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Müller S, DeLeon O, Atkinson SN, Saravia F, Kellogg S, Shank EA, Kirby JR. Thiocillin contributes to the ecological fitness of Bacillus cereus ATCC 14579 during interspecies interactions with Myxococcus xanthus. Front Microbiol 2023; 14:1295262. [PMID: 38075900 PMCID: PMC10704990 DOI: 10.3389/fmicb.2023.1295262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/09/2023] [Indexed: 02/12/2024] Open
Abstract
The soil-dwelling delta-proteobacterium Myxococcus xanthus is a model organism to study predation and competition. M. xanthus preys on a broad range of bacteria mediated by lytic enzymes, exopolysaccharides, Type-IV pilus-based motility, and specialized metabolites. Competition between M. xanthus and prey bacterial strains with various specialized metabolite profiles indicates a range of fitness, suggesting that specialized metabolites contribute to prey survival. To expand our understanding of how specialized metabolites affect predator-prey dynamics, we assessed interspecies interactions between M. xanthus and two strains of Bacillus cereus. While strain ATCC 14579 resisted predation, strain T was found to be highly sensitive to M. xanthus predation. The interaction between B. cereus ATCC 14579 and M. xanthus appears to be competitive, resulting in population loss for both predator and prey. Genome analysis revealed that ATCC 14579 belongs to a clade that possesses the biosynthetic gene cluster for production of thiocillins, whereas B. cereus strain T lacks those genes. Further, purified thiocillin protects B. cereus strains unable to produce this specialized metabolite, strengthening the finding that thiocillin protects against predation and contributes to the ecological fitness of B. cereus ATCC 14579. Lastly, strains that produce thiocillin appear to confer some level of protection to their own antibiotic by encoding an additional copy of the L11 ribosomal protein, a known target for thiopeptides. This work highlights the importance of specialized metabolites affecting predator-prey dynamics in soil microenvironments.
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Affiliation(s)
- Susanne Müller
- Department of Microbiology & Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Orlando DeLeon
- Department of Medicine, University of Chicago Pritzker School of Medicine, Chicago, IL, United States
| | - Samantha N. Atkinson
- Department of Microbiology & Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Fatima Saravia
- Department of Microbiology & Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Stephanie Kellogg
- Department of Microbiology & Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Elizabeth A. Shank
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worchester, MA, United States
| | - John R. Kirby
- Department of Microbiology & Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
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Frazier K, Manzoor S, Carroll K, DeLeon O, Miyoshi S, Miyoshi J, St. George M, Tan A, Chrisler EA, Izumo M, Takahashi JS, Rao MC, Leone VA, Chang EB. Gut microbes and the liver circadian clock partition glucose and lipid metabolism. J Clin Invest 2023; 133:e162515. [PMID: 37712426 PMCID: PMC10503806 DOI: 10.1172/jci162515] [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: 06/09/2022] [Accepted: 07/18/2023] [Indexed: 09/16/2023] Open
Abstract
Circadian rhythms govern glucose homeostasis, and their dysregulation leads to complex metabolic diseases. Gut microbes exhibit diurnal rhythms that influence host circadian networks and metabolic processes, yet underlying mechanisms remain elusive. Here, we showed hierarchical, bidirectional communication among the liver circadian clock, gut microbes, and glucose homeostasis in mice. To assess this relationship, we utilized mice with liver-specific deletion of the core circadian clock gene Bmal1 via Albumin-cre maintained in either conventional or germ-free housing conditions. The liver clock, but not the forebrain clock, required gut microbes to drive glucose clearance and gluconeogenesis. Liver clock dysfunctionality expanded proportions and abundances of oscillating microbial features by 2-fold relative to that in controls. The liver clock was the primary driver of differential and rhythmic hepatic expression of glucose and fatty acid metabolic pathways. Absent the liver clock, gut microbes provided secondary cues that dampened these rhythms, resulting in reduced lipid fuel utilization relative to carbohydrates. All together, the liver clock transduced signals from gut microbes that were necessary for regulating glucose and lipid metabolism and meeting energy demands over 24 hours.
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Affiliation(s)
- Katya Frazier
- Department of Medicine and
- Committee on Molecular Metabolism and Nutrition, The University of Chicago, Chicago, Illinois, USA
| | | | | | | | | | - Jun Miyoshi
- Department of Gastroenterology and Hepatology, Kyorin University School of Medicine, Tokyo, Japan
| | | | | | - Evan A. Chrisler
- Department of Animal & Dairy Sciences, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | | | - Joseph S. Takahashi
- Department of Neuroscience and
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | | | - Vanessa A. Leone
- Department of Animal & Dairy Sciences, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Eugene B. Chang
- Department of Medicine and
- Committee on Molecular Metabolism and Nutrition, The University of Chicago, Chicago, Illinois, USA
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Kennedy MS, Zhang M, DeLeon O, Bissell J, Trigodet F, Lolans K, Temelkova S, Carroll KT, Fiebig A, Deutschbauer A, Sidebottom AM, Lake J, Henry C, Rice PA, Bergelson J, Chang EB. Dynamic genetic adaptation of Bacteroides thetaiotaomicron during murine gut colonization. Cell Rep 2023; 42:113009. [PMID: 37598339 PMCID: PMC10528517 DOI: 10.1016/j.celrep.2023.113009] [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: 05/08/2022] [Revised: 05/17/2023] [Accepted: 08/03/2023] [Indexed: 08/22/2023] Open
Abstract
To understand how a bacterium ultimately succeeds or fails in adapting to a new host, it is essential to assess the temporal dynamics of its fitness over the course of colonization. Here, we introduce a human-derived commensal organism, Bacteroides thetaiotaomicron (Bt), into the guts of germ-free mice to determine whether and how the genetic requirements for colonization shift over time. Combining a high-throughput functional genetics assay and transcriptomics, we find that gene usage changes drastically during the first days of colonization, shifting from high expression of amino acid biosynthesis genes to broad upregulation of diverse polysaccharide utilization loci. Within the first week, metabolism becomes centered around utilization of a predominant dietary oligosaccharide, and these changes are largely sustained through 6 weeks of colonization. Spontaneous mutations in wild-type Bt also evolve around this locus. These findings highlight the importance of considering temporal colonization dynamics in developing more effective microbiome-based therapies.
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Affiliation(s)
- Megan S Kennedy
- Medical Scientist Training Program, Pritzker School of Medicine, The University of Chicago, Chicago, IL, USA; Department of Ecology & Evolution, The University of Chicago, Chicago, IL, USA
| | - Manjing Zhang
- Committee on Microbiology, The University of Chicago, Chicago, IL, USA
| | - Orlando DeLeon
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Jacie Bissell
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Florian Trigodet
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Karen Lolans
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Sara Temelkova
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | | | - Aretha Fiebig
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Adam Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ashley M Sidebottom
- Duchossois Family Institute, Department of Biomedical Sciences, The University of Chicago, Chicago, IL, USA
| | - Joash Lake
- Committee on Immunology, The University of Chicago, Chicago, IL, USA
| | - Chris Henry
- Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, IL, USA
| | - Phoebe A Rice
- Department of Biochemistry & Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Joy Bergelson
- Committee on Microbiology, The University of Chicago, Chicago, IL, USA
| | - Eugene B Chang
- Department of Medicine, The University of Chicago, Chicago, IL, USA.
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Fei N, Miyoshi S, Hermanson JB, Miyoshi J, Xie B, DeLeon O, Hawkins M, Charlton W, D’Souza M, Hart J, Sulakhe D, Martinez-Guryn KB, Chang EB, Charlton MR, Leone VA. Imbalanced gut microbiota predicts and drives the progression of nonalcoholic fatty liver disease and nonalcoholic steatohepatitis in a fast-food diet mouse model. bioRxiv 2023:2023.01.09.523249. [PMID: 36712061 PMCID: PMC9882021 DOI: 10.1101/2023.01.09.523249] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is multifactorial in nature, affecting over a billion people worldwide. The gut microbiome has emerged as an associative factor in NAFLD, yet mechanistic contributions are unclear. Here, we show fast food (FF) diets containing high fat, added cholesterol, and fructose/glucose drinking water differentially impact short- vs. long-term NAFLD severity and progression in conventionally-raised, but not germ-free mice. Correlation and machine learning analyses independently demonstrate FF diets induce early and specific gut microbiota changes that are predictive of NAFLD indicators, with corresponding microbial community instability relative to control-fed mice. Shotgun metagenomics showed FF diets containing high cholesterol elevate fecal pro-inflammatory effectors over time, relating to a reshaping of host hepatic metabolic and inflammatory transcriptomes. FF diet-induced gut dysbiosis precedes onset and is highly predictive of NAFLD outcomes, providing potential insights into microbially-based pathogenesis and therapeutics.
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Affiliation(s)
- Na Fei
- Department of Medicine, University of Chicago Medical Center, University of Chicago, Chicago, IL, 60637, USA
| | - Sawako Miyoshi
- Department of General Medicine, Kyorin University School of Medicine, Tokyo 1818611, Japan
| | - Jake B. Hermanson
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jun Miyoshi
- Department of Gastroenterology and Hepatology, Kyorin University School of Medicine, Tokyo 1818611, Japan
| | - Bingqing Xie
- Department of Medicine, University of Chicago Medical Center, University of Chicago, Chicago, IL, 60637, USA
| | - Orlando DeLeon
- Department of Medicine, University of Chicago Medical Center, University of Chicago, Chicago, IL, 60637, USA
| | - Maximilian Hawkins
- Department of Medicine, University of Chicago Medical Center, University of Chicago, Chicago, IL, 60637, USA
| | - William Charlton
- Department of Medicine, University of Chicago Medical Center, University of Chicago, Chicago, IL, 60637, USA
| | - Mark D’Souza
- Duchossois Family Institute, University of Chicago, Chicago, IL, 60637, USA
| | - John Hart
- Department of Medicine, University of Chicago Medical Center, University of Chicago, Chicago, IL, 60637, USA
| | - Dinanath Sulakhe
- Duchossois Family Institute, University of Chicago, Chicago, IL, 60637, USA
| | | | - Eugene B. Chang
- Department of Medicine, University of Chicago Medical Center, University of Chicago, Chicago, IL, 60637, USA
| | - Michael R. Charlton
- Department of Medicine, University of Chicago Medical Center, University of Chicago, Chicago, IL, 60637, USA
| | - Vanessa A. Leone
- Department of Animal & Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
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Mark J, Phoenix D, Gutierrez C, Morrell K, Eng K, Mayor P, Akers S, Lele S, Odunsi K, DeLeon O, Frederick P, Zsiros E. Tackling the opioid crisis: Implementation of an ultra-restrictive opioid prescription protocol in patients undergoing major gynecologic surgery radically decreased dispensed opioid without reducing pain control. Gynecol Oncol 2018. [DOI: 10.1016/j.ygyno.2018.04.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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DeLeon O, Hodis H, O’Malley Y, Johnson J, Salimi H, Zhai Y, Winter E, Remec C, Eichelberger N, Van Cleave B, Puliadi R, Harrington RD, Stapleton JT, Haim H. Accurate predictions of population-level changes in sequence and structural properties of HIV-1 Env using a volatility-controlled diffusion model. PLoS Biol 2017; 15:e2001549. [PMID: 28384158 PMCID: PMC5383018 DOI: 10.1371/journal.pbio.2001549] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [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: 11/11/2016] [Accepted: 03/06/2017] [Indexed: 01/08/2023] Open
Abstract
The envelope glycoproteins (Envs) of HIV-1 continuously evolve in the host by random mutations and recombination events. The resulting diversity of Env variants circulating in the population and their continuing diversification process limit the efficacy of AIDS vaccines. We examined the historic changes in Env sequence and structural features (measured by integrity of epitopes on the Env trimer) in a geographically defined population in the United States. As expected, many Env features were relatively conserved during the 1980s. From this state, some features diversified whereas others remained conserved across the years. We sought to identify “clues” to predict the observed historic diversification patterns. Comparison of viruses that cocirculate in patients at any given time revealed that each feature of Env (sequence or structural) exists at a defined level of variance. The in-host variance of each feature is highly conserved among individuals but can vary between different HIV-1 clades. We designate this property “volatility” and apply it to model evolution of features as a linear diffusion process that progresses with increasing genetic distance. Volatilities of different features are highly correlated with their divergence in longitudinally monitored patients. Volatilities of features also correlate highly with their population-level diversification. Using volatility indices measured from a small number of patient samples, we accurately predict the population diversity that developed for each feature over the course of 30 years. Amino acid variants that evolved at key antigenic sites are also predicted well. Therefore, small “fluctuations” in feature values measured in isolated patient samples accurately describe their potential for population-level diversification. These tools will likely contribute to the design of population-targeted AIDS vaccines by effectively capturing the diversity of currently circulating strains and addressing properties of variants expected to appear in the future. HIV-1 is the causative agent of the global AIDS pandemic. The envelope glycoproteins (Envs) of HIV-1 constitute a primary target for antibody-based vaccines. However, the diversity of Envs in the population limits the potential efficacy of this approach. Accurate estimates of the range of variants that currently infect patients and those expected to appear in the future will likely contribute to the design of population-targeted immunogens. We found that different properties (features) of Env have different propensities for small “fluctuations” in their values among viruses that infect patients at any given time point. This propensity of each feature for in-host variance, which we designate “volatility”, is conserved among patients. We apply this parameter to model the evolution of features (in patients and population) as a diffusion process driven by their “diffusion coefficients” (volatilities). Using volatilities measured from a few patient samples from the 1980s, we accurately predict properties of viruses that evolved in the population over the course of 30 years. The diffusion-based model described here efficiently captures evolution of phenotypes in biological systems controlled by a dominant random component.
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Affiliation(s)
- Orlando DeLeon
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Hagit Hodis
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Yunxia O’Malley
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Jacklyn Johnson
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Hamid Salimi
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Yinjie Zhai
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Elizabeth Winter
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Claire Remec
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Noah Eichelberger
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Brandon Van Cleave
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Ramya Puliadi
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Robert D. Harrington
- Center for AIDS Research (CFAR) at the University of Washington, Seattle, Washington, United States of America
| | - Jack T. Stapleton
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
- Veterans Affairs Medical Center, Iowa City, Iowa, United States of America
| | - Hillel Haim
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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DeLeon O, Roseman M, Chang Y. Relationship between Race/Ethnicity and Parents Including Functional Foods in Their Children’s Diet. J Acad Nutr Diet 2016. [DOI: 10.1016/j.jand.2016.06.336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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DeLeon O, Chang Y, Roseman M. Relationship between Income and Parents Including Functional Foods in Their Children’s Diet. J Acad Nutr Diet 2015. [DOI: 10.1016/j.jand.2015.06.321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Grobe J, Bahr S, Weidemann B, Burnett C, Pearson N, DeLeon O, Murry D, Kirby J. Transfer of Obesity via the Gut Microbiome is Mediated Specifically through Suppression of Non‐Aerobic Resting Metabolism. FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.857.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Justin Grobe
- PharmacologyUniversity of IowaIowa CityIAUnited States
| | - Sarah Bahr
- MicrobiologyUniversity of IowaIowa CityIAUnited States
| | | | - Colin Burnett
- PharmacologyUniversity of IowaIowa CityIAUnited States
| | | | | | - Daryl Murry
- Pharmaceutics & Translational Therapeutics University of IowaIowa CityIAUnited States
| | - John Kirby
- MicrobiologyUniversity of IowaIowa CityIAUnited States
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Goldsmith RH, DeLeon O, Wilson TM, Finkelstein-Shapiro D, Ratner MA, Wasielewski MR. Challenges in distinguishing superexchange and hopping mechanisms of intramolecular charge transfer through fluorene oligomers. J Phys Chem A 2008; 112:4410-4. [PMID: 18422290 DOI: 10.1021/jp801084v] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The temperature dependence of intramolecular charge separation in a series of donor-bridge-acceptor molecules having phenothiazine (PTZ) donors, 2,7-oligofluorene FL(n) (n = 1-4) bridges, and perylene-3,4:9,10-bis(dicarboximide) (PDI) acceptors was studied. Photoexcitation of PDI to its lowest excited singlet state results in oxidation of PTZ via the FL(n) bridge. In toluene, the temperature dependence of the charge separation rate constants for PTZ-FL(n)-PDI, (n = 1-4) is relatively weak and is successfully described by the semiclassical Marcus equation. The activation energies for charge separation suggest that bridge charge carrier injection is not the rate limiting step. The difficulty of using temperature and length dependence to differentiate hopping and superexchange is discussed, with difficulties in the latter topic explored via an extension of a kinetic model proposed by Bixon and Jortner.
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Affiliation(s)
- Randall H Goldsmith
- Department of Chemistry, Argonne-Northwestern Solar Energy Research Center, and International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208-3113, USA
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