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Wang L, Liu P, Wu Y, Pei H, Cao X. Inhibitory effect of Lonicera japonica flos on Streptococcus mutans biofilm and mechanism exploration through metabolomic and transcriptomic analyses. Front Microbiol 2024; 15:1435503. [PMID: 39027105 PMCID: PMC11256199 DOI: 10.3389/fmicb.2024.1435503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 06/05/2024] [Indexed: 07/20/2024] Open
Abstract
Introduction Streptococcus mutans was the primary pathogenic organism responsible for dental caries. Lonicera japonica flos (LJF) is a traditional herb in Asia and Europe and consumed as a tea beverage for thousands of years. Methods The inhibitory effect and mechanism of LJF on biofilm formation by S. mutans was investigated. The active extracts of LJF were validated for their inhibitory activity by examining changes in surface properties such as adherence, hydrophobicity, auto-aggregation abilities, and exopolysaccharides (EPS) production, including water-soluble glucan and water-insoluble glucan. Results and discussion LJF primarily inhibited biofilm formation through the reduction of EPS production, resulting in alterations in cell surface characteristics and growth retardation in biofilm formation cycles. Integrated transcriptomic and untargeted metabolomics analyses revealed that EPS production was modulated through two-component systems (TCS), quorum sensing (QS), and phosphotransferase system (PTS) pathways under LJF stress conditions. The sensing histidine kinase VicK was identified as an important target protein, as LJF caused its dysregulated expression and blocked the sensing of autoinducer II (AI-2). This led to the inhibition of response regulator transcriptional factors, down-regulated glycosyltransferase (Gtf) activity, and decreased production of water-insoluble glucans (WIG) and water-soluble glucans (WSG). This is the first exploration of the inhibitory effect and mechanism of LJF on S. mutans, providing a theoretical basis for the application of LJF in functional food, oral health care, and related areas.
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Affiliation(s)
| | | | | | | | - Xueli Cao
- Beijing Technology and Business University, Beijing Advanced Innovation Centre for Food Nutrition and Human Health, Beijing, China
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2
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Liu P, Wang L, Song Y, Pei H, Cao X. Virtual Screening of Inhibitors of Streptococcus mutans Biofilm from Lonicera japonica flos and Activity Validation. ACS Med Chem Lett 2024; 15:781-790. [PMID: 38894900 PMCID: PMC11181501 DOI: 10.1021/acsmedchemlett.4c00051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 06/21/2024] Open
Abstract
In this study, potential inhibitors of Streptococcus mutans biofilm were screened from Lonicera japonica flos using semiflexible molecular docking. A total of 88 metabolites from L. japonica flos and 14 biofilm-related proteins of S. mutans were analyzed, and 25 compounds were initially screened out. Subsequently, 9 compounds with higher availability were subjected to experimental validation, confirming that 6 of them effectively inhibit the S. mutans biofilm formation. Notably, chlorogenic acid was found to potentially disrupt the GbpC protein, which plays a role in the sucrose-dependent adhesion pathway. Similarly, oleanolic acid appeared to impede the adhesin P1 protein involved in the sucrose-independent adhesion mechanism, corroborating the computational predictions. The results of this study provide essential insights for leveraging L. japonica flos in the creation of dental-care-related products and food items aimed at oral health.
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Affiliation(s)
- Ping Liu
- Beijing Advanced
Innovation
Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China
| | - Lin Wang
- Beijing Advanced
Innovation
Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China
| | - Ya Song
- Beijing Advanced
Innovation
Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China
| | - Hairun Pei
- Beijing Advanced
Innovation
Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China
| | - Xueli Cao
- Beijing Advanced
Innovation
Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China
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3
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Gao S, Wang Y, Yuan S, Zuo J, Jin W, Shen Y, Grenier D, Yi L, Wang Y. Cooperation of quorum sensing and central carbon metabolism in the pathogenesis of Gram-positive bacteria. Microbiol Res 2024; 282:127655. [PMID: 38402726 DOI: 10.1016/j.micres.2024.127655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/25/2024] [Accepted: 02/17/2024] [Indexed: 02/27/2024]
Abstract
Quorum sensing (QS), an integral component of bacterial communication, is essential in coordinating the collective response of diverse bacterial pathogens. Central carbon metabolism (CCM), serving as the primary metabolic hub for substances such as sugars, lipids, and amino acids, plays a crucial role in the life cycle of bacteria. Pathogenic bacteria often utilize CCM to regulate population metabolism and enhance the synthesis of specific cellular structures, thereby facilitating in adaptation to the host microecological environment and expediting infection. Research has demonstrated that QS can both directly or indirectly affect the CCM of numerous pathogenic bacteria, thus altering their virulence and pathogenicity. This article reviews the interplay between QS and CCM in Gram-positive pathogenic bacteria, details the molecular mechanisms by which QS modulates CCM, and lays the groundwork for investigating bacterial pathogenicity and developing innovative infection treatment drugs.
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Affiliation(s)
- Shuji Gao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China; Henan Provincial Engineering Research Center for Detection and Prevention and Control of Emerging Infectious Diseases in Livestock and Poultry, Luoyang 471003, China
| | - Yuxin Wang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China; Henan Provincial Engineering Research Center for Detection and Prevention and Control of Emerging Infectious Diseases in Livestock and Poultry, Luoyang 471003, China
| | - Shuo Yuan
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China; Henan Provincial Engineering Research Center for Detection and Prevention and Control of Emerging Infectious Diseases in Livestock and Poultry, Luoyang 471003, China
| | - Jing Zuo
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China; Henan Provincial Engineering Research Center for Detection and Prevention and Control of Emerging Infectious Diseases in Livestock and Poultry, Luoyang 471003, China
| | - Wenjie Jin
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China; Henan Provincial Engineering Research Center for Detection and Prevention and Control of Emerging Infectious Diseases in Livestock and Poultry, Luoyang 471003, China
| | - Yamin Shen
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China; Henan Provincial Engineering Research Center for Detection and Prevention and Control of Emerging Infectious Diseases in Livestock and Poultry, Luoyang 471003, China
| | - Daniel Grenier
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Quebec City, Quebec, Canada
| | - Li Yi
- Henan Provincial Engineering Research Center for Detection and Prevention and Control of Emerging Infectious Diseases in Livestock and Poultry, Luoyang 471003, China; College of Life Science, Luoyang Normal University, Luoyang 471934, China.
| | - Yang Wang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China; Henan Provincial Engineering Research Center for Detection and Prevention and Control of Emerging Infectious Diseases in Livestock and Poultry, Luoyang 471003, China.
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4
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Fine DH, Schreiner H. Oral microbial interactions from an ecological perspective: a narrative review. FRONTIERS IN ORAL HEALTH 2023; 4:1229118. [PMID: 37771470 PMCID: PMC10527376 DOI: 10.3389/froh.2023.1229118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/16/2023] [Indexed: 09/30/2023] Open
Abstract
Landscape ecology is a relatively new field of study within the sub-specialty of ecology that considers time and space in addition to structure and function. Landscape ecology contends that both the configuration (spatial pattern) and the composition (organisms both at the macro and or micro level) of an ecology can change over time. The oral cavity is an ideal place to study landscape ecology because of the variety of landscapes, the dynamic nature of plaque biofilm development, and the easy access to biofilm material. This review is intended to provide some specific clinical examples of how landscape ecology can influence the understanding of oral diseases and act as a supplement to diagnosis and treatment. The purpose of this review is two-fold; (1) to illustrate how landscape ecology can be used to clarify the two most prominent microbiologically induced infections in the oral cavity, and (2) how studies of oral microbiology can be used to enhance the understanding of landscape ecology. The review will distinguish between "habitat" and "niche" in a landscape and extend the concept that a "patch", is the demarcating unit of a habitat within a landscape. The review will describe how; (1) an individual patch, defined by its shape, edges and internal components can have an influence on species within the patch, (2) spatial dynamics over time within a patch can lead to variations or diversities of species within that patch space, and (3) an unwelcoming environment can promote species extinction or departure/dispersion into a more favorable habitat. Understanding this dynamic in relationship to caries and periodontal disease is the focus of this review.
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Affiliation(s)
- Daniel H. Fine
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, United States
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5
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Zheng T, Jing M, Gong T, Yan J, Wang X, Xu M, Zhou X, Zeng J, Li Y. Regulatory mechanisms of exopolysaccharide synthesis and biofilm formation in Streptococcus mutans. J Oral Microbiol 2023; 15:2225257. [PMID: 37346997 PMCID: PMC10281425 DOI: 10.1080/20002297.2023.2225257] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/23/2023] Open
Abstract
Background Dental caries is a chronic, multifactorial and biofilm-mediated oral bacterial infection affecting almost every age group and every geographical region. Streptococcus mutans is considered an important pathogen responsible for the initiation and development of dental caries. It produces exopolysaccharides in situ to promote the colonization of cariogenic bacteria and coordinate dental biofilm development. Objective The understanding of the regulatory mechanism of S. mutans biofilm formation can provide a theoretical basis for the prevention and treatment of caries. Design At present, an increasing number of studies have identified many regulatory systems in S. mutans that regulate biofilm formation, including second messengers (e.g. c-di-AMP, Ap4A), transcription factors (e.g. EpsR, RcrR, StsR, AhrC, FruR), two-component systems (e.g. CovR, VicR), small RNA (including sRNA0426, srn92532, and srn133489), acetylation modifications (e.g. ActG), CRISPR-associated proteins (e.g. Cas3), PTS systems (e.g. EIIAB), quorum-sensing signaling system (e.g. LuxS), enzymes (including Dex, YidC, CopZ, EzrA, lmrB, SprV, RecA, PdxR, MurI) and small-molecule metabolites. Results This review summarizes the recent progress in the molecular regulatory mechanisms of exopolysaccharides synthesis and biofilm formation in S. mutans.
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Affiliation(s)
- Ting Zheng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Meiling Jing
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Tao Gong
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jiangchuan Yan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xiaowan Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Mai Xu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jumei Zeng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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6
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Detection of changes in biological characteristics of Aeromonas veronii TH0426 after deletion of lsrB gene by homologous recombination. Microb Pathog 2023; 174:105938. [PMID: 36526036 DOI: 10.1016/j.micpath.2022.105938] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/11/2022] [Accepted: 12/08/2022] [Indexed: 12/15/2022]
Abstract
Aeromonas veronii is a widespread pathogenic microorganism that can infect humans, animals, and a variety of aquatilia, at the same time, can cause diseases, mainly sepsis and ulcer syndrome. In this research, we first deleted the gene of lsrB's nucleotide sequences by homologous recombination. The results showed that the median lethal dose (LD50) of the mutant strain (ΔlsrB) for zebrafish was 1.28-times higher than that of the TH0426 strain. The toxicity of TH0426 to epithelioma papulosum cyprini (EPC) cells was 1.15-times and 1.64-times higher than that of ΔlsrB, 1 and 2 h after infection. The production ability of the biofilm of ΔlsrB decreased by 1.38-times, and the adhesion ability of ΔlsrB to EPC cells greatly decreased by 1.96-times than the TH0426. The result of motility detection pointed out that the swimming ability of ΔlsrB was down by 1.67-times. The results indicated that almost all of them lost their flagella after deleting the lsrB gene. In general, the virulence of TH0426 was reduced after deleting the lsrB gene. The final results point out that the lsrB gene of TH0426 is related to motility, biofilm formation, adhesion, and virulence.
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Falà AK, Álvarez-Ordóñez A, Filloux A, Gahan CGM, Cotter PD. Quorum sensing in human gut and food microbiomes: Significance and potential for therapeutic targeting. Front Microbiol 2022; 13:1002185. [PMID: 36504831 PMCID: PMC9733432 DOI: 10.3389/fmicb.2022.1002185] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 10/17/2022] [Indexed: 11/27/2022] Open
Abstract
Human gut and food microbiomes interact during digestion. The outcome of these interactions influences the taxonomical composition and functional capacity of the resident human gut microbiome, with potential consequential impacts on health and disease. Microbe-microbe interactions between the resident and introduced microbiomes, which likely influence host colonisation, are orchestrated by environmental conditions, elements of the food matrix, host-associated factors as well as social cues from other microorganisms. Quorum sensing is one example of a social cue that allows bacterial communities to regulate genetic expression based on their respective population density and has emerged as an attractive target for therapeutic intervention. By interfering with bacterial quorum sensing, for instance, enzymatic degradation of signalling molecules (quorum quenching) or the application of quorum sensing inhibitory compounds, it may be possible to modulate the microbial composition of communities of interest without incurring negative effects associated with traditional antimicrobial approaches. In this review, we summarise and critically discuss the literature relating to quorum sensing from the perspective of the interactions between the food and human gut microbiome, providing a general overview of the current understanding of the prevalence and influence of quorum sensing in this context, and assessing the potential for therapeutic targeting of quorum sensing mechanisms.
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Affiliation(s)
- A. Kate Falà
- APC Microbiome Ireland, University College Cork, Cork, Ireland,School of Microbiology, University College Cork, Cork, Ireland,Food Bioscience Department, Teagasc Food Research Centre, Fermoy, Ireland
| | - Avelino Álvarez-Ordóñez
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Cormac G. M. Gahan
- APC Microbiome Ireland, University College Cork, Cork, Ireland,School of Microbiology, University College Cork, Cork, Ireland,School of Pharmacy, University College Cork, Cork, Ireland
| | - Paul D. Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland,Food Bioscience Department, Teagasc Food Research Centre, Fermoy, Ireland,*Correspondence: Paul D. Cotter,
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Naka S, Matsuoka D, Goto K, Misaki T, Nagasawa Y, Ito S, Nomura R, Nakano K, Matsumoto-Nakano M. Cnm of Streptococcus mutans is important for cell surface structure and membrane permeability. Front Cell Infect Microbiol 2022; 12:994014. [PMID: 36176579 PMCID: PMC9513430 DOI: 10.3389/fcimb.2022.994014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/18/2022] [Indexed: 11/18/2022] Open
Abstract
Streptococcus mutans, a Gram-positive facultative anaerobic bacterium, is a major pathogen of dental caries. The protein Cnm of S. mutans is involved in collagen binding, but its other biological functions are unknown. In this study, a Cnm-deficient isogenic mutant and a complementation strain were generated from a Cnm-positive S. mutans strain to help determine the properties of Cnm. Initially, comparison of the cell surface structure was performed by electron microscopy, which demonstrated that Cnm appears to be localized on the cell surface and associated with a protruding cell surface structure. Deep RNA sequencing of the strains revealed that the defect in Cnm caused upregulated expression of many genes related to ABC transporters and cell-surface proteins, while a few genes were downregulated. The amount of biofilm formed by the Cnm-defective strain increased compared with the parental and complemented strains, but the biofilm structure was thinner because of elevated expression of genes encoding glucan synthesis enzymes, leading to increased production of extracellular polysaccharides. Particular antibiotics, including bacitracin and chloramphenicol, had a lower minimum inhibitory concentration for the Cnm-defective strain than particular antibiotics, including bacitracin and chloramphenicol, compared with the parental and complemented strains. Our results suggest that S. mutans Cnm is located on the cell surface, gives rise to the observed protruding cell surface, and is associated with several biological properties related to membrane permeability.
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Affiliation(s)
- Shuhei Naka
- Department of Pediatric Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Daiki Matsuoka
- Department of Pediatric Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Kana Goto
- Department of Pediatric Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Taro Misaki
- Division of Nephrology, Seirei Hamamatsu General Hospital, Hamamatsu, Japan
- Department of Nursing, Faculty of Nursing, Seirei Christopher University, Hamamatsu, Japan
| | - Yasuyuki Nagasawa
- Department of General Internal Medicine, Hyogo College of Medicine, Nishinomiya, Japan
| | - Seigo Ito
- Department of Internal Medicine, Japan Self-Defense Iruma Hospital, Iruma, Japan
| | - Ryota Nomura
- Department of Pediatric Dentistry, Division of Oral infection and Disease Control, Osaka University Graduate School of Dentistry, Suita, Japan
| | - Kazuhiko Nakano
- Department of Pediatric Dentistry, Division of Oral infection and Disease Control, Osaka University Graduate School of Dentistry, Suita, Japan
| | - Michiyo Matsumoto-Nakano
- Department of Pediatric Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
- *Correspondence: Michiyo Matsumoto-Nakano,
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9
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Quorum Sensing and Quorum Quenching with a Focus on Cariogenic and Periodontopathic Oral Biofilms. Microorganisms 2022; 10:microorganisms10091783. [PMID: 36144385 PMCID: PMC9503171 DOI: 10.3390/microorganisms10091783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022] Open
Abstract
Numerous in vitro studies highlight the role of quorum sensing in the pathogenicity and virulence of biofilms. This narrative review discusses general principles in quorum sensing, including Gram-positive and Gram-negative models and the influence of flow, before focusing on quorum sensing and quorum quenching in cariogenic and periodontopathic biofilms. In cariology, quorum sensing centres on the role of Streptococcus mutans, and to a lesser extent Candida albicans, while Fusobacterium nucleatum and the red complex pathogens form the basis of the majority of the quorum sensing research on periodontopathic biofilms. Recent research highlights developments in quorum quenching, also known as quorum sensing inhibition, as a potential antimicrobial tool to attenuate the pathogenicity of oral biofilms by the inhibition of bacterial signalling networks. Quorum quenchers may be synthetic or derived from plant or bacterial products, or human saliva. Furthermore, biofilm inhibition by coating quorum sensing inhibitors on dental implant surfaces provides another potential application of quorum quenching technologies in dentistry. While the body of predominantly in vitro research presented here is steadily growing, the clinical value of quorum sensing inhibitors against in vivo oral polymicrobial biofilms needs to be ascertained.
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10
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Wang Q, Wang P, Liu P, Ou J. Comparative Transcriptome Analysis Reveals Regulatory Factors Involved in Vibrio Parahaemolyticus Biofilm Formation. Front Cell Infect Microbiol 2022; 12:917131. [PMID: 35899046 PMCID: PMC9309355 DOI: 10.3389/fcimb.2022.917131] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 06/10/2022] [Indexed: 11/13/2022] Open
Abstract
Vibrio parahaemolyticus biofilm poses a serious threat to food safety and human health. However, there is limited knowledge of transcriptional regulatory mechanism during the biofilm formation of this organism. Hence, the RNA sequencing technique was employed to compare the differences in transcriptome profiles between planktonic and biofilm state of V. parahaemolyticus ATCC33847 in this study. Collections of mRNA from planktonic and biofilm cells cultured at 25°C for 36 h were sequenced by studying their biological characteristics. The results showed that there were significant differences in the expression levels of 956 genes in biofilms compared with planktonic cells. These differences suggested that two-component regulatory system (TCS) and quorum sensing (QS) regulated V. parahaemolyticus biofilm formation by affecting important factors such as flagellar motility, Extracellular polymeric substance (EPS) secretion, tripartite ATP-independent (TRAP) transport system and ATP binding cassette (ABC) transport system. The present work in transcriptomics serves as a basis for future studies examining the complex network systems that regulate bacterial biofilm formation.
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Affiliation(s)
- Qiuyu Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Pengfei Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Pingping Liu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Jie Ou
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai, China
- Shanghai Engineering Research Center of Aquatic-Product Processing and Preservation, Shanghai, China
- *Correspondence: Jie Ou,
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11
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Ruiz Puentes P, Rueda-Gensini L, Valderrama N, Hernández I, González C, Daza L, Muñoz-Camargo C, Cruz JC, Arbeláez P. Predicting target-ligand interactions with graph convolutional networks for interpretable pharmaceutical discovery. Sci Rep 2022; 12:8434. [PMID: 35589824 PMCID: PMC9119967 DOI: 10.1038/s41598-022-12180-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/05/2022] [Indexed: 02/08/2023] Open
Abstract
Drug Discovery is an active research area that demands great investments and generates low returns due to its inherent complexity and great costs. To identify potential therapeutic candidates more effectively, we propose protein–ligand with adversarial augmentations network (PLA-Net), a deep learning-based approach to predict target–ligand interactions. PLA-Net consists of a two-module deep graph convolutional network that considers ligands’ and targets’ most relevant chemical information, successfully combining them to find their binding capability. Moreover, we generate adversarial data augmentations that preserve relevant biological backgrounds and improve the interpretability of our model, highlighting the relevant substructures of the ligands reported to interact with the protein targets. Our experiments demonstrate that the joint ligand–target information and the adversarial augmentations significantly increase the interaction prediction performance. PLA-Net achieves 86.52% in mean average precision for 102 target proteins with perfect performance for 30 of them, in a curated version of actives as decoys dataset. Lastly, we accurately predict pharmacologically-relevant molecules when screening the ligands of ChEMBL and drug repurposing Hub datasets with the perfect-scoring targets.
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Affiliation(s)
- Paola Ruiz Puentes
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogotá, 111711, Colombia.,Department of Biomedical Engineering, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Laura Rueda-Gensini
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogotá, 111711, Colombia.,Department of Biomedical Engineering, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Natalia Valderrama
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogotá, 111711, Colombia.,Department of Biomedical Engineering, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Isabela Hernández
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogotá, 111711, Colombia.,Department of Biomedical Engineering, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Cristina González
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogotá, 111711, Colombia.,Department of Biomedical Engineering, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Laura Daza
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogotá, 111711, Colombia.,Department of Biomedical Engineering, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Carolina Muñoz-Camargo
- Department of Biomedical Engineering, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Juan C Cruz
- Department of Biomedical Engineering, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Pablo Arbeláez
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogotá, 111711, Colombia. .,Department of Biomedical Engineering, Universidad de los Andes, Bogotá, 111711, Colombia.
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12
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Quorum quenching of Streptococcus mutans via the nano-quercetin-based antimicrobial photodynamic therapy as a potential target for cariogenic biofilm. BMC Microbiol 2022; 22:125. [PMID: 35538403 PMCID: PMC9088123 DOI: 10.1186/s12866-022-02544-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 04/28/2022] [Indexed: 12/12/2022] Open
Abstract
Background Quorum sensing (QS) system can regulate the expression of virulence factors and biofilm formation in Streptococcus mutans. Antimicrobial photodynamic therapy (aPDT) inhibits quorum quenching (QQ), and can be used to prevent microbial biofilm. We thereby aimed to evaluate the anti-biofilm potency and anti-metabolic activity of nano-quercetin (N-QCT)-mediated aPDT against S. mutans. Also, in silico evaluation of the inhibitory effect of N-QCT on the competence-stimulating peptide (CSP) of S. mutans was performed to elucidate the impact of aPDT on various QS-regulated genes. Methods Cytotoxicity and intracellular reactive oxygen species (ROS) generation were assessed following synthesis and confirmation of N-QCT. Subsequently, the minimum biofilm inhibitory concentration (MBIC) of N-QCT against S. mutans and anti-biofilm effects of aPDT were assessed using colorimetric assay and plate counting. Molecular modeling and docking analysis were performed to confirm the connection of QCT to CSP. The metabolic activity of S. mutans and the expression level of various genes involved in QS were evaluated by flow cytometry and reverse transcription quantitative real-time PCR, respectively. Results Successful synthesis of non-toxic N-QCT was confirmed through several characterization tests. The MBIC value of N-QCT against S. mutans was 128 μg/mL. Similar to the crystal violet staining, the results log10 CFU/mL showed a significant degradation of preformed biofilms in the group treated with aPDT compared to the control group (P < 0.05). Following aPDT, metabolic activity of S. mutans also decreased by 85.7% (1/2 × MBIC of N-QCT) and 77.3% (1/4 × MBIC of N-QCT), as compared to the control values (P < 0.05). In silico analysis showed that the QCT molecule was located in the site formed by polypeptide helices of CSP. The relative expression levels of the virulence genes were significantly decreased in the presence of N-QCT-mediated aPDT (P < 0.05). Conclusions The combination of N-QCT with blue laser as a QQ-strategy leads to maximum ROS generation, disrupts the microbial biofilm of S. mutans, reduces metabolic activity, and downregulates the expression of genes involved in the QS pathway by targeting genes of the QS signaling system of S. mutans.
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Zhao Y, Min H, Luo K, Zhang R, Chen Q, Chen Z. Transcriptomics and proteomics revealed the psychrotolerant and antibiotic-resistant mechanisms of strain Pseudomonas psychrophila RNC-1 capable of assimilatory nitrate reduction and aerobic denitrification. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 820:153169. [PMID: 35051480 DOI: 10.1016/j.scitotenv.2022.153169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Aerobic denitrification has been proved to be profoundly affected by temperature and antibiotics, but little is known about how aerobic denitrifiers respond to temperature and antibiotic stress. In this study, the nitrate reduction performance and the intracellular metabolism by a psychrotolerant aerobic denitrifying bacteria, named Pseudomonas psychrophila RNC-1, were systematically investigated at different temperatures (10 °C, 20 °C, 30 °C) and different sulfamethoxazole (SMX) concentrations (0 mg/L, 0.1 mg/L, 0.5 mg/L, 1.0 mg/L, and 5.0 mg/L). The results showed that strain RNC-1 performed satisfactory nitrate removal at 10 °C and 20 °C, but its growth was significantly inhibited at 30 °C. Nitrate removal by strain RNC-1 was slightly promoted in the presence of 0.5 mg/L SMX, whereas it was significantly suppressed with 5.0 mg/L SMX. Nitrogen balance analysis indicated that assimilatory nitrate reduction and dissimilatory aerobic denitrification jointly dominated in the nitrate removal process of strain RNC-1, in which the inhibition effected on assimilation process was much higher than that on the aerobic denitrification process under SMX exposure. Further transcriptomics and proteomics analysis revealed that the psychrotolerant mechanism of strain RNC-1 could be attributed to the up-regulation of RNA translation, energy metabolism, ABC transporters and the over-expression of cold shock proteins, while the down-regulation of oxidative phosphorylation pathway was the primary reason for the deteriorative cell growth at 30 °C. The promotion of nitrate reduction with 0.5 mg/L SMX was related to the up-regulation of amino acid metabolism pathways, while the down-regulation of folate cycle, glycolysis/gluconeogenesis and bacterial chemotaxis pathways were responsible for the inhibition effect at 5.0 mg/L SMX. This work provides a mechanistic understanding of the metabolic adaption of strain RNC-1 under different stress, which is of significance for its application in nitrogen contaminated wastewater treatment processes.
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Affiliation(s)
- Yuanyi Zhao
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, PR China; State Environmental Protection Key Laboratory of All Materials Flux in River Ecosystems, Beijing 100871, PR China; College of Environment and Resources, Dalian Minzu University, Dalian 116600, PR China
| | - Hongchao Min
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Kongyan Luo
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, PR China; State Environmental Protection Key Laboratory of All Materials Flux in River Ecosystems, Beijing 100871, PR China; College of Environment and Resources, Dalian Minzu University, Dalian 116600, PR China
| | - Ruijie Zhang
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, PR China; State Environmental Protection Key Laboratory of All Materials Flux in River Ecosystems, Beijing 100871, PR China
| | - Qian Chen
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, PR China; State Environmental Protection Key Laboratory of All Materials Flux in River Ecosystems, Beijing 100871, PR China.
| | - Zhaobo Chen
- College of Environment and Resources, Dalian Minzu University, Dalian 116600, PR China.
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Li X, Liu Y, Yang X, Li C, Song Z. The Oral Microbiota: Community Composition, Influencing Factors, Pathogenesis, and Interventions. Front Microbiol 2022; 13:895537. [PMID: 35572634 PMCID: PMC9100676 DOI: 10.3389/fmicb.2022.895537] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/06/2022] [Indexed: 12/12/2022] Open
Abstract
The human oral cavity provides a habitat for oral microbial communities. The complexity of its anatomical structure, its connectivity to the outside, and its moist environment contribute to the complexity and ecological site specificity of the microbiome colonized therein. Complex endogenous and exogenous factors affect the occurrence and development of the oral microbiota, and maintain it in a dynamic balance. The dysbiotic state, in which the microbial composition is altered and the microecological balance between host and microorganisms is disturbed, can lead to oral and even systemic diseases. In this review, we discuss the current research on the composition of the oral microbiota, the factors influencing it, and its relationships with common oral diseases. We focus on the specificity of the microbiota at different niches in the oral cavity, the communities of the oral microbiome, the mycobiome, and the virome within oral biofilms, and interventions targeting oral pathogens associated with disease. With these data, we aim to extend our understanding of oral microorganisms and provide new ideas for the clinical management of infectious oral diseases.
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Affiliation(s)
- Xinyi Li
- School of Stomatology, Southwest Medical University, Luzhou, China
| | - Yanmei Liu
- School of Stomatology, Southwest Medical University, Luzhou, China
| | - Xingyou Yang
- Molecular Biotechnology Platform, Public Center of Experimental Technology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
| | - Chengwen Li
- Molecular Biotechnology Platform, Public Center of Experimental Technology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
- *Correspondence: Chengwen Li,
| | - Zhangyong Song
- Molecular Biotechnology Platform, Public Center of Experimental Technology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
- Zhangyong Song,
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Li J, Zhang Q, Zhao J, Zhang H, Chen W. Streptococcus mutans and Candida albicans Biofilm Inhibitors Produced by Lactiplantibacillus plantarum CCFM8724. Curr Microbiol 2022; 79:143. [PMID: 35325333 DOI: 10.1007/s00284-022-02833-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/10/2022] [Indexed: 12/24/2022]
Abstract
Lactiplantibacillus plantarum CCFM8724 inhibits the growth of Streptococcus mutans and Candida albicans in mixed-species biofilm formation. In this study, bioactive compound including cyclo (leu-pro), cyclo (phe-pro), and some organic acids, such as 3-phenyllactic acid, hydrocinnamic acid, and palmitic acid, were identified through GC-MS analysis. At 50 μg·mL-1, cyclo (leu-pro) reduced biofilm mass (OD600) from 3.00 to 2.00, and hydrocinnamic acid at 25 μg·mL-1 reduced biofilm mass (OD600) from 3.00 to 1.00. The expression of ALS3 and HWP1 was downregulated by cyclo (leu-pro). Furthermore, a mixture of cyclo (leu-pro), cyclo (phe-pro), 3-phenyllactic acid, hydrocinnamic acid, and palmitic acid, had anti-biofilm activity. Overall, the results provide promising baseline information for the potential use of this probiotic and its components in preventing biofilm formation.
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Affiliation(s)
- Jiaxun Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Qiuxiang Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China. .,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China. .,(Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, 225004, China.
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, Jiangsu, China
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