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Woo AYM, Aguilar Ramos MA, Narayan R, Richards-Corke KC, Wang ML, Sandoval-Espinola WJ, Balskus EP. Targeting the human gut microbiome with small-molecule inhibitors. NATURE REVIEWS. CHEMISTRY 2023; 7:319-339. [PMID: 37117817 DOI: 10.1038/s41570-023-00471-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/20/2023] [Indexed: 04/30/2023]
Abstract
The human gut microbiome is a complex microbial community that is strongly linked to both host health and disease. However, the detailed molecular mechanisms underlying the effects of these microorganisms on host biology remain largely uncharacterized. The development of non-lethal, small-molecule inhibitors that target specific gut microbial activities enables a powerful but underutilized approach to studying the gut microbiome and a promising therapeutic strategy. In this Review, we will discuss the challenges of studying this microbial community, the historic use of small-molecule inhibitors in microbial ecology, and recent applications of this strategy. We also discuss the evidence suggesting that host-targeted drugs can affect the growth and metabolism of gut microbes. Finally, we address the issues of developing and implementing microbiome-targeted small-molecule inhibitors and define important future directions for this research.
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Affiliation(s)
- Amelia Y M Woo
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, MA, USA
| | | | - Rohan Narayan
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, MA, USA
| | | | - Michelle L Wang
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, MA, USA
| | - Walter J Sandoval-Espinola
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, MA, USA
- Universidad Nacional de Asunción, Facultad de Ciencias Exactas y Naturales, Departamento de Biotecnología, Laboratorio de Biotecnología Microbiana, San Lorenzo, Paraguay
| | - Emily P Balskus
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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Identification of salt tolerance-related genes of Lactobacillus plantarum D31 and T9 strains by genomic analysis. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01551-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Abstract
Purpose
The aim of this study was to identify salt tolerance-related genes of Lactobacillus plantarum D31 and T9 strains, isolated from Chinese traditional fermented food, by genomic analysis.
Methods
Tolerance of L. plantarum D31 and T9 strains was evaluated at different stress conditions (temperatures, acid, osmolality, and artificial gastrointestinal fluids). Draft genomes of the two strains were determined using the Illumina sequencing technique. Comparative genomic analysis and gene transcriptional analysis were performed to identify and validate the salt tolerance-related genes.
Results
Both L. plantarum D31 and T9 strains were able to withstand high osmotic pressure caused by 5.0% NaCl, and L. plantarum D31 even to tolerate 8.0% NaCl. L. plantarum D31 genome contained 3,315,786 bp (44.5% GC content) with 3106 predicted protein-encoding genes, while L. plantarum T9 contained 3,388,070 bp (44.1% GC content) with 3223 genes. Comparative genomic analysis revealed a number of genes involved in the maintenance of intracellular ion balance, absorption or synthesis of compatible solutes, stress response, and modulation of membrane composition in L. plantarum D31 and or T9 genomes. Gene transcriptional analysis validated that most of these genes were coupled with the stress-resistance phenotypes of the two strains.
Conclusions
L. plantarum D31 and T9 strains tolerated 5.0% NaCl, and D31 even tolerated 8.0% NaCl. The draft genomes of these two strains were determined, and comparative genomic analysis revealed multiple molecular coping strategies for the salt stress tolerance in L. plantarum D31 and T9 strains.
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Li T, Wu C, Liao J, Jiang T, Xu H, Lei H. Application of Protein Hydrolysates from Defatted Walnut Meal in High-Gravity Brewing to Improve Fermentation Performance of Lager Yeast. Appl Biochem Biotechnol 2019; 190:360-372. [PMID: 31352671 DOI: 10.1007/s12010-019-03109-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 07/18/2019] [Indexed: 11/25/2022]
Abstract
Protein hydrolysates were prepared from an industrially defatted walnut meal (DWMPH) by enzymolysis employing Neutrase, Protamex, and Flavorzyme, respectively, with/without ultrasonic treatment. The effects of DWMPH supplementations on fermentation performance of lager yeast in high-gravity brewing were investigated. Results showed that ultrasonic-assisted enzymolysis simultaneous treatment (UAE) and ultrasonic pretreatment followed by enzymolysis (UPE) significantly increased degree of hydrolysis (DH) by 1.43 times and 0.71 times of traditional enzymolysis (TE) at least, respectively, Protamex treatment exhibited higher DH (13.3-32.8%) than Neutrase (9.2-25.3%) or Flavorzyme (11.8-28.7%). Compared with control, DWMPH supplementations prepared by UAE using Protamex (UAE-P), Neutrase (UAE-N), or Flavorzyme (UAE-F) significantly improved fermentation performance of lager yeast, especially for UAE-P with the highest major fractions of Mw < 1 kDa, increased wort fermentability and ethanol production by 15% and 17%, respectively, while UAE-F with the highest major fractions of Mw > 3 kDa obviously improved the foam stability of final beers. Furthermore, DWMPH supplementations significantly increased yeast growth and cell viability, promoted glycogen and trehalose accumulation, upregulated stress markers HSP12 and SSA3 expression in yeast cells, improved the formation of higher alcohols and esters, and increased the ratio of higher alcohol to ester indicating a better balanced taste of final beers.
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Affiliation(s)
- Tianlin Li
- College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, China
| | - Caiyun Wu
- College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, China
| | - Jianqiao Liao
- College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, China
| | - Tian Jiang
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Huaide Xu
- College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, China
| | - Hongjie Lei
- College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, China.
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Li L, Tian X, Chen J, Li P, Zheng Q, Hou J. Griffithsin inhibits porcine reproductive and respiratory syndrome virus infection in vitro. Arch Virol 2018; 163:3317-3325. [PMID: 30220033 PMCID: PMC7087274 DOI: 10.1007/s00705-018-4029-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 08/01/2018] [Indexed: 11/28/2022]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is a pathogen that severely disrupts swine production. Despite sustained efforts, the disease is still endemic, with high mortality and morbidity. New antiviral strategies to control PRRSV are needed. Griffithsin, a red algal lectin, has potent antiviral effect on several human enveloped viruses, but this effect has not been demonstrated on PRRSV. Here, we first tested the in vitro antiviral activity of Griffithsin against PRRSV. Griffithsin exerted strong saccharide-dependent antiviral activity against PRRSV, probably through interactions with glycans on the surface of PRRSV that interfered with virus entry. Furthermore we revealed that Griffithsin's action on PRRSV involved blocking viral adsorption, and it had no effect on viral penetration. Besides Our findings also suggested that Griffithsin may interfere with cell-to-cell spread to prevent virus transmission. The remarkable potency profile of Griffithsin supports its potential value as an antiviral agent against PRRSV.
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Affiliation(s)
- Lan Li
- National Research, Center of Engineering and Technology for Veterinary Biologicals, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 Jiangsu People’s Republic of China
| | - Xiaoning Tian
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095 Jiangsu People’s Republic of China
| | - Jin Chen
- National Research, Center of Engineering and Technology for Veterinary Biologicals, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 Jiangsu People’s Republic of China
| | - Pengcheng Li
- National Research, Center of Engineering and Technology for Veterinary Biologicals, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 Jiangsu People’s Republic of China
| | - Qisheng Zheng
- National Research, Center of Engineering and Technology for Veterinary Biologicals, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 Jiangsu People’s Republic of China
| | - Jibo Hou
- National Research, Center of Engineering and Technology for Veterinary Biologicals, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 Jiangsu People’s Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009 Jiangsu People’s Republic of China
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Nolan JA, Skuse P, Govindarajan K, Patterson E, Konstantinidou N, Casey PG, MacSharry J, Shanahan F, Stanton C, Hill C, Cotter PD, Joyce SA, Gahan CGM. The influence of rosuvastatin on the gastrointestinal microbiota and host gene expression profiles. Am J Physiol Gastrointest Liver Physiol 2017; 312:G488-G497. [PMID: 28209601 DOI: 10.1152/ajpgi.00149.2016] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 02/01/2017] [Accepted: 02/08/2017] [Indexed: 01/31/2023]
Abstract
Statins are the most widely prescribed medications worldwide for the treatment of hypercholesterolemia. They inhibit the activity of 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMG-R), an enzyme involved in cholesterol synthesis in higher organisms and in isoprenoid biosynthesis in some bacteria. We hypothesized that statins may influence the microbial community in the gut through either direct inhibition or indirect mechanisms involving alterations to host responses. We therefore examined the impact of rosuvastatin (RSV) on the community structure of the murine gastrointestinal microbiota. RSV was orally administered to mice and the effects on the gut microbiota, host bile acid profiles, and markers of inflammation were analyzed. RSV significantly influenced the microbial community in both the cecum and feces, causing a significant decrease in α-diversity in the cecum and resulting in a reduction of several physiologically relevant bacterial groups. RSV treatment of mice significantly affected bile acid metabolism and impacted expression of inflammatory markers known to influence microbial community structure (including RegIIIγ and Camp) in the gut. This study suggests that a commonly used statin (RSV) leads to an altered gut microbial composition in normal mice with attendant impacts on local gene expression profiles, a finding that should prompt further studies to investigate the implications of statins for gut microbiota stability and health in humans.NEW & NOTEWORTHY This work demonstrates that rosuvastatin administration in mice affects the gastrointestinal microbiota, influences bile acid metabolism, and alters transcription of genes encoding factors involved in gut homeostasis and immunity in the gastrointestinal tract.
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Affiliation(s)
- J A Nolan
- APC Microbiome Institute, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - P Skuse
- Teagasc Food Research Centre, Biosciences Department, Moorepark, Fermoy, Cork, Ireland
| | - K Govindarajan
- APC Microbiome Institute, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - E Patterson
- APC Microbiome Institute, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland.,Teagasc Food Research Centre, Biosciences Department, Moorepark, Fermoy, Cork, Ireland
| | | | - P G Casey
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - J MacSharry
- APC Microbiome Institute, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland.,School of Medicine, University College Cork, Cork, Ireland; and
| | - F Shanahan
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - C Stanton
- APC Microbiome Institute, University College Cork, Cork, Ireland.,Teagasc Food Research Centre, Biosciences Department, Moorepark, Fermoy, Cork, Ireland
| | - C Hill
- APC Microbiome Institute, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - P D Cotter
- APC Microbiome Institute, University College Cork, Cork, Ireland.,Teagasc Food Research Centre, Biosciences Department, Moorepark, Fermoy, Cork, Ireland
| | - S A Joyce
- APC Microbiome Institute, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland.,School of Medicine, University College Cork, Cork, Ireland; and
| | - C G M Gahan
- APC Microbiome Institute, University College Cork, Cork, Ireland; .,School of Microbiology, University College Cork, Cork, Ireland.,School of Pharmacy, University College Cork, Cork, Ireland
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Vandevelde NM, Tulkens PM, Van Bambeke F. Modulating antibiotic activity towards respiratory bacterial pathogens by co-medications: a multi-target approach. Drug Discov Today 2016; 21:1114-29. [PMID: 27094105 DOI: 10.1016/j.drudis.2016.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 03/17/2016] [Accepted: 04/05/2016] [Indexed: 01/01/2023]
Abstract
Non-antibiotic drugs can modulate bacterial physiology and/or antibiotic activity, opening perspectives for innovative therapeutic strategies. Focusing on respiratory pathogens and considering in vitro, in vivo, and clinical data, here we examine the effect of these drugs on the expression of resistance mechanisms, biofilm formation, and intracellular survival, as well as their influence on the activity of antibiotics on bacteria. Beyond the description of the effects observed, we also comment on concentrations that are active and discuss the mechanisms of drug-drug or drug-target interactions. This discussion should be helpful in defining useful targets for adjuvant therapy and establishing the corresponding pharmacophores for further drug fine-tuning.
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Affiliation(s)
- Nathalie M Vandevelde
- Pharmacologie cellulaire et moléculaire, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Paul M Tulkens
- Pharmacologie cellulaire et moléculaire, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Françoise Van Bambeke
- Pharmacologie cellulaire et moléculaire, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium.
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