studying Brevibacillus, Paenibacillus, and other disease-relevant bacteria commonly found in beehives.
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Affiliation(s)
- Jordan A Berg
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Bryan D Merrill
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Donald P Breakwell
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Sandra Hope
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Julianne H Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
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12
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Merrill BD, Fajardo CP, Hilton JA, Payne AM, Ward AT, Walker JK, Dhalai A, Imahara C, Mangohig J, Monk J, Pascacio C, Rai P, Salisbury A, Velez K, Bloomfield TJ, Buhler B, Duncan SG, Fuhriman DA, George J, Graves K, Heaton K, Hill HL, Kim M, Knabe BK, Ririe DB, Rogers SL, Stamereilers C, Stephenson MB, Usher BK, Ward CS, Withers JM, Wright CK, Breakwell DP, Grose JH, Hope S, Tsourkas PK. Complete Genome Sequences of 18 Paenibacillus larvae Phages from the Western United States. Microbiol Resour Announc 2018; 7:e00966-18. [PMID: 30533693 PMCID: PMC6256562 DOI: 10.1128/mra.00966-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 09/05/2018] [Indexed: 11/28/2022] Open
Abstract
We present here the complete genomes of 18 phages that infect Paenibacillus larvae, the causative agent of American foulbrood in honeybees. The phages were isolated between 2014 and 2016 as part of an undergraduate phage discovery course at Brigham Young University. The phages were isolated primarily from bee debris and lysogens.
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Affiliation(s)
- Bryan D. Merrill
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Christopher P. Fajardo
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Jared A. Hilton
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Ashley M. Payne
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Andy T. Ward
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Jamison K. Walker
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Aziza Dhalai
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA
| | - Cameron Imahara
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA
| | - James Mangohig
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA
| | - Josh Monk
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA
| | - Cristian Pascacio
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA
| | - Padmani Rai
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA
| | - Alicia Salisbury
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA
| | - Kathie Velez
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA
| | - Travis J. Bloomfield
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Brett Buhler
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Steven G. Duncan
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - David A. Fuhriman
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Josil George
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA
| | - Kiel Graves
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Karli Heaton
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Hunter L. Hill
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Michelle Kim
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA
| | - Bradley K. Knabe
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Devin B. Ririe
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Spencer L. Rogers
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | | | - Michael B. Stephenson
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Brittian K. Usher
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Colton S. Ward
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Jacob M. Withers
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Cole K. Wright
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Donald P. Breakwell
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Julianne H. Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Sandra Hope
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
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13
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Walker JK, Merrill BD, Berg JA, Dhalai A, Dingman DW, Fajardo CP, Graves K, Hill HL, Hilton JA, Imahara C, Knabe BK, Mangohig J, Monk J, Mun H, Payne AM, Salisbury A, Stamereilers C, Velez K, Ward AT, Breakwell DP, Grose JH, Hope S, Tsourkas PK. Complete Genome Sequences of Paenibacillus larvae Phages BN12, Dragolir, Kiel007, Leyra, Likha, Pagassa, PBL1c, and Tadhana. Genome Announc 2018; 6:e01602-17. [PMID: 29903825 PMCID: PMC6003738 DOI: 10.1128/genomea.01602-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 05/08/2018] [Indexed: 11/25/2022]
Abstract
We present here the complete genomes of eight phages that infect Paenibacillus larvae, the causative agent of American foulbrood in honeybees. Phage PBL1c was originally isolated in 1984 from a P. larvae lysogen, while the remaining phages were isolated in 2014 from bee debris, honeycomb, and lysogens from three states in the USA.
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Affiliation(s)
- Jamison K Walker
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Bryan D Merrill
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Jordan A Berg
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Aziza Dhalai
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA
| | - Douglas W Dingman
- Department of Entomology, Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
| | - Chris P Fajardo
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Kiel Graves
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Hunter L Hill
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Jared A Hilton
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Cameron Imahara
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA
| | - Bradley K Knabe
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - James Mangohig
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA
| | - Josh Monk
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA
| | - Heejin Mun
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA
| | - Ashley M Payne
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Alicia Salisbury
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA
| | | | - Kathie Velez
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA
| | - Andy T Ward
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Donald P Breakwell
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Julianne H Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Sandra Hope
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
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14
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Lumb JH, Li Q, Popov LM, Ding S, Keith MT, Merrill BD, Greenberg HB, Li JB, Carette JE. DDX6 Represses Aberrant Activation of Interferon-Stimulated Genes. Cell Rep 2018; 20:819-831. [PMID: 28746868 DOI: 10.1016/j.celrep.2017.06.085] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/30/2017] [Accepted: 06/28/2017] [Indexed: 12/31/2022] Open
Abstract
The innate immune system tightly regulates activation of interferon-stimulated genes (ISGs) to avoid inappropriate expression. Pathological ISG activation resulting from aberrant nucleic acid metabolism has been implicated in autoimmune disease; however, the mechanisms governing ISG suppression are unknown. Through a genome-wide genetic screen, we identified DEAD-box helicase 6 (DDX6) as a suppressor of ISGs. Genetic ablation of DDX6 induced global upregulation of ISGs and other immune genes. ISG upregulation proved cell intrinsic, imposing an antiviral state and making cells refractory to divergent families of RNA viruses. Epistatic analysis revealed that ISG activation could not be overcome by deletion of canonical RNA sensors. However, DDX6 deficiency was suppressed by disrupting LSM1, a core component of mRNA degradation machinery, suggesting that dysregulation of RNA processing underlies ISG activation in the DDX6 mutant. DDX6 is distinct among DExD/H helicases that regulate the antiviral response in its singular ability to negatively regulate immunity.
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Affiliation(s)
- Jennifer H Lumb
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Qin Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Lauren M Popov
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Siyuan Ding
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA; Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Palo Alto Veterans Institute of Research, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Marie T Keith
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Bryan D Merrill
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Harry B Greenberg
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA; Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Palo Alto Veterans Institute of Research, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA.
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15
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Dodd D, Spitzer MH, Van Treuren W, Merrill BD, Hryckowian AJ, Higginbottom SK, Le A, Cowan TM, Nolan GP, Fischbach MA, Sonnenburg JL. A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites. Nature 2017; 551:648-652. [PMID: 29168502 DOI: 10.1038/nature24661] [Citation(s) in RCA: 688] [Impact Index Per Article: 98.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 10/25/2017] [Indexed: 12/30/2022]
Abstract
The human gut microbiota produces dozens of metabolites that accumulate in the bloodstream, where they can have systemic effects on the host. Although these small molecules commonly reach concentrations similar to those achieved by pharmaceutical agents, remarkably little is known about the microbial metabolic pathways that produce them. Here we use a combination of genetics and metabolic profiling to characterize a pathway from the gut symbiont Clostridium sporogenes that generates aromatic amino acid metabolites. Our results reveal that this pathway produces twelve compounds, nine of which are known to accumulate in host serum. All three aromatic amino acids (tryptophan, phenylalanine and tyrosine) serve as substrates for the pathway, and it involves branching and alternative reductases for specific intermediates. By genetically manipulating C. sporogenes, we modulate serum levels of these metabolites in gnotobiotic mice, and show that in turn this affects intestinal permeability and systemic immunity. This work has the potential to provide the basis of a systematic effort to engineer the molecular output of the gut bacterial community.
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Affiliation(s)
- Dylan Dodd
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Matthew H Spitzer
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - William Van Treuren
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Bryan D Merrill
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Andrew J Hryckowian
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Steven K Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Anthony Le
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Tina M Cowan
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Garry P Nolan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Michael A Fischbach
- California Institute for Quantitative Bioscience and Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco 94143, California, USA
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
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16
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Brady TS, Merrill BD, Hilton JA, Payne AM, Stephenson MB, Hope S. Bacteriophages as an alternative to conventional antibiotic use for the prevention or treatment of Paenibacillus larvae in honeybee hives. J Invertebr Pathol 2017; 150:94-100. [PMID: 28917651 DOI: 10.1016/j.jip.2017.09.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/06/2017] [Accepted: 09/11/2017] [Indexed: 02/07/2023]
Abstract
American Foulbrood (AFB) is an infectious disease caused by the bacteria, Paenibacillus larvae. P. larvae phages were isolated and tested to determine each phages' host range amongst 59 field isolate strains of P. larvae. Three phages were selected to create a phage cocktail for the treatment of AFB infections according to the combined phages' ability to lyse all tested strains of bacteria. Studies were performed to demonstrate the safety and efficacy of the phage cocktail treatment as a replacement for traditional antibiotics for the prevention of AFB and the treatment of active infections. Safety verification studies confirmed that the phage cocktail did not adversely affect the rate of bee death even when administered as an overdose. In a comparative study of healthy hives, traditional prophylactic antibiotic treatment experienced a 38±0.7% decrease in overall hive health, which was statistically lower than hive health observed in control hives. Hives treated with phage cocktail decreased 19±0.8%, which was not statistically different than control hives, which decreased by 10±1.0%. In a study of beehives at-risk for a natural infection, 100±0.5% of phage-treated hives were protected from AFB infection, while 80±0.5% of untreated controls became infected. AFB infected hives began with an average Hitchcock score of 2.25 out of 4 and 100±0.5% of the hives recovered completely within two weeks of treatment with phage cocktail. While the n numbers for the latter two studies are small, the results for both the phage protection rate and the phage cure rate were statistically significant (α=0.05). These studies demonstrate the powerful potential of using a phage cocktail against AFB and establish phage therapy as a feasible treatment.
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Affiliation(s)
- T Scott Brady
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, USA
| | - Bryan D Merrill
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, USA
| | - Jared A Hilton
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, USA
| | - Ashley M Payne
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, USA
| | - Michael B Stephenson
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, USA
| | - Sandra Hope
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, USA.
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17
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Asare PT, Jeong TY, Ryu S, Klumpp J, Loessner MJ, Merrill BD, Kim KP. Putative type 1 thymidylate synthase and dihydrofolate reductase as signature genes of a novel Bastille-like group of phages in the subfamily Spounavirinae. BMC Genomics 2015; 16:582. [PMID: 26250905 PMCID: PMC4528723 DOI: 10.1186/s12864-015-1757-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 07/07/2015] [Indexed: 12/12/2022] Open
Abstract
Background Spounavirinae viruses have received an increasing interest as tools for the control of harmful bacteria due to their relatively broad host range and strictly virulent phenotype. Results In this study, we collected and analyzed the complete genome sequences of 61 published phages, either ICTV-classified or candidate members of the Spounavirinae subfamily of the Myoviridae. A set of comparative analyses identified a distinct, recently proposed Bastille-like phage group within the Spounavirinae. More importantly, type 1 thymidylate synthase (TS1) and dihydrofolate reductase (DHFR) genes were shown to be unique for the members of the proposed Bastille-like phage group, and are suitable as molecular markers. We also show that the members of this group encode beta-lactamase and/or sporulation-related SpoIIIE homologs, possibly questioning their suitability as biocontrol agents. Conclusions We confirm the creation of a new genus—the “Bastille-like group”—in Spounavirinae, and propose that the presence of TS1- and DHFR-encoding genes could serve as signatures for the new Bastille-like group. In addition, the presence of metallo-beta-lactamase and/or SpoIIIE homologs in all members of Bastille-like group phages makes questionable their suitability for use in biocontrol. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1757-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paul Tetteh Asare
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do, 561-756, Korea.
| | - Tae-Yong Jeong
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do, 561-756, Korea.
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, Korea. .,Department of Agricultural Biotechnology, Center for Agricultural Biomaterials, Seoul National University, Seoul, Korea. .,Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Korea.
| | - Jochen Klumpp
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland.
| | - Martin J Loessner
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland.
| | - Bryan D Merrill
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, USA.
| | - Kwang-Pyo Kim
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do, 561-756, Korea.
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18
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Merrill BD, Grose JH, Breakwell DP, Burnett SH. Characterization of Paenibacillus larvae bacteriophages and their genomic relationships to firmicute bacteriophages. BMC Genomics 2014; 15:745. [PMID: 25174730 PMCID: PMC4168068 DOI: 10.1186/1471-2164-15-745] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 08/26/2014] [Indexed: 01/10/2023] Open
Abstract
Background Paenibacillus larvae is a Firmicute bacterium that causes American Foulbrood, a lethal disease in honeybees and is a major source of global agricultural losses. Although P. larvae phages were isolated prior to 2013, no full genome sequences of P. larvae bacteriophages were published or analyzed. This report includes an in-depth analysis of the structure, genomes, and relatedness of P. larvae myoviruses Abouo, Davis, Emery, Jimmer1, Jimmer2, and siphovirus phiIBB_Pl23 to each other and to other known phages. Results P. larvae phages Abouo, Davies, Emery, Jimmer1, and Jimmer2 are myoviruses with ~50 kbp genomes. The six P. larvae phages form three distinct groups by dotplot analysis. An annotated linear genome map of these six phages displays important identifiable genes and demonstrates the relationship between phages. Sixty phage assembly or structural protein genes and 133 regulatory or other non-structural protein genes were identifiable among the six P. larvae phages. Jimmer1, Jimmer2, and Davies formed stable lysogens resistant to superinfection by genetically similar phages. The correlation between tape measure protein gene length and phage tail length allowed identification of co-isolated phages Emery and Abouo in electron micrographs. A Phamerator database was assembled with the P. larvae phage genomes and 107 genomes of Firmicute-infecting phages, including 71 Bacillus phages. Phamerator identified conserved domains in 1,501 of 6,181 phamilies (only 24.3%) encoded by genes in the database and revealed that P. larvae phage genomes shared at least one phamily with 72 of the 107 other phages. The phamily relationship of large terminase proteins was used to indicate putative DNA packaging strategies. Analyses from CoreGenes, Phamerator, and electron micrograph measurements indicated Jimmer1, Jimmer2, Abouo and Davies were related to phages phiC2, EJ-1, KC5a, and AQ113, which are small-genome myoviruses that infect Streptococcus, Lactobacillus, and Clostridium, respectively. Conclusions This paper represents the first comparison of phage genomes in the Paenibacillus genus and the first organization of P. larvae phages based on sequence and structure. This analysis provides an important contribution to the field of bacteriophage genomics by serving as a foundation on which to build an understanding of the natural predators of P. larvae. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-745) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Sandra H Burnett
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, UT, USA.
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