1
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Kirsch JM, Hryckowian AJ, Duerkop BA. A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota. Cell Host Microbe 2024:S1931-3128(24)00085-4. [PMID: 38565143 DOI: 10.1016/j.chom.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/06/2024] [Accepted: 03/08/2024] [Indexed: 04/04/2024]
Abstract
Insertion sequence (IS) elements are mobile genetic elements in bacterial genomes that support adaptation. We developed a database of IS elements coupled to a computational pipeline that identifies IS element insertions in the microbiota. We discovered that diverse IS elements insert into the genomes of intestinal bacteria regardless of human host lifestyle. These insertions target bacterial accessory genes that aid in their adaptation to unique environmental conditions. Using IS expansion in Bacteroides, we show that IS activity leads to the insertion of "hot spots" in accessory genes. We show that IS insertions are stable and can be transferred between humans. Extreme environmental perturbations force IS elements to fall out of the microbiota, and many fail to rebound following homeostasis. Our work shows that IS elements drive bacterial genome diversification within the microbiota and establishes a framework for understanding how strain-level variation within the microbiota impacts human health.
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Affiliation(s)
- Joshua M Kirsch
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, CO 80045, USA
| | - Andrew J Hryckowian
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA; Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Breck A Duerkop
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, CO 80045, USA.
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2
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Pensinger DA, Dobrila HA, Stevenson DM, Hryckowian ND, Amador-Noguez D, Hryckowian AJ. Exogenous butyrate inhibits butyrogenic metabolism and alters virulence phenotypes in Clostridioides difficile. mBio 2024; 15:e0253523. [PMID: 38289141 PMCID: PMC10936429 DOI: 10.1128/mbio.02535-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/20/2023] [Indexed: 02/13/2024] Open
Abstract
The gut microbiome engenders colonization resistance against the diarrheal pathogen Clostridioides difficile, but the molecular basis of this colonization resistance is incompletely understood. A prominent class of gut microbiome-produced metabolites important for colonization resistance against C. difficile is short-chain fatty acids (SCFAs). In particular, one SCFA (butyrate) decreases the fitness of C. difficile in vitro and is correlated with C. difficile-inhospitable gut environments, both in mice and in humans. Here, we demonstrate that butyrate-dependent growth inhibition in C. difficile occurs under conditions where C. difficile also produces butyrate as a metabolic end product. Furthermore, we show that exogenous butyrate is internalized into C. difficile cells and is incorporated into intracellular CoA pools where it is metabolized in a reverse (energetically unfavorable) direction to crotonyl-CoA and (S)-3-hydroxybutyryl-CoA and/or 4-hydroxybutyryl-CoA. This internalization of butyrate and reverse metabolic flow of a butyrogenic pathway(s) in C. difficile coincides with alterations in toxin release and sporulation. Together, this work highlights butyrate as a marker of a C. difficile-inhospitable environment to which C. difficile responds by releasing its diarrheagenic toxins and producing environmentally resistant spores necessary for transmission between hosts. These findings provide foundational data for understanding the molecular and genetic basis of how C. difficile growth is inhibited by butyrate and how butyrate alters C. difficile virulence in the face of a highly competitive and dynamic gut environment.IMPORTANCEThe gut microbiome engenders colonization resistance against the diarrheal pathogen Clostridioides difficile, but the molecular basis of this colonization resistance is incompletely understood, which hinders the development of novel therapeutic interventions for C. difficile infection (CDI). We investigated how C. difficile responds to butyrate, an end-product of gut microbiome community metabolism which inhibits C. difficile growth. We show that exogenously produced butyrate is internalized into C. difficile, which inhibits C. difficile growth by interfering with its own butyrate production. This growth inhibition coincides with increased toxin release from C. difficile cells and the production of environmentally resistant spores necessary for transmission between hosts. Future work to disentangle the molecular mechanisms underlying these growth and virulence phenotypes will likely lead to new strategies to restrict C. difficile growth in the gut and minimize its pathogenesis during CDI.
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Affiliation(s)
- Daniel A. Pensinger
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Horia A. Dobrila
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David M. Stevenson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nicole D. Hryckowian
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Andrew J. Hryckowian
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
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3
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Kirsch JM, Hryckowian AJ, Duerkop BA. A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota. bioRxiv 2024:2023.10.06.561241. [PMID: 37873088 PMCID: PMC10592638 DOI: 10.1101/2023.10.06.561241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Insertion sequence (IS) elements are mobile genetic elements in bacterial genomes that support adaptation. We developed a database of IS elements coupled to a computational pipeline that identifies IS element insertions in the microbiota. We discovered that diverse IS elements insert into the genomes of intestinal bacteria regardless of human host lifestyle. These insertions target bacterial accessory genes that aid in their adaptation to unique environmental conditions. Using IS expansion in Bacteroides, we show that IS activity leads to insertion "hot spots" in accessory genes. We show that IS insertions are stable and can be transferred between humans. Extreme environmental perturbations force IS elements to fall out of the microbiota and many fail to rebound following homeostasis. Our work shows that IS elements drive bacterial genome diversification within the microbiota and establishes a framework for understanding how strain level variation within the microbiota impacts human health.
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Affiliation(s)
- Joshua M. Kirsch
- Department of Immunology and Microbiology, University of Colorado - Anschutz Medical Campus, School of Medicine, Aurora, Colorado, 80045, USA
| | - Andrew J. Hryckowian
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, 53706, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, 53706, USA
| | - Breck A. Duerkop
- Department of Immunology and Microbiology, University of Colorado - Anschutz Medical Campus, School of Medicine, Aurora, Colorado, 80045, USA
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4
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Ling J, Hryckowian AJ. Re-framing the importance of Group B Streptococcus as a gut-resident pathobiont. Infect Immun 2024:e0047823. [PMID: 38436256 DOI: 10.1128/iai.00478-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2024] Open
Abstract
Streptococcus agalactiae (Group B Streptococcus, GBS) is a Gram-positive bacterial species that causes disease in humans across the lifespan. While antibiotics are used to mitigate GBS infections, it is evident that antibiotics disrupt human microbiomes (which can predispose people to other diseases later in life), and antibiotic resistance in GBS is on the rise. Taken together, these unintended negative impacts of antibiotics highlight the need for precision approaches for minimizing GBS disease. One possible approach involves selectively depleting GBS in its commensal niches before it can cause disease at other body sites or be transmitted to at-risk individuals. One understudied commensal niche of GBS is the adult gastrointestinal (GI) tract, which may predispose colonization at other body sites in individuals at risk for GBS disease. However, a better understanding of the host-, microbiome-, and GBS-determined variables that dictate GBS GI carriage is needed before precise GI decolonization approaches can be developed. In this review, we synthesize current knowledge of the diverse body sites occupied by GBS as a pathogen and as a commensal. We summarize key molecular factors GBS utilizes to colonize different host-associated niches to inform future efforts to study GBS in the GI tract. We also discuss other GI commensals that are pathogenic in other body sites to emphasize the broader utility of precise de-colonization approaches for mitigating infections by GBS and other bacterial pathogens. Finally, we highlight how GBS treatments could be improved with a more holistic understanding of GBS enabled by continued GI-focused study.
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Affiliation(s)
- Joie Ling
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Healthon, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Andrew J Hryckowian
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Healthon, Madison, Wisconsin, USA
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5
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Cowley ES, Chaves IZ, Osman F, Suen G, Anantharaman K, Hryckowian AJ. Determinants of Gastrointestinal Group B Streptococcus Carriage in Adults. bioRxiv 2023:2023.08.17.553755. [PMID: 37645860 PMCID: PMC10462156 DOI: 10.1101/2023.08.17.553755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Background Streptococcus agalactiae (Group B Streptococcus, GBS) is a commensal Gram-positive bacterium found in the human gastrointestinal and urogenital tracts. Much of what is known about GBS relates to the diseases it causes in pregnant people and neonates. However, GBS is a common cause of disease in the general population with 90% of GBS mortality occurring in non-pregnant people. There are limited data about the predisposing factors for GBS and the reservoirs in the body. To gain an understanding of the determinants of gastrointestinal GBS carriage, we used stool samples and associated metadata to determine the prevalence and abundance of GBS in the gut microbiome of adults and find risk factors for GBS status. Methods We used 754 stool samples collected from adults in Wisconsin from 2016-2017 to test for the prevalence and abundance of GBS using a Taqman probe-based qPCR assay targeting two GBS-specific genes: cfp and sip. We compared the microbiome compositions of the stool samples by GBS status using 16S rRNA analysis. We compared associations with GBS status and 557 survey variables collected during sample acquisition (demographics, diet, overall health, and reproductive health) using univariate and multivariate analyses. Results We found 137/754 (18%) of participants had detectable GBS in their stool samples with a median abundance of 104 copies per nanogram of starting DNA. There was no difference in GBS status or abundance based on gender. Beta-diversity, Bray-Curtis and Unweighted UniFrac, was significantly different based on carrier status of the participant. Prior to p-value correction, 59/557 (10.6%) survey variables were significantly associated with GBS carrier status and 11/547 (2.0%) variables were significantly associated with abundance (p-value<0.05). After p-value correction, 2/547 (0.4%) variables were associated with GBS abundance: an increased abundance of GBS was associated with a decreased frequency since last dental checkup (p<0.001) and last dental cleaning (p<0.001). Increased GBS abundance was significantly associated with increased frequency of iron consumption (p=0.007) after p-value correction in multivariate models. Conclusions GBS is found in stool samples from adults in Wisconsin at similar frequencies as pregnant individuals screened with rectovaginal swabs. We did not find associations between risk factors historically associated with GBS in pregnant people, suggesting that risk factors for GBS carriage in pregnancy may differ from those in the general population. We found that frequency of iron consumption and dental hygiene are risk factors for GBS carriage in Wisconsin adults. Given that these variables were not assayed in previous GBS surveys, it is possible they also influence carriage in pregnant people. Taken together, this work serves as a foundation for future work in developing approaches to decrease GBS abundance in carriers.
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Affiliation(s)
- Elise S. Cowley
- Department of Bacteriology, University of Wisconsin-Madison
- Microbiology Doctoral Training Program, University of Wisconsin-Madison
| | - Ibrahim Zuniga Chaves
- Department of Bacteriology, University of Wisconsin-Madison
- Microbiology Doctoral Training Program, University of Wisconsin-Madison
| | - Fauzia Osman
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison
| | | | - Andrew J. Hryckowian
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison
- Department of Medicine (Division of Gastroenterology & Hepatology), School of Medicine and Public Health, University of Wisconsin-Madison
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6
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Pensinger DA, Dobrila HA, Stevenson DM, Davis NM, Amador-Noguez D, Hryckowian AJ. Exogenous butyrate inhibits butyrogenic metabolism and alters expression of virulence genes in Clostridioides difficile. bioRxiv 2023:2023.07.06.548018. [PMID: 37461482 PMCID: PMC10350080 DOI: 10.1101/2023.07.06.548018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
The gut microbiome engenders colonization resistance against the diarrheal pathogen Clostridioides difficile but the molecular basis of this colonization resistance is incompletely understood. A prominent class of gut microbiome-produced metabolites important for colonization resistance against C. difficile is short chain fatty acids (SCFAs). In particular, one SCFA (butyrate) decreases the fitness of C. difficile in vitro and is correlated with C. difficile-inhospitable gut environments, both in mice and in humans. Here, we demonstrate that butyrate-dependent growth inhibition in C. difficile occurs under conditions where C. difficile also produces butyrate as a metabolic end product. Furthermore, we show that exogenous butyrate is internalized into C. difficile cells, is incorporated into intracellular CoA pools where it is metabolized in a reverse (energetically unfavorable) direction to crotonyl-CoA and (S)-3-hydroxybutyryl-CoA and/or 4-hydroxybutyryl-CoA. This internalization of butyrate and reverse metabolic flow of butyrogenic pathway(s) in C. difficile coincides with alterations in toxin production and sporulation. Together, this work highlights butyrate as a signal of a C. difficile inhospitable environment to which C. difficile responds by producing its diarrheagenic toxins and producing environmentally-resistant spores necessary for transmission between hosts. These findings provide foundational data for understanding the molecular and genetic basis of how C. difficile growth is inhibited by butyrate and how butyrate serves as a signal to alter C. difficile virulence in the face of a highly competitive and dynamic gut environment.
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Affiliation(s)
- Daniel A. Pensinger
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Horia A. Dobrila
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - David M. Stevenson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Nicole M. Davis
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | | | - Andrew J. Hryckowian
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
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7
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Hanson L, VandeVusse L, Forgie M, Malloy E, Singh M, Scherer M, Kleber D, Dixon J, Hryckowian AJ, Safdar N. A randomized controlled trial of an oral probiotic to reduce antepartum group B Streptococcus colonization and gastrointestinal symptoms. Am J Obstet Gynecol MFM 2023; 5:100748. [PMID: 36108911 DOI: 10.1016/j.ajogmf.2022.100748] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 09/06/2022] [Indexed: 11/18/2022]
Abstract
BACKGROUND Probiotics have been suggested as a strategy to reduce antenatal group B Streptococcus colonization. Although probiotics are known to improve gastrointestinal symptoms, this has not been studied during pregnancy. OBJECTIVE This study aimed to evaluate the efficacy of a probiotic to reduce: (1) standard-of-care antenatal group B Streptococcus colonization and colony counts and (2) gastrointestinal symptoms of pregnancy. STUDY DESIGN In a double-blind fashion, 109 healthy adult pregnant people were randomized to Florajen3 probiotic or placebo capsules once daily from 28 weeks' gestation until labor onset. Baseline vaginal and rectal study swabs for group B Streptococcus colony-forming units and microbiome analysis were collected at 28 and 36 weeks' gestation. Standard-of-care vaginal to rectal group B Streptococcus swabs were collected from all participants at 36 weeks' gestation and determined the need for intrapartum antibiotic prophylaxis. Data collection included solicitation of adverse events, demographic information, Antepartum Gastrointestinal Symptom Assessment score, yogurt ingestion, sexual activity, and vaginal cleaning practices. RESULTS A total of 83 participants completed the study to 36 weeks' gestation with no adverse events. Standard-of-care group B Streptococcus colonization was 20.4% in the control group and 15.4% in probiotic group participants (-5%; P=.73). The relative risk for positive standard-of-care vaginal-rectal group B Streptococcus colonization was 1.33 (95% confidence interval, 0.5-3.40) times higher in the control group than in the probiotic group (P=.55). There were no differences in median vaginal (P=.16) or rectal (P=.20) group B streptococcus colony-forming units at baseline or at 36 weeks (vaginal P>.999; rectal P=.56). Antepartum Gastrointestinal Symptom Assessment scores were similar at baseline (P=.19), but significantly decreased in probiotic group participants at 36 weeks (P=.02). No covariates significantly altered group B Streptococcus colonization. Significantly more Florajen3 bacteria components were recovered from the vaginal-rectal samples of probiotic group participants (32%; P=.04) compared with controls. CONCLUSION The findings of this study provided insufficient evidence for the clinical application of the Florajen3 probiotic intervention to reduce standard-of-care vaginal-rectal group B Streptococcus colonization. The prevalence of group B Streptococcus was lower than expected in the study population, and intervention adherence was poor. Probiotic bacteria colonization of the genitourinary tract occurred more in intervention group participants than in controls and significantly reduced gastrointestinal symptoms of pregnancy.
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Affiliation(s)
- Lisa Hanson
- Marquette University College of Nursing, Milwaukee, WI (Drs Hanson, VandeVusse, Malloy, and Singh).
| | - Leona VandeVusse
- Marquette University College of Nursing, Milwaukee, WI (Drs Hanson, VandeVusse, Malloy, and Singh)
| | - Marie Forgie
- Advocate Aurora UW Medical Group, Aurora Sinai Medical Center, Milwaukee, WI (Drs Forgie and Malloy)
| | - Emily Malloy
- Advocate Aurora UW Medical Group, Aurora Sinai Medical Center, Milwaukee, WI (Drs Forgie and Malloy); Advocate Aurora Sinai Midwifery and Wellness Center, Milwaukee, WI (Dr Malloy and Ms Scherer)
| | - Maharaj Singh
- Marquette University College of Nursing, Milwaukee, WI (Drs Hanson, VandeVusse, Malloy, and Singh); Advocate Aurora Research Institute, Milwaukee, WI (Dr Singh and Ms Kleber)
| | - MaryAnne Scherer
- Advocate Aurora Sinai Midwifery and Wellness Center, Milwaukee, WI (Dr Malloy and Ms Scherer)
| | - Diana Kleber
- Advocate Aurora Research Institute, Milwaukee, WI (Dr Singh and Ms Kleber)
| | - Jonah Dixon
- University of Wisconsin School of Medicine and Public Health, Madison, WI (Mr Dixon and Dr Safdar)
| | - Andrew J Hryckowian
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Wisconsin-Madison, Madison, WI (Dr Hryckowian); Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI (Dr Hryckowian)
| | - Nasia Safdar
- University of Wisconsin School of Medicine and Public Health, Madison, WI (Mr Dixon and Dr Safdar)
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8
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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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9
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Pruss KM, Enam F, Battaglioli E, DeFeo M, Diaz OR, Higginbottom SK, Fischer CR, Hryckowian AJ, Van Treuren W, Dodd D, Kashyap P, Sonnenburg JL. Oxidative ornithine metabolism supports non-inflammatory C. difficile colonization. Nat Metab 2022; 4:19-28. [PMID: 34992297 PMCID: PMC8803604 DOI: 10.1038/s42255-021-00506-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 11/12/2021] [Indexed: 01/08/2023]
Abstract
The enteric pathogen Clostridioides difficile (Cd) is responsible for a toxin-mediated infection that causes more than 200,000 recorded hospitalizations and 13,000 deaths in the United States every year1. However, Cd can colonize the gut in the absence of disease symptoms. Prevalence of asymptomatic colonization by toxigenic Cd in healthy populations is high; asymptomatic carriers are at increased risk of infection compared to noncolonized individuals and may be a reservoir for transmission of Cd infection2,3. Elucidating the molecular mechanisms by which Cd persists in the absence of disease is necessary for understanding pathogenesis and developing refined therapeutic strategies. Here, we show with gut microbiome metatranscriptomic analysis that mice recalcitrant to Cd infection and inflammation exhibit increased community-wide expression of arginine and ornithine metabolic pathways. To query Cd metabolism specifically, we leverage RNA sequencing in gnotobiotic mice infected with two wild-type strains (630 and R20291) and isogenic toxin-deficient mutants of these strains to differentiate inflammation-dependent versus -independent transcriptional states. A single operon encoding oxidative ornithine degradation is consistently upregulated across non-toxigenic Cd strains. Combining untargeted and targeted metabolomics with bacterial and host genetics, we demonstrate that both diet- and host-derived sources of ornithine provide a competitive advantage to Cd, suggesting a mechanism for Cd persistence within a non-inflammatory, healthy gut.
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Affiliation(s)
- Kali M Pruss
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Fatima Enam
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Eric Battaglioli
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, GA, USA
| | - Mary DeFeo
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Oscar R Diaz
- 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
| | - Curt R Fischer
- ChEM-H, Stanford University, Stanford, CA, USA
- Octant Bio, Emeryville, CA, USA
| | - Andrew J Hryckowian
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - William Van Treuren
- Department of Microbiology and Immunology, 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
| | - Purna Kashyap
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
- Center for Human Microbiome Studies, Stanford, CA, USA.
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10
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Abstract
Clostridioides difficile is an opportunistic diarrheal pathogen responsible for significant morbidity and mortality worldwide. A disrupted (dysbiotic) gut microbiome, commonly engendered by antibiotic treatment, is the primary risk factor for C. difficile infection, highlighting that C. difficile–microbiome interactions are critical for determining the fitness of this pathogen. Here, we review short chain fatty acids (SCFAs): a major class of metabolites present in the gut, their production by the gut microbiome, and their impacts on the biology of the host and of C. difficile. We use these observations to illustrate a conceptual model whereby C. difficile senses and responds to SCFAs as a marker of a healthy gut and tunes its virulence accordingly in order to maintain dysbiosis. Future work to learn the molecular mechanisms and genetic circuitry underlying the relationships between C. difficile and SCFAs will help to identify precision approaches, distinct from antibiotics and fecal transplant, for mitigating disease caused by C. difficile and will inform similar investigations into other gastrointestinal pathogens.
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Affiliation(s)
- Anna L. Gregory
- Department of Medicine, University of Wisconsin School of Medicine & Public Health, Madison, Wisconsin, United States of America
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine & Public Health, Madison, Wisconsin, United States of America
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Daniel A. Pensinger
- Department of Medicine, University of Wisconsin School of Medicine & Public Health, Madison, Wisconsin, United States of America
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine & Public Health, Madison, Wisconsin, United States of America
| | - Andrew J. Hryckowian
- Department of Medicine, University of Wisconsin School of Medicine & Public Health, Madison, Wisconsin, United States of America
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine & Public Health, Madison, Wisconsin, United States of America
- * E-mail:
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11
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Flaherty KE, Grembi JA, Ramachandran VV, Haque F, Khatun S, Rahman M, Maples S, Becker TK, Spormann AM, Schoolnik GK, Hryckowian AJ, Nelson EJ. High-throughput low-cost nl-qPCR for enteropathogen detection: A proof-of-concept among hospitalized patients in Bangladesh. PLoS One 2021; 16:e0257708. [PMID: 34597302 PMCID: PMC8486112 DOI: 10.1371/journal.pone.0257708] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 09/07/2021] [Indexed: 11/25/2022] Open
Abstract
Background Diarrheal disease is a leading cause of morbidity and mortality globally, especially in low- and middle-income countries. High-throughput and low-cost approaches to identify etiologic agents are needed to guide public health mitigation. Nanoliter-qPCR (nl-qPCR) is an attractive alternative to more expensive methods yet is nascent in application and without a proof-of-concept among hospitalized patients. Methods A census-based study was conducted among diarrheal patients admitted at two government hospitals in rural Bangladesh during a diarrheal outbreak period. DNA was extracted from stool samples and assayed by nl-qPCR for common bacterial, protozoan, and helminth enteropathogens as the primary outcome. Results A total of 961 patients were enrolled; stool samples were collected from 827 patients. Enteropathogens were detected in 69% of patient samples; More than one enteropathogen was detected in 32%. Enteropathogens most commonly detected were enteroaggregative Escherichia coli (26.0%), Shiga toxin-producing E.coli (18.3%), enterotoxigenic E. coli (15.5% heat stable toxin positive, 2.2% heat labile toxin positive), Shigella spp. (14.8%), and Vibrio cholerae (9.0%). Geospatial analysis revealed that the median number of pathogens per patient and the proportion of cases presenting with severe dehydration were greatest amongst patients residing closest to the study hospitals.” Conclusions This study demonstrates a proof-of-concept for nl-qPCR as a high-throughput low-cost method for enteropathogen detection among hospitalized patients.
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Affiliation(s)
- Katelyn E. Flaherty
- Department Environmental and Global Health, University of Florida, Gainesville, Florida, United States of America
- Department of Emergency Medicine, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
| | - Jessica A. Grembi
- Department of Civil and Environmental Engineering, Stanford University, Stanford, California, United States of America
- Department of Medicine, School of Medicine, Stanford University, Stanford, California, United States of America
| | - Vasavi V. Ramachandran
- Department of Pediatrics, School of Medicine, Stanford University, Stanford, California, United States of America
| | - Farhana Haque
- Institute of Epidemiology, Disease Control and Research, Ministry of Health and Family Welfare, Government of Bangladesh, Dhaka, Bangladesh
- Institute for Global Health, University College London, London, United Kingdom
| | - Selina Khatun
- Institute of Epidemiology, Disease Control and Research, Ministry of Health and Family Welfare, Government of Bangladesh, Dhaka, Bangladesh
| | - Mahmudu Rahman
- Institute of Epidemiology, Disease Control and Research, Ministry of Health and Family Welfare, Government of Bangladesh, Dhaka, Bangladesh
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Stace Maples
- Geospatial Center, Branner Library, Stanford University, Stanford, California, United States of America
| | - Torben K. Becker
- Department Environmental and Global Health, University of Florida, Gainesville, Florida, United States of America
- Department of Emergency Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Alfred M. Spormann
- Department of Civil and Environmental Engineering, Stanford University, Stanford, California, United States of America
| | - Gary K. Schoolnik
- Department of Medicine, School of Medicine, Stanford University, Stanford, California, United States of America
| | - Andrew J. Hryckowian
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Eric J. Nelson
- Department Environmental and Global Health, University of Florida, Gainesville, Florida, United States of America
- Department of Medicine, School of Medicine, Stanford University, Stanford, California, United States of America
- Department of Pediatrics, University of Florida, Gainesville, Florida, United States of America
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12
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Abstract
As we learn about the sophisticated and far-reaching impacts that our resident microbiomes have on our biology, it is apparent that the tools we have for managing our microbiomes are rudimentary at best. For example, though antibiotics rid our microbiomes of bacterial pathogens, they target pathogens and commensals alike. Additional approaches, such as fecal microbiome transplant, seem to restore a healthy microbiome in some applications, but the mechanisms underlying this treatment and its long-term effects are poorly understood. Here, I discuss my laboratory's research, which uses two major drivers of gut microbiome ecology, diet and bacteriophages, as tools to develop new concepts and approaches for managing microbiomes. I speculate on the anticipated impacts of this research and how it will influence the way that we treat the kaleidoscope of microbe-microbe and microbe-host interactions central to our health.
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Affiliation(s)
- Andrew J Hryckowian
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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13
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Shkoporov AN, Khokhlova EV, Stephens N, Hueston C, Seymour S, Hryckowian AJ, Scholz D, Ross RP, Hill C. Long-term persistence of crAss-like phage crAss001 is associated with phase variation in Bacteroides intestinalis. BMC Biol 2021; 19:163. [PMID: 34407825 PMCID: PMC8375218 DOI: 10.1186/s12915-021-01084-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [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: 02/19/2021] [Accepted: 07/01/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The crAss-like phages are ubiquitous and highly abundant members of the human gut virome that infect commensal bacteria of the order Bacteroidales. Although incapable of lysogeny, these viruses demonstrate long-term persistence in the human gut microbiome, dominating the virome in some individuals. RESULTS Here we show that rapid phase variation of alternate capsular polysaccharides in Bacteroides intestinalis cultures plays an important role in a dynamic equilibrium between phage sensitivity and resistance, allowing phage and bacteria to multiply in parallel. The data also suggests the role of a concomitant phage persistence mechanism associated with delayed lysis of infected cells, similar to carrier state infection. From an ecological and evolutionary standpoint, this type of phage-host interaction is consistent with the Piggyback-the-Winner model, which suggests a preference towards lysogenic or other "benign" forms of phage infection when the host is stably present at high abundance. CONCLUSION Long-term persistence of bacteriophage and host could result from mutually beneficial mechanisms driving bacterial strain-level diversity and phage survival in complex environments.
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Affiliation(s)
- Andrey N Shkoporov
- School of Microbiology, University College Cork, Cork, Ireland.
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
| | | | - Niamh Stephens
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Cara Hueston
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Samuel Seymour
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Andrew J Hryckowian
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, USA
| | - Dimitri Scholz
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - R Paul Ross
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Colin Hill
- School of Microbiology, University College Cork, Cork, Ireland.
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
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14
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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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15
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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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16
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Nelson EJ, Grembi JA, Chao DL, Andrews JR, Alexandrova L, Rodriguez PH, Ramachandran VV, Sayeed MA, Wamala JF, Debes AK, Sack DA, Hryckowian AJ, Haque F, Khatun S, Rahman M, Chien A, Spormann AM, Schoolnik GK. Gold Standard Cholera Diagnostics Are Tarnished by Lytic Bacteriophage and Antibiotics. J Clin Microbiol 2020; 58:e00412-20. [PMID: 32611794 PMCID: PMC7448619 DOI: 10.1128/jcm.00412-20] [Citation(s) in RCA: 8] [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: 03/10/2020] [Accepted: 06/25/2020] [Indexed: 01/22/2023] Open
Abstract
A fundamental, clinical, and scientific concern is how lytic bacteriophage, as well as antibiotics, impact diagnostic positivity. Cholera was chosen as a model disease to investigate this important question, because cholera outbreaks enable large enrollment, field methods are well established, and the predatory relationship between lytic bacteriophage and the etiologic agent Vibrio cholerae share commonalities across bacterial taxa. Patients with diarrheal disease were enrolled at two remote hospitals in Bangladesh. Diagnostic performance was assessed as a function of lytic bacteriophage detection and exposure to the first-line antibiotic azithromycin, detected in stool samples by mass spectrometry. Among diarrheal samples positive by nanoliter quantitative PCR (qPCR) for V. cholerae (n = 78/849), the odds that a rapid diagnostic test (RDT) or qPCR was positive was reduced by 89% (odds ratio [OR], 0.108; 95% confidence interval [CI], 0.002 to 0.872) and 87% (OR, 0.130; 95% CI, 0.022 to 0.649), respectively, when lytic bacteriophage were detected. The odds that an RDT or qPCR was positive was reduced by more than 99% (OR, 0.00; 95% CI, 0.00 to 0.28) and 89% (OR, 0.11; 95% CI, 0.03 to 0.44), respectively, when azithromycin was detected. Analysis of additional samples from South Sudan found similar phage effects on RDTs; antibiotics were not assayed. Cholera burden estimates may improve by accommodating for the negative effects of lytic bacteriophage and antibiotic exposure on diagnostic positivity. One accommodation is using bacteriophage detection as a proxy for pathogen detection. These findings have relevance for other diagnostic settings where bacterial pathogens are vulnerable to lytic bacteriophage predation.
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Affiliation(s)
- E J Nelson
- Departments of Pediatrics and Environmental and Global Health, University of Florida, Gainesville, Florida, USA
- Department of Pediatrics, School of Medicine, Stanford University, Stanford, California, USA
| | - J A Grembi
- Department of Civil and Environmental Engineering, Stanford University, Stanford, California, USA
| | - D L Chao
- Institute for Disease Modeling, Bellevue, Washington, USA
| | - J R Andrews
- Department of Medicine, School of Medicine, Stanford University, Stanford, California, USA
| | - L Alexandrova
- Vincent Coates Foundation Mass Spectrometry Laboratory, Stanford University, Stanford, California, USA
| | - P H Rodriguez
- Departments of Pediatrics and Environmental and Global Health, University of Florida, Gainesville, Florida, USA
| | - V V Ramachandran
- Department of Pediatrics, School of Medicine, Stanford University, Stanford, California, USA
| | - M A Sayeed
- Departments of Pediatrics and Environmental and Global Health, University of Florida, Gainesville, Florida, USA
| | - J F Wamala
- Country Preparedness and IHR (CPI), World Health Organization (South Sudan), Juba, South Sudan
| | - A K Debes
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - D A Sack
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - A J Hryckowian
- Department of Microbiology, School of Medicine, Stanford University, Stanford, California, USA
| | - F Haque
- Institute of Epidemiology, Disease Control and Research, Ministry of Health and Family Welfare, Government of Bangladesh, Dhaka, Bangladesh
| | - S Khatun
- Institute of Epidemiology, Disease Control and Research, Ministry of Health and Family Welfare, Government of Bangladesh, Dhaka, Bangladesh
| | - M Rahman
- Institute of Epidemiology, Disease Control and Research, Ministry of Health and Family Welfare, Government of Bangladesh, Dhaka, Bangladesh
| | - A Chien
- Vincent Coates Foundation Mass Spectrometry Laboratory, Stanford University, Stanford, California, USA
| | - A M Spormann
- Department of Civil and Environmental Engineering, Stanford University, Stanford, California, USA
| | - G K Schoolnik
- Department of Medicine, School of Medicine, Stanford University, Stanford, California, USA
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17
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Alexandrova L, Haque F, Rodriguez P, Marrazzo AC, Grembi JA, Ramachandran V, Hryckowian AJ, Adams CM, Siddique MSA, Khan AI, Qadri F, Andrews JR, Rahman M, Spormann AM, Schoolnik GK, Chien A, Nelson EJ. Identification of Widespread Antibiotic Exposure in Patients With Cholera Correlates With Clinically Relevant Microbiota Changes. J Infect Dis 2020; 220:1655-1666. [PMID: 31192364 PMCID: PMC6782107 DOI: 10.1093/infdis/jiz299] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/11/2019] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND A first step to combating antimicrobial resistance in enteric pathogens is to establish an objective assessment of antibiotic exposure. Our goal was to develop and evaluate a liquid chromatography-ion trap mass spectrometry (LC/MS) method to determine antibiotic exposure in patients with cholera. METHODS A priority list for targeted LC/MS was generated from medication-vendor surveys in Bangladesh. A study of patients with and those without cholera was conducted to collect and analyze paired urine and stool samples. RESULTS Among 845 patients, 11% (90) were Vibrio cholerae positive; among these 90 patients, analysis of stool specimens revealed ≥1 antibiotic in 86% and ≥2 antibiotics in 52%. Among 44 patients with cholera and paired urine and stool specimens, ≥1 antibiotic was detected in 98% and ≥2 antibiotics were detected in 84%, despite 55% self-reporting medication use. Compared with LC/MS, a low-cost antimicrobial detection bioassay lacked a sufficient negative predictive value (10%; 95% confidence interval, 6%-16%). Detection of guideline-recommended antibiotics in stool specimens did (for azithromycin; P = .040) and did not (for ciprofloxacin) correlate with V. cholerae suppression. A nonrecommended antibiotic (metronidazole) was associated with decreases in anaerobes (ie, Prevotella organisms; P < .001). CONCLUSION These findings suggest that there may be no true negative control group when attempting to account for antibiotic exposure in settings like those in this study.
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Affiliation(s)
- Ludmila Alexandrova
- Vincent Coates Foundation Mass Spectrometry Laboratory, School of Medicine, Stanford University, California
| | - Farhana Haque
- Institute of Epidemiology, Disease Control, and Research, Ministry of Health and Family Welfare, Government of Bangladesh, Dhaka, Bangladesh
| | - Patricia Rodriguez
- Department of Pediatrics, University of Florida, Gainesville.,Department of Environmental and Global Health, University of Florida, Gainesville
| | - Ashton C Marrazzo
- Department of Pediatrics, University of Florida, Gainesville.,Department of Environmental and Global Health, University of Florida, Gainesville
| | - Jessica A Grembi
- Department of Civil and Environmental Engineering, School of Medicine, Stanford University, California
| | - Vasavi Ramachandran
- Department of Pediatrics, School of Medicine, Stanford University, California
| | - Andrew J Hryckowian
- Department of Microbiology, School of Medicine, Stanford University, California
| | - Christopher M Adams
- Vincent Coates Foundation Mass Spectrometry Laboratory, School of Medicine, Stanford University, California
| | - Md Shah A Siddique
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Ashraful I Khan
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Firdausi Qadri
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Jason R Andrews
- Department of Medicine, School of Medicine, Stanford University, California
| | - Mahmudur Rahman
- Institute of Epidemiology, Disease Control, and Research, Ministry of Health and Family Welfare, Government of Bangladesh, Dhaka, Bangladesh
| | - Alfred M Spormann
- Department of Civil and Environmental Engineering, School of Medicine, Stanford University, California
| | - Gary K Schoolnik
- Department of Medicine, School of Medicine, Stanford University, California
| | - Allis Chien
- Vincent Coates Foundation Mass Spectrometry Laboratory, School of Medicine, Stanford University, California
| | - Eric J Nelson
- Department of Pediatrics, School of Medicine, Stanford University, California
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18
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Hryckowian AJ, Van Treuren W, Smits SA, Davis NM, Gardner JO, Bouley DM, Sonnenburg JL. Microbiota-accessible carbohydrates suppress Clostridium difficile infection in a murine model. Nat Microbiol 2018; 3:662-669. [PMID: 29686297 PMCID: PMC6126909 DOI: 10.1038/s41564-018-0150-6] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 03/21/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Andrew J Hryckowian
- 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
| | - Samuel A Smits
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicole M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jackson O Gardner
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Donna M Bouley
- Department of Comparative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
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19
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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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20
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Hryckowian AJ, Pruss KM, Sonnenburg JL. The emerging metabolic view of Clostridium difficile pathogenesis. Curr Opin Microbiol 2017; 35:42-47. [PMID: 27997854 PMCID: PMC5474191 DOI: 10.1016/j.mib.2016.11.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [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] [Received: 09/25/2016] [Revised: 11/23/2016] [Accepted: 11/30/2016] [Indexed: 12/20/2022]
Abstract
It is widely accepted that Clostridium difficile exploits dysbiosis and leverages inflammation to thrive in the gut environment, where it can asymptomatically colonize humans or cause a toxin-mediated disease ranging in severity from frequent watery diarrhea to pseudomembranous colitis or toxic megacolon. Here, we synthesize recent findings from the gut microbiota and enteric pathogenesis fields to inform the next steps toward a better understanding of C. difficile infection (CDI). In this review, we present a model in which the lifestyle of C. difficile is dictated by the metabolic state of the distal gut ecosystem. Contributions by C. difficile (specifically the production and action of the large glycosylating toxins TcdA and TcdB), the microbiota, and the host dictate whether the gut environment is supportive to the pathogen. Mechanistic, metabolic pathway-focused approaches encompassing the roles of all of these players are helping to elucidate the molecular ecology of the distal gut underlying a diseased or healthy ecosystem. A new generation of therapeutic strategies that are more targeted (and palatable) than fecal microbiota transplants or broad-spectrum antibiotics will be fueled by insight into the interspecies (host-microbe and microbe-microbe) interactions that differentiate healthy from pathogen-infested microbiotas.
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Affiliation(s)
- Andrew J Hryckowian
- Department of Microbiology and Immunology, Stanford University, CA, United States
| | - Kali M Pruss
- Department of Microbiology and Immunology, Stanford University, CA, United States
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University, CA, United States.
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21
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Bender KO, Garland M, Ferreyra JA, Hryckowian AJ, Child MA, Puri AW, Solow-Cordero DE, Higginbottom SK, Segal E, Banaei N, Shen A, Sonnenburg JL, Bogyo M. A small-molecule antivirulence agent for treating Clostridium difficile infection. Sci Transl Med 2015; 7:306ra148. [PMID: 26400909 DOI: 10.1126/scitranslmed.aac9103] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/04/2015] [Indexed: 12/22/2022]
Abstract
Clostridium difficile infection (CDI) is a worldwide health threat that is typically triggered by the use of broad-spectrum antibiotics, which disrupt the natural gut microbiota and allow this Gram-positive anaerobic pathogen to thrive. The increased incidence and severity of disease coupled with decreased response, high recurrence rates, and emergence of multiple antibiotic-resistant strains have created an urgent need for new therapies. We describe pharmacological targeting of the cysteine protease domain (CPD) within the C. difficile major virulence factor toxin B (TcdB). Through a targeted screen with an activity-based probe for this protease domain, we identified a number of potent CPD inhibitors, including one bioactive compound, ebselen, which is currently in human clinical trials for a clinically unrelated indication. This drug showed activity against both major virulence factors, TcdA and TcdB, in biochemical and cell-based studies. Treatment in a mouse model of CDI that closely resembles the human infection confirmed a therapeutic benefit in the form of reduced disease pathology in host tissues that correlated with inhibition of the release of the toxic glucosyltransferase domain (GTD). Our results show that this non-antibiotic drug can modulate the pathology of disease and therefore could potentially be developed as a therapeutic for the treatment of CDI.
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Affiliation(s)
- Kristina Oresic Bender
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305-5324, USA
| | - Megan Garland
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305-5324, USA
| | - Jessica A Ferreyra
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305-5124, USA
| | - Andrew J Hryckowian
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305-5124, USA
| | - Matthew A Child
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305-5324, USA
| | - Aaron W Puri
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305-5324, USA
| | - David E Solow-Cordero
- Stanford University High-Throughput Bioscience Center, 1291 Welch Road, Stanford, CA 94305-5174, USA
| | - Steven K Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305-5124, USA
| | - Ehud Segal
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305-5324, USA
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305-5324, USA. Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305-5107, USA
| | - Aimee Shen
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305-5124, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305-5324, USA. Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305-5124, USA.
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22
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Ferreyra JA, Wu KJ, Hryckowian AJ, Bouley DM, Weimer BC, Sonnenburg JL. Gut microbiota-produced succinate promotes C. difficile infection after antibiotic treatment or motility disturbance. Cell Host Microbe 2015; 16:770-7. [PMID: 25498344 DOI: 10.1016/j.chom.2014.11.003] [Citation(s) in RCA: 236] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 08/15/2014] [Accepted: 10/28/2014] [Indexed: 12/29/2022]
Abstract
Clostridium difficile is a leading cause of antibiotic-associated diarrhea. The mechanisms underlying C. difficile expansion after microbiota disturbance are just emerging. We assessed the gene expression profile of C. difficile within the intestine of gnotobiotic mice to identify genes regulated in response to either dietary or microbiota compositional changes. In the presence of the gut symbiont Bacteroides thetaiotaomicron, C. difficile induces a pathway that metabolizes the microbiota fermentation end-product succinate to butyrate. The low concentration of succinate present in the microbiota of conventional mice is transiently elevated upon antibiotic treatment or chemically induced intestinal motility disturbance, and C. difficile exploits this succinate spike to expand in the perturbed intestine. A C. difficile mutant compromised in succinate utilization is at a competitive disadvantage during these perturbations. Understanding the metabolic mechanisms involved in microbiota-C. difficile interactions may help to identify approaches for the treatment and prevention of C. difficile-associated diseases.
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Affiliation(s)
- Jessica A Ferreyra
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Katherine J Wu
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew J Hryckowian
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Donna M Bouley
- Department of Comparative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bart C Weimer
- Department of Population Health and Reproduction, University of California, Davis, Davis, CA 95616, USA
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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23
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Hatfull GF, Jacobs-Sera D, Lawrence JG, Pope WH, Russell DA, Ko CC, Weber RJ, Patel MC, Germane KL, Edgar RH, Hoyte NN, Bowman CA, Tantoco AT, Paladin EC, Myers MS, Smith AL, Grace MS, Pham TT, O'Brien MB, Vogelsberger AM, Hryckowian AJ, Wynalek JL, Donis-Keller H, Bogel MW, Peebles CL, Cresawn SG, Hendrix RW. Comparative genomic analysis of 60 Mycobacteriophage genomes: genome clustering, gene acquisition, and gene size. J Mol Biol 2010; 397:119-43. [PMID: 20064525 DOI: 10.1016/j.jmb.2010.01.011] [Citation(s) in RCA: 234] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Revised: 12/08/2009] [Accepted: 01/05/2010] [Indexed: 10/20/2022]
Abstract
Mycobacteriophages are viruses that infect mycobacterial hosts. Expansion of a collection of sequenced phage genomes to a total of 60-all infecting a common bacterial host-provides further insight into their diversity and evolution. Of the 60 phage genomes, 55 can be grouped into nine clusters according to their nucleotide sequence similarities, 5 of which can be further divided into subclusters; 5 genomes do not cluster with other phages. The sequence diversity between genomes within a cluster varies greatly; for example, the 6 genomes in Cluster D share more than 97.5% average nucleotide similarity with one another. In contrast, similarity between the 2 genomes in Cluster I is barely detectable by diagonal plot analysis. In total, 6858 predicted open-reading frames have been grouped into 1523 phamilies (phams) of related sequences, 46% of which possess only a single member. Only 18.8% of the phams have sequence similarity to non-mycobacteriophage database entries, and fewer than 10% of all phams can be assigned functions based on database searching or synteny. Genome clustering facilitates the identification of genes that are in greatest genetic flux and are more likely to have been exchanged horizontally in relatively recent evolutionary time. Although mycobacteriophage genes exhibit a smaller average size than genes of their host (205 residues compared with 315), phage genes in higher flux average only 100 amino acids, suggesting that the primary units of genetic exchange correspond to single protein domains.
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Affiliation(s)
- Graham F Hatfull
- Department of Biological Sciences, Pittsburgh Bacteriophage Institute, Pittsburgh, PA 15260, USA.
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24
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Hatfull GF, Pedulla ML, Jacobs-Sera D, Cichon PM, Foley A, Ford ME, Gonda RM, Houtz JM, Hryckowian AJ, Kelchner VA, Namburi S, Pajcini KV, Popovich MG, Schleicher DT, Simanek BZ, Smith AL, Zdanowicz GM, Kumar V, Peebles CL, Jacobs WR, Lawrence JG, Hendrix RW. Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform. PLoS Genet 2006; 2:e92. [PMID: 16789831 PMCID: PMC1475703 DOI: 10.1371/journal.pgen.0020092] [Citation(s) in RCA: 211] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2006] [Accepted: 05/04/2006] [Indexed: 01/18/2023] Open
Abstract
Bacteriophages are the most abundant forms of life in the biosphere and carry genomes characterized by high genetic diversity and mosaic architectures. The complete sequences of 30 mycobacteriophage genomes show them collectively to encode 101 tRNAs, three tmRNAs, and 3,357 proteins belonging to 1,536 "phamilies" of related sequences, and a statistical analysis predicts that these represent approximately 50% of the total number of phamilies in the mycobacteriophage population. These phamilies contain 2.19 proteins on average; more than half (774) of them contain just a single protein sequence. Only six phamilies have representatives in more than half of the 30 genomes, and only three-encoding tape-measure proteins, lysins, and minor tail proteins-are present in all 30 phages, although these phamilies are themselves highly modular, such that no single amino acid sequence element is present in all 30 mycobacteriophage genomes. Of the 1,536 phamilies, only 230 (15%) have amino acid sequence similarity to previously reported proteins, reflecting the enormous genetic diversity of the entire phage population. The abundance and diversity of phages, the simplicity of phage isolation, and the relatively small size of phage genomes support bacteriophage isolation and comparative genomic analysis as a highly suitable platform for discovery-based education.
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Affiliation(s)
- Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
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