1
|
Fan Y, Keerthisinghe TP, Nian M, Cao X, Chen X, Yang Q, Sampathkumar K, Loo JSC, Ng KW, Demokritou P, Fang M. Comparative secretome metabolic dysregulation by six engineered dietary nanoparticles (EDNs) on the simulated gut microbiota. J Hazard Mater 2024; 465:133003. [PMID: 38029586 DOI: 10.1016/j.jhazmat.2023.133003] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/27/2023] [Accepted: 11/12/2023] [Indexed: 12/01/2023]
Abstract
The potential use of engineered dietary nanoparticles (EDNs) in diet has been increasing and poses a risk of exposure. The effect of EDNs on gut bacterial metabolism remains largely unknown. In this study, liquid chromatography-mass spectrometry (LC-MS) based metabolomics was used to reveal significantly altered metabolites and metabolic pathways in the secretome of simulated gut microbiome exposed to six different types of EDNs (Chitosan, cellulose nanocrystals (CNC), cellulose nanofibrils (CNF) and polylactic-co-glycolic acid (PLGA); two inorganic EDNs including TiO2 and SiO2) at two dietary doses. We demonstrated that all six EDNs can alter the composition in the secretome with distinct patterns. Chitosan, followed by PLGA and SiO2, has shown the highest potency in inducing the secretome change with major pathways in tryptophan and indole metabolism, bile acid metabolism, tyrosine and phenol metabolism. Metabolomic alterations with clear dose response were observed in most EDNs. Overall, phenylalanine has been shown as the most sensitive metabolites, followed by bile acids such as chenodeoxycholic acid and cholic acid. Those metabolites might be served as the representative metabolites for the EDNs-gut bacteria interaction. Collectively, our studies have demonstrated the sensitivity and feasibility of using metabolomic signatures to understand and predict EDNs-gut microbiome interaction.
Collapse
Affiliation(s)
- Yijun Fan
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Anhui Medical University, No 678 Furong Road, Hefei 230601, Anhui, China
| | | | - Min Nian
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Xiaoqiong Cao
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T.H. Chan School of Public Health, Harvard University, 655 Huntington Ave, Boston, MA 02115, USA
| | - Xing Chen
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Qin Yang
- Nanyang Environment and Water Research Institute, Nanyang Technological University, 637141, Singapore
| | - Kaarunya Sampathkumar
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
| | - Joachim Say Chye Loo
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
| | - Kee Woei Ng
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
| | - Philip Demokritou
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T.H. Chan School of Public Health, Harvard University, 655 Huntington Ave, Boston, MA 02115, USA
| | - Mingliang Fang
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China; Institute of Eco-Chongming, Shanghai 202162, China.
| |
Collapse
|
2
|
Keerthisinghe TP, Yang Q, Chow A, Fang M. Feeding state greatly modulates the effect of xenobiotics on gut microbiome metabolism: A case study of tetracycline. J Hazard Mater 2021; 413:125441. [PMID: 33930963 DOI: 10.1016/j.jhazmat.2021.125441] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 02/01/2021] [Accepted: 02/14/2021] [Indexed: 06/12/2023]
Abstract
The human gut microbiome is crucial in modulating host health mostly through bacterial metabolites. Chemical exposure is typical external stress which alters its composition and functionality. To date, very few studies have investigated the effect of feeding state on chemical-induced gut microbial metabolic dysregulations. Here, we set up an in vitro human gut microbiome and incorporated a metabolomics approach to investigate the effect of tetracycline (TET) at multiple doses (i.e., 10, 1, and 0.01 mg/L) on gut microbiome under the fed and fasted states. Overall, the metabolome was highly responsive at the fed state with 62 metabolites dysregulated while only 14 were altered at the fasted state under 10 mg/L (clinical TET dose). As expected, nutrient consumption was significantly inhibited under clinical TET dose at the fed state accumulating nutrients such as glutamate and leucine. Interestingly, at the fed state, TET could increase the synthesis of indole and phenyl derivatives including indole-3-aldehyde and hydrocinnamate, while inhibiting indoxyl, tryptamine, and vitamin B production, all of which have host health implications. Furthermore, metabolites like indoxyl and xanthurenic acid were still responsive at 0.01 mg/L (dietary TET dose). Collectively, results demonstrated that the feeding state greatly modulates the chemical-induced gut microbial metabolic alterations.
Collapse
Affiliation(s)
- Tharushi Prabha Keerthisinghe
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798; Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore 637141
| | - Qin Yang
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798; Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore 637141
| | - Agnes Chow
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798; Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore 637141
| | - Mingliang Fang
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798; Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore 637141; Singapore Phenome Center, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921.
| |
Collapse
|
3
|
Zhao F, Li L, Chen Y, Huang Y, Keerthisinghe TP, Chow A, Dong T, Jia S, Xing S, Warth B, Huan T, Fang M. Risk-Based Chemical Ranking and Generating a Prioritized Human Exposome Database. Environ Health Perspect 2021; 129:47014. [PMID: 33929905 PMCID: PMC8086799 DOI: 10.1289/ehp7722] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 03/17/2021] [Accepted: 04/01/2021] [Indexed: 05/26/2023]
Abstract
BACKGROUND Due to the ubiquitous use of chemicals in modern society, humans are increasingly exposed to thousands of chemicals that contribute to a major portion of the human exposome. Should a comprehensive and risk-based human exposome database be created, it would be conducive to the rapid progress of human exposomics research. In addition, once a xenobiotic is biotransformed with distinct half-lives upon exposure, monitoring the parent compounds alone may not reflect the actual human exposure. To address these questions, a comprehensive and risk-prioritized human exposome database is needed. OBJECTIVES Our objective was to set up a comprehensive risk-prioritized human exposome database including physicochemical properties as well as risk prediction and develop a graphical user interface (GUI) that has the ability to conduct searches for content associated with chemicals in our database. METHODS We built a comprehensive risk-prioritized human exposome database by text mining and database fusion. Subsequently, chemicals were prioritized by integrating exposure level obtained from the Systematic Empirical Evaluation of Models with toxicity data predicted by the Toxicity Estimation Software Tool and the Toxicological Priority Index calculated from the ToxCast database. The biotransformation half-lives (HLBs) of all the chemicals were assessed using the Iterative Fragment Selection approach and biotransformation products were predicted using the previously developed BioTransformer machine-learning method. RESULTS We compiled a human exposome database of >20,000 chemicals, prioritized 13,441 chemicals based on probabilistic hazard quotient and 7,770 chemicals based on risk index, and provided a predicted biotransformation metabolite database of >95,000 metabolites. In addition, a user-interactive Java software (Oracle)-based search GUI was generated to enable open access to this new resource. DISCUSSION Our database can be used to guide chemical management and enhance scientific understanding to rapidly and effectively prioritize chemicals for comprehensive biomonitoring in epidemiological investigations. https://doi.org/10.1289/EHP7722.
Collapse
Affiliation(s)
- Fanrong Zhao
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore
- Nanyang Environment & Water Research Institute, Nanyang Technological University, Singapore, Singapore
| | - Li Li
- School of Community Health Sciences, University of Nevada, Reno, Nevada, USA
| | - Yue Chen
- School of Computer Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Yichao Huang
- School of Environment, Jinan University, Guangdong Guangzhou, P.R. China
| | - Tharushi Prabha Keerthisinghe
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore
- Nanyang Environment & Water Research Institute, Nanyang Technological University, Singapore, Singapore
| | - Agnes Chow
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore
- Nanyang Environment & Water Research Institute, Nanyang Technological University, Singapore, Singapore
| | - Ting Dong
- School of Environment, Jinan University, Guangdong Guangzhou, P.R. China
| | - Shenglan Jia
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore
- Nanyang Environment & Water Research Institute, Nanyang Technological University, Singapore, Singapore
| | - Shipei Xing
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Benedikt Warth
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Tao Huan
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mingliang Fang
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore
- Nanyang Environment & Water Research Institute, Nanyang Technological University, Singapore, Singapore
- Singapore Phenome Center, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| |
Collapse
|
4
|
Yang Q, Keerthisinghe TP, Tan TRJ, Cao X, Setyawati MI, DeLoid G, Ng KW, Loo SCJ, Demokritou P, Fang M. A high-throughput method to characterize the gut bacteria growth upon engineered nanomaterial treatment. Environ Sci Nano 2020; 7:3155-3166. [PMID: 33101690 PMCID: PMC7577393 DOI: 10.1039/d0en00568a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Human are increasingly exposed to various types of engineered nanomaterials (ENMs) via dietary ingestion of nano-enabled food products, but these ENMs' impact on the gut bacteria health is still poorly understood. Current efforts in understanding the impact of these ENMs are hampered by their optical interferences in conventional quantification and viability assays, such as optical density and whole cell fluorescence staining assays. Therefore, there is a need to develop a more reliable bacteria quantification method in the presence of ENMs to effectively screen the potential adverse effects arising from the exposure of increasing ENMs on human gut microbiome. In this study, we developed a DNA-based quantification (DBQ) method in a 96-well plate format. Post-spiking method was used to correct the interference from ENMs on the reading. We showed the applicability of this method for several types of ENMs, i.e., cellulose nanofiber (CNF), graphene oxide (GO), silicon dioxide (SiO2), and chitosan, both in pure bacterial culture and in vitro human gut microbiome community. The detection limit for the highest dosing of CNF, GO, SiO2, and chitosan ENMs was approximately 0.18, 0.19, 0.05, and 0.24 as OD600, respectively. The method was also validated by a dose response experiment of E. coli with chitosan in the course of 8 hr. We believe that this method has great potential to be used in screening the effect of ENMs on the growth of gut bacteria or any other in vitro models and normalization for metabolites or proteins analysis.
Collapse
Affiliation(s)
- Qin Yang
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
- Nanyang Environment and Water Research Institute, Nanyang Technological University, 637141, Singapore
| | - Tharushi Prabha Keerthisinghe
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
- Nanyang Environment and Water Research Institute, Nanyang Technological University, 637141, Singapore
| | - Tiffany Rou Jie Tan
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
- Nanyang Environment and Water Research Institute, Nanyang Technological University, 637141, Singapore
| | - Xiaoqiong Cao
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T.H. Chan School of Public Health, Harvard University, 655 Huntington Ave, Boston, MA, 02115 USA
| | - Magdiel Inggrid Setyawati
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Glen DeLoid
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T.H. Chan School of Public Health, Harvard University, 655 Huntington Ave, Boston, MA, 02115 USA
| | - Kee Woei Ng
- Nanyang Environment and Water Research Institute, Nanyang Technological University, 637141, Singapore
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T.H. Chan School of Public Health, Harvard University, 655 Huntington Ave, Boston, MA, 02115 USA
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Say Chye Joachim Loo
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T.H. Chan School of Public Health, Harvard University, 655 Huntington Ave, Boston, MA, 02115 USA
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Philip Demokritou
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T.H. Chan School of Public Health, Harvard University, 655 Huntington Ave, Boston, MA, 02115 USA
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Mingliang Fang
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
- Nanyang Environment and Water Research Institute, Nanyang Technological University, 637141, Singapore
- Singapore Phenome Center, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, Singapore
| |
Collapse
|
5
|
Keerthisinghe TP, Wang F, Wang M, Yang Q, Li J, Yang J, Xi L, Dong W, Fang M. Long-term exposure to TET increases body weight of juvenile zebrafish as indicated in host metabolism and gut microbiome. Environ Int 2020; 139:105705. [PMID: 32283355 DOI: 10.1016/j.envint.2020.105705] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 03/16/2020] [Accepted: 03/29/2020] [Indexed: 06/11/2023]
Abstract
The application of tetracycline (TET) is very common in medical treatment, fisheries, and animal husbandry, resulting in its frequent detection with abundant concentrations in the aquatic environment. Though the effects of TET on zebrafish (Danio rerio) at embryonic and larval stages have been reported, there is very limited information on the possible long-term effect on aquatic fishes at the juvenile stage, especially at environmentally relevant levels. In this study, we have exposed juvenile zebrafish to two levels of TET at 1 and 100 µg/L for one month until their adulthood. The result showed that both levels of TET can significantly increase the body weight of the zebrafish, while there is no change in the body length. TET exposure also affected the liver microstructure by lipid vacuoles generation and global lipidomics analysis revealed a significant upregulation in hepatic triglyceride (TAG) levels. The metabolomics analysis showed great dysregulations in hepatic metabolic pathways including linoleic acid metabolism, tyrosine metabolism, and methionine metabolism, which are known to be linked with increased body weight gain through hepatic lipid accumulation. The hepatic gene expression involved in lipid transport (e.g., apoa4 and fabp11) and lipogenic factors (e.g., ppar) have been significantly upregulated in the livers of TET exposed zebrafish. Interestingly, the 16 rRNA gene sequence-based zebrafish gut microbial community analysis revealed an enhanced community diversity and altered microbial community composition upon TET exposure. To our knowledge, this is the first study showing that TET exposure can increase the body weight in juvenile zebrafish and the study on the ecotoxicity of antibiotic occurrences in the aquatic system can be further warranted.
Collapse
Affiliation(s)
- Tharushi Prabha Keerthisinghe
- Inner Mongolia Key Laboratory of Toxicant Monitoring and Toxicology, College of Animal Science and Technology, Inner Mongolia University for the Nationalities, Tongliao, Inner Mongolia 028000, China; School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore; Nanyang Environment and Water Research Institute, Nanyang Technological University, 637141, Singapore
| | - Feng Wang
- Inner Mongolia Key Laboratory of Toxicant Monitoring and Toxicology, College of Animal Science and Technology, Inner Mongolia University for the Nationalities, Tongliao, Inner Mongolia 028000, China; Laboratory of Developmental Nutrition, Department of Animal Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Mengjing Wang
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Qin Yang
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Jiawei Li
- Inner Mongolia Key Laboratory of Toxicant Monitoring and Toxicology, College of Animal Science and Technology, Inner Mongolia University for the Nationalities, Tongliao, Inner Mongolia 028000, China
| | - Jingfeng Yang
- Inner Mongolia Key Laboratory of Toxicant Monitoring and Toxicology, College of Animal Science and Technology, Inner Mongolia University for the Nationalities, Tongliao, Inner Mongolia 028000, China
| | - Lin Xi
- Laboratory of Developmental Nutrition, Department of Animal Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Wu Dong
- Inner Mongolia Key Laboratory of Toxicant Monitoring and Toxicology, College of Animal Science and Technology, Inner Mongolia University for the Nationalities, Tongliao, Inner Mongolia 028000, China.
| | - Mingliang Fang
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore; Nanyang Environment and Water Research Institute, Nanyang Technological University, 637141, Singapore; Singapore Phenome Center, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, Singapore.
| |
Collapse
|
6
|
Zhang Y, Keerthisinghe TP, Han Y, Liu M, Wanjaya ER, Fang M. "Cocktail" of Xenobiotics at Human Relevant Levels Reshapes the Gut Bacterial Metabolome in a Species-Specific Manner. Environ Sci Technol 2018; 52:11402-11410. [PMID: 30153011 DOI: 10.1021/acs.est.8b02629] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The human gut microbiome experiences long-term exposure to numerous organic contaminants (e.g., xenobiotics) in the digestive tract, and the possible consequences have rarely been characterized. To date, very few studies have investigated the metabolic variation from different species of gut bacteria in response to xenobiotic mixtures. In this study, we applied liquid chromatography mass spectrometry-based global metabolomics, coupled with targeted metabolomics, to characterize the model gut bacterial responses toward the xenobiotic mixture, covering diverse classes of compounds at human relevant concentrations. The xenobiotic "cocktail" will not likely affect the growth or morphological properties of model bacteria at human relevant concentrations. However, the metabolic results were distinct between four model bacteria and dose levels, showing species-specific and dose-dependent responsive patterns among different commensal gut bacteria. The key metabolites responsive to xenobiotic exposure are mainly involved in amino acid metabolism and central carbon metabolism, including sulfur-containing amino acids, aromatic amino acids, amino sugars, neurotransmitters, and energy-related metabolic pathways. Many of those metabolites also play an important role in the host's health. In summary, our results show that the gut microbiome can be significantly perturbed by exposure to xenobiotic mixtures at human relevant levels, providing key information on susceptibilities of individuals with diverse gut microbial structures.
Collapse
Affiliation(s)
- Yingdan Zhang
- School of Civil and Environmental Engineering , Nanyang Technological University , Singapore 639798
| | - Tharushi Prabha Keerthisinghe
- School of Civil and Environmental Engineering , Nanyang Technological University , Singapore 639798
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute , Nanyang Technological University , Singapore 63714
| | - Yuan Han
- Analytical Cluster, Nanyang Environment & Water Research Institute , Nanyang Technological University , Singapore 637141
| | - Min Liu
- School of Civil and Environmental Engineering , Nanyang Technological University , Singapore 639798
| | - Elvy Riani Wanjaya
- Analytical Cluster, Nanyang Environment & Water Research Institute , Nanyang Technological University , Singapore 637141
| | - Mingliang Fang
- School of Civil and Environmental Engineering , Nanyang Technological University , Singapore 639798
- Analytical Cluster, Nanyang Environment & Water Research Institute , Nanyang Technological University , Singapore 637141
| |
Collapse
|