1
|
De Filippis F, Valentino V, Sequino G, Borriello G, Riccardi MG, Pierri B, Cerino P, Pizzolante A, Pasolli E, Esposito M, Limone A, Ercolini D. Exposure to environmental pollutants selects for xenobiotic-degrading functions in the human gut microbiome. Nat Commun 2024; 15:4482. [PMID: 38802370 PMCID: PMC11130323 DOI: 10.1038/s41467-024-48739-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 05/08/2024] [Indexed: 05/29/2024] Open
Abstract
Environmental pollutants from different chemical families may reach the gut microbiome, where they can be metabolized and transformed. However, how our gut symbionts respond to the exposure to environmental pollution is still underexplored. In this observational, cohort study, we aim to investigate the influence of environmental pollution on the gut microbiome composition and potential activity by shotgun metagenomics. We select as a case study a population living in a highly polluted area in Campania region (Southern Italy), proposed as an ideal field for exposomic studies and we compare the fecal microbiome of 359 subjects living in areas with high, medium and low environmental pollution. We highlight changes in gut microbiome composition and functionality that were driven by pollution exposure. Subjects from highly polluted areas show higher blood concentrations of dioxin and heavy metals, as well as an increase in microbial genes related to degradation and/or resistance to these molecules. Here we demonstrate the dramatic effect that environmental xenobiotics have on gut microbial communities, shaping their composition and boosting the selection of strains with degrading capacity. The gut microbiome can be considered as a pivotal player in the environment-health interaction that may contribute to detoxifying toxic compounds and should be taken into account when developing risk assessment models. The study was registered at ClinicalTrials.gov with the identifier NCT05976126.
Collapse
Affiliation(s)
- Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, Via Università, 100, Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Corso Umberto I, 40, Napoli, Italy
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute, 2, Portici, Italy
| | - Vincenzo Valentino
- Department of Agricultural Sciences, University of Naples Federico II, Via Università, 100, Portici, Italy
| | - Giuseppina Sequino
- Department of Agricultural Sciences, University of Naples Federico II, Via Università, 100, Portici, Italy
| | - Giorgia Borriello
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute, 2, Portici, Italy
| | | | - Biancamaria Pierri
- National Reference Centre for the Analysis and Study of the Correlation between Environment, Animal and Human, Via Salute, 2, Portici, Italy
| | - Pellegrino Cerino
- National Reference Centre for the Analysis and Study of the Correlation between Environment, Animal and Human, Via Salute, 2, Portici, Italy
| | - Antonio Pizzolante
- National Reference Centre for the Analysis and Study of the Correlation between Environment, Animal and Human, Via Salute, 2, Portici, Italy
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, Via Università, 100, Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Corso Umberto I, 40, Napoli, Italy
| | - Mauro Esposito
- National Reference Centre for the Analysis and Study of the Correlation between Environment, Animal and Human, Via Salute, 2, Portici, Italy
| | - Antonio Limone
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute, 2, Portici, Italy
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, Via Università, 100, Portici, Italy.
- Task Force on Microbiome Studies, University of Naples Federico II, Corso Umberto I, 40, Napoli, Italy.
| |
Collapse
|
2
|
Dahiya P, Kumari S, Behl M, Kashyap A, Kumari D, Thakur K, Devi M, Kumari N, Kaushik N, Walia A, Bhatt AK, Bhatia RK. Guardians of the Gut: Harnessing the Power of Probiotic Microbiota and Their Exopolysaccharides to Mitigate Heavy Metal Toxicity in Human for Better Health. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10281-9. [PMID: 38733461 DOI: 10.1007/s12602-024-10281-9] [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] [Accepted: 04/26/2024] [Indexed: 05/13/2024]
Abstract
Heavy metal pollution is a significant global health concern, posing risks to both the environment and human health. Exposure to heavy metals happens through various channels like contaminated water, food, air, and workplaces, resulting in severe health implications. Heavy metals also disrupt the gut's microbial balance, leading to dysbiosis characterized by a decrease in beneficial microorganisms and proliferation in harmful ones, ultimately exacerbating health problems. Probiotic microorganisms have demonstrated their ability to adsorb and sequester heavy metals, while their exopolysaccharides (EPS) exhibit chelating properties, aiding in mitigating heavy metal toxicity. These beneficial microorganisms aid in restoring gut integrity through processes like biosorption, bioaccumulation, and biotransformation of heavy metals. Incorporating probiotic strains with high affinity for heavy metals into functional foods and supplements presents a practical approach to mitigating heavy metal toxicity while enhancing gut health. Utilizing probiotic microbiota and their exopolysaccharides to address heavy metal toxicity offers a novel method for improving human health through modulation of the gut microbiome. By combining probiotics and exopolysaccharides, a distinctive strategy emerges for mitigating heavy metal toxicity, highlighting promising avenues for therapeutic interventions and health improvements. Further exploration in this domain could lead to groundbreaking therapies and preventive measures, underscoring probiotic microbiota and exopolysaccharides as natural and environmentally friendly solutions to heavy metal toxicity. This, in turn, could enhance public health by safeguarding the gut from environmental contaminants.
Collapse
Affiliation(s)
- Pushpak Dahiya
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla, 171005, Himachal Pradesh, India
| | - Sangeeta Kumari
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla, 171005, Himachal Pradesh, India
| | - Manya Behl
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla, 171005, Himachal Pradesh, India
| | - Aakash Kashyap
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla, 171005, Himachal Pradesh, India
| | - Deeksha Kumari
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla, 171005, Himachal Pradesh, India
| | - Kalpana Thakur
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla, 171005, Himachal Pradesh, India
| | - Mamta Devi
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla, 171005, Himachal Pradesh, India
| | - Neelam Kumari
- Department of Biosciences, Himachal Pradesh University, Summer Hill, Shimla, 171005, Himachal Pradesh, India
| | - Neelam Kaushik
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla, 171005, Himachal Pradesh, India
| | - Abhishek Walia
- Department of Microbiology, College of Basic Sciences, CSK HPKV, Palampur, HP, 176062, India
| | - Arvind Kumar Bhatt
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla, 171005, Himachal Pradesh, India
| | - Ravi Kant Bhatia
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla, 171005, Himachal Pradesh, India.
| |
Collapse
|
3
|
Lopez-Moreno A, Cerk K, Rodrigo L, Suarez A, Aguilera M, Ruiz-Rodriguez A. Bisphenol A exposure affects specific gut taxa and drives microbiota dynamics in childhood obesity. mSystems 2024; 9:e0095723. [PMID: 38426791 PMCID: PMC10949422 DOI: 10.1128/msystems.00957-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/15/2024] [Indexed: 03/02/2024] Open
Abstract
Cumulative xenobiotic exposure has an environmental and human health impact which is currently assessed under the One Health approach. Bisphenol A (BPA) exposure and its potential link with childhood obesity that has parallelly increased during the last decades deserve special attention. It stands during prenatal or early life and could trigger comorbidities and non-communicable diseases along life. Accumulation in the nature of synthetic chemicals supports the "environmental obesogen" hypothesis, such as BPA. This estrogen-mimicking xenobiotic has shown endocrine disruptive and obesogenic effects accompanied by gut microbiota misbalance that is not yet well elucidated. This study aimed to investigate specific microbiota taxa isolated and selected by direct BPA exposure and reveal its role on the overall children microbiota community and dynamics, driving toward specific obesity dysbiosis. A total of 333 BPA-resistant isolated species obtained through culturing after several exposure conditions were evaluated for their role and interplay with the global microbial community. The selected BPA-cultured taxa biomarkers showed a significant impact on alpha diversity. Specifically, Clostridium and Romboutsia were positively associated promoting the richness of microbiota communities, while Intestinibacter, Escherichia-Shigella, Bifidobacterium, and Lactobacillus were negatively associated. Microbial community dynamics and networks analyses showed differences according to the study groups. The normal-weight children group exhibited a more enriched, structured, and connected taxa network compared to overweight and obese groups, which could represent a more resilient community to xenobiotic substances. In this sense, subnetwork analysis generated with the BPA-cultured genera showed a correlation between taxa connectivity and more diverse potential enzymatic BPA degradation capacities.IMPORTANCEOur findings indicate how gut microbiota taxa with the capacity to grow in BPA were differentially represented within differential body mass index children study groups and how these taxa affected the overall dynamics toward patterns of diversity generally recognized in dysbiosis. Community network and subnetwork analyses corroborated the better connectedness and stability profiles for normal-weight group compared to the overweight and obese groups.
Collapse
Affiliation(s)
- Ana Lopez-Moreno
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus of Cartuja, Granada, Spain
- Institute of Nutrition and Food Technology "José Mataix" (INYTA), Centre of Biomedical Research, University of Granada, Granada, Spain
- />Instituto de Investigación Biosanitaria ibs, Granada, Spain
| | - Klara Cerk
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, United Kingdom
| | - Lourdes Rodrigo
- Institute of Nutrition and Food Technology "José Mataix" (INYTA), Centre of Biomedical Research, University of Granada, Granada, Spain
| | - Antonio Suarez
- Institute of Nutrition and Food Technology "José Mataix" (INYTA), Centre of Biomedical Research, University of Granada, Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, Campus of Cartuja, University of Granada, Granada, Spain
| | - Margarita Aguilera
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus of Cartuja, Granada, Spain
- Institute of Nutrition and Food Technology "José Mataix" (INYTA), Centre of Biomedical Research, University of Granada, Granada, Spain
- />Instituto de Investigación Biosanitaria ibs, Granada, Spain
| | - Alicia Ruiz-Rodriguez
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus of Cartuja, Granada, Spain
- Institute of Nutrition and Food Technology "José Mataix" (INYTA), Centre of Biomedical Research, University of Granada, Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, Campus of Cartuja, University of Granada, Granada, Spain
| |
Collapse
|
4
|
Liang X, Liu J, Di J, Xiao N, Peng Y, Tian Q, Chen L. Toxicity evaluation of processing Evodiae fructus based on intestinal microbiota. Front Microbiol 2024; 15:1336777. [PMID: 38435687 PMCID: PMC10904473 DOI: 10.3389/fmicb.2024.1336777] [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: 11/11/2023] [Accepted: 02/06/2024] [Indexed: 03/05/2024] Open
Abstract
Background With the development of healthcare services, drug efficacy, and safety have become the focus of drug use, and processing alters drug toxicity and efficacy, exploring the effects of processing on Evodiae fructus (EF) can guide the clinical use of drugs. Methods Fifty male Kunming mice were randomly divided into the control group (CCN), raw small-flowered EF group (CRSEF), raw medium-flowered EF group (CRMEF), processing small-flowered EF group (CPSEF), and processing medium-flowered EF group (CPMEF). The CRSEF, CRMEF, CPSEF, and CPMEF groups were gavaged with aqueous extracts of raw small-flowered EF dry paste (RSEF), medium-flowered EF dry paste (RMEF), processing small-flowered EF dry paste (PSEF) and processing medium-flowered EF dry paste (PMEF), respectively, for 21 days at 5 times the pharmacopeial dosage. Upon concluding the experiment, histopathological sections of liver and kidney tissues were examined. Additionally, levels of aspartate aminotransferase (AST), alanine aminotransferase (ALT), serum creatinine (SCr), and blood urea nitrogen (BUN) were determined. DNA from the intestinal contents of the mice was extracted, and 16S rRNA full-length high-throughput sequencing was performed. Results After fed EF 21 days, mice exhibited a decreasing trend in body weight. Comparative analysis with the CCN group revealed an upward trend in SCr, BUN, AST, and ALT levels in both CRSEF and CRMEF groups. The CRMEF group displayed notably elevated BUN and AST levels, with an observed increasing trend in Scr and ALT. Kidney sections unveiled cellular edema and considerable inflammatory cell infiltrates, whereas significant liver damage was not evident. Compared with CRSEF, Bun levels were significantly lower while AST levels were significantly higher in the CPMEF group. Additionally, the intestinal microbiota diversity and the relative abundance of Psychrobacter decreased significantly, and the relative abundance of Staphylococcus, Jeotgalicoccus, and Salinicoccus increased significantly in the CPMEF group. AST, ALT, and SCr were positively correlated with Staphylococcus, Jeotgalicoccus, and Salinicoccus. Conclusion In conclusion, PMEF significantly increased harmful bacteria (Staphylococcus, Jeotgalicoccus, and Salinicoccu) and decreased beneficial bacteria. SEF with 5 times the clinical dose showed nephrotoxicity and SEF nephrotoxicity decreased after processing, but EF hepatotoxicity was not significant, which may be due to insufficient dose concentration and time.
Collapse
Affiliation(s)
| | - Jing Liu
- Hunan University of Chinese Medicine, Changsha, China
| | - Jiaxin Di
- Hunan University of Chinese Medicine, Changsha, China
| | - Nenqun Xiao
- Hunan University of Chinese Medicine, Changsha, China
| | - Yanmei Peng
- Hunan Academy of Chinese Medicine, Changsha, China
| | - Qixue Tian
- Hunan Province Hospital of Integrated Traditional Chinese and Western Medicine (The Affiliated Hospital of Hunan Academy of Traditional Chinese Medicine), Changsha, China
- National Traditional Chinese Medicine Processing Technology Inheritance Base of the Affiliated Hospital of Hunan Academy of Traditional Chinese Medicine, Changsha, China
| | - Linglong Chen
- Hunan Academy of Chinese Medicine, Changsha, China
- National Traditional Chinese Medicine Processing Technology Inheritance Base of the Affiliated Hospital of Hunan Academy of Traditional Chinese Medicine, Changsha, China
| |
Collapse
|
5
|
Attia H, ElBanna SA, Khattab RA, Farag MA, Yassin AS, Aziz RK. Integrating Microbiome Analysis, Metabolomics, Bioinformatics, and Histopathology to Elucidate the Protective Effects of Pomegranate Juice against Benzo-alpha-pyrene-Induced Colon Pathologies. Int J Mol Sci 2023; 24:10691. [PMID: 37445869 DOI: 10.3390/ijms241310691] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Polycyclic aromatic hydrocarbons, e.g., benzo[a]pyrene (BaP), are common dietary pollutants with potential carcinogenic activity, while polyphenols are potential chemopreventive antioxidants. Although several health benefits are attributed to polyphenol-rich pomegranate, little is known about its interaction with BaP. This study integrates histochemical, microbiomic, and metabolomic approaches to investigate the protective effects of pomegranate juice from BaP-induced pathologies. To this end, 48 Sprague-Dawley rats received, for four weeks, either pomegranate, BaP, both, or neither (n = 12 rats per group). Whereas histochemical examination of the colon indicated tissue damage marked by mucin depletion in BaP-fed animals, which was partially restored by administration of pomegranate juice, the fecal microbiome and metabolome retained their resilience, except for key changes related to pomegranate and BaP biotransformation. Meanwhile, dramatic microbiome restructuring and metabolome shift were observed as a consequence of the elapsed time (age factor). Additionally, the analysis allowed a thorough examination of fecal microbiome-metabolome associations, which delineated six microbiome clusters (marked by a differential abundance of Lactobacillaceae and Prevotellaceae, Rumincococcaceae, and Erysipelotrichaceae) and two major metabolome clusters (a sugar- and amino-acids-dominated metabotype vs. a cluster of fatty acids and hydrocarbons), with sugar alcohols maintaining a unique signature. In conclusion, using paired comparisons to minimize inter-individual animal variations allowed the dissection of temporal vs. treatment-derived variations. Microbiome-metabolome association clusters may be further exploited for metabotype prediction and gut-health biomarker discovery.
Collapse
Affiliation(s)
- Heba Attia
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
- Center for Genome and Microbiome Research, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Shahira A ElBanna
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
- Center for Genome and Microbiome Research, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Rania A Khattab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Mohamed A Farag
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Aymen S Yassin
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
- Center for Genome and Microbiome Research, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
- Center for Genome and Microbiome Research, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
- Microbiology and Immunology Research Program, Children's Cancer Hospital Egypt 57357, Cairo 11617, Egypt
| |
Collapse
|
6
|
Key Stratification of Microbiota Taxa and Metabolites in the Host Metabolic Health-Disease Balance. Int J Mol Sci 2023; 24:ijms24054519. [PMID: 36901949 PMCID: PMC10003303 DOI: 10.3390/ijms24054519] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
Human gut microbiota seems to drive the interaction with host metabolism through microbial metabolites, enzymes, and bioactive compounds. These components determine the host health-disease balance. Recent metabolomics and combined metabolome-microbiome studies have helped to elucidate how these substances could differentially affect the individual host pathophysiology according to several factors and cumulative exposures, such as obesogenic xenobiotics. The present work aims to investigate and interpret newly compiled data from metabolomics and microbiota composition studies, comparing controls with patients suffering from metabolic-related diseases (diabetes, obesity, metabolic syndrome, liver and cardiovascular diseases, etc.). The results showed, first, a differential composition of the most represented genera in healthy individuals compared to patients with metabolic diseases. Second, the analysis of the metabolite counts exhibited a differential composition of bacterial genera in disease compared to health status. Third, qualitative metabolite analysis revealed relevant information about the chemical nature of metabolites related to disease and/or health status. Key microbial genera were commonly considered overrepresented in healthy individuals together with specific metabolites, e.g., Faecalibacterium and phosphatidylethanolamine; and the opposite, Escherichia and Phosphatidic Acid, which is converted into the intermediate Cytidine Diphosphate Diacylglycerol-diacylglycerol (CDP-DAG), were overrepresented in metabolic-related disease patients. However, it was not possible to associate most specific microbiota taxa and metabolites according to their increased and decreased profiles analyzed with health or disease. Interestingly, positive association of essential amino acids with the genera Bacteroides were observed in a cluster related to health, and conversely, benzene derivatives and lipidic metabolites were related to the genera Clostridium, Roseburia, Blautia, and Oscillibacter in a disease cluster. More studies are needed to elucidate the microbiota species and their corresponding metabolites that are key in promoting health or disease status. Moreover, we propose that greater attention should be paid to biliary acids and to microbiota-liver cometabolites and its detoxification enzymes and pathways.
Collapse
|
7
|
Effect of in vitro cultivation on human gut microbiota composition using 16S rDNA amplicon sequencing and metabolomics approach. Sci Rep 2023; 13:3026. [PMID: 36810418 PMCID: PMC9945476 DOI: 10.1038/s41598-023-29637-2] [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: 10/04/2022] [Accepted: 02/08/2023] [Indexed: 02/23/2023] Open
Abstract
Gut microbiota (GM) plays many key functions and helps maintain the host's health. Consequently, the development of GM cultivation under in vitro stimulating physiological conditions has gained extreme interest in different fields. In this study, we evaluated the impact of four culture media: Gut Microbiota Medium (GMM), Schaedler Broth (SM), Fermentation Medium (FM), and Carbohydrate Free Basal Medium (CFBM) on preserving the biodiversity and metabolic activity of human GM in batch in vitro cultures using PMA treatment coupled with 16S rDNA sequencing (PMA-seq) and LC-HR-MS/MS untargeted metabolomics supplemented with GC-MS SCFA profiling. Before the experiments, we determined the possibility of using the pooled faecal samples (MIX) from healthy donors (n = 15) as inoculum to reduce the number of variables and ensure the reproducibility of in vitro cultivation tests. Results showed the suitability of pooling faecal samples for in vitro cultivation study. Non-cultured MIX inoculum was characterized by higher α-diversity (Shannon effective count, and Effective microbial richness) compared to inocula from individual donors. After 24 h of cultivation, a significant effect of culture media composition on GM taxonomic and metabolomic profiles was observed. The SM and GMM had the highest α-diversity (Shannon effective count). The highest number of core ASVs (125) shared with non-cultured MIX inoculum and total SCFAs production was observed in the SM. These results might contribute to the development of standardized protocols for human GM in vitro cultivation by preventing methodological bias in the data.
Collapse
|
8
|
Using chemical and biological data to predict drug toxicity. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 28:53-64. [PMID: 36639032 DOI: 10.1016/j.slasd.2022.12.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/19/2022] [Accepted: 12/31/2022] [Indexed: 01/12/2023]
Abstract
Various sources of information can be used to better understand and predict compound activity and safety-related endpoints, including biological data such as gene expression and cell morphology. In this review, we first introduce types of chemical, in vitro and in vivo information that can be used to describe compounds and adverse effects. We then explore how compound descriptors based on chemical structure or biological perturbation response can be used to predict safety-related endpoints, and how especially biological data can help us to better understand adverse effects mechanistically. Overall, the described applications demonstrate how large-scale biological information presents new opportunities to anticipate and understand the biological effects of compounds, and how this can support predictive toxicology and drug discovery projects.
Collapse
|
9
|
Merenstein D, Pot B, Leyer G, Ouwehand AC, Preidis GA, Elkins CA, Hill C, Lewis ZT, Shane AL, Zmora N, Petrova MI, Collado MC, Morelli L, Montoya GA, Szajewska H, Tancredi DJ, Sanders ME. Emerging issues in probiotic safety: 2023 perspectives. Gut Microbes 2023; 15:2185034. [PMID: 36919522 PMCID: PMC10026873 DOI: 10.1080/19490976.2023.2185034] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
Probiotics are used for both generally healthy consumers and in clinical settings. However, theoretical and proven adverse events from probiotic consumption exist. New probiotic strains and products, as well as expanding use of probiotics into vulnerable populations, warrants concise, and actionable recommendations on how to work toward their safe and effective use. The International Scientific Association for Probiotics and Prebiotics convened a meeting to discuss and produce evidence-based recommendations on potential acute and long-term risks, risks to vulnerable populations, the importance for probiotic product quality to match the needs of vulnerable populations, and the need for adverse event reporting related to probiotic use. The importance of whole genome sequencing, which enables determination of virulence, toxin, and antibiotic resistance genes, as well as clear assignment of species and strain identity, is emphasized. We present recommendations to guide the scientific and medical community on judging probiotic safety.
Collapse
Affiliation(s)
- Daniel Merenstein
- Department of Family Medicine, Georgetown University Medical Center, Washington, DC USA
| | - Bruno Pot
- Yakult Europe BV, Almere, Netherlands
| | | | - Arthur C Ouwehand
- Global Health & Nutrition Sciences, International Flavors & Fragrances, Kantvik, Finland
| | - Geoffrey A Preidis
- Division of Gastroenterology, Hepatology & Nutrition, Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Christopher A Elkins
- Clinical and Environmental Microbiology Branch, Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Andrea L Shane
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Emory Children's Center, Atlanta, Georgia
| | - Niv Zmora
- Scientific consultant, Elinav Lab, Immunology Department, Weizmann Institute of Science, Department of Gastroenterology and Liver Diseases, Tel Aviv, Israel
| | | | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Valencia, Spain
| | - Lorenzo Morelli
- Department of Food Science and Technology, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Gina A Montoya
- Department of Chemical Risk Assessment, Nestlé S.A., Lausanne, Switzerland
| | - Hania Szajewska
- Department of Paediatrics, The Medical University of Warsaw, Warsaw, Poland
| | - Daniel J Tancredi
- Department of Pediatrics, UC Davis School of Medicine, Sacramento, CA, USA
| | - Mary Ellen Sanders
- International Scientific Association for Probiotics and Prebiotics, Centennial, CO, USA
| |
Collapse
|
10
|
Djokoski F, Hiljadnikova-Bajro M. Novel insights in pharmacomicrobiomics. MAKEDONSKO FARMACEVTSKI BILTEN 2022. [DOI: 10.33320/maced.pharm.bull.2022.68.03.170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
- Filip Djokoski
- Faculty of Pharmacy, Institute of Applied Biochemistry, Ss. Cyril and Methodius University in Skopje, Mother Theresa 47, 1000 Skopje, Republic of North Macedonia
| | - Marija Hiljadnikova-Bajro
- Faculty of Pharmacy, Institute of Applied Biochemistry, Ss. Cyril and Methodius University in Skopje, Mother Theresa 47, 1000 Skopje, Republic of North Macedonia
| |
Collapse
|
11
|
Conti G, D’Amico F, Fabbrini M, Brigidi P, Barone M, Turroni S. Pharmacomicrobiomics in Anticancer Therapies: Why the Gut Microbiota Should Be Pointed Out. Genes (Basel) 2022; 14:55. [PMID: 36672796 PMCID: PMC9859289 DOI: 10.3390/genes14010055] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/09/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Anticancer treatments have shown a variable therapeutic outcome that may be partly attributable to the activity of the gut microbiota on the pathology and/or therapies. In recent years, microbiota-drug interactions have been extensively investigated, but most of the underlying molecular mechanisms still remain unclear. In this review, we discuss the relationship between the gut microbiota and some of the most commonly used drugs in oncological diseases. Different strategies for manipulating the gut microbiota layout (i.e., prebiotics, probiotics, antibiotics, and fecal microbiota transplantation) are then explored in order to optimize clinical outcomes in cancer patients. Anticancer technologies that exploit tumor-associated bacteria to target tumors and biotransform drugs are also briefly discussed. In the field of pharmacomicrobiomics, multi-omics strategies coupled with machine and deep learning are urgently needed to bring to light the interaction among gut microbiota, drugs, and host for the development of truly personalized precision therapies.
Collapse
Affiliation(s)
- Gabriele Conti
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Federica D’Amico
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Marco Fabbrini
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Patrizia Brigidi
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
| | - Monica Barone
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| |
Collapse
|
12
|
Ampatzoglou A, Gruszecka‐Kosowska A, Aguilera‐Gómez M. Microbiota analysis for risk assessment of xenobiotics: toxicomicrobiomics, incorporating the gut microbiome in the risk assessment of xenobiotics and identifying beneficial components for One Health. EFSA J 2022; 20:e200915. [PMID: 36531267 PMCID: PMC9749437 DOI: 10.2903/j.efsa.2022.e200915] [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] [Indexed: 12/23/2022] Open
Abstract
This work explores three areas of relevance to the gut microbiome in the context of One Health; the incorporation of the microbiome in food safety risk assessment of xenobiotics; the identification and application of beneficial microbial components to various areas under One Health, and specifically, in the context of antimicrobial resistance. We conclude that, although challenging, focusing on the microbiota resilience, function and active components, are critical for advancing the incorporation of the gut microbiome in the risk assessment of xenobiotics. Moreover, research technologies, such as toxicomicrobiomics, culturomics and genomics, especially in combination, have revealed that the human microbiota may be a promising source of beneficial taxa or other components, with the potential to metabolise and biodegrade xenobiotics. These may have possible applications in several health areas, including in animals or plants for detoxification or in the environment for bioremediation. This approach would be of particular interest for antimicrobials, with the potential to ameliorate antimicrobial resistance development. Finally, we propose that the concept of resistance to xenobiotics in the context of the gut microbiome may deserve further investigation in the pursuit of holistically elucidating their involvement in the balance between health and disease.
Collapse
Affiliation(s)
- Antonios Ampatzoglou
- "José Mataix Verdú" Institute of Nutrition and Food TechnologyUniversity of Granada (INYTA‐UGR)GranadaSpain
| | | | - Margarita Aguilera‐Gómez
- "José Mataix Verdú" Institute of Nutrition and Food TechnologyUniversity of Granada (INYTA‐UGR)GranadaSpain
| |
Collapse
|
13
|
Gruszecka‐Kosowska A, Ampatzoglou A, Aguilera‐Gómez M. Microbiota analysis for risk assessment of xenobiotics: cumulative xenobiotic exposure and impact on human gut microbiota under One Health approach. EFSA J 2022; 20:e200916. [DOI: 10.2903/j.efsa.2022.e200916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
|
14
|
Torres-Sánchez A, Ruiz-Rodríguez A, Ortiz P, Moreno MA, Ampatzoglou A, Gruszecka-Kosowska A, Monteoliva-Sánchez M, Aguilera M. Exploring Next Generation Probiotics for Metabolic and Microbiota Dysbiosis Linked to Xenobiotic Exposure: Holistic Approach. Int J Mol Sci 2022; 23:12917. [PMID: 36361709 PMCID: PMC9655105 DOI: 10.3390/ijms232112917] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 07/30/2023] Open
Abstract
Variation of gut microbiota in metabolic diseases seems to be related to dysbiosis induced by exposure to multiple substances called Microbiota Disrupting Chemicals (MDCs), which are present as environmental and dietary contaminants. Some recent studies have focused on elucidating the alterations of gut microbiota taxa and their metabolites as a consequence of xenobiotic exposures to find possible key targets involved in the severity of the host disease triggered. Compilation of data supporting the triad of xenobiotic-microbiota-metabolic diseases would subsequently allow such health misbalances to be prevented or treated by identifying beneficial microbe taxa that could be Next Generation Probiotics (NGPs) with metabolic enzymes for MDC neutralisation and mitigation strategies. In this review, we aim to compile the available information and reports focused on variations of the main gut microbiota taxa in metabolic diseases associated with xenobiotic exposure and related microbial metabolite profiles impacting the host health status. We performed an extensive literature search using SCOPUS, Web of Science, and PubMed databases. The data retrieval and thorough analyses highlight the need for more combined metagenomic and metabolomic studies revealing signatures for xenobiotics and triggered metabolic diseases. Moreover, metabolome and microbiome compositional taxa analyses allow further exploration of how to target beneficial NGP candidates according to their alleged variability abundance and potential therapeutic significance. Furthermore, this holistic approach has identified limitations and the need of future directions to expand and integrate key knowledge to design appropriate clinical and interventional studies with NGPs. Apart from human health, the beneficial microbes and metabolites identified could also be proposed for various applications under One Health, such as probiotics for animals, plants and environmental bioremediation.
Collapse
Affiliation(s)
- Alfonso Torres-Sánchez
- Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain
| | - Alicia Ruiz-Rodríguez
- Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain
- Institute of Nutrition and Food Technology “José Mataix” (INYTA), Centre of Biomedical Research, University of Granada, 18016 Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain
| | - Pilar Ortiz
- Institute of Nutrition and Food Technology “José Mataix” (INYTA), Centre of Biomedical Research, University of Granada, 18016 Granada, Spain
| | - María Alejandra Moreno
- Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain
| | - Antonis Ampatzoglou
- Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain
- Institute of Nutrition and Food Technology “José Mataix” (INYTA), Centre of Biomedical Research, University of Granada, 18016 Granada, Spain
| | - Agnieszka Gruszecka-Kosowska
- Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain
- Institute of Nutrition and Food Technology “José Mataix” (INYTA), Centre of Biomedical Research, University of Granada, 18016 Granada, Spain
- Department of Environmental Protection, Faculty of Geology, Geophysics, and Environmental Protection, AGH University of Science and Technology, Al. Mickiewicza 30, 30-059 Krakow, Poland
| | - Mercedes Monteoliva-Sánchez
- Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain
- Institute of Nutrition and Food Technology “José Mataix” (INYTA), Centre of Biomedical Research, University of Granada, 18016 Granada, Spain
| | - Margarita Aguilera
- Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain
- Institute of Nutrition and Food Technology “José Mataix” (INYTA), Centre of Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria ibs, 18012 Granada, Spain
| |
Collapse
|
15
|
Peskett ST, Rand AA. The human fecal microbiome contributes to the biotransformation of the PFAS surfactant 8:2 monosubstituted polyfluoroalkyl phosphate ester. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2022; 24:1758-1768. [PMID: 35979739 DOI: 10.1039/d2em00225f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Polyfluoroalkyl phosphate esters (PAPs) can be found throughout society due to their numerous commercial applications. However, they also pose an environmental and health concern given their ability to undergo hydrolysis and oxidation to several bioactive and persistent products, including the perfluorocarboxylic acids (PFCAs). The metabolism of PAPs has been shown to occur in mammalian liver and intestine, however metabolism by the gut microbiome has not yet been investigated. In this study, human fecal samples were used to model the microbial population of the colon, to test whether these anaerobic microbes could facilitate 8:2 monosubstituted PAP (monoPAP) transformation. In vitro testing was completed by incubating the fecal samples with 8:2 monoPAP (400-10,000 nM) up to 120 minutes in an anaerobic chamber. Reactions were then terminated and the samples prepared for GC- and LC-MS/MS analysis. Metabolites of interest were the immediate hydrolysis product, the 8:2 fluorotelomer alcohol (FTOH), and 11 additional metabolites previously shown to form from 8:2 FTOH in both oxic and anoxic environments. The kinetics of 8:2 monoPAP transformation by gut microbiota were compared to those in human S9 liver and intestine fractions, both of which have active levels of hydrolyzing and oxidative enzymes that transform 8:2 monoPAP. Transformation rates from 8:2 monoPAP to 8:2 FTOH were highest in liver S9 > intestine S9 > fecal suspensions. The gut microbiome also produced a unique composition of oxidative metabolites, where the following intermediate metabolites were more abundant than terminal PFCAs: 8:2 fluorotelomer unsaturated carboxylic acid (FTUCA) > 8:2 fluorotelomer carboxylic acid (FTCA) > 7:2 Ketone ≈ perfluorohexanoic acid (PFHxA). Hydrolytic and oxidative metabolites contributed up to 30% of the molar balance after microbial 8:2 monoPAP transformation. Together, the results suggest that the gut microbiome can play a notable role in PAP biotransformation.
Collapse
Affiliation(s)
- Sierra T Peskett
- Department of Chemistry and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, USA.
| | - Amy A Rand
- Department of Chemistry and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, USA.
| |
Collapse
|
16
|
In silico identification of the potential molecular mechanisms involved in protective effects of prolactin on motor and memory deficits induced by 1,2-Diacetylbenzene in young and old rats. Neurotoxicology 2022; 93:45-59. [PMID: 36100143 DOI: 10.1016/j.neuro.2022.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 02/06/2023]
Abstract
We aimed to identify the molecular mechanisms through which prolactin protects against 1,2-Diacetylbenzene (DAB)-induced memory and motor impairments. The gene expression omnibus database (no. GSE119435), transcriptomic data, GeneMANIA, ToppGeneSuite, Metascape, STRING database, Cytoscape, and Autodock were used as the core tools in in-silico analyses. We observed that prolactin may improve memory and motor deficits caused by DAB via 13 genes (Scn5a, Lmntd1, LOC100360619, Rgs9, Srpk3, Syndig1l, Gpr88, Egr2, Ctxn3, Drd2, Ttr, Gpr6, and Ecel1) in young rats and 9 genes (Scn5a, Chat, RGD1560608, Ucma, Lrrc31, Gpr88, Col1a2, Cnbd1, and Ttr) in old rats. Almost all of these genes were downregulated in both young and old rats given DAB, but they were increased in both young and old rats given prolactin. Co-expression interactions were identified as the most important interactions (83.2 % for young rats and 100 % for old rats). The most important mechanisms associated with prolactin's ability to counteract DAB were identified, including "learning and memory," and "positive regulation of ion transport" in young rats, as well as "acetylcholine related pathways," "inflammatory response pathway," and "neurotransmitter release cycle" in old rats. We also identified several key miRNAs associated with memory and motor deficits, as well as prolactin and DAB exposure (rno-miR-141-3p, rno-miR-200a-3p, rno-miR-124-3p, rno-miR-26, and rno-let-7 families). The most significant transcription factors associated with differentially expressed gene regulation were Six3, Rxrg, Nkx26, and Tbx20. These findings will contribute to our understanding of the processes through which prolactin's beneficial effects counteract DAB-induced memory and motor deficits.
Collapse
|
17
|
Maheshwari N, Khan AA, Ali A, Mahmood R. Oral administration of pentachlorophenol impairs antioxidant system, inhibits enzymes of brush border membrane, causes DNA damage and histological changes in rat intestine. Toxicol Res (Camb) 2022; 11:616-627. [PMID: 36051662 PMCID: PMC9424705 DOI: 10.1093/toxres/tfac035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 05/05/2022] [Accepted: 05/11/2022] [Indexed: 10/28/2023] Open
Abstract
Pentachlorophenol (PCP) is a broad spectrum biocide that has many domestic and industrial applications. PCP enters the environment due to its wide use, especially as a wood preservative. Human exposure to PCP is through contaminated water and adulterated food products. PCP is highly toxic and is classified as class 2B or probable human carcinogen. In this study, we explored the effect of PCP on rat intestine. Adult rats were orally given different doses of PCP (25-150-mg/kg body weight/day) in corn oil for 5 days, whereas controls were given similar amount of corn oil. The rats were sacrificed 24 h after the last treatment. A marked increase in lipid peroxidation, carbonyl content, and hydrogen peroxide level was seen. The glutathione and sulfhydryl group content was decreased in all PCP treated groups. This strongly suggests the generation of reactive oxygen species (ROS) in the intestine. PCP administration suppressed carbohydrate metabolism, inhibited enzymes of brush border membrane (BBM), and antioxidant defense system. It also led to increase in DNA damage, which was evident from comet assay, DNA-protein cross-linking, and DNA fragmentation. Histological studies supported the biochemical results showing marked dose-dependent tissue damage in intestines from PCP treated animals. This study reports for the first time that oral administration of PCP induces ROS, impairs the antioxidant system, damages DNA, and alters the enzyme activities of BBM and metabolic pathways in rat intestine.
Collapse
Affiliation(s)
- Nikhil Maheshwari
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Aijaz Ahmed Khan
- Departments of Anatomy, J. N. Medical College and Hospital, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Asif Ali
- Departments of Biochemistry, J. N. Medical College and Hospital, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Riaz Mahmood
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, U.P., India
| |
Collapse
|
18
|
Gruszecka-Kosowska A, Ampatzoglou A, Aguilera M. Integration of Omics Approaches Enhances the Impact of Scientific Research in Environmental Applications. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19148758. [PMID: 35886610 PMCID: PMC9317225 DOI: 10.3390/ijerph19148758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/14/2022] [Indexed: 12/04/2022]
Abstract
In the original article [...]
Collapse
Affiliation(s)
- Agnieszka Gruszecka-Kosowska
- Department of Environmental Protection, Faculty of Geology, Geophysics, and Environmental Protection, AGH University of Science and Technology, Al. Mickiewicza 30, 30-059 Krakow, Poland
- Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada (UGR), 18071 Granada, Spain;
- Institute of Nutrition and Food Technology “José Mataix” (INYTA), Centre of Biomedical Research, University of Granada (UGR-INYTA), 18016 Granada, Spain
- Correspondence: (A.G.-K.); (M.A.)
| | - Antonis Ampatzoglou
- Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada (UGR), 18071 Granada, Spain;
- Institute of Nutrition and Food Technology “José Mataix” (INYTA), Centre of Biomedical Research, University of Granada (UGR-INYTA), 18016 Granada, Spain
| | - Margarita Aguilera
- Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada (UGR), 18071 Granada, Spain;
- Institute of Nutrition and Food Technology “José Mataix” (INYTA), Centre of Biomedical Research, University of Granada (UGR-INYTA), 18016 Granada, Spain
- IBS—Instituto de Investigación Biosanitaria, 18012 Granada, Spain
- Correspondence: (A.G.-K.); (M.A.)
| |
Collapse
|
19
|
Miryala SK, Anbarasu A, Ramaiah S. Organ-specific host differential gene expression analysis in systemic candidiasis: A systems biology approach. Microb Pathog 2022; 169:105677. [PMID: 35839997 PMCID: PMC9283004 DOI: 10.1016/j.micpath.2022.105677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/08/2022] [Accepted: 07/08/2022] [Indexed: 12/19/2022]
Abstract
Patients admitted to the hospital with coronavirus disease (COVID-19) are at risk for acquiring mycotic infections in particular Candidemia. Candida albicans (C. albicans) constitutes an important component of the human mycobiome and the most common cause of invasive fungal infections. Invasive yeast infections are gaining interest among the scientific community as a consequence of complications associated with severe COVID-19 infections. Early identification and surveillance for Candida infections is critical for decreasing the COVID-19 mortality. Our current study attempted to understand the molecular-level interactions between the human genes in different organs during systematic candidiasis. Our research findings have shed light on the molecular events that occur during Candidiasis in organs such as the kidney, liver, and spleen. The differentially expressed genes (up and down-regulated) in each organ will aid in designing organ-specific therapeutic protocols for systemic candidiasis. We observed organ-specific immune responses such as the development of the acute phase response in the liver; TGF-pathway and genes involved in lymphocyte activation, and leukocyte proliferation in the kidney. We have also observed that in the kidney, filament production, up-regulation of iron acquisition mechanisms, and metabolic adaptability are aided by the late initiation of innate defense mechanisms, which is likely related to the low number of resident immune cells and the sluggish recruitment of new effector cells. Our findings point to major pathways that play essential roles in specific organs during systemic candidiasis. The hub genes discovered in the study can be used to develop novel drugs for clinical management of Candidiasis.
Collapse
Affiliation(s)
- Sravan Kumar Miryala
- Medical and Biological Computing Laboratory, School of Biosciences and Technology Vellore Institute of Technology (VIT), Vellore, 632014, Tamil Nadu, India
| | - Anand Anbarasu
- Medical and Biological Computing Laboratory, School of Biosciences and Technology Vellore Institute of Technology (VIT), Vellore, 632014, Tamil Nadu, India
| | - Sudha Ramaiah
- Medical and Biological Computing Laboratory, School of Biosciences and Technology Vellore Institute of Technology (VIT), Vellore, 632014, Tamil Nadu, India.
| |
Collapse
|
20
|
Lindell AE, Zimmermann-Kogadeeva M, Patil KR. Multimodal interactions of drugs, natural compounds and pollutants with the gut microbiota. Nat Rev Microbiol 2022; 20:431-443. [PMID: 35102308 PMCID: PMC7615390 DOI: 10.1038/s41579-022-00681-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2022] [Indexed: 02/08/2023]
Abstract
The gut microbiota contributes to diverse aspects of host physiology, ranging from immunomodulation to drug metabolism. Changes in the gut microbiota composition are associated with various diseases as well as with the response to medications. It is therefore important to understand how different lifestyle and environmental factors shape gut microbiota composition. Beyond the commonly considered factor of diet, small-molecule drugs have recently been identified as major effectors of the microbiota composition. Other xenobiotics, such as environmental or chemical pollutants, can also impact gut bacterial communities. Here, we review the mechanisms of interactions between gut bacteria and antibiotics, host-targeted drugs, natural food compounds, food additives and environmental pollutants. While xenobiotics can impact bacterial growth and metabolism, bacteria in turn can bioaccumulate or chemically modify these compounds. These reciprocal interactions can manifest in complex xenobiotic-microbiota-host relationships. Our Review highlights the need to study mechanisms underlying interactions with pollutants and food additives towards deciphering the dynamics and evolution of the gut microbiota.
Collapse
Affiliation(s)
- Anna E Lindell
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | | | - Kiran R Patil
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK.
| |
Collapse
|
21
|
Miri AH, Kamankesh M, Llopis-Lorente A, Liu C, Wacker MG, Haririan I, Asadzadeh Aghdaei H, Hamblin MR, Yadegar A, Rad-Malekshahi M, Zali MR. The Potential Use of Antibiotics Against Helicobacter pylori Infection: Biopharmaceutical Implications. Front Pharmacol 2022; 13:917184. [PMID: 35833028 PMCID: PMC9271669 DOI: 10.3389/fphar.2022.917184] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
Helicobacter pylori (H. pylori) is a notorious, recalcitrant and silent germ, which can cause a variety of debilitating stomach diseases, including gastric and duodenal ulcers and gastric cancer. This microbe predominantly colonizes the mucosal layer of the human stomach and survives in the inhospitable gastric microenvironment, by adapting to this hostile milieu. In this review, we first discuss H. pylori colonization and invasion. Thereafter, we provide a survey of current curative options based on polypharmacy, looking at pharmacokinetics, pharmacodynamics and pharmaceutical microbiology concepts, in the battle against H. pylori infection.
Collapse
Affiliation(s)
- Amir Hossein Miri
- Department of Pharmaceutical Biomaterials and Medical Biomaterials Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mojtaba Kamankesh
- Polymer Chemistry Department, School of Science, University of Tehran, Tehran, Iran
| | - Antoni Llopis-Lorente
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Chenguang Liu
- College of Marine Life Science, Ocean University of China, Qingdao, China
| | - Matthias G. Wacker
- Department of Pharmacy, National University of Singapore, Singapore, Singapore
| | - Ismaeil Haririan
- Department of Pharmaceutical Biomaterials and Medical Biomaterials Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Michael R. Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, South Africa
- *Correspondence: Michael R. Hamblin, ; Abbas Yadegar, ; Mazda Rad-Malekshahi, ; Mohammad Reza Zali,
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- *Correspondence: Michael R. Hamblin, ; Abbas Yadegar, ; Mazda Rad-Malekshahi, ; Mohammad Reza Zali,
| | - Mazda Rad-Malekshahi
- Department of Pharmaceutical Biomaterials and Medical Biomaterials Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- *Correspondence: Michael R. Hamblin, ; Abbas Yadegar, ; Mazda Rad-Malekshahi, ; Mohammad Reza Zali,
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- *Correspondence: Michael R. Hamblin, ; Abbas Yadegar, ; Mazda Rad-Malekshahi, ; Mohammad Reza Zali,
| |
Collapse
|
22
|
Yin Q, Sun Y, Li B, Feng Z, Wu G. The r/K selection theory and its application in biological wastewater treatment processes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 824:153836. [PMID: 35176382 DOI: 10.1016/j.scitotenv.2022.153836] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/23/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Understanding the characteristics of functional organisms is the key to managing and updating biological processes for wastewater treatment. This review, for the first time, systematically characterized two typical types of strategists in wastewater treatment ecosystems via the r/K selection theory and provided novel strategies for selectively enriching microbial community. Functional organisms involved in nitrification (e.g., Nitrosomonas and Nitrosococcus), anammox (Candidatus Brocadia), and methanogenesis (Methanosarcinaceae) are identified as r-strategists with fast growth capacities and low substrate affinities. These r-strategists can achieve high pollutant removal loading rates. On the other hand, other organisms such as Nitrosospira spp., Candidatus Kuenenia, and Methanosaetaceae, are characterized as K-strategists with slow growth rates but high substrate affinities, which can decrease the pollutant concentration to low levels. More importantly, K-strategists may play crucial roles in the biodegradation of recalcitrant organic pollutants. The food-to-microorganism ratio, mass transfer, cell size, and biomass morphology are the key factors determining the selection of r-/K-strategists. These factors can be related with operating parameters (e.g., solids and hydraulic retention time), biomass morphology (biofilm or granules), and operating modes (continuous-flow or sequencing batch), etc., to achieve the efficient acclimation of targeted r-/K-strategists. For practical applications, the concept of substrate flux was put forward to further benefit the selective enrichment of r-/K-strategists, fulfilling effective management and improvement of engineered pollution control bioprocesses. Finally, the future perspectives regarding the development of the r/K selection theory in wastewater treatment processes were discussed.
Collapse
Affiliation(s)
- Qidong Yin
- College of Science and Engineering, National University of Ireland, Galway, Galway H91 TK33, Ireland; Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong, China
| | - Yuepeng Sun
- Department of Civil and Environmental Engineering, Virginia Tech, Ashburn, VA 20147, United States
| | - Bo Li
- Department of Civil & Environmental Engineering, University of Washington, Seattle, WA 98105, United States
| | - Zhaolu Feng
- Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong, China
| | - Guangxue Wu
- College of Science and Engineering, National University of Ireland, Galway, Galway H91 TK33, Ireland.
| |
Collapse
|
23
|
Patel SM, Young MC. The Identification and Management of Small Intestinal Bacterial Overgrowth. Phys Med Rehabil Clin N Am 2022; 33:587-603. [DOI: 10.1016/j.pmr.2022.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
24
|
Dikeocha IJ, Al-Kabsi AM, Miftahussurur M, Alshawsh MA. Pharmacomicrobiomics: Influence of gut microbiota on drug and xenobiotic metabolism. FASEB J 2022; 36:e22350. [PMID: 35579628 DOI: 10.1096/fj.202101986r] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 04/28/2022] [Accepted: 05/02/2022] [Indexed: 11/11/2022]
Abstract
Gut microbiota is the most diverse and complex biological ecosystem, which is estimated to consist of greater than 5 million distinct genes and 100 trillion cells which are in constant communication with the host environment. The interaction between the gut microbiota and drugs and other xenobiotic compounds is bidirectional, quite complicated, and not fully understood yet. The impact of xenobiotics from pollution, manufacturing processes or from the environment is harmful to human health at varying degrees and this needs to be recognized and addressed. The gut microbiota is capable of biotransforming/metabolizing of various drugs and xenobiotic compounds as well as altering the activity and toxicity of these substances, thereby influencing how a host responds to drugs and xenobiotics and this emerging field is known as pharmacomicrobiomics. In this review, we discussed different mechanisms of drug-gut microbiota interaction and highlighted the influence of drug-gut microbiome interactions on the clinical response in humans.
Collapse
Affiliation(s)
| | | | - Muhammad Miftahussurur
- Helicobacter Pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.,Division of Gastroentero-Hepatology, Department of Internal Medicine, Faculty of Medicine, Dr. Soetomo Teaching Hospital, Universitas Airlangga, Surabaya, Indonesia
| | | |
Collapse
|
25
|
Ampatzoglou A, Gruszecka-Kosowska A, Torres-Sánchez A, López-Moreno A, Cerk K, Ortiz P, Monteoliva-Sánchez M, Aguilera M. Incorporating the Gut Microbiome in the Risk Assessment of Xenobiotics and Identifying Beneficial Components for One Health. Front Microbiol 2022; 13:872583. [PMID: 35602014 PMCID: PMC9116292 DOI: 10.3389/fmicb.2022.872583] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/31/2022] [Indexed: 12/12/2022] Open
Abstract
Three areas of relevance to the gut microbiome in the context of One Health were explored; the incorporation of the microbiome in food safety risk assessment of xenobiotics; the identification and application of beneficial microbial components to various areas under One Health, and; specifically, in the context of antimicrobial resistance. Although challenging, focusing on the microbiota resilience, function and active components is critical for advancing the incorporation of microbiome data in the risk assessment of xenobiotics. Moreover, the human microbiota may be a promising source of beneficial components, with the potential to metabolize xenobiotics. These may have possible applications in several areas, e.g., in animals or plants for detoxification or in the environment for biodegradation. This approach would be of particular interest for antimicrobials, with the potential to ameliorate antimicrobial resistance development. Finally, the concept of resistance to xenobiotics in the context of the gut microbiome may deserve further investigation.
Collapse
Affiliation(s)
- Antonis Ampatzoglou
- Department of Microbiology, Faculty of Pharmacy, University of Granada (UGR), Granada, Spain
- Centre of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix” (INYTA), UGR, Granada, Spain
| | - Agnieszka Gruszecka-Kosowska
- Department of Microbiology, Faculty of Pharmacy, University of Granada (UGR), Granada, Spain
- Centre of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix” (INYTA), UGR, Granada, Spain
- Department of Environmental Protection, Faculty of Geology, Geophysics, and Environmental Protection, AGH University of Science and Technology, Kraków, Poland
| | - Alfonso Torres-Sánchez
- Department of Microbiology, Faculty of Pharmacy, University of Granada (UGR), Granada, Spain
- Centre of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix” (INYTA), UGR, Granada, Spain
| | - Ana López-Moreno
- Department of Microbiology, Faculty of Pharmacy, University of Granada (UGR), Granada, Spain
- Centre of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix” (INYTA), UGR, Granada, Spain
- IBS: Instituto de Investigación Biosanitaria ibs., Granada, Spain
| | - Klara Cerk
- Department of Microbiology, Faculty of Pharmacy, University of Granada (UGR), Granada, Spain
- Centre of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix” (INYTA), UGR, Granada, Spain
| | - Pilar Ortiz
- Department of Microbiology, Faculty of Pharmacy, University of Granada (UGR), Granada, Spain
- Centre of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix” (INYTA), UGR, Granada, Spain
| | - Mercedes Monteoliva-Sánchez
- Department of Microbiology, Faculty of Pharmacy, University of Granada (UGR), Granada, Spain
- Centre of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix” (INYTA), UGR, Granada, Spain
| | - Margarita Aguilera
- Department of Microbiology, Faculty of Pharmacy, University of Granada (UGR), Granada, Spain
- Centre of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix” (INYTA), UGR, Granada, Spain
- IBS: Instituto de Investigación Biosanitaria ibs., Granada, Spain
| |
Collapse
|
26
|
The Soil Microbiota Recovery in the Agroecosystem: Minimal Information and a New Framework for Sustainable Agriculture. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19095423. [PMID: 35564818 PMCID: PMC9105074 DOI: 10.3390/ijerph19095423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/15/2022] [Accepted: 02/20/2022] [Indexed: 02/05/2023]
Abstract
The efficient management of soil represents a mission of vital importance for meeting the continuously increasing agricultural demand in a sustainable way. Decades of research identified in the biotechnological potential of soil microorganisms an always more practicable channel for achieving these goals. Due to the complexity of soil microbial communities and their tight connection to soil characteristics, it is still difficult to define universal strategies for an efficient and sustainable agroecosystem management. We here propose a new framework for the assessment of the impact of agricultural practices in the agroecosystem that revolves around the concept of microbial community recovery. This assessment is based on the selection of (i) a representative temporal interval, (ii) a representative agricultural system and (iii) monitoring tools able to assess the expression levels of microbial functionality in soil. This approach can be especially valuable for evaluating the effects of agrochemicals and other agronomical amendments (of different nature: biological, physical, chemical) on the soil microbiota. In the same way precision-medicine tries to tailor drugs on an always smaller subset of patients' characteristics, a new generation of agrochemicals can be developed and tested considering soil characteristics in order to minimize their off-target effects. What remains central in this paradigm is the promotion of Soil Health maintenance practices. As for healthy humans, a healthy soil is more resilient and tolerates treatments and stresses better while recovering more quickly.
Collapse
|
27
|
Ortiz P, Torres-Sánchez A, López-Moreno A, Cerk K, Ruiz-Moreno Á, Monteoliva-Sánchez M, Ampatzoglou A, Aguilera M, Gruszecka-Kosowska A. Impact of Cumulative Environmental and Dietary Xenobiotics on Human Microbiota: Risk Assessment for One Health. J Xenobiot 2022; 12:56-63. [PMID: 35323221 PMCID: PMC8949313 DOI: 10.3390/jox12010006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/03/2022] [Accepted: 03/10/2022] [Indexed: 12/11/2022] Open
Abstract
Chemical risk assessment in the context of the risk analysis framework was initially designed to evaluate the impact of hazardous substances or xenobiotics on human health. As the need of multiple stressors assessment was revealed to be more reliable regarding the occurrence and severity of the adverse effects in the exposed organisms, the cumulative risk assessment started to be the recommended approach. As toxicant mixtures and their "cocktail effects" are considered to be main hazards, the most important exposure for these xenobiotics would be of dietary and environmental origin. In fact, even a more holistic prism should currently be considered. In this sense, the definition of One Health refers to simultaneous actions for improving human, animal, and environmental health through transdisciplinary cooperation. Global policies necessitate going beyond the classical risk assessment for guaranteeing human health through actions and implementation of the One Health approach. In this context, a new perspective is proposed for the integration of microbiome biomarkers and next generation probiotics potentially impacting and modulating not only human health, but plant, animal health, and the environment.
Collapse
Affiliation(s)
- Pilar Ortiz
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus of Cartuja, 18071 Granada, Spain; (P.O.); (A.T.-S.); (A.L.-M.); (K.C.); (Á.R.-M.); (M.M.-S.); (A.A.)
- Institute of Nutrition and Food Technology “José Mataix” (UGR-INYTA), Centre of Biomedical Research, University of Granada, 18016 Granada, Spain
| | - Alfonso Torres-Sánchez
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus of Cartuja, 18071 Granada, Spain; (P.O.); (A.T.-S.); (A.L.-M.); (K.C.); (Á.R.-M.); (M.M.-S.); (A.A.)
- Institute of Nutrition and Food Technology “José Mataix” (UGR-INYTA), Centre of Biomedical Research, University of Granada, 18016 Granada, Spain
| | - Ana López-Moreno
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus of Cartuja, 18071 Granada, Spain; (P.O.); (A.T.-S.); (A.L.-M.); (K.C.); (Á.R.-M.); (M.M.-S.); (A.A.)
- Institute of Nutrition and Food Technology “José Mataix” (UGR-INYTA), Centre of Biomedical Research, University of Granada, 18016 Granada, Spain
- IBS (Instituto de Investigación Biosanitaria ibs.), 18012 Granada, Spain
| | - Klara Cerk
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus of Cartuja, 18071 Granada, Spain; (P.O.); (A.T.-S.); (A.L.-M.); (K.C.); (Á.R.-M.); (M.M.-S.); (A.A.)
- Institute of Nutrition and Food Technology “José Mataix” (UGR-INYTA), Centre of Biomedical Research, University of Granada, 18016 Granada, Spain
| | - Ángel Ruiz-Moreno
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus of Cartuja, 18071 Granada, Spain; (P.O.); (A.T.-S.); (A.L.-M.); (K.C.); (Á.R.-M.); (M.M.-S.); (A.A.)
- Institute of Nutrition and Food Technology “José Mataix” (UGR-INYTA), Centre of Biomedical Research, University of Granada, 18016 Granada, Spain
| | - Mercedes Monteoliva-Sánchez
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus of Cartuja, 18071 Granada, Spain; (P.O.); (A.T.-S.); (A.L.-M.); (K.C.); (Á.R.-M.); (M.M.-S.); (A.A.)
- Institute of Nutrition and Food Technology “José Mataix” (UGR-INYTA), Centre of Biomedical Research, University of Granada, 18016 Granada, Spain
| | - Antonis Ampatzoglou
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus of Cartuja, 18071 Granada, Spain; (P.O.); (A.T.-S.); (A.L.-M.); (K.C.); (Á.R.-M.); (M.M.-S.); (A.A.)
- Institute of Nutrition and Food Technology “José Mataix” (UGR-INYTA), Centre of Biomedical Research, University of Granada, 18016 Granada, Spain
| | - Margarita Aguilera
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus of Cartuja, 18071 Granada, Spain; (P.O.); (A.T.-S.); (A.L.-M.); (K.C.); (Á.R.-M.); (M.M.-S.); (A.A.)
- Institute of Nutrition and Food Technology “José Mataix” (UGR-INYTA), Centre of Biomedical Research, University of Granada, 18016 Granada, Spain
- IBS (Instituto de Investigación Biosanitaria ibs.), 18012 Granada, Spain
| | - Agnieszka Gruszecka-Kosowska
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus of Cartuja, 18071 Granada, Spain; (P.O.); (A.T.-S.); (A.L.-M.); (K.C.); (Á.R.-M.); (M.M.-S.); (A.A.)
- Institute of Nutrition and Food Technology “José Mataix” (UGR-INYTA), Centre of Biomedical Research, University of Granada, 18016 Granada, Spain
- Department of Environmental Protection, Faculty of Geology, Geophysics and Environmental Protection, AGH University of Science and Technology, Al. Mickiewicza 30, 30-059 Krakow, Poland
| |
Collapse
|
28
|
Giambò F, Costa C, Teodoro M, Fenga C. Role-Playing Between Environmental Pollutants and Human Gut Microbiota: A Complex Bidirectional Interaction. Front Med (Lausanne) 2022; 9:810397. [PMID: 35252248 PMCID: PMC8888443 DOI: 10.3389/fmed.2022.810397] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 01/18/2022] [Indexed: 12/12/2022] Open
Abstract
There is a growing interest in the characterization of the involvement of toxicant and pollutant exposures in the development and the progression of several diseases such as obesity, diabetes, cancer, as well as in the disruption of the immune and reproductive homeostasis. The gut microbiota is considered a pivotal player against the toxic properties of chemicals with the establishment of a dynamic bidirectional relationship, underlining the toxicological significance of this mutual interplay. In fact, several environmental chemicals have been demonstrated to affect the composition, the biodiversity of the intestinal microbiota together with the underlining modulated metabolic pathways, which may play an important role in tailoring the microbiotype of an individual. In this review, we aimed to discuss the latest updates concerning the environmental chemicals–microbiota dual interaction, toward the identification of a distinctiveness of the gut microbial community, which, in turn, may allow to adopt personalized preventive strategies to improve risk assessment for more susceptible workers.
Collapse
Affiliation(s)
- Federica Giambò
- Occupational Medicine Section, Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Chiara Costa
- Clinical and Experimental Medicine Department, University of Messina, Messina, Italy
| | - Michele Teodoro
- Occupational Medicine Section, Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Concettina Fenga
- Occupational Medicine Section, Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| |
Collapse
|
29
|
Zheng S, Wang L, Xiong J, Liang G, Xu Y, Lin F. Consensus Prediction of Human Gut Microbiota-Mediated Metabolism Susceptibility for Small Molecules by Machine Learning, Structural Alerts, and Dietary Compounds-Based Average Similarity Methods. J Chem Inf Model 2022; 62:1078-1099. [PMID: 35156807 DOI: 10.1021/acs.jcim.1c00948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The human gut microbiota (HGM) colonizing human gastrointestinal tract (HGT) confers a repertoire of dynamic and unique metabolic capacities that are not possessed by the host and therefore is tentatively perceived as an alternative metabolic ″organ″ besides the liver in the host. Nevertheless, the significant contribution of HGM to the overall human metabolism is often overlooked in the modern drug discovery pipeline. Hence, a systematic evaluation of HGM-mediated drug metabolism is gradually important, and its computational prediction becomes increasingly necessary. In this work, a new data set containing both the HGM-mediated metabolism susceptible (HGMMS) and insusceptible (HGMMI) compounds (329 vs 320) was manually curated. Based on this data set, the first machine learning (ML) model, a new structural alerts (SA) model, and the K-nearest neighboring dietary compounds-based average similarity (AS) model were proposed to directly predict the HGM-mediated metabolism susceptibility for small molecules, and exhibit promising performance on three independent test sets. Finally, consensus prediction (ML/SA/AS) for DrugBank molecules revealed an intriguing phenomenon that a typical Michael acceptor ″α,β-unsaturated carbonyl group″ is a very common warhead for the design of covalent inhibitors and inclined to be metabolized by HGM in anaerobic HGT to generate the reduced metabolite without the reactive warhead, which could be a new concern to medicinal chemists. To the best of our knowledge, we gleaned the first HGMMS/HGMMI data set, developed the first HGMMS/HGMMI classification model, implemented a relatively comprehensive program based on ML/SA/AS approaches, and found a new phenomenon on the HGM-mediated deactivation of an extensively used warhead for covalent inhibitors.
Collapse
Affiliation(s)
- Suqing Zheng
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China.,Chemical Biology Research Center, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China
| | - Lei Wang
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China
| | - Jun Xiong
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China
| | - Guang Liang
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China.,Chemical Biology Research Center, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China
| | - Yong Xu
- Center of Chemical Biology, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, P.R. China
| | - Fu Lin
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China
| |
Collapse
|
30
|
López-Moreno A, Ruiz-Moreno Á, Pardo-Cacho J, Cerk K, Torres-Sánchez A, Ortiz P, Úbeda M, Aguilera M. Culturing and Molecular Approaches for Identifying Microbiota Taxa Impacting Children's Obesogenic Phenotypes Related to Xenobiotic Dietary Exposure. Nutrients 2022; 14:nu14020241. [PMID: 35057422 PMCID: PMC8778816 DOI: 10.3390/nu14020241] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/31/2021] [Accepted: 01/03/2022] [Indexed: 12/11/2022] Open
Abstract
Integrated data from molecular and improved culturomics studies might offer holistic insights on gut microbiome dysbiosis triggered by xenobiotics, such as obesity and metabolic disorders. Bisphenol A (BPA), a dietary xenobiotic obesogen, was chosen for a directed culturing approach using microbiota specimens from 46 children with obesity and normal-weight profiles. In parallel, a complementary molecular analysis was carried out to estimate the BPA metabolising capacities. Firstly, catalogues of 237 BPA directed-cultured microorganisms were isolated using five selected media and several BPA treatments and conditions. Taxa from Firmicutes, Proteobacteria, and Actinobacteria were the most abundant in normal-weight and overweight/obese children, with species belonging to the genera Enterococcus, Escherichia, Staphylococcus, Bacillus, and Clostridium. Secondly, the representative isolated taxa from normal-weight vs. overweight/obese were grouped as BPA biodegrader, tolerant, or resistant bacteria, according to the presence of genes encoding BPA enzymes in their whole genome sequences. Remarkably, the presence of sporobiota and concretely Bacillus spp. showed the higher BPA biodegradation potential in overweight/obese group compared to normal-weight, which could drive a relevant role in obesity and metabolic dysbiosis triggered by these xenobiotics.
Collapse
Affiliation(s)
- Ana López-Moreno
- Department of Microbiology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (J.P.-C.); (K.C.); (A.T.-S.); (P.O.); (M.Ú.)
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, 18016 Granada, Spain
- Microbiota Laboratory, IBS: Instituto de Investigación Biosanitaria ibs, 18012 Granada, Spain
- Correspondence: (A.L.-M.); (M.A.); Tel.: +34-9-5824-5129 (M.A.)
| | - Ángel Ruiz-Moreno
- Department of Microbiology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (J.P.-C.); (K.C.); (A.T.-S.); (P.O.); (M.Ú.)
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, 18016 Granada, Spain
| | - Jesús Pardo-Cacho
- Department of Microbiology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (J.P.-C.); (K.C.); (A.T.-S.); (P.O.); (M.Ú.)
| | - Klara Cerk
- Department of Microbiology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (J.P.-C.); (K.C.); (A.T.-S.); (P.O.); (M.Ú.)
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, 18016 Granada, Spain
| | - Alfonso Torres-Sánchez
- Department of Microbiology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (J.P.-C.); (K.C.); (A.T.-S.); (P.O.); (M.Ú.)
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, 18016 Granada, Spain
| | - Pilar Ortiz
- Department of Microbiology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (J.P.-C.); (K.C.); (A.T.-S.); (P.O.); (M.Ú.)
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, 18016 Granada, Spain
| | - Marina Úbeda
- Department of Microbiology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (J.P.-C.); (K.C.); (A.T.-S.); (P.O.); (M.Ú.)
| | - Margarita Aguilera
- Department of Microbiology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (J.P.-C.); (K.C.); (A.T.-S.); (P.O.); (M.Ú.)
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, 18016 Granada, Spain
- Microbiota Laboratory, IBS: Instituto de Investigación Biosanitaria ibs, 18012 Granada, Spain
- Correspondence: (A.L.-M.); (M.A.); Tel.: +34-9-5824-5129 (M.A.)
| |
Collapse
|
31
|
Ahrodia T, Das S, Bakshi S, Das B. Structure, functions, and diversity of the healthy human microbiome. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 191:53-82. [DOI: 10.1016/bs.pmbts.2022.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
32
|
Dhurjad P, Dhavaliker C, Gupta K, Sonti R. Exploring drug metabolism by the gut microbiota: modes of metabolism and experimental approaches. Drug Metab Dispos 2021; 50:224-234. [PMID: 34969660 DOI: 10.1124/dmd.121.000669] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 09/08/2021] [Indexed: 11/22/2022] Open
Abstract
Increasing evidence uncovers the involvement of gut microbiota in the metabolism of numerous pharmaceutical drugs. The human gut microbiome harbours 10-100 trillion symbiotic gut microbial bacteria that utilize drugs as substrates for enzymatic processes to alter host metabolism. Thus, microbiota-mediated drug metabolism can change the conventional drug action course and cause inter-individual differences in efficacy and toxicity, making it vital for drug discovery and development. This review focuses on drug biotransformation pathways and discusses different models for evaluating gut microbiota role in drug metabolism. Significance Statement This review emphasizes the importance of gut microbiota and different modes of drug metabolism mediated by them. It provides information on in vivo, in vitro, ex vivo, in silico and multi-omics approaches for identifying the role of gut microbiota in the metabolism. Further, it highlights the significance of gut microbiota mediated metabolism in the process of new drug discovery and development as a rationale for safe and efficacious drug therapy.
Collapse
Affiliation(s)
- Pooja Dhurjad
- National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Chinmayi Dhavaliker
- National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Kajal Gupta
- National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Rajesh Sonti
- National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| |
Collapse
|
33
|
Commensal-Related Changes in the Epidermal Barrier Function Lead to Alterations in the Benzo[ a]Pyrene Metabolite Profile and Its Distribution in 3D Skin. mBio 2021; 12:e0122321. [PMID: 34579573 PMCID: PMC8546866 DOI: 10.1128/mbio.01223-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Polycyclic aromatic hydrocarbons (PAH) such as benzo[a]pyrene (B[a]P) are among the most abundant environmental pollutants, resulting in continuous exposure of human skin and its microbiota. However, effects of the latter on B[a]P toxicity, absorption, metabolism, and distribution in humans remain unclear. Here, we demonstrate that the skin microbiota does metabolize B[a]P on and in human skin in situ, using a recently developed commensal skin model. In this model, microbial metabolism leads to high concentrations of known microbial B[a]P metabolites on the surface as well as in the epidermal layers. In contrast to what was observed for uncolonized skin, B[a]P and its metabolites were subject to altered rates of skin penetration and diffusion, resulting in up to 58% reduction of metabolites recovered from basal culture medium. The results indicate the reason for this altered behavior to be a microbially induced strengthening of the epidermal barrier. Concomitantly, colonized models showed decreased formation and penetration of the ultimate carcinogen B[a]P-7,8-dihydrodiol-9,10-epoxide (BPDE), leading, in consequence, to fewer BPDE-DNA adducts being formed. Befittingly, transcript and expression levels of key proteins for repairing environmentally induced DNA damage such as xeroderma pigmentosum complementation group C (XPC) were also found to be reduced in the commensal models, as was expression of B[a]P-associated cytochrome P450-dependent monooxygenases (CYPs). The results show that the microbiome can have significant effects on the toxicology of external chemical impacts. The respective effects rely on a complex interplay between microbial and host metabolism and microbe-host interactions, all of which cannot be adequately assessed using single-system studies.
Collapse
|
34
|
Zahran SA, Ali-Tammam M, Ali AE, Aziz RK. Compositional variation of the human fecal microbiome in relation to azo-reducing activity: a pilot study. Gut Pathog 2021; 13:58. [PMID: 34625106 PMCID: PMC8499468 DOI: 10.1186/s13099-021-00454-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/23/2021] [Indexed: 12/01/2022] Open
Abstract
Background Through an arsenal of microbial enzymes, the gut microbiota considerably contributes to human metabolic processes, affecting nutrients, drugs, and environmental poisons. Azoreductases are a predominant group of microbiota-derived enzymes involved in xenobiotic metabolism and drug activation, but little is known about how compositional changes in the gut microbiota correlate with its azo-reducing activity. Results To this end, we used high-throughput 16S rRNA amplicon sequencing, with Illumina MiSeq, to determine the microbial community composition of stool samples from 16 adults with different azo-reducing activity. High azo-reducing activity positively
correlated with the relative abundance of phylum Firmicutes (especially genera Streptococcus and Coprococcus) but negatively with phylum Bacteroidetes (especially genus Bacteroides). Typical variations in the Firmicutes-to-Bacteroidetes and Prevotella-to-Bacteroides ratios were observed among samples. Multivariate analysis of the relative abundance of key microbial taxa and other diversity parameters confirmed the Firmicutes proportion as a major variable differentiating high and non-azo-reducers, while Bacteroidetes relative abundance was correlated with azo-reduction, sex, and BMI. Conclusions This pilot study showed that stool samples with higher azo-reducing activity were enriched in Firmicutes but with relatively fewer Bacteroidetes. More samples and studies from different geographical areas are needed to bolster this conclusion. Better characterization of different azoreductase-producing gut microbes will increase our knowledge about the fate and differential human responses to azodye-containing drugs or orally consumed chemicals, thus contributing to efforts towards implementing microbiome testing in precision medicine and toxicology. Supplementary Information The online version contains supplementary material available at 10.1186/s13099-021-00454-0.
Collapse
Affiliation(s)
- Sara A Zahran
- Department of Microbiology and Immunology, Faculty of Pharmacy, Future University in Egypt, New Cairo, 11835, Egypt
| | - Marwa Ali-Tammam
- Department of Microbiology and Immunology, Faculty of Pharmacy, Future University in Egypt, New Cairo, 11835, Egypt
| | - Amal E Ali
- Department of Microbiology and Immunology, Faculty of Pharmacy, Future University in Egypt, New Cairo, 11835, Egypt
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt. .,The Center for Genome and Microbiome Research, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt. .,Microbiology and Immunology Research Program, Children's Cancer Hospital Egypt 57357, Cairo, 11617, Egypt.
| |
Collapse
|
35
|
Food-grade lactic acid bacteria and probiotics as a potential protective tool against erythrotoxic dietary xenobiotics. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
36
|
Ma Y, Liu H, Du X, Shi Z, Liu X, Wang R, Zhang S, Tian Z, Shi L, Guo H, Zhang H. Advances in the toxicology research of microcystins based on Omics approaches. ENVIRONMENT INTERNATIONAL 2021; 154:106661. [PMID: 34077854 DOI: 10.1016/j.envint.2021.106661] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 06/12/2023]
Abstract
Microcystins (MCs) are the most widely distributed cyanotoxins, which can be ingested by animals and human body in multiple ways, resulting in a threat to human health and the biodiversity of wildlife. Therefore, the study on toxic effects and mechanisms of MCs is one of the focuses of attention. Recently, the Omics techniques, i.e. genomics, transcriptomics, proteomics and metabolomics, have significantly contributed to the comprehensive understanding and revealing of the molecular mechanisms about the toxicity of MCs. This paper mainly reviews current literature using the Omics approaches to explore the toxicity mechanism of MCs in liver, gonad, spleen, brain, intestine and lung of multiple species. It was found that MCs can exert strong toxic effects on various metabolic activities and cell signal transduction in cell cycle, apoptosis, destruction of cell cytoskeleton and redox disorder, at protein, transcription and metabolism level. Meanwhile, it was also revealed that the alteration of non-coding RNAs (miRNA, circRNA and lncRNA, etc.) and gut microbiota plays an essential regulatory role in the toxic effects of MCs, especially in hepatotoxicity and reproductive toxicity. In addition, we summarized current research gaps and pointed out the future directions for research. The detailed information in this paper shows that the application and development of Omics techniques have significantly promoted the research on MCs toxicity, and it is also a valuable resource for exploring the toxic mechanism of MCs.
Collapse
Affiliation(s)
- Ya Ma
- College of Public Health, Zhengzhou University, Zhengzhou, PR China
| | - Haohao Liu
- College of Public Health, Zhengzhou University, Zhengzhou, PR China
| | - Xingde Du
- College of Public Health, Zhengzhou University, Zhengzhou, PR China
| | - Ziang Shi
- Department of Clinical Medicine, Zhengzhou University, Zhengzhou, PR China
| | - Xiaohui Liu
- School of Basic Medical Sciences, Henan University of Chinese Medicine, Zhengzhou 450046, PR China
| | - Rui Wang
- College of Public Health, Zhengzhou University, Zhengzhou, PR China
| | - Shiyu Zhang
- College of Public Health, Zhengzhou University, Zhengzhou, PR China
| | - Zhihui Tian
- College of Public Health, Zhengzhou University, Zhengzhou, PR China
| | - Linjia Shi
- College of Public Health, Zhengzhou University, Zhengzhou, PR China
| | - Hongxiang Guo
- College of Life Sciences, Henan Agricultural University, Zhengzhou, PR China
| | - Huizhen Zhang
- College of Public Health, Zhengzhou University, Zhengzhou, PR China.
| |
Collapse
|
37
|
Kim HM, Kang JS. Metabolomic Studies for the Evaluation of Toxicity Induced by Environmental Toxicants on Model Organisms. Metabolites 2021; 11:485. [PMID: 34436425 PMCID: PMC8402193 DOI: 10.3390/metabo11080485] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 12/11/2022] Open
Abstract
Environmental pollution causes significant toxicity to ecosystems. Thus, acquiring a deeper understanding of the concentration of environmental pollutants in ecosystems and, clarifying their potential toxicities is of great significance. Environmental metabolomics is a powerful technique in investigating the effects of pollutants on living organisms in the environment. In this review, we cover the different aspects of the environmental metabolomics approach, which allows the acquisition of reliable data. A step-by-step procedure from sample preparation to data interpretation is also discussed. Additionally, other factors, including model organisms and various types of emerging environmental toxicants are discussed. Moreover, we cover the considerations for successful environmental metabolomics as well as the identification of toxic effects based on data interpretation in combination with phenotype assays. Finally, the effects induced by various types of environmental toxicants in model organisms based on the application of environmental metabolomics are also discussed.
Collapse
Affiliation(s)
- Hyung Min Kim
- College of Pharmacy, Chungnam National University, Daejeon 34134, Korea
| | - Jong Seong Kang
- College of Pharmacy, Chungnam National University, Daejeon 34134, Korea
| |
Collapse
|
38
|
Fournier E, Roussel C, Dominicis A, Ley D, Peyron MA, Collado V, Mercier-Bonin M, Lacroix C, Alric M, Van de Wiele T, Chassard C, Etienne-Mesmin L, Blanquet-Diot S. In vitro models of gut digestion across childhood: current developments, challenges and future trends. Biotechnol Adv 2021; 54:107796. [PMID: 34252564 DOI: 10.1016/j.biotechadv.2021.107796] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 02/08/2023]
Abstract
The human digestion is a multi-step and multi-compartment process essential for human health, at the heart of many issues raised by academics, the medical world and industrials from the food, nutrition and pharma fields. In the first years of life, major dietary changes occur and are concomitant with an evolution of the whole child digestive tract anatomy and physiology, including colonization of gut microbiota. All these phenomena are influenced by child exposure to environmental compounds, such as drugs (especially antibiotics) and food pollutants, but also childhood infections. Due to obvious ethical, regulatory and technical limitations, in vivo approaches in animal and human are more and more restricted to favor complementary in vitro approaches. This review summarizes current knowledge on the evolution of child gut physiology from birth to 3 years old regarding physicochemical, mechanical and microbial parameters. Then, all the available in vitro models of the child digestive tract are described, ranging from the simplest static mono-compartmental systems to the most sophisticated dynamic and multi-compartmental models, and mimicking from the oral phase to the colon compartment. Lastly, we detail the main applications of child gut models in nutritional, pharmaceutical and microbiological studies and discuss the limitations and challenges facing this field of research.
Collapse
Affiliation(s)
- Elora Fournier
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, Microbiologie Environnement Digestif et Santé, CRNH Auvergne, 63000 Clermont-Ferrand, France; Toxalim, Research Centre in Food Toxicology, INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, 31000 Toulouse, France
| | - Charlène Roussel
- Laval University, INAF Institute of Nutrition and Functional Foods, G1V 0A6 Quebec, Canada
| | - Alessandra Dominicis
- European Reference Laboratory for E. coli, Istituto Superiore di Sanità, Rome, Italy
| | - Delphine Ley
- Université Lille 2, Faculté de Médecine, Inserm U995 Nutritional Modulation of Infection and Inflammation, 59045 Lille, France
| | - Marie-Agnès Peyron
- Université Clermont Auvergne, INRAE, UNH, Unité de Nutrition Humaine, CRNH Auvergne, 63000 Clermont-Ferrand, France
| | - Valérie Collado
- Université Clermont Auvergne, EA 4847, CROC, Centre de Recherche en Odontologie Clinique, 63000 Clermont-Ferrand, France
| | - Muriel Mercier-Bonin
- Toxalim, Research Centre in Food Toxicology, INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, 31000 Toulouse, France
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zürich, Switzerland
| | - Monique Alric
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, Microbiologie Environnement Digestif et Santé, CRNH Auvergne, 63000 Clermont-Ferrand, France
| | - Tom Van de Wiele
- Ghent University, Center for Microbial Ecology and Technology (CMET), Coupure Links 653, 9000 Ghent, Belgium
| | - Christophe Chassard
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMRF, 15000 Aurillac, France
| | - Lucie Etienne-Mesmin
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, Microbiologie Environnement Digestif et Santé, CRNH Auvergne, 63000 Clermont-Ferrand, France
| | - Stéphanie Blanquet-Diot
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, Microbiologie Environnement Digestif et Santé, CRNH Auvergne, 63000 Clermont-Ferrand, France.
| |
Collapse
|
39
|
Ahn J, Hayes RB. Environmental Influences on the Human Microbiome and Implications for Noncommunicable Disease. Annu Rev Public Health 2021; 42:277-292. [PMID: 33798404 DOI: 10.1146/annurev-publhealth-012420-105020] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The human microbiome contributes metabolic functions, protects against pathogens, educates the immune system, and through these basic functions, directly or indirectly, affects most of our physiologic functions. Here, we consider the human microbiome and its relationship to several major noncommunicable human conditions, including orodigestive tract cancers, neurologic diseases, diabetes, and obesity. We also highlight the scope of contextual macroenvironmental factors (toxicological and chemical environment, built environment, and socioeconomic environment) and individual microenvironmental factors (smoking, alcohol, and diet) that may push the microbiota toward less healthy or more healthy conditions, influencing the development of these diseases. Last, we highlight current uncertainties and challenges in the study of environmental influences on the human microbiome and implications for understanding noncommunicable disease, suggesting a research agenda to strengthen the scientific evidence base.
Collapse
Affiliation(s)
- Jiyoung Ahn
- Department of Population Health, Grossman School of Medicine, New York University, New York, NY 10016, USA.,Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA; ,
| | - Richard B Hayes
- Department of Population Health, Grossman School of Medicine, New York University, New York, NY 10016, USA.,Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA; ,
| |
Collapse
|
40
|
van den Bogaard EH, Esser C, Perdew GH. The aryl hydrocarbon receptor at the forefront of host-microbe interactions in the skin: A perspective on current knowledge gaps and directions for future research and therapeutic applications. Exp Dermatol 2021; 30:1477-1483. [PMID: 34105853 PMCID: PMC8518783 DOI: 10.1111/exd.14409] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/11/2021] [Accepted: 05/22/2021] [Indexed: 02/06/2023]
Abstract
The skin is home to a community of skin microbiota including bacteria, viruses and fungi, which are widely accepted to be of importance for skin homeostasis but also associated with skin diseases. Detailed knowledge on the skin microbiota composition and its changes in a number of skin diseases is available. Yet, specific interactions between microbes and the host skin cells or how they communicate with each other are less well understood. To identify, understand and eventually therapeutically exploit causal relationships of microbial dysbiosis with disease, studies are required that address the receptors and mediators involved in host‐microbe interactions. In this perspective article, we provide an outlook on one of such receptors, namely the aryl hydrocarbon receptor (AHR). The AHR is well known for being a ligand‐activated transcription factor regulating the proliferation, differentiation and function of many cell types present in the skin. Its targeting by anti‐inflammatory therapeutics such as coal tar and Tapinarof is effective in atopic dermatitis and psoriasis. AHR signalling is activated upon binding of wide variety of small chemicals or ligands, including microbiota‐derived metabolites. New evidence has emerged pointing towards a key role for epidermal AHR signalling through skin microbiota‐derived metabolites. In response, AHR‐driven expression of antimicrobial peptides and stratum corneum formation may alter the skin microbiota composition. This a self‐perpetuating feedback loop calls for novel therapeutic intervention strategies for which we herein discuss the requirements in future mechanistic studies.
Collapse
Affiliation(s)
- Ellen H van den Bogaard
- Department of Dermatology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Charlotte Esser
- IUF-Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Gary H Perdew
- Department of Veterinary and Biomedical Sciences, Center for Molecular Toxicology and Carcinogenesis, The Pennsylvania State University, University Park, PA, USA
| |
Collapse
|
41
|
López-Moreno A, Acuña I, Torres-Sánchez A, Ruiz-Moreno Á, Cerk K, Rivas A, Suárez A, Monteoliva-Sánchez M, Aguilera M. Next Generation Probiotics for Neutralizing Obesogenic Effects: Taxa Culturing Searching Strategies. Nutrients 2021; 13:1617. [PMID: 34065873 PMCID: PMC8151043 DOI: 10.3390/nu13051617] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/06/2021] [Accepted: 05/08/2021] [Indexed: 12/12/2022] Open
Abstract
The combination of diet, lifestyle, and the exposure to food obesogens categorized into "microbiota disrupting chemicals" (MDC) could determine obesogenic-related dysbiosis and modify the microbiota diversity that impacts on individual health-disease balances, inducing altered pathogenesis phenotypes. Specific, complementary, and combined treatments are needed to face these altered microbial patterns and the specific misbalances triggered. In this sense, searching for next-generation beneficial microbes or next-generation probiotics (NGP) by microbiota culturing, and focusing on their demonstrated, extensive scope and well-defined functions could contribute to counteracting and repairing the effects of obesogens. Therefore, this review presents a perspective through compiling information and key strategies for directed searching and culturing of NGP that could be administered for obesity and endocrine-related dysbiosis by (i) observing the differential abundance of specific microbiota taxa in obesity-related patients and analyzing their functional roles, (ii) developing microbiota-directed strategies for culturing these taxa groups, and (iii) applying the successful compiled criteria from recent NGP clinical studies. New isolated or cultivable microorganisms from healthy gut microbiota specifically related to obesogens' neutralization effects might be used as an NGP single strain or in consortia, both presenting functions and the ability to palliate metabolic-related disorders. Identification of holistic approaches for searching and using potential NGP, key aspects, the bias, gaps, and proposals of solutions are also considered in this review.
Collapse
Affiliation(s)
- Ana López-Moreno
- Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (K.C.); (M.M.-S.)
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, Armilla, 18016 Granada, Spain; (I.A.); (A.S.)
| | - Inmaculada Acuña
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, Armilla, 18016 Granada, Spain; (I.A.); (A.S.)
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain
| | - Alfonso Torres-Sánchez
- Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (K.C.); (M.M.-S.)
| | - Ángel Ruiz-Moreno
- Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (K.C.); (M.M.-S.)
| | - Klara Cerk
- Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (K.C.); (M.M.-S.)
| | - Ana Rivas
- IBS, Instituto de Investigación Biosanitaria, 18012 Granada, Spain;
- Department of Nutrition and Food Science, Campus of Cartuja, University of Granada, 18071 Granada, Spain
| | - Antonio Suárez
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, Armilla, 18016 Granada, Spain; (I.A.); (A.S.)
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain
| | - Mercedes Monteoliva-Sánchez
- Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (K.C.); (M.M.-S.)
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, Armilla, 18016 Granada, Spain; (I.A.); (A.S.)
| | - Margarita Aguilera
- Department of Microbiology, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain; (Á.R.-M.); (K.C.); (M.M.-S.)
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, Armilla, 18016 Granada, Spain; (I.A.); (A.S.)
- IBS, Instituto de Investigación Biosanitaria, 18012 Granada, Spain;
| |
Collapse
|
42
|
Effect of Gut Microbiota Biotransformation on Dietary Tannins and Human Health Implications. Microorganisms 2021; 9:microorganisms9050965. [PMID: 33947064 PMCID: PMC8145700 DOI: 10.3390/microorganisms9050965] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/25/2021] [Accepted: 04/27/2021] [Indexed: 12/17/2022] Open
Abstract
Tannins represent a heterogeneous group of high-molecular-weight polyphenols that are ubiquitous among plant families, especially in cereals, as well as in many fruits and vegetables. Hydrolysable and condensed tannins, in addition to phlorotannins from marine algae, are the main classes of these bioactive compounds. Despite their low bioavailability, tannins have many beneficial pharmacological effects, such as anti-inflammatory, antioxidant, antidiabetic, anticancer, and cardioprotective effects. Microbiota-mediated hydrolysis of tannins produces highly bioaccessible metabolites, which have been extensively studied and account for most of the health effects attributed to tannins. This review article summarises the effect of the human microbiota on the metabolism of different tannin groups and the expected health benefits that may be induced by such mutual interactions. Microbial metabolism of tannins yields highly bioaccessible microbial metabolites that account for most of the systemic effects of tannins. This article also uses explainable artificial intelligence to define the molecular signatures of gut-biotransformed tannin metabolites that are correlated with chemical and biological activity. An understanding of microbiota–tannin interactions, tannin metabolism-related phenotypes (metabotypes) and chemical tannin-metabolites motifs is of great importance for harnessing the biological effects of tannins for drug discovery and other health benefits.
Collapse
|
43
|
Bland JS. Why the Pegan Diet Makes Sense. Integr Med (Encinitas) 2021; 20:16-19. [PMID: 34373678 PMCID: PMC8325496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In 1985, S. Boyd Eaton and Melvin Konner published a landmark paper in the New England Journal of Medicine. The title was "Paleolithic Nutrition: A Consideration of Its Nature and Current Implications," and this work postulated that an increase in the prevalence of chronic disease among modern humans is the result of a dietary composition that is incompatible with both our genetic ancestry and natural metabolic function. Over the intervening decades, numerous theories about optimal dietary approaches have been put forth and much debate has ensued. Among researchers and the public, we have witnessed vocal advocates emerge in support of the paleolithic philosophy of encouraging mild ketosis, while others passionately argue for plant-based vegetarianism. There is now evidence that neither extreme provides superior health benefits in isolation. According to numerous clinical studies, a hybrid approach may convey a positive and multifactorial influence on the intestinal microbiome, the metabolome, proteomics, and overall health outcomes. A Mediterranean-style diet has been widely studied, and a new concept-Pegan, which is a contraction of the words paleo and vegan-is now gaining worldwide attention.
Collapse
|
44
|
Calatayud Arroyo M, García Barrera T, Callejón Leblic B, Arias Borrego A, Collado MC. A review of the impact of xenobiotics from dietary sources on infant health: Early life exposures and the role of the microbiota. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 269:115994. [PMID: 33310490 DOI: 10.1016/j.envpol.2020.115994] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 09/22/2020] [Accepted: 11/02/2020] [Indexed: 06/12/2023]
Abstract
Xenobiotics are worldwide distributed and humans are unavoidably exposed to multiple chemical compounds during life, from preconception to adulthood. The human microbiota is mainly settled during early life and modulate host health and fitness. One of the main routes for chemical exposure is by intake of contaminated food and water. Thus, the interplay between diet-xenobiotics-microbiota during pregnancy and perinatal period may have relevant consequences for infant and adult health. Maternal exposure to metal(oid)s, persistent organic pollutants, and some food additives can modify the infant's microbiota with unknown consequences for child or adult health. Toxicants' exposure may also modulate the maternal transfer of microorganisms to the progeny during birth and breastfeeding; however, scarce information is available. The rapid increase in releasing novel chemicals to the environment, the exposure to chemical mixtures, the chronic/low dose scenario, and the delay in science-stakeholders action call for novel and groundbreaking approaches to improve a comprehensive risk assessment in sensitive population groups like pregnant women and neonates, with emphasis on microbiota as modulating factor and target-organ of xenobiotic's toxicity.
Collapse
Affiliation(s)
- M Calatayud Arroyo
- Department of Biotechnology, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Agustin Escardino 7, Paterna, Valencia, 46980, Spain.
| | - T García Barrera
- Research Center on Natural Resources, Health and the Environment (RENSMA), Department of Chemistry "Prof. J.C. Vílchez Martín", University of Huelva, Fuerzas Armadas Ave., Huelva, 21120, Spain
| | - B Callejón Leblic
- Research Center on Natural Resources, Health and the Environment (RENSMA), Department of Chemistry "Prof. J.C. Vílchez Martín", University of Huelva, Fuerzas Armadas Ave., Huelva, 21120, Spain
| | - A Arias Borrego
- Research Center on Natural Resources, Health and the Environment (RENSMA), Department of Chemistry "Prof. J.C. Vílchez Martín", University of Huelva, Fuerzas Armadas Ave., Huelva, 21120, Spain
| | - M C Collado
- Department of Biotechnology, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Agustin Escardino 7, Paterna, Valencia, 46980, Spain.
| |
Collapse
|
45
|
Abstract
The field of pharmacogenetic testing was hailed as one of the early successful clinical applications arising from the personalized (or precision) medicine revolution. Substantial progress has been made to identify genes and genetic variants involved in drug response and establish clinical implementation programs. Yet, drug response is a complex trait and recent work has highlighted the key role played by the gut microbiome. As the study of the gut microbiome and pharmacogenetics converge, it may be possible to generate more precise predictions of drug response and improve health outcomes to treatments. Substantial effort will be needed to understand the dynamic impact of the microbiome and the interplay with host genetics and how to implement expanded pharmacogenetic testing.
Collapse
Affiliation(s)
- Susanne B Haga
- Center for Applied Genomics & Precision Medicine, Duke University School of Medicine, 101 Science Drive, Box 3382, Durham, NC 27708, USA
| |
Collapse
|