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Ratheesh A, Shibli SMA. Biochar supported Pseudomonas putida based globules for effective removal of Bisphenol A with a practical approach. CHEMOSPHERE 2024; 361:142496. [PMID: 38825245 DOI: 10.1016/j.chemosphere.2024.142496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 05/21/2024] [Accepted: 05/30/2024] [Indexed: 06/04/2024]
Abstract
The widespread and inevitable use of plastic has led to prospective ecological problems through Bisphenol A (BPA), a synthetic chemical in plastic manufacturing. The present study addresses a unique methodology for eliminating BPA using the assistance of Pseudomonas putida. In the present work, biomass was torrefied to generate biochar with highly porous networks that could accommodate the bacterial species for effective colonization and multiplication. The designed biochar-bacterial globules demonstrated the ability to effectively remove BPA (96.88%) at a concentration of up to 2 g/L. The biochar-bacterial globules could effectively adsorb BPA at a low concentration of 20 mg/L. The alteration in pH did not impact the globule's performance, providing additional support for the practical utilization of these globules in polluted water bodies. In addition, the biochar-bacterial globules exhibited superior effectiveness in degradation compared to the standard levels, particularly in saline conditions. The simplicity and effectiveness of the approach make it promising for real-world implementation in addressing ecological problems associated with BPA contamination.
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Affiliation(s)
- Anjana Ratheesh
- Department of Biotechnology, University of Kerala, Kariavattom Campus, Thiruvananthapuram, Kerala, 695 581, India
| | - S M A Shibli
- Department of Chemistry, University of Kerala, Kariavattom Campus, Thiruvananthapuram, Kerala, 695 581, India; Centre for Renewable Energy and Materials, University of Kerala, Kariavattom Campus, Thiruvananthapuram, Kerala, 695 581, India.
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2
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Zampolli J, De Giani A, Rossi M, Finazzi M, Di Gennaro P. Who inhabits the built environment? A microbiological point of view on the principal bacteria colonizing our urban areas. Front Microbiol 2024; 15:1380953. [PMID: 38863750 PMCID: PMC11165352 DOI: 10.3389/fmicb.2024.1380953] [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: 02/02/2024] [Accepted: 05/09/2024] [Indexed: 06/13/2024] Open
Abstract
Modern lifestyle greatly influences human well-being. Indeed, nowadays people are centered in the cities and this trend is growing with the ever-increasing population. The main habitat for modern humans is defined as the built environment (BE). The modulation of life quality in the BE is primarily mediated by a biodiversity of microbes. They derive from different sources, such as soil, water, air, pets, and humans. Humans are the main source and vector of bacterial diversity in the BE leaving a characteristic microbial fingerprint on the surfaces and spaces. This review, focusing on articles published from the early 2000s, delves into bacterial populations present in indoor and outdoor urban environments, exploring the characteristics of primary bacterial niches in the BE and their native habitats. It elucidates bacterial interconnections within this context and among themselves, shedding light on pathways for adaptation and survival across diverse environmental conditions. Given the limitations of culture-based methods, emphasis is placed on culture-independent approaches, particularly high-throughput techniques to elucidate the genetic and -omic features of BE bacteria. By elucidating these microbiota profiles, the review aims to contribute to understanding the implications for human health and the assessment of urban environmental quality in modern cities.
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Affiliation(s)
| | | | | | | | - Patrizia Di Gennaro
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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3
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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.
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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.
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4
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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.
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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.
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Rio P, Gasbarrini A, Gambassi G, Cianci R. Pollutants, microbiota and immune system: frenemies within the gut. Front Public Health 2024; 12:1285186. [PMID: 38799688 PMCID: PMC11116734 DOI: 10.3389/fpubh.2024.1285186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 04/24/2024] [Indexed: 05/29/2024] Open
Abstract
Pollution is a critical concern of modern society for its heterogeneous effects on human health, despite a widespread lack of awareness. Environmental pollutants promote several pathologies through different molecular mechanisms. Pollutants can affect the immune system and related pathways, perturbing its regulation and triggering pro-inflammatory responses. The exposure to several pollutants also leads to alterations in gut microbiota with a decreasing abundance of beneficial microbes, such as short-chain fatty acid-producing bacteria, and an overgrowth of pro-inflammatory species. The subsequent intestinal barrier dysfunction, together with oxidative stress and increased inflammatory responses, plays a role in the pathogenesis of gastrointestinal inflammatory diseases. Moreover, pollutants encourage the inflammation-dysplasia-carcinoma sequence through various mechanisms, such as oxidative stress, dysregulation of cellular signalling pathways, cell cycle impairment and genomic instability. In this narrative review, we will describe the interplay between pollutants, gut microbiota, and the immune system, focusing on their relationship with inflammatory bowel diseases and colorectal cancer. Understanding the biological mechanisms underlying the health-to-disease transition may allow the design of public health policies aimed at reducing the burden of disease related to pollutants.
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Affiliation(s)
| | | | | | - Rossella Cianci
- Department of Translational Medicine and Surgery, Catholic University of Sacred Heart, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
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6
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Huang C, Li X, Li H, Chen R, Li Z, Li D, Xu X, Zhang G, Qin L, Li B, Chu XM. Role of gut microbiota in doxorubicin-induced cardiotoxicity: from pathogenesis to related interventions. J Transl Med 2024; 22:433. [PMID: 38720361 PMCID: PMC11077873 DOI: 10.1186/s12967-024-05232-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
Doxorubicin (DOX) is a broad-spectrum and highly efficient anticancer agent, but its clinical implication is limited by lethal cardiotoxicity. Growing evidences have shown that alterations in intestinal microbial composition and function, namely dysbiosis, are closely linked to the progression of DOX-induced cardiotoxicity (DIC) through regulating the gut-microbiota-heart (GMH) axis. The role of gut microbiota and its metabolites in DIC, however, is largely unelucidated. Our review will focus on the potential mechanism between gut microbiota dysbiosis and DIC, so as to provide novel insights into the pathophysiology of DIC. Furthermore, we summarize the underlying interventions of microbial-targeted therapeutics in DIC, encompassing dietary interventions, fecal microbiota transplantation (FMT), probiotics, antibiotics, and natural phytochemicals. Given the emergence of microbial investigation in DIC, finally we aim to point out a novel direction for future research and clinical intervention of DIC, which may be helpful for the DIC patients.
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Affiliation(s)
- Chao Huang
- Department of Cardiology, The Affiliated Hospital of Qingdao University, No. 59 Haier Road, Qingdao, Shandong, 266100, China
| | - Xiaoxia Li
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, No. 308 Ningxia Road, Qingdao, Shandong, 266000, China
| | - Hanqing Li
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, No. 16 Jiangsu Road, Qingdao, 266000, China
| | - Ruolan Chen
- Department of Cardiology, The Affiliated Hospital of Qingdao University, No. 59 Haier Road, Qingdao, Shandong, 266100, China
| | - Zhaoqing Li
- Department of Cardiology, The Affiliated Hospital of Qingdao University, No. 59 Haier Road, Qingdao, Shandong, 266100, China
| | - Daisong Li
- Department of Cardiology, The Affiliated Hospital of Qingdao University, No. 59 Haier Road, Qingdao, Shandong, 266100, China
| | - Xiaojian Xu
- Department of Cardiology, The Affiliated Hospital of Qingdao University, No. 59 Haier Road, Qingdao, Shandong, 266100, China
| | - Guoliang Zhang
- Department of Cardiology, The Affiliated Hospital of Qingdao University, No. 59 Haier Road, Qingdao, Shandong, 266100, China
| | - Luning Qin
- Department of Cardiology, The Affiliated Hospital of Qingdao University, No. 59 Haier Road, Qingdao, Shandong, 266100, China
| | - Bing Li
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, No. 308 Ningxia Road, Qingdao, Shandong, 266000, China.
- Department of Dermatology, The Affiliated Haici Hospital of Qingdao University, Qingdao, 266033, China.
| | - Xian-Ming Chu
- Department of Cardiology, The Affiliated Hospital of Qingdao University, No. 59 Haier Road, Qingdao, Shandong, 266100, China.
- The Affiliated Cardiovascular Hospital of Qingdao University, No. 5 Zhiquan Road, Qingdao, 266071, China.
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7
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Guo J, Zhao Y, Kang SG, Huang K, Tong T. Differential effects of four laboratory animal control diets on gut microbiota in mice. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:4438-4452. [PMID: 38323712 DOI: 10.1002/jsfa.13331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 01/16/2024] [Accepted: 01/23/2024] [Indexed: 02/08/2024]
Abstract
BACKGROUND The gut microbiota is intricate and susceptible to multiple factors, with diet being a major contributor. The present study aimed to investigate the impact of four commonly used laboratory animal control diets, namely Keao Xieli's maintenance diet (KX), HFK's 1025 (HF), Research Diets' D12450B (RD), and Lab Diet's 5CC4 (LD), on the gut microbiota of mice. RESULTS A total of 40 mice were randomly assigned to four groups, and each group was fed one of the four diets for a duration of 8 weeks. The assessment of gut microbiota was conducted using 16S rRNA sequencing both at the beginning of the study (week 0) and the end (week 8), which served as the baseline and endpoint samples, respectively. Following the 8-week feeding period, no significant differences were observed in physiological parameters, including body weight, visceral weight, and blood biochemical indices, across the four groups. Nonetheless, relative to the baseline, discernible alterations in the gut microbiota were observed in all groups, encompassing shifts in beta-diversity, hierarchical clustering, and key genera. Among the four diets, HF diet exhibited a significant influence on alpha-diversity, RD diet brought about notable changes in microbial composition at the phylum level, and LD diet demonstrated an interconnected co-occurrence network. Mantel analysis indicated no significant correlation between physiological parameters and gut microbiota in the four groups. CONCLUSION Overall, our study demonstrated that the four control diets had a minimal impact on physiological parameters, while exerting a distinct influence on the gut microbiota after 8 weeks. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Jingya Guo
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, P. R. China
| | - Yuhan Zhao
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, P. R. China
| | - Seong-Gook Kang
- Department of Food Engineering and Solar Salt Research Center, Mokpo National University, Muangun, Republic of Korea
| | - Kunlun Huang
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, P. R. China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing, P. R. China
- Beijing Laboratory for Food Quality and Safety, Beijing, P. R. China
| | - Tao Tong
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, P. R. China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing, P. R. China
- Beijing Laboratory for Food Quality and Safety, Beijing, P. R. China
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8
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Li B, Zhang B, Zhang F, Liu X, Zhang Y, Peng W, Teng D, Mao R, Yang N, Hao Y, Wang J. Interaction between Dietary Lactoferrin and Gut Microbiota in Host Health. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:7596-7606. [PMID: 38557058 DOI: 10.1021/acs.jafc.3c09050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The gut microbiota are known to play an important role in host health and disease. Alterations in the gut microbiota composition can disrupt the stability of the gut ecosystem, which may result in noncommunicable chronic diseases (NCCDs). Remodeling the gut microbiota through personalized nutrition is a novel therapeutic avenue for both disease control and prevention. However, whether there are commonly used gut microbiota-targeted diets and how gut microbiota-diet interactions combat NCCDs and improve health remain questions to be addressed. Lactoferrin (LF), which is broadly used in dietary supplements, acts not only as an antimicrobial in the defense against enteropathogenic bacteria but also as a prebiotic to propagate certain probiotics. Thus, LF-induced gut microbiota alterations can be harnessed to induce changes in host physiology, and the underpinnings of their relationships and mechanisms are beginning to unravel in studies involving humans and animal models.
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Affiliation(s)
- Bing Li
- Institute of Translational Medicine, College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou 466001, Henan, PR China
| | - Bo Zhang
- International Joint Research Laboratory for Biomedical Nanomaterials of Henan, Zhoukou Normal University, Zhoukou 466001, Henan, PR China
| | - Fuli Zhang
- Institute of Translational Medicine, College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou 466001, Henan, PR China
| | - Xiaomeng Liu
- Institute of Translational Medicine, College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou 466001, Henan, PR China
| | - Yunxia Zhang
- Institute of Translational Medicine, College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou 466001, Henan, PR China
| | - Weifeng Peng
- Institute of Translational Medicine, College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou 466001, Henan, PR China
| | - Da Teng
- Gene Engineering Lab, Feed Research Institute, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, P. R. China
| | - Ruoyu Mao
- Gene Engineering Lab, Feed Research Institute, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, P. R. China
| | - Na Yang
- Gene Engineering Lab, Feed Research Institute, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, P. R. China
| | - Ya Hao
- Gene Engineering Lab, Feed Research Institute, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, P. R. China
| | - Jianhua Wang
- Gene Engineering Lab, Feed Research Institute, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, P. R. China
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9
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Boston RH, Guan R, Kalmar L, Beier S, Horner EC, Beristain-Covarrubias N, Yam-Puc JC, Pereyra Gerber P, Faria L, Kuroshchenkova A, Lindell AE, Blasche S, Correa-Noguera A, Elmer A, Saunders C, Bermperi A, Jose S, Kingston N, Grigoriadou S, Staples E, Buckland MS, Lear S, Matheson NJ, Benes V, Parkinson C, Thaventhiran JE, Patil KR. Stability of gut microbiome after COVID-19 vaccination in healthy and immuno-compromised individuals. Life Sci Alliance 2024; 7:e202302529. [PMID: 38316462 PMCID: PMC10844540 DOI: 10.26508/lsa.202302529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 02/07/2024] Open
Abstract
Bidirectional interactions between the immune system and the gut microbiota are key contributors to various physiological functions. Immune-associated diseases such as cancer and autoimmunity, and efficacy of immunomodulatory therapies, have been linked to microbiome variation. Although COVID-19 infection has been shown to cause microbial dysbiosis, it remains understudied whether the inflammatory response associated with vaccination also impacts the microbiota. Here, we investigate the temporal impact of COVID-19 vaccination on the gut microbiome in healthy and immuno-compromised individuals; the latter included patients with primary immunodeficiency and cancer patients on immunomodulating therapies. We find that the gut microbiome remained remarkably stable post-vaccination irrespective of diverse immune status, vaccine response, and microbial composition spanned by the cohort. The stability is evident at all evaluated levels including diversity, phylum, species, and functional capacity. Our results indicate the resilience of the gut microbiome to host immune changes triggered by COVID-19 vaccination and suggest minimal, if any, impact on microbiome-mediated processes. These findings encourage vaccine acceptance, particularly when contrasted with the significant microbiome shifts observed during COVID-19 infection.
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Affiliation(s)
- Rebecca H Boston
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Rui Guan
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Lajos Kalmar
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Sina Beier
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Emily C Horner
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | | | - Juan Carlos Yam-Puc
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Pehuén Pereyra Gerber
- https://ror.org/013meh722 Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- https://ror.org/013meh722 Department of Medicine, University of Cambridge, Cambridge, UK
| | - Luisa Faria
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Anna Kuroshchenkova
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Anna E Lindell
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Sonja Blasche
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Andrea Correa-Noguera
- Department of Clinical Immunology, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Anne Elmer
- NIHR Cambridge Clinical Research Facility, Cambridge, UK
| | | | - Areti Bermperi
- NIHR Cambridge Clinical Research Facility, Cambridge, UK
| | - Sherly Jose
- NIHR Cambridge Clinical Research Facility, Cambridge, UK
| | - Nathalie Kingston
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Emily Staples
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Matthew S Buckland
- Department of Clinical Immunology, Barts Health, London, UK
- UCL GOSH Institute of Child Health Division of Infection and Immunity, Section of Cellular and Molecular Immunology, London, UK
| | - Sara Lear
- Department of Clinical Immunology, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Nicholas J Matheson
- https://ror.org/013meh722 Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- https://ror.org/013meh722 Department of Medicine, University of Cambridge, Cambridge, UK
- NHS Blood and Transplant, Cambridge, UK
| | - Vladimir Benes
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Christine Parkinson
- Department of Clinical Immunology, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - James Ed Thaventhiran
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
- Department of Clinical Immunology, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Kiran R Patil
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
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10
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Müller P, de la Cuesta-Zuluaga J, Kuhn M, Baghai Arassi M, Treis T, Blasche S, Zimmermann M, Bork P, Patil KR, Typas A, Garcia-Santamarina S, Maier L. High-throughput anaerobic screening for identifying compounds acting against gut bacteria in monocultures or communities. Nat Protoc 2024; 19:668-699. [PMID: 38092943 DOI: 10.1038/s41596-023-00926-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 10/05/2023] [Indexed: 03/10/2024]
Abstract
The human gut microbiome is a key contributor to health, and its perturbations are linked to many diseases. Small-molecule xenobiotics such as drugs, chemical pollutants and food additives can alter the microbiota composition and are now recognized as one of the main factors underlying microbiome diversity. Mapping the effects of such compounds on the gut microbiome is challenging because of the complexity of the community, anaerobic growth requirements of individual species and the large number of interactions that need to be quantitatively assessed. High-throughput screening setups offer a promising solution for probing the direct inhibitory effects of hundreds of xenobiotics on tens of anaerobic gut bacteria. When automated, such assays enable the cost-effective investigation of a wide range of compound-microbe combinations. We have developed an experimental setup and protocol that enables testing of up to 5,000 compounds on a target gut species under strict anaerobic conditions within 5 d. In addition, with minor modifications to the protocol, drug effects can be tested on microbial communities either assembled from isolates or obtained from stool samples. Experience in working in an anaerobic chamber, especially in performing delicate work with thick chamber gloves, is required for implementing this protocol. We anticipate that this protocol will accelerate the study of interactions between small molecules and the gut microbiome and provide a deeper understanding of this microbial ecosystem, which is intimately intertwined with human health.
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Affiliation(s)
- Patrick Müller
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Jacobo de la Cuesta-Zuluaga
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Michael Kuhn
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Maral Baghai Arassi
- European Molecular Biology Laboratory, Heidelberg, Germany
- Department of Pediatrics I, University Children's Hospital Heidelberg, Heidelberg, Germany
| | - Tim Treis
- European Molecular Biology Laboratory, Heidelberg, Germany
- Institute of Computational Biology, Helmholtz Center München, Neuherberg, Germany
| | - Sonja Blasche
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | | | - Peer Bork
- European Molecular Biology Laboratory, Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, Berlin, Germany
- Yonsei Frontier Lab (YFL), Yonsei University, Seoul, South Korea
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Kiran Raosaheb Patil
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | | | | | - Lisa Maier
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany.
- Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany.
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11
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Hu ZQ, Hung YM, Chen LH, Lai LC, Pan MH, Chuang EY, Tsai MH. NURECON: A Novel Online System for Determining Nutrition Requirements Based on Microbial Composition. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024; 21:254-264. [PMID: 38568776 DOI: 10.1109/tcbb.2024.3349572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Dietary habits have been proven to have an impact on the microbial composition and health of the human gut. Over the past decade, researchers have discovered that gut microbiota can use nutrients to produce metabolites that have major implications for human physiology. However, there is no comprehensive system that specifically focuses on identifying nutrient deficiencies based on gut microbiota, making it difficult to interpret and compare gut microbiome data in the literature. This study proposes an analytical platform, NURECON, that can predict nutrient deficiency information in individuals by comparing their metagenomic information to a reference baseline. NURECON integrates a next-generation bacterial 16S rRNA analytical pipeline (QIIME2), metabolic pathway prediction tools (PICRUSt2 and KEGG), and a food compound database (FooDB) to enable the identification of missing nutrients and provide personalized dietary suggestions. Metagenomic information from total number of 287 healthy subjects was used to establish baseline microbial composition and metabolic profiles. The uploaded data is analyzed and compared to the baseline for nutrient deficiency assessment. Visualization results include gut microbial composition, related enzymes, pathways, and nutrient abundance. NURECON is a user-friendly online platform that provides nutritional advice to support dietitians' research or menu design.
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12
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Michaelis L, Berg L, Maier L. Confounder or Confederate? The Interactions Between Drugs and the Gut Microbiome in Psychiatric and Neurological Diseases. Biol Psychiatry 2024; 95:361-369. [PMID: 37331548 DOI: 10.1016/j.biopsych.2023.06.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/20/2023]
Abstract
The gut microbiome is emerging as an important factor in signaling along the gut-brain axis. The intimate physiological connection between the gut and the brain allows perturbations in the microbiome to be directly transmitted to the central nervous system and thereby contribute to psychiatric and neurological diseases. Common microbiome perturbations result from the ingestion of xenobiotic compounds including pharmaceuticals such as psychotropic drugs. In recent years, a variety of interactions between these drug classes and the gut microbiome have been reported, ranging from direct inhibitory effects on gut bacteria to microbiome-mediated drug degradation or sequestration. Consequently, the microbiome may play a critical role in influencing the intensity, duration, and onset of therapeutic effects, as well as in influencing the side effects that patients may experience. Furthermore, because the composition of the microbiome varies from person to person, the microbiome may contribute to the frequently observed interpersonal differences in the response to these drugs. In this review, we first summarize the known interactions between xenobiotics and the gut microbiome. Then, for psychopharmaceuticals, we address the question of whether these interactions with gut bacteria are irrelevant for the host (i.e., merely confounding factors in metagenomic analyses) or whether they may even have therapeutic or adverse effects.
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Affiliation(s)
- Lena Michaelis
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany; and the Cluster of Excellence EXC 2124 (Controlling Microbes to Fight Infections), University of Tübingen, Tübingen, Germany
| | - Lara Berg
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany; and the Cluster of Excellence EXC 2124 (Controlling Microbes to Fight Infections), University of Tübingen, Tübingen, Germany
| | - Lisa Maier
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany; and the Cluster of Excellence EXC 2124 (Controlling Microbes to Fight Infections), University of Tübingen, Tübingen, Germany.
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13
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Li T, Ding N, Guo H, Hua R, Lin Z, Tian H, Yu Y, Fan D, Yuan Z, Gonzalez FJ, Wu Y. A gut microbiota-bile acid axis promotes intestinal homeostasis upon aspirin-mediated damage. Cell Host Microbe 2024; 32:191-208.e9. [PMID: 38237593 PMCID: PMC10922796 DOI: 10.1016/j.chom.2023.12.015] [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: 07/10/2023] [Revised: 11/18/2023] [Accepted: 12/21/2023] [Indexed: 02/17/2024]
Abstract
Aspirin-related gastrointestinal damage is of growing concern. Aspirin use modulates the gut microbiota and associated metabolites, such as bile acids (BAs), but how this impacts intestinal homeostasis remains unclear. Herein, using clinical cohorts and aspirin-treated mice, we identified an intestinal microbe, Parabacteroides goldsteinii, whose growth is suppressed by aspirin. Mice supplemented with P. goldsteinii or its BA metabolite, 7-keto-lithocholic acid (7-keto-LCA), showed reduced aspirin-mediated damage of the intestinal niche and gut barrier, effects that were lost with a P. goldsteinii hdhA mutant unable to generate 7-keto-LCA. Specifically, 7-keto-LCA promotes repair of the intestinal epithelium by suppressing signaling by the intestinal BA receptor, farnesoid X receptor (FXR). 7-Keto-LCA was confirmed to be an FXR antagonist that facilitates Wnt signaling and thus self-renewal of intestinal stem cells. These results reveal the impact of oral aspirin on the gut microbiota and intestinal BA metabolism that in turn modulates gastrointestinal homeostasis.
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Affiliation(s)
- Ting Li
- Department of Cardiovascular Medicine, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China; Key Laboratory of Molecular Cardiology, Xi'an, Shaanxi, China; Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, China
| | - Ning Ding
- Department of Cardiovascular Medicine, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China; Key Laboratory of Molecular Cardiology, Xi'an, Shaanxi, China; Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, China
| | - Hanqing Guo
- Department of Gastroenterology, Xi'an Central Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Rui Hua
- Department of Cardiovascular Medicine, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Zehao Lin
- Department of Cardiovascular Medicine, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Huohuan Tian
- Department of Cardiovascular Medicine, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yue Yu
- Department of Cardiovascular Medicine, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Daiming Fan
- Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Zuyi Yuan
- Department of Cardiovascular Medicine, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China; Key Laboratory of Molecular Cardiology, Xi'an, Shaanxi, China; Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, China.
| | - Frank J Gonzalez
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Yue Wu
- Department of Cardiovascular Medicine, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China; Key Laboratory of Molecular Cardiology, Xi'an, Shaanxi, China; Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, China.
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14
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Liu C, Xu Q, Dong S, Ding H, Li B, Zhang D, Liang Y, Li L, Liu Q, Cheng Y, Wu J, Zhu J, Zhong M, Cao Y, Zhang G. New mechanistic insights of anti-obesity by sleeve gastrectomy-altered gut microbiota and lipid metabolism. Front Endocrinol (Lausanne) 2024; 15:1338147. [PMID: 38375198 PMCID: PMC10875461 DOI: 10.3389/fendo.2024.1338147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/09/2024] [Indexed: 02/21/2024] Open
Abstract
Background The obesity epidemic has been on the rise due to changes in living standards and lifestyles. To combat this issue, sleeve gastrectomy (SG) has emerged as a prominent bariatric surgery technique, offering substantial weight reduction. Nevertheless, the mechanisms that underlie SG-related bodyweight loss are not fully understood. Methods In this study, we conducted a collection of preoperative and 3-month postoperative serum and fecal samples from patients who underwent laparoscopic SG at the First Affiliated Hospital of Shandong First Medical University (Jinan, China). Here, we took an unbiased approach of multi-omics to investigate the role of SG-altered gut microbiota in anti-obesity of these patients. Non-target metabolome sequencing was performed using the fecal and serum samples. Results Our data show that SG markedly increased microbiota diversity and Rikenellaceae, Alistipes, Parabacteroides, Bactreoidales, and Enterobacteraies robustly increased. These compositional changes were positively correlated with lipid metabolites, including sphingolipids, glycerophospholipids, and unsaturated fatty acids. Increases of Rikenellaceae, Alistipes, and Parabacteroide were reversely correlated with body mass index (BMI). Conclusion In conclusion, our findings provide evidence that SG induces significant alterations in the abundances of Rikenellaceae, Alistipes, Parabacteroides, and Bacteroidales, as well as changes in lipid metabolism-related metabolites. Importantly, these changes were found to be closely linked to the alleviation of obesity. On the basis of these findings, we have identified a number of microbiotas that could be potential targets for treatment of obesity.
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Affiliation(s)
- Chuxuan Liu
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, Shandong, China
| | - Qian Xu
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, Shandong, China
| | - Shuohui Dong
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, Shandong, China
| | - Huanxin Ding
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, Shandong, China
| | - Bingjun Li
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, Shandong, China
| | - Dexu Zhang
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, Shandong, China
| | - Yongjuan Liang
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, Shandong, China
| | - Linchuan Li
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, Shandong, China
| | - Qiaoran Liu
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, Shandong, China
| | - Yugang Cheng
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, Shandong, China
| | - Jing Wu
- Department of Clinical Pharmacy, The First Affiliated Hospital of Shandong First Medical University, Jinan, Shandong, China
| | - Jiankang Zhu
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, Shandong, China
| | - Mingwei Zhong
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, Shandong, China
| | - Yihai Cao
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Guangyong Zhang
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, Shandong, China
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15
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Chan M, Ghadieh C, Irfan I, Khair E, Padilla N, Rebeiro S, Sidgreaves A, Patravale V, Disouza J, Catanzariti R, Pont L, Williams K, De Rubis G, Mehndiratta S, Dhanasekaran M, Dua K. Exploring the influence of the microbiome on the pharmacology of anti-asthmatic drugs. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:751-762. [PMID: 37650889 PMCID: PMC10791706 DOI: 10.1007/s00210-023-02681-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/18/2023] [Indexed: 09/01/2023]
Abstract
The microbiome is increasingly implicated in playing a role in physiology and pharmacology; in this review, we investigate the literature on the possibility of bacterial influence on the pharmacology of anti-asthmatic drugs, and the potential impact this has on asthmatic patients. Current knowledge in this area of research reveals an interaction between the gut and lung microbiome and the development of asthma. The influence of microbiome on the pharmacokinetics and pharmacodynamics of anti-asthmatic drugs is limited; however, understanding this interaction will assist in creating a more efficient treatment approach. This literature review highlighted that bioaccumulation and biotransformation in the presence of certain gut bacterial strains could affect drug metabolism in anti-asthmatic drugs. Furthermore, the bacterial richness in the lungs and the gut can influence drug efficacy and could also play a role in drug response. The implications of the above findings suggest that the microbiome is a contributing factor to an individuals' pharmacological response to anti-asthmatic drugs. Hence, future directions for research should follow investigating how these processes affect asthmatic patients and consider the role of the microbiome on drug efficacy and modify treatment guidelines accordingly.
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Affiliation(s)
- Michael Chan
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Chloe Ghadieh
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Isphahan Irfan
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Eamen Khair
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Natasha Padilla
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Sanshya Rebeiro
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Annabel Sidgreaves
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Vandana Patravale
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Matunga, Mumbai, Maharashtra, India
| | - John Disouza
- Department of Pharmaceutics, Tatyasaheb Kore College of Pharmacy, Warananagar, Tal: Panhala, Maharashtra, 416113, India
| | - Rachelle Catanzariti
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Lisa Pont
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Kylie Williams
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Gabriele De Rubis
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, NSW, 2007, Australia
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Sydney, Australia
| | - Samir Mehndiratta
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, NSW, 2007, Australia
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Sydney, Australia
| | | | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Sydney, Australia.
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16
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Zeng Y, Wu Y, Zhang Q, Xiao X. Crosstalk between glucagon-like peptide 1 and gut microbiota in metabolic diseases. mBio 2024; 15:e0203223. [PMID: 38055342 PMCID: PMC10790698 DOI: 10.1128/mbio.02032-23] [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] [Indexed: 12/08/2023] Open
Abstract
Gut microbiota exert influence on gastrointestinal mucosal permeability, bile acid metabolism, short-chain fatty acid synthesis, dietary fiber fermentation, and farnesoid X receptor/Takeda G protein-coupled receptor 5 (TGR5) signal transduction. The incretin glucagon-like peptide 1 (GLP-1) is mainly produced by L cells in the gut and regulates postprandial blood glucose. Changes in gut microbiota composition and function have been observed in obesity and type 2 diabetes (T2D). Meanwhile, the function and rhythm of GLP-1 have also been affected in subjects with obesity or T2D. Therefore, it is necessary to discuss the link between the gut microbiome and GLP-1. In this review, we describe the interaction between GLP-1 and the gut microbiota in metabolic diseases. On the one hand, gut microbiota metabolites stimulate GLP-1 secretion, and gut microbiota affect GLP-1 function and rhythm. On the other hand, the mechanism of action of GLP-1 on gut microbiota involves the inflammatory response. Additionally, we discuss the effects and mechanism of various interventions, such as prebiotics, probiotics, antidiabetic drugs, and bariatric surgery, on the crosstalk between gut microbiota and GLP-1. Finally, we stress that gut microbiota can be used as a target for metabolic diseases, and the clinical application of GLP-1 receptor agonists should be individualized.
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Grants
- 81870545, 81870579, 82170854, 81570715, 81170736 MOST | National Natural Science Foundation of China (NSFC)
- 7202163 Natural Science Foundation of Beijing Municipality (Beijing Natural Science Foundation)
- Z201100005520011 Beijing Municipal Science and Technology Commission, Adminitrative Commission of Zhongguancun Science Park
- 2017YFC1309603, 2021YFC2501700, 2016YFA0101002, 2018YFC2001100 MOST | National Key Research and Development Program of China (NKPs)
- 2019DCT-M-05 Beijing Municipal Human Resources and Social Security Bureau (BMHRSSB)
- 2017PT31036, 2018PT31021 Chinese Academy of Medical Sciences (CAMS)
- 2017PT32020, 2018PT32001 Chinese Academy of Medical Sciences (CAMS)
- CIFMS2017-I2M-1-008, CIFMS2021-I2M-1-002 Chinese Academy of Medical Sciences (CAMS)
- 2022-PUMCH- C-019, 2022-PUMCH-B-121 National High Level Hospital Clinical Research Funding
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Affiliation(s)
- Yuan Zeng
- Department of Endocrinology, Key Laboratory of Endocrinology, Ministry of Health, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yifan Wu
- Department of Endocrinology, Key Laboratory of Endocrinology, Ministry of Health, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Qian Zhang
- Department of Endocrinology, Key Laboratory of Endocrinology, Ministry of Health, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xinhua Xiao
- Department of Endocrinology, Key Laboratory of Endocrinology, Ministry of Health, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
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17
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Zhou Y, Zhang Y, Zhao D, Yu X, Shen X, Zhou Y, Wang S, Qiu Y, Chen Y, Zhu F. TTD: Therapeutic Target Database describing target druggability information. Nucleic Acids Res 2024; 52:D1465-D1477. [PMID: 37713619 PMCID: PMC10767903 DOI: 10.1093/nar/gkad751] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/31/2023] [Accepted: 09/05/2023] [Indexed: 09/17/2023] Open
Abstract
Target discovery is one of the essential steps in modern drug development, and the identification of promising targets is fundamental for developing first-in-class drug. A variety of methods have emerged for target assessment based on druggability analysis, which refers to the likelihood of a target being effectively modulated by drug-like agents. In the therapeutic target database (TTD), nine categories of established druggability characteristics were thus collected for 426 successful, 1014 clinical trial, 212 preclinical/patented, and 1479 literature-reported targets via systematic review. These characteristic categories were classified into three distinct perspectives: molecular interaction/regulation, human system profile and cell-based expression variation. With the rapid progression of technology and concerted effort in drug discovery, TTD and other databases were highly expected to facilitate the explorations of druggability characteristics for the discovery and validation of innovative drug target. TTD is now freely accessible at: https://idrblab.org/ttd/.
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Affiliation(s)
- Ying Zhou
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
- National Key Laboratory of Diagnosis and Treatment of Severe Infectious Disease, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang 310000, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Yintao Zhang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Donghai Zhao
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xinyuan Yu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xinyi Shen
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven 06510, USA
| | - Yuan Zhou
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Shanshan Wang
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China
| | - Yunqing Qiu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
- National Key Laboratory of Diagnosis and Treatment of Severe Infectious Disease, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang 310000, China
| | - Yuzong Chen
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, The Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518000, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
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18
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Panigrahi P. The neonatal gut microbiome and global health. Gut Microbes 2024; 16:2352175. [PMID: 38743045 PMCID: PMC11095572 DOI: 10.1080/19490976.2024.2352175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 05/02/2024] [Indexed: 05/16/2024] Open
Abstract
The role of gut microbiome in health, a century-old concept, has been on the center stage of medical research recently. While different body sites, disease conditions, and populations have been targeted, neonatal and early infancy appear to be the most suitable period for such interventions. It is intriguing to note that, unlike traditional use in diarrhea and maintenance of gastrointestinal health, microbiome-mediating therapies have now addressed the most serious medical conditions in young infants such as necrotizing enterocolitis and neonatal sepsis. Unfortunately, almost all new endeavors in this space have been carried out in the Western world leaving behind millions of neonates that can benefit from such manipulations while serving as a large resource for further learning. In this review, an attempt has been made to quantify the global burden of neonatal morbidity and mortality, examples presented on interventions that have failed as a result of drawing from studies conducted in the West, and a case made for manipulating the neonatal gut microbiome to address the biggest killers in early life. A brief comparative analysis has been made to demonstrate the differences in the gut microbiota of North and South and a large clinical trial of synbiotics conducted by our group in a South Asian setting has been presented. Although challenging, the value of conducting such global health research is introduced with an intent to invite medical scientists to engage in well-planned, scientifically robust research endeavors. This can bring about innovation while saving and serving the most vulnerable citizens now and protecting them from the negative health consequences in the later part of their lives, ultimately shaping a resilient and equitable world as pledged by 193 United Nations member countries in 2015.
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Affiliation(s)
- Pinaki Panigrahi
- Department of Pediatrics, Division of Neonatal Perinatal Medicine, International Microbiome Research, Georgetown University Medical Center, Georgetown, WA, USA
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19
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Teng M, Zhao X, Zhou L, Yan H, Zhao L, Sun J, Li Y, Zhu W, Wu F. An integrated analysis of the fecal metabolome and metagenome reveals the distinct effects of differentially charged nanoplastics on the gut microbiota-associated metabolites in mice. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167287. [PMID: 37748599 DOI: 10.1016/j.scitotenv.2023.167287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/14/2023] [Accepted: 09/20/2023] [Indexed: 09/27/2023]
Abstract
Whether nanoplastics with differential charges cause intestinal impairment via distinct mechanisms remains unclear. We investigated the relationship between fecal metabolites and the gut microbiome, and potential biomarkers thereof, in mice following exposure to differentially charged polystyrene nanoplastics (PS-NPs). Metagenomic analysis revealed that exposure to differentially charged PS-NPs resulted in alterations in the abundances of Bilophila_wadsworthia, Helicobacter apodemus, and Helicobacter typhlonius. A total of 237 fecal metabolites were significantly altered in mice that exhibited intestinal impairment, and these included 10 gut microbiota-related fecal metabolites that accurately discriminated impaired intestinal samples from the control. Additionally, the specific gut microbiome-related fecal metabolite-based model approach for the prediction of intestinal impairment in mice had an area under the curve (AUC) of 1.0 in the PS (without charge) group, an AUC of 0.94 in the PS-NH2 (positive charge) group, and an AUC of 0.86 in the PS-COOH (negative charge) group. Thus, the model showed promising evaluable accuracy for the prediction of intestinal impairment induced by nanoplastics in a charge-specific manner. Our study demonstrates that the fecal metabolome of mice with intestinal impairment following exposure to differentially charged nanoplastics is associated with changes in the gut microbiome. The identified biomarkers have potential application for the detection of intestinal impairment after exposure to negative, positive, or noncharged nanomaterials.
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Affiliation(s)
- Miaomiao Teng
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Xiaoli Zhao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Lingfeng Zhou
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Hong Yan
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, USA
| | - Lihui Zhao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Jiaqi Sun
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Yunxia Li
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Wentao Zhu
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Fengchang Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
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20
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Tan Y, Liang J, Lai M, Wan S, Luo X, Li F. Advances in synthetic biology toolboxes paving the way for mechanistic understanding and strain engineering of gut commensal Bacteroides spp. and Clostridium spp. Biotechnol Adv 2023; 69:108272. [PMID: 37844770 DOI: 10.1016/j.biotechadv.2023.108272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023]
Abstract
The gut microbiota plays a significant role in influencing human immunity, metabolism, development, and behavior by producing a wide range of metabolites. While there is accumulating data on several microbiota-derived small molecules that contribute to host health and disease, our knowledge regarding the molecular mechanisms underlying metabolite-mediated microbe-host interactions remains limited. This is primarily due to the lack of efficient genetic tools for most commensal bacteria, especially those belonging to the dominant phyla Bacteroides spp. and Clostridium spp., which hinders the application of synthetic biology to these gut commensal bacteria. In this review, we provide an overview of recent advances in synthetic biology tools developed for the two dominant genera, as well as their applications in deciphering the mechanisms of microbe-host interactions mediated by microbiota-derived small molecules. We also discuss the potential biomedical applications of engineering commensal bacteria using these toolboxes. Finally, we share our perspective on the future development of synthetic biology tools for a better understanding of small molecule-mediated microbe-host interactions and their engineering for biomedical purposes.
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Affiliation(s)
- Yang Tan
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao 266101, China.
| | - Jing Liang
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Mingchi Lai
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Sai Wan
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Xiaozhou Luo
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Fuli Li
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao 266101, China.
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21
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Fishbein SRS, Mahmud B, Dantas G. Antibiotic perturbations to the gut microbiome. Nat Rev Microbiol 2023; 21:772-788. [PMID: 37491458 DOI: 10.1038/s41579-023-00933-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2023] [Indexed: 07/27/2023]
Abstract
Antibiotic-mediated perturbation of the gut microbiome is associated with numerous infectious and autoimmune diseases of the gastrointestinal tract. Yet, as the gut microbiome is a complex ecological network of microorganisms, the effects of antibiotics can be highly variable. With the advent of multi-omic approaches for systems-level profiling of microbial communities, we are beginning to identify microbiome-intrinsic and microbiome-extrinsic factors that affect microbiome dynamics during antibiotic exposure and subsequent recovery. In this Review, we discuss factors that influence restructuring of the gut microbiome on antibiotic exposure. We present an overview of the currently complex picture of treatment-induced changes to the microbial community and highlight essential considerations for future investigations of antibiotic-specific outcomes. Finally, we provide a synopsis of available strategies to minimize antibiotic-induced damage or to restore the pretreatment architectures of the gut microbial community.
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Affiliation(s)
- Skye R S Fishbein
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Bejan Mahmud
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.
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22
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Fu Y, Dou Q, Smalla K, Wang Y, Johnson TA, Brandt KK, Mei Z, Liao M, Hashsham SA, Schäffer A, Smidt H, Zhang T, Li H, Stedtfeld R, Sheng H, Chai B, Virta M, Jiang X, Wang F, Zhu Y, Tiedje JM. Gut microbiota research nexus: One Health relationship between human, animal, and environmental resistomes. MLIFE 2023; 2:350-364. [PMID: 38818274 PMCID: PMC10989101 DOI: 10.1002/mlf2.12101] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 06/01/2024]
Abstract
The emergence and rapid spread of antimicrobial resistance is of global public health concern. The gut microbiota harboring diverse commensal and opportunistic bacteria that can acquire resistance via horizontal and vertical gene transfers is considered an important reservoir and sink of antibiotic resistance genes (ARGs). In this review, we describe the reservoirs of gut ARGs and their dynamics in both animals and humans, use the One Health perspective to track the transmission of ARG-containing bacteria between humans, animals, and the environment, and assess the impact of antimicrobial resistance on human health and socioeconomic development. The gut resistome can evolve in an environment subject to various selective pressures, including antibiotic administration and environmental and lifestyle factors (e.g., diet, age, gender, and living conditions), and interventions through probiotics. Strategies to reduce the abundance of clinically relevant antibiotic-resistant bacteria and their resistance determinants in various environmental niches are needed to ensure the mitigation of acquired antibiotic resistance. With the help of effective measures taken at the national, local, personal, and intestinal management, it will also result in preventing or minimizing the spread of infectious diseases. This review aims to improve our understanding of the correlations between intestinal microbiota and antimicrobial resistance and provide a basis for the development of management strategies to mitigate the antimicrobial resistance crisis.
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Affiliation(s)
- Yuhao Fu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil ScienceChinese Academy of SciencesNanjingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Qingyuan Dou
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil ScienceChinese Academy of SciencesNanjingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Kornelia Smalla
- Julius Kühn Institute (JKI) Federal Research Centre for Cultivated PlantsBraunschweigGermany
| | - Yu Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil ScienceChinese Academy of SciencesNanjingChina
- University of Chinese Academy of SciencesBeijingChina
| | | | - Kristian K. Brandt
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
- Sino‐Danish Center (SDC)BeijingChina
| | - Zhi Mei
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil ScienceChinese Academy of SciencesNanjingChina
- University of Chinese Academy of SciencesBeijingChina
- Department of MicrobiologyUniversity of HelsinkiHelsinkiFinland
| | - Maoyuan Liao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil ScienceChinese Academy of SciencesNanjingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Syed A. Hashsham
- Department of Plant, Soil and Microbial Sciences, Center for Microbial EcologyMichigan State UniversityMichiganUSA
- Department of Civil and Environmental EngineeringMichigan State UniversityMichiganUSA
| | - Andreas Schäffer
- Institute for Environmental ResearchRWTH Aachen UniversityAachenGermany
| | - Hauke Smidt
- Laboratory of MicrobiologyWageningen University & ResearchWageningenThe Netherlands
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil EngineeringThe University of Hong KongPokfulamHong KongChina
| | - Hui Li
- Department of Plant, Soil and Microbial Sciences, Center for Microbial EcologyMichigan State UniversityMichiganUSA
| | - Robert Stedtfeld
- Department of Civil and Environmental EngineeringMichigan State UniversityMichiganUSA
| | - Hongjie Sheng
- Institute of Agricultural Resources and EnvironmentJiangsu Academy of Agricultural SciencesNanjingChina
| | - Benli Chai
- Department of Plant, Soil and Microbial Sciences, Center for Microbial EcologyMichigan State UniversityMichiganUSA
| | - Marko Virta
- Department of MicrobiologyUniversity of HelsinkiHelsinkiFinland
| | - Xin Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil ScienceChinese Academy of SciencesNanjingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Fang Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil ScienceChinese Academy of SciencesNanjingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yong‐Guan Zhu
- University of Chinese Academy of SciencesBeijingChina
- Key Laboratory of Urban Environment and Health, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
- State Key Laboratory of Urban and Regional EcologyChinese Academy of SciencesBeijingChina
| | - James M. Tiedje
- Department of Plant, Soil and Microbial Sciences, Center for Microbial EcologyMichigan State UniversityMichiganUSA
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23
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Tan H, Chen X, Wang C, Song J, Xu J, Zhang Y, Suo H. Intestinal organoid technology and applications in probiotics. Crit Rev Food Sci Nutr 2023:1-15. [PMID: 38032232 DOI: 10.1080/10408398.2023.2288887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
The impacts of probiotics on maintaining the host's intestinal health have been extensively confirmed. Organoid technology revolutionizes intestinal health research by providing a unique platform to study the effects of probiotics. It overcomes challenges posed by animal models and 2D cell models in accurately simulating the in vivo environment. This review summarizes the development of intestinal organoid technology and its potential applications in intestinal health research as well as highlights the regulatory mechanisms of probiotics on intestinal health, which have been revealed using intestinal organoid technology. Furthermore, an overview of its potential applications in probiotic research has also been provided. This review aims to improve the understanding of intestinal organoid technology's applications in this field as well as to contribute to its further development.
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Affiliation(s)
- Han Tan
- College of Food Science, Southwest University, Chongqing, China
| | - Xiaoyong Chen
- College of Food Science, Southwest University, Chongqing, China
- Chongqing Agricultural Product Processing Technology Innovation Platform, Chongqing, China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing, China
- Citrus Research Institute, National Citrus Engineering Research Center, Southwest University, Chongqing, China
| | - Chen Wang
- College of Food Science, Southwest University, Chongqing, China
- Chongqing Agricultural Product Processing Technology Innovation Platform, Chongqing, China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing, China
- Citrus Research Institute, National Citrus Engineering Research Center, Southwest University, Chongqing, China
| | - Jiajia Song
- College of Food Science, Southwest University, Chongqing, China
- Chongqing Agricultural Product Processing Technology Innovation Platform, Chongqing, China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing, China
- Citrus Research Institute, National Citrus Engineering Research Center, Southwest University, Chongqing, China
| | - Jiahui Xu
- College of Food Science, Southwest University, Chongqing, China
| | - Yuhong Zhang
- Institute of Food Sciences and Technology, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Huayi Suo
- College of Food Science, Southwest University, Chongqing, China
- Chongqing Agricultural Product Processing Technology Innovation Platform, Chongqing, China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing, China
- Citrus Research Institute, National Citrus Engineering Research Center, Southwest University, Chongqing, China
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24
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Xiao X, Cui Y, Lu H, Wang J, Yang J, Liu L, Liu Z, Peng X, Cao H, Liu X, Wei X. Strontium ranelate enriched Ruminococcus albus in the gut microbiome of Sprague-Dawley rats with postmenopausal osteoporosis. BMC Microbiol 2023; 23:365. [PMID: 38008735 PMCID: PMC10680188 DOI: 10.1186/s12866-023-03109-z] [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: 02/06/2023] [Accepted: 11/03/2023] [Indexed: 11/28/2023] Open
Abstract
BACKGROUND Gut microbiome is critical to our human health and is related to postmenopausal osteoporosis (PMO). Strontium ranelate (SrR) is an anti-osteoporosis oral drug that can promote osteoblast formation and inhibit osteoclast formation. However, the effect of SrR on gut microbiome has been rarely studied. Therefore, we investigated the effect of oral SrR on gut microbiome and metabolic profiles. RESULTS In this study, we used ovariectomized (OVX) Sprague-Dawley rats to construct a PMO model and applied oral SrR for 6 weeks. The relative abundance of intestinal microbiome was investigated by 16S rRNA metagenomic sequencing. Ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS) was used to analyze changes in metabolites of intestinal contents. Results demonstrated that 6-week oral SrR alleviated osteoporosis and significantly changed the composition of the gut microbiome and metabolic profiles of OVX rats. Ruminococcus, Akkermansia and Oscillospira were significantly enriched in the gut of OVX rats after 6-week oral SrR. Especially, the species R. albus showed the greatest importance by a random forest classifier between OVX and OVX_Sr group. The enrichment of R. albus in the gut was positively correlated with bone mineral density and the accumulation of lycopene and glutaric acid, which also significantly elevated after oral SrR. CONCLUSIONS We discovered that oral SrR can improve bone health while stimulate the accumulation of gut microbe R. albus and metabolites (lycopene and glutaric acid). The results suggested possible connections between oral SrR and the gut-bone axis, which may provide new insight into the treatment/prevention of osteoporosis.
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Affiliation(s)
- Xiao Xiao
- School of Basic Medicine, Hubei University of Medicine, Shiyan, Hubei, PR China
| | - Yuanyuan Cui
- School of Basic Medicine, Hubei University of Medicine, Shiyan, Hubei, PR China
| | - Huigai Lu
- School of Basic Medicine, Hubei University of Medicine, Shiyan, Hubei, PR China
| | - Jiaqi Wang
- School of Basic Medicine, Hubei University of Medicine, Shiyan, Hubei, PR China
| | - Jing Yang
- School of Basic Medicine, Hubei University of Medicine, Shiyan, Hubei, PR China
| | - Long Liu
- School of Basic Medicine, Hubei University of Medicine, Shiyan, Hubei, PR China
| | - Zhixin Liu
- School of Basic Medicine, Hubei University of Medicine, Shiyan, Hubei, PR China
| | - Xiaohong Peng
- Key Laboratory of Pathogenic Biology, Guilin Medical University, Guilin, Guangxi, PR China
| | - Hong Cao
- Department of Orthopedics, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei, PR China
| | - Xinghui Liu
- School of Basic Medicine, Hubei University of Medicine, Shiyan, Hubei, PR China.
| | - Xiuli Wei
- School of Basic Medicine, Hubei University of Medicine, Shiyan, Hubei, PR China.
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25
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López‐Moreno A, Langella P, Martín R, Aguilera M. Microbiota analysis for risk assessment of xenobiotic exposure and the impact on dysbiosis: identifying potential next-generation probiotics. EFSA J 2023; 21:e211010. [PMID: 38047127 PMCID: PMC10687753 DOI: 10.2903/j.efsa.2023.e211010] [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: 12/05/2023] Open
Abstract
On-going projects of the team are currently dealing with microbiota, xenobiotics, endocrine-disrupting chemicals (EDCs), obesity, inflammation and probiotics. The combination of diet, lifestyle and the exposure to dietary xenobiotics categorised into microbiota-disrupting chemicals (MDCs) could determine obesogenic-related dysbiosis. This modification of the microbiota diversity impacts on individual health-disease balance, inducing altered phenotypes. Specific, complementary, and combined prevention and treatments are needed to face these altered microbial patterns and the specific misbalances triggered. In this sense, searching for 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, EU-FORA project contributes to present a perspective through compiling information and key strategies for directed taxa searching and culturing of NGP that could be administered for preventing obesity and endocrine-related dysbiosis by (i) observing the differential abundance of specific microbiota taxa in obesity-related patients and analysing their functional roles, (ii) developing microbiota-directed strategies for culturing these taxa groups, and (iii) design and applying the successful compiled criteria from recent NGP clinical studies. New isolated or cultivable microorganisms from healthy gut microbiota specifically related to xenobiotic obesogens' neutralisation 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 were also considered in this workplan.
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Affiliation(s)
- Ana López‐Moreno
- Microbiology Department, Faculty of PharmacyUniversity of GranadaSpain
- "José Mataix Verdú" Institute of Nutrition and Food Technology, University of Granada (INYTA‐UGR)GranadaSpain
| | - Philippe Langella
- Commensal and Probiotics‐Host Interactions Laboratory, INRAE, AgroParisTech, Micalis Institute, Université Paris‐Saclay78350Jouy‐en‐JosasFrance
| | - Rebeca Martín
- Commensal and Probiotics‐Host Interactions Laboratory, INRAE, AgroParisTech, Micalis Institute, Université Paris‐Saclay78350Jouy‐en‐JosasFrance
| | - Margarita Aguilera
- Microbiology Department, Faculty of PharmacyUniversity of GranadaSpain
- "José Mataix Verdú" Institute of Nutrition and Food Technology, University of Granada (INYTA‐UGR)GranadaSpain
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26
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Sun H, Li H, Zhang X, Liu Y, Chen H, Zheng L, Zhai Y, Zheng H. The honeybee gut resistome and its role in antibiotic resistance dissemination. Integr Zool 2023; 18:1014-1026. [PMID: 36892101 DOI: 10.1111/1749-4877.12714] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
There is now general concern about widespread antibiotic resistance, and growing evidence indicates that gut microbiota is critical in providing antibiotic resistance. Honeybee is an important pollinator; the incidence of antibiotic resistance genes in honeybee gut causes potential risks to not only its own health but also to public and animal health, for its potential disseminator role, thus receiving more attention from the public. Recent analysis results reveal that the gut of honeybee serves as a reservoir of antibiotic resistance genes, probably due to antibiotics application history in beekeeping and horizontal gene transfer from the highly polluted environment. These antibiotic resistance genes accumulate in the honeybee gut and could be transferred to the pathogen, even having the potential to spread during pollination, tending, social interactions, etc. Newly acquired resistance traits may cause fitness reduction in bacteria whereas facilitating adaptive evolution as well. This review outlines the current knowledge about the resistome in honeybee gut and emphasizes its role in antibiotic resistance dissemination.
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Affiliation(s)
- Huihui Sun
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Sanya Institute of China Agricultural University, Sanya, China
| | - Hu Li
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xue Zhang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Yan Liu
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
- Shandong Provincial Engineering Technology Research Center on Biocontrol of Crops Diseases and Insect Pests, Jinan, China
| | - Hao Chen
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
- Shandong Provincial Engineering Technology Research Center on Biocontrol of Crops Diseases and Insect Pests, Jinan, China
| | - Li Zheng
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
- Shandong Provincial Engineering Technology Research Center on Biocontrol of Crops Diseases and Insect Pests, Jinan, China
| | - Yifan Zhai
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
- Shandong Provincial Engineering Technology Research Center on Biocontrol of Crops Diseases and Insect Pests, Jinan, China
| | - Hao Zheng
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
- Shandong Provincial Engineering Technology Research Center on Biocontrol of Crops Diseases and Insect Pests, Jinan, China
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27
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Yin J, Li D, Zheng T, Hu B, Wang P. Gastrointestinal Degradation and Toxicity of Disinfection Byproducts in Drinking Water Using In Vitro Models and the Roles of Gut Microbiota. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:16219-16231. [PMID: 37847491 DOI: 10.1021/acs.est.3c04483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Disinfection byproducts (DBPs) in drinking water are mainly exposed to the human body after oral ingestion and degradation in the gastrointestinal tract. The role of gastrointestinal degradation in the toxic effects of DBPs still needs further investigation. In this study, the degradation of five categories of DBPs (22 DBPs) in the stomach and small intestine was investigated based on a semicontinuous steady-state gastrointestinal simulation system, and 22 DBPs can be divided into three groups based on their residual proportions. The degradation of chloroacetonitrile (CAN), dibromoacetic acid (DBAA), and tetrabromopyrrole (FBPy) was further analyzed based on the Simulator of the Human Intestinal Microbial Ecosystem inoculating the gut microbiota, and approximately 60% of CAN, 45% of DBAA, and 80% of FBPy were degraded in the stomach and small intestine, followed by the complete degradation of remaining DBPs in the colon. Meanwhile, gastrointestinal degradation can reduce oxidative stress-mediated DNA damage and apoptosis induced by DBPs in DLD-1 cells, but the toxicity of DBPs did not disappear with the complete degradation of DBPs, possibly because of their interferences on gut microbiota. This study provides new insights into investigating the gastrointestinal toxic effects and mechanisms of DBPs through oral exposure.
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Affiliation(s)
- Jinbao Yin
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, China
| | - Dingxin Li
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, China
| | - Tianming Zheng
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, China
| | - Bin Hu
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, China
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, China
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28
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Wang W, Xia J, Wang Z, Shao Z. Bacterial cell sensing and signaling pathway for external polycyclic aromatic hydrocarbons (PAHs). iScience 2023; 26:107912. [PMID: 37841585 PMCID: PMC10570129 DOI: 10.1016/j.isci.2023.107912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/19/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023] Open
Abstract
The mechanism by which a bacterial cell senses external nutrients remains largely unknown. In this study, we identified a bacterial cell sensing system for polycyclic aromatic hydrocarbons (PAHs) in a common marine PAH-using bacterium, Cycloclasticus. It consists of an outer membrane receptor (PahS) and a periplasmic protein (PahP) in combination with a two-component sensing system (TCS) that ensures a rapid response to PAH occurrence by directly controlling serial reactions including chemotactic sensing and movement, PAH uptake and intracellular PAH metabolism. PahS protrudes from the cell and acts as a PAH sensor, transducing the PAH signal across the outer membrane to its periplasmic partner PahP, which in turn transduces the PAH signal across the periplasm to a specialized TCS. This sensing system plays a critical role in sensing and promoting the metabolism of PAHs, which can be scavenged by various hydrocarbon-degrading bacteria.
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Affiliation(s)
- Wanpeng Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Jingyu Xia
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Zining Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
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Zhao Q, Chen Y, Huang W, Zhou H, Zhang W. Drug-microbiota interactions: an emerging priority for precision medicine. Signal Transduct Target Ther 2023; 8:386. [PMID: 37806986 PMCID: PMC10560686 DOI: 10.1038/s41392-023-01619-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 07/20/2023] [Accepted: 08/24/2023] [Indexed: 10/10/2023] Open
Abstract
Individual variability in drug response (IVDR) can be a major cause of adverse drug reactions (ADRs) and prolonged therapy, resulting in a substantial health and economic burden. Despite extensive research in pharmacogenomics regarding the impact of individual genetic background on pharmacokinetics (PK) and pharmacodynamics (PD), genetic diversity explains only a limited proportion of IVDR. The role of gut microbiota, also known as the second genome, and its metabolites in modulating therapeutic outcomes in human diseases have been highlighted by recent studies. Consequently, the burgeoning field of pharmacomicrobiomics aims to explore the correlation between microbiota variation and IVDR or ADRs. This review presents an up-to-date overview of the intricate interactions between gut microbiota and classical therapeutic agents for human systemic diseases, including cancer, cardiovascular diseases (CVDs), endocrine diseases, and others. We summarise how microbiota, directly and indirectly, modify the absorption, distribution, metabolism, and excretion (ADME) of drugs. Conversely, drugs can also modulate the composition and function of gut microbiota, leading to changes in microbial metabolism and immune response. We also discuss the practical challenges, strategies, and opportunities in this field, emphasizing the critical need to develop an innovative approach to multi-omics, integrate various data types, including human and microbiota genomic data, as well as translate lab data into clinical practice. To sum up, pharmacomicrobiomics represents a promising avenue to address IVDR and improve patient outcomes, and further research in this field is imperative to unlock its full potential for precision medicine.
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Affiliation(s)
- Qing Zhao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, PR China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, PR China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, PR China
| | - Yao Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, PR China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, PR China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, PR China
| | - Weihua Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, PR China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, PR China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, PR China
| | - Honghao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, PR China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, PR China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, PR China
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, PR China.
- The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, PR China.
- The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080, PR China.
- Central Laboratory of Hunan Cancer Hospital, Central South University, 283 Tongzipo Road, Changsha, 410013, PR China.
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30
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Pedroza Matute S, Iyavoo S. Exploring the gut microbiota: lifestyle choices, disease associations, and personal genomics. Front Nutr 2023; 10:1225120. [PMID: 37867494 PMCID: PMC10585655 DOI: 10.3389/fnut.2023.1225120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 09/19/2023] [Indexed: 10/24/2023] Open
Abstract
The gut microbiota is a rich and dynamic ecosystem that actively interacts with the human body, playing a significant role in the state of health and disease of the host. Diet, exercise, mental health, and other factors have exhibited the ability to influence the gut bacterial composition, leading to changes that can prevent and improve, or favor and worsen, both intestinal and extra-intestinal conditions. Altered gut microbial states, or 'dysbiosis', associated with conditions and diseases are often characterized by shifts in bacterial abundance and diversity, including an impaired Firmicutes to Bacteroidetes ratio. By understanding the effect of lifestyle on the gut microbiota, personalized advice can be generated to suit each individual profile and foster the adoption of lifestyle changes that can both prevent and ameliorate dysbiosis. The delivery of effective and reliable advice, however, depends not only on the available research and current understanding of the topic, but also on the methods used to assess individuals and to discover the associations, which can introduce bias at multiple stages. The aim of this review is to summarize how human gut microbial variability is defined and what lifestyle choices and diseases have shown association with gut bacterial composition. Furthermore, popular methods to investigate the human gut microbiota are outlined, with a focus on the possible bias caused by the lack of use of standardized methods. Finally, an overview of the current state of personalized advice based on gut microbiota testing is presented, underlining its power and limitations.
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Affiliation(s)
| | - Sasitaran Iyavoo
- Nkaarco Diagnostics Limited, Norwich, United Kingdom
- School of Chemistry, College of Health and Science, University of Lincoln, Lincoln, United Kingdom
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31
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Wuyts S, Alves R, Zimmermann‐Kogadeeva M, Nishijima S, Blasche S, Driessen M, Geyer PE, Hercog R, Kartal E, Maier L, Müller JB, Garcia Santamarina S, Schmidt TSB, Sevin DC, Telzerow A, Treit PV, Wenzel T, Typas A, Patil KR, Mann M, Kuhn M, Bork P. Consistency across multi-omics layers in a drug-perturbed gut microbial community. Mol Syst Biol 2023; 19:e11525. [PMID: 37485738 PMCID: PMC10495815 DOI: 10.15252/msb.202311525] [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: 01/09/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/25/2023] Open
Abstract
Multi-omics analyses are used in microbiome studies to understand molecular changes in microbial communities exposed to different conditions. However, it is not always clear how much each omics data type contributes to our understanding and whether they are concordant with each other. Here, we map the molecular response of a synthetic community of 32 human gut bacteria to three non-antibiotic drugs by using five omics layers (16S rRNA gene profiling, metagenomics, metatranscriptomics, metaproteomics and metabolomics). We find that all the omics methods with species resolution are highly consistent in estimating relative species abundances. Furthermore, different omics methods complement each other for capturing functional changes. For example, while nearly all the omics data types captured that the antipsychotic drug chlorpromazine selectively inhibits Bacteroidota representatives in the community, the metatranscriptome and metaproteome suggested that the drug induces stress responses related to protein quality control. Metabolomics revealed a decrease in oligosaccharide uptake, likely caused by Bacteroidota depletion. Our study highlights how multi-omics datasets can be utilized to reveal complex molecular responses to external perturbations in microbial communities.
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Affiliation(s)
- Sander Wuyts
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Renato Alves
- European Molecular Biology LaboratoryHeidelbergGermany
| | | | | | - Sonja Blasche
- European Molecular Biology LaboratoryHeidelbergGermany
- Medical Research Council Toxicology UnitCambridgeUK
| | | | - Philipp E Geyer
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Rajna Hercog
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Ece Kartal
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Lisa Maier
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Johannes B Müller
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Sarela Garcia Santamarina
- European Molecular Biology LaboratoryHeidelbergGermany
- Present address:
MOSTMICRO Unit, Instituto de Tecnologia Quimica e BiologicaUniversidade Nova de LisboaOeirasPortugal
| | | | | | - Anja Telzerow
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Peter V Treit
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Tobias Wenzel
- European Molecular Biology LaboratoryHeidelbergGermany
- Present address:
Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological SciencesPontificia Universidad Catolica de ChileSantiagoChile
| | | | - Kiran R Patil
- European Molecular Biology LaboratoryHeidelbergGermany
- Medical Research Council Toxicology UnitCambridgeUK
| | - Matthias Mann
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
- Proteomics Program, NNF Center for Protein Research, Faculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Michael Kuhn
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Peer Bork
- European Molecular Biology LaboratoryHeidelbergGermany
- Max Delbrück Centre for Molecular MedicineBerlinGermany
- Yonsei Frontier Lab (YFL)Yonsei UniversitySeoulSouth Korea
- Department of Bioinformatics, BiocenterUniversity of WürzburgWürzburgGermany
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32
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Katagiri S, Ohsugi Y, Shiba T, Yoshimi K, Nakagawa K, Nagasawa Y, Uchida A, Liu A, Lin P, Tsukahara Y, Iwata T, Tohara H. Homemade blenderized tube feeding improves gut microbiome communities in children with enteral nutrition. Front Microbiol 2023; 14:1215236. [PMID: 37680532 PMCID: PMC10482415 DOI: 10.3389/fmicb.2023.1215236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 08/09/2023] [Indexed: 09/09/2023] Open
Abstract
Enteral nutrition for children is supplied through nasogastric or gastrostomy tubes. Diet not only influences nutritional intake but also interacts with the composition and function of the gut microbiota. Homemade blenderized tube feeding has been administered to children receiving enteral nutrition, in addition to ready-made tube feeding. The purpose of this study was to evaluate the oral/gut microbial communities in children receiving enteral nutrition with or without homemade blenderized tube feeding. Among a total of 30 children, 6 receiving mainly ready-made tube feeding (RTF) and 5 receiving mainly homemade blenderized tube feeding (HBTF) were analyzed in this study. Oral and gut microbiota community profiles were evaluated through 16S rRNA sequencing of saliva and fecal samples. The α-diversity representing the number of observed features, Shannon index, and Chao1 in the gut were significantly increased in HBTF only in the gut microbiome but not in the oral microbiome. In addition, the relative abundances of the phylum Proteobacteria, class Gammaproteobacteria, and genus Escherichia-Shigella were significantly low, whereas that of the genus Ruminococcus was significantly high in the gut of children with HBTF, indicating HBTF altered the gut microbial composition and reducing health risks. Metagenome prediction showed enrichment of carbon fixation pathways in prokaryotes at oral and gut microbiomes in children receiving HBTF. In addition, more complex network structures were observed in the oral cavity and gut in the HBTF group than in the RTF group. In conclusion, HBTF not only provides satisfaction and enjoyment during meals with the family but also alters the gut microbial composition to a healthy state.
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Affiliation(s)
- Sayaka Katagiri
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yujin Ohsugi
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Takahiko Shiba
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, MA, United States
| | - Kanako Yoshimi
- Department of Dysphagia Rehabilitation, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Kazuharu Nakagawa
- Department of Dysphagia Rehabilitation, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yuki Nagasawa
- Department of Dysphagia Rehabilitation, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Aritoshi Uchida
- Department of Dysphagia Rehabilitation, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Anhao Liu
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Peiya Lin
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yuta Tsukahara
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Takanori Iwata
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Haruka Tohara
- Department of Dysphagia Rehabilitation, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
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Yan Y, Wang Z, Zhou YL, Gao Z, Ning L, Zhao Y, Xuan B, Ma Y, Tong T, Huang X, Hu M, Fang JY, Cui Z, Chen H, Hong J. Commensal bacteria promote azathioprine therapy failure in inflammatory bowel disease via decreasing 6-mercaptopurine bioavailability. Cell Rep Med 2023; 4:101153. [PMID: 37586320 PMCID: PMC10439275 DOI: 10.1016/j.xcrm.2023.101153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 06/07/2023] [Accepted: 07/18/2023] [Indexed: 08/18/2023]
Abstract
Azathioprine (AZA) therapy failure, though not the primary cause, contributes to disease relapse and progression in inflammatory bowel disease (IBD). However, the role of gut microbiota in AZA therapy failure remains poorly understood. We found a high prevalence of Blautia wexlerae in patients with IBD with AZA therapy failure, associated with shorter disease flare survival time. Colonization of B. wexlerae increased inflammatory macrophages and compromised AZA's therapeutic efficacy in mice with intestinal colitis. B. wexlerae colonization reduced 6-mercaptopurine (6-MP) bioavailability by enhancing selenium-dependent xanthine dehydrogenase (sd-XDH) activity. The enzyme sd-XDH converts 6-MP into its inactive metabolite, 6-thioxanthine (6-TX), thereby impairing its ability to inhibit inflammation in mice. Supplementation with Bacillus (B.) subtilis enriched in hypoxanthine phosphoribosyltransferase (HPRT) effectively mitigated B. wexlerae-induced AZA treatment failure in mice with intestinal colitis. These findings emphasize the need for tailored management strategies based on B. wexlerae levels in patients with IBD.
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Affiliation(s)
- Yuqing Yan
- State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Zhenhua Wang
- State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Yi-Lu Zhou
- State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Ziyun Gao
- State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Lijun Ning
- State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Ying Zhao
- State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Baoqin Xuan
- State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Yanru Ma
- State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Tianying Tong
- State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Xiaowen Huang
- State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Muni Hu
- State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Jing-Yuan Fang
- State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Zhe Cui
- Department of Gastrointestinal Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 145 Middle Shandong Road, Shanghai 200001, China.
| | - Haoyan Chen
- State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China.
| | - Jie Hong
- State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China.
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34
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Hou R, Zhang S, Huang Q, Lin L, Li H, Li J, Liu S, Sun C, Xu X. Role of Gastrointestinal Microbiota from Crucian Carp in Microbial Transformation and Estrogenicity Modification of Novel Plastic Additives. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:11476-11488. [PMID: 37462611 DOI: 10.1021/acs.est.3c03595] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Ingestion is a major exposure route for hydrophobic organic pollutants in fish, but the microbial transformation and estrogenic modification of the novel plastic additives by the gut microbiota of fish remain obscure. Using an in vitro approach, we provide evidence that structure-related transformation of various plastic additives by the gastric and intestinal (GI) microbiota from crucian carp, with the degradation ratio of bisphenols and triphenyl phosphate faster than those of brominated compounds. The degradation kinetics for these pollutants could be limited by oxygen and cometabolic substrates (i.e., glucose). The fish GI microbiota could utilize the vast majority of carbon sources in a Biolog EcoPlate, suggesting their high metabolic potential and ability to transform various organic compounds. Unique microorganisms associated with transformation of the plastic additives including genera of Citrobacter, Klebsiella, and some unclassified genera in Enterobacteriaceae were identified by combining high-throughput genetic analyses and metagenomic analyses. Through identification of anaerobic transformation products by high-resolution mass spectrometry, alkyl-cleavage was found the common transformation mechanism, and hydrolysis was the major pathway for ester-containing pollutants. After anaerobic incubation, the estrogenic activities of triphenyl phosphate and bisphenols A, F, and AF declined, whereas that of bisphenol AP increased.
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Affiliation(s)
- Rui Hou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Siqi Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qianyi Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lang Lin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Hengxiang Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Sanya 572100, China
| | - Jingxi Li
- Key Laboratory of Marine Eco-environmental Science and Technology, Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Shan Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Sanya 572100, China
| | - Chengjun Sun
- Key Laboratory of Marine Eco-environmental Science and Technology, Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Xiangrong Xu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Sanya 572100, China
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Barouki R, Samson M, Blanc EB, Colombo M, Zucman-Rossi J, Lazaridis KN, Miller GW, Coumoul X. The exposome and liver disease - how environmental factors affect liver health. J Hepatol 2023; 79:492-505. [PMID: 36889360 PMCID: PMC10448911 DOI: 10.1016/j.jhep.2023.02.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 03/10/2023]
Abstract
Since the initial development of the exposome concept, much effort has been devoted to the characterisation of the exposome through analytical, epidemiological, and toxicological/mechanistic studies. There is now an urgent need to link the exposome to human diseases and to include exposomics in the characterisation of environment-linked pathologies together with genomics and other omics. Liver diseases are particularly well suited for such studies since major functions of the liver include the detection, detoxification, and elimination of xenobiotics, as well as inflammatory responses. It is well known that several liver diseases are associated with i) addictive behaviours such as alcohol consumption, smoking, and to a certain extent dietary imbalance and obesity, ii) viral and parasitic infections, and iii) exposure to toxins and occupational chemicals. Recent studies indicate that environmental exposures are also significantly associated with liver diseases, and these include air pollution (particulate matter and volatile chemicals), contaminants such as polyaromatic hydrocarbons, bisphenol A and per-and poly-fluorinated substances, and physical stressors such as radiation. Furthermore, microbial metabolites and the "gut-liver" axis play a major role in liver diseases. Exposomics is poised to play a major role in the field of liver pathology. Methodological advances such as the exposomics-metabolomics framework, the determination of risk factors' genomic and epigenomic signatures, and cross-species biological pathway analysis should further delineate the impact of the exposome on the liver, opening the way for improved prevention, as well as the identification of new biomarkers of exposure and effects, and additional therapeutic targets.
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Affiliation(s)
| | - Michel Samson
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | | | - Massimo Colombo
- San Raffaele Hospital, Liver Center, Via Olgettina 60, 20132, Milan, Italy
| | - Jessica Zucman-Rossi
- Centre de Recherche des Cordeliers, Université Paris Cité, Sorbonne Université, Inserm, AP-HP, Hôpital Européen Georges Pompidou, Institut du Cancer Paris CARPEM, F-75006, Paris, France
| | | | - Gary W Miller
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, 10032, USA
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36
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Koukou Z, Papadopoulou E, Panteris E, Papadopoulou S, Skordou A, Karamaliki M, Diamanti E. The Effect of Breastfeeding on Food Allergies in Newborns and Infants. CHILDREN (BASEL, SWITZERLAND) 2023; 10:1046. [PMID: 37371277 DOI: 10.3390/children10061046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 05/10/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023]
Abstract
Breastfeeding is the preferred method of infant feeding and its establishment is one of the primary goals for the infant. Allergic diseases are common in childhood, with increased morbidity. Food allergies are also associated with a strong negative impact on health-related quality of life and is a major public health problem. In addition, maternal exclusion of common allergens during pregnancy and/or lactation suggests that supplementation with regular cow's milk formula during the first week of life should be avoided. Breast milk contains many active immune factors, such as cytokines, inflammatory mediators, signaling molecules and soluble receptors, which may also reduce the risk of allergic disease. The prophylactic effects of breastfeeding have been the subject of many studies, some with weak evidence. In this narrative review, we aim to provide an up-to-date account of the effects of prophylactic breastfeeding on food allergy and other common allergies in infants and children up to 5 years of age. Colostrum in particular has been shown to be prophylactic against food allergy. The American Academy of Pediatrics cautions that the relationship between duration of breastfeeding and incidence of food allergy in early childhood is unclear. The protective role of breastfeeding has a positive effect on allergy prevention, which is opposed by the early introduction of solid foods, but larger studies are needed to confirm the evidence. There is evidence that breastfeeding is effective in providing partial protection to infants.
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Affiliation(s)
- Zoi Koukou
- School of Health Sciences, International Hellenic University (IHU), Sindos, 57400 Thessaloniki, Greece
| | | | - Eleftherios Panteris
- Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Styliani Papadopoulou
- School of Health Sciences, International Hellenic University (IHU), Sindos, 57400 Thessaloniki, Greece
| | - Anna Skordou
- School of Health Sciences, International Hellenic University (IHU), Sindos, 57400 Thessaloniki, Greece
| | - Maria Karamaliki
- School of Health Sciences, International Hellenic University (IHU), Sindos, 57400 Thessaloniki, Greece
| | - Elisavet Diamanti
- School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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Zheng DW, Qiao JY, Ma JC, An JX, Yang CH, Zhang Y, Cheng Q, Rao ZY, Zeng SM, Wang L, Zhang XZ. A Microbial Community Cultured in Gradient Hydrogel for Investigating Gut Microbiome-Drug Interaction and Guiding Therapeutic Decisions. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2300977. [PMID: 37029611 DOI: 10.1002/adma.202300977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/29/2023] [Indexed: 06/02/2023]
Abstract
Despite the recognition that the gut microbiota acts a clinically significant role in cancer chemotherapy, both mechanistic understanding and translational research are still limited. Maximizing drug efficacy requires an in-depth understanding of how the microbiota contributes to therapeutic responses, while microbiota modulation is hindered by the complexity of the human body. To address this issue, a 3D experimental model named engineered microbiota (EM) is reported for bridging microbiota-drug interaction research and therapeutic decision-making. EM can be manipulated in vitro and faithfully recapitulate the human gut microbiota at the genus/species level while allowing co-culture with cells, organoids, and isolated tissues for testing drug responses. Examination of various clinical and experimental drugs by EM reveales that the gut microbiota affects drug efficacy through three pathways: immunological effects, bioaccumulation, and drug metabolism. Guided by discovered mechanisms, custom-tailored strategies are adopted to maximize the therapeutic efficacy of drugs on orthotopic tumor models with patient-derived gut microbiota. These strategies include immune synergy, nanoparticle encapsulation, and host-guest complex formation, respectively. Given the important role of the gut microbiota in influencing drug efficacy, EM will likely become an indispensable tool to guide drug translation and clinical decision-making.
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Affiliation(s)
- Di-Wei Zheng
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, P. R. China
| | - Ji-Yan Qiao
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, P. R. China
| | - Jun-Chi Ma
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, P. R. China
| | - Jia-Xin An
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, P. R. China
| | - Chi-Hui Yang
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, P. R. China
| | - Yu Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, P. R. China
| | - Qian Cheng
- Research Center for Tissue Engineering and Regenerative Medicine & Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, P. R. China
- Research Center for Tissue Engineering and Regenerative Medicine & Department of Clinical Laboratory, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, P. R. China
| | - Zhi-Yong Rao
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, P. R. China
| | - Si-Min Zeng
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, P. R. China
| | - Lin Wang
- Research Center for Tissue Engineering and Regenerative Medicine & Department of Clinical Laboratory, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, P. R. China
| | - Xian-Zheng Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, P. R. China
- Department of Traditional Chinese Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, P. R. China
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Du B, Xiao X, Wang H, Li W, Xia Z, Yang P, Huang SK, Yuan R, Liu J, Han M, Zou Y, Zhu J, He D, Lyu J, Jin X, Xu X, Wang J, Yang H, Xiao L, Liu X, Kristiansen K. Evaluation of the Impact of BaP Exposure on the Gut Microbiota and Allergic Responses in an OVA-Sensitized Mouse Model. ENVIRONMENTAL HEALTH PERSPECTIVES 2023; 131:67004. [PMID: 37267060 DOI: 10.1289/ehp11874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
BACKGROUND Exposure to environmental pollutants, including benzo[a]pyrene (BaP), has been implicated in allergic diseases and intestinal microbiota homeostasis, but the environment-microbiota-immunity triangular relationship and to what extent BaP-induced remodeling of the gut microbiota contributes to intestinal allergic inflammation remain to be established. OBJECTIVES We investigated the impact of BaP on intestinal allergic inflammation and examined the relationship between this effect and gut microbiota dysbiosis. We explored the potential ability of intestinal bacteria to degrade BaP and alleviate cytotoxicity as a detoxification strategy to counteract the effects of BaP exposure. METHODS We combined microbiome shotgun metagenomics with animal histological and intestinal allergic inflammatory responses to assess the effects of BaP (50μg/mouse per day) in a 23-d toxicity test in antigen-induced allergic female mice. In addition, genome annotation, quantitative analysis of BaP, and in vitro cytotoxicity-tests using CaCo-2 cells were conducted to infer the role of intestinal bacteria in BaP detoxification. RESULTS BaP exposure impacted the taxonomic composition and the functional potential of the gut microbiota and aggravated antigen-induced intestinal allergic inflammatory responses. The level of inflammatory cytokines correlated with the abundance of specific bacterial taxa, including Lachnospiraceae bacterium 28-4 and Alistipes inops. We identified 614 bacteria harboring genes implicated in the degradation of BaP, and 4 of these bacterial strains were shown to significantly reduce the cytotoxicity of BaP to CaCo-2 cells in vitro. DISCUSSION Using allergic female mice as a model, we investigated the relationship between BaP, microbiota, and host immune reactions, highlighting the role of gut bacteria in BaP-aggravated allergic reactions. Our findings offer novel insight toward establishing the causal relationship between BaP exposure and the occurrence of allergic disorders. Identifying gut bacteria that degrade BaP may provide new strategies for ameliorating BaP cytotoxicity. https://doi.org/10.1289/EHP11874.
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Affiliation(s)
- Beibei Du
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Xiaojun Xiao
- State Key Laboratory of Respiratory Disease for Allergy at Shenzhen University, Shenzhen Key Laboratory of Allergy and Immunology, Shenzhen University School of Medicine, Shenzhen, China
| | - Huailing Wang
- State Key Laboratory of Respiratory Disease for Allergy at Shenzhen University, Shenzhen Key Laboratory of Allergy and Immunology, Shenzhen University School of Medicine, Shenzhen, China
| | - Wenxi Li
- BGI-Shenzhen, Shenzhen, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | | | - Pingchang Yang
- State Key Laboratory of Respiratory Disease for Allergy at Shenzhen University, Shenzhen Key Laboratory of Allergy and Immunology, Shenzhen University School of Medicine, Shenzhen, China
- National Institute of Environmental Health Sciences, National Health Research Institutes, Taiwan, China
| | - Shau-Ku Huang
- National Institute of Environmental Health Sciences, National Health Research Institutes, Taiwan, China
- Department of Allergy, Third Affiliated Hospital of Shenzhen University, Shenzhen, China
- Department of Medicine, Division of Allergy and Clinical Immunology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ruyi Yuan
- State Key Laboratory of Respiratory Disease for Allergy at Shenzhen University, Shenzhen Key Laboratory of Allergy and Immunology, Shenzhen University School of Medicine, Shenzhen, China
| | - Jie Liu
- State Key Laboratory of Respiratory Disease for Allergy at Shenzhen University, Shenzhen Key Laboratory of Allergy and Immunology, Shenzhen University School of Medicine, Shenzhen, China
| | - Mo Han
- BGI-Shenzhen, Shenzhen, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, Shenzhen, China
| | - Yuanqiang Zou
- BGI-Shenzhen, Shenzhen, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, Shenzhen, China
- Qingdao-Europe Advanced Institute for Life Sciences, Qingdao, China
| | | | | | | | - Xin Jin
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China
| | | | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China
- Qingdao-Europe Advanced Institute for Life Sciences, Qingdao, China
| | - Liang Xiao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, Shenzhen, China
- Qingdao-Europe Advanced Institute for Life Sciences, Qingdao, China
| | - Xiaoyu Liu
- State Key Laboratory of Respiratory Disease for Allergy at Shenzhen University, Shenzhen Key Laboratory of Allergy and Immunology, Shenzhen University School of Medicine, Shenzhen, China
| | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Qingdao-Europe Advanced Institute for Life Sciences, Qingdao, China
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Pinto CJG, Ávila-Gálvez MÁ, Lian Y, Moura-Alves P, Nunes Dos Santos C. Targeting the aryl hydrocarbon receptor by gut phenolic metabolites: A strategy towards gut inflammation. Redox Biol 2023; 61:102622. [PMID: 36812782 PMCID: PMC9958510 DOI: 10.1016/j.redox.2023.102622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/25/2023] [Accepted: 01/30/2023] [Indexed: 02/04/2023] Open
Abstract
The Aryl Hydrocarbon Receptor (AHR) is a ligand-dependent transcription factor able to control complex transcriptional processes in several cell types, which has been correlated with various diseases, including inflammatory bowel diseases (IBD). Numerous studies have described different compounds as ligands of this receptor, like xenobiotics, natural compounds, and several host-derived metabolites. Dietary (poly)phenols have been studied regarding their pleiotropic activities (e.g., neuroprotective and anti-inflammatory), but their AHR modulatory capabilities have also been considered. However, dietary (poly)phenols are submitted to extensive metabolism in the gut (e.g., gut microbiota). Thus, the resulting gut phenolic metabolites could be key players modulating AHR since they are the ones that reach the cells and may exert effects on the AHR throughout the gut and other organs. This review aims at a comprehensive search for the most abundant gut phenolic metabolites detected and quantified in humans to understand how many have been described as AHR modulators and what could be their impact on inflammatory gut processes. Even though several phenolic compounds have been studied regarding their anti-inflammatory capacities, only 1 gut phenolic metabolite, described as AHR modulator, has been evaluated on intestinal inflammatory models. Searching for AHR ligands could be a novel strategy against IBD.
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Affiliation(s)
- Catarina J G Pinto
- iNOVA4Health, NOVA Medical School
- Faculdade de Ciências Médicas, NMS
- FCM, Universidade Nova de Lisboa, Lisboa, Portugal; IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal; I3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - María Ángeles Ávila-Gálvez
- iNOVA4Health, NOVA Medical School
- Faculdade de Ciências Médicas, NMS
- FCM, Universidade Nova de Lisboa, Lisboa, Portugal; iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras, Portugal
| | - Yilong Lian
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, OX3 7DQ, Oxford, United Kingdom
| | - Pedro Moura-Alves
- IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal; I3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal; Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, OX3 7DQ, Oxford, United Kingdom.
| | - Cláudia Nunes Dos Santos
- iNOVA4Health, NOVA Medical School
- Faculdade de Ciências Médicas, NMS
- FCM, Universidade Nova de Lisboa, Lisboa, Portugal; iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras, Portugal.
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Lomakin IB, Devarkar SC, Patel S, Grada A, Bunick C. Sarecycline inhibits protein translation in Cutibacterium acnes 70S ribosome using a two-site mechanism. Nucleic Acids Res 2023; 51:2915-2930. [PMID: 36864821 PMCID: PMC10085706 DOI: 10.1093/nar/gkad103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 03/04/2023] Open
Abstract
Acne vulgaris is a chronic disfiguring skin disease affecting ∼1 billion people worldwide, often having persistent negative effects on physical and mental health. The Gram-positive anaerobe, Cutibacterium acnes is implicated in acne pathogenesis and is, therefore, a main target for antibiotic-based acne therapy. We determined a 2.8-Å resolution structure of the 70S ribosome of Cutibacterium acnes by cryogenic electron microscopy and discovered that sarecycline, a narrow-spectrum antibiotic against Cutibacterium acnes, may inhibit two active sites of this bacterium's ribosome in contrast to the one site detected previously on the model ribosome of Thermus thermophilus. Apart from the canonical binding site at the mRNA decoding center, the second binding site for sarecycline exists at the nascent peptide exit tunnel, reminiscent of the macrolides class of antibiotics. The structure also revealed Cutibacterium acnes-specific features of the ribosomal RNA and proteins. Unlike the ribosome of the Gram-negative bacterium Escherichia coli, Cutibacterium acnes ribosome has two additional proteins, bS22 and bL37, which are also present in the ribosomes of Mycobacterium smegmatis and Mycobacterium tuberculosis. We show that bS22 and bL37 have antimicrobial properties and may be involved in maintaining the healthy homeostasis of the human skin microbiome.
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Affiliation(s)
- Ivan B Lomakin
- Department of Dermatology, Yale University School of Medicine, New Haven, CT06520, USA
| | - Swapnil C Devarkar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06520, USA
| | - Shivali Patel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06520, USA
| | - Ayman Grada
- Department of Dermatology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Christopher G Bunick
- Department of Dermatology, Yale University School of Medicine, New Haven, CT06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06520, USA
- Program in Translational Biomedicine, Yale University School of Medicine, New Haven, CT 06520, USA
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Kelly JR, Clarke G, Harkin A, Corr SC, Galvin S, Pradeep V, Cryan JF, O'Keane V, Dinan TG. Seeking the Psilocybiome: Psychedelics meet the microbiota-gut-brain axis. Int J Clin Health Psychol 2023; 23:100349. [PMID: 36605409 PMCID: PMC9791138 DOI: 10.1016/j.ijchp.2022.100349] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/16/2022] [Indexed: 12/15/2022] Open
Abstract
Moving towards a systems psychiatry paradigm embraces the inherent complex interactions across all levels from micro to macro and necessitates an integrated approach to treatment. Cortical 5-HT2A receptors are key primary targets for the effects of serotonergic psychedelics. However, the therapeutic mechanisms underlying psychedelic therapy are complex and traverse molecular, cellular, and network levels, under the influence of biofeedback signals from the periphery and the environment. At the interface between the individual and the environment, the gut microbiome, via the gut-brain axis, plays an important role in the unconscious parallel processing systems regulating host neurophysiology. While psychedelic and microbial signalling systems operate over different timescales, the microbiota-gut-brain (MGB) axis, as a convergence hub between multiple biofeedback systems may play a role in the preparatory phase, the acute administration phase, and the integration phase of psychedelic therapy. In keeping with an interconnected systems-based approach, this review will discuss the gut microbiome and mycobiome and pathways of the MGB axis, and then explore the potential interaction between psychedelic therapy and the MGB axis and how this might influence mechanism of action and treatment response. Finally, we will discuss the possible implications for a precision medicine-based psychedelic therapy paradigm.
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Affiliation(s)
- John R. Kelly
- Department of Psychiatry, Trinity College, Dublin, Ireland
- Tallaght University Hospital, Dublin, Ireland
| | - Gerard Clarke
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Sinead C. Corr
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Microbiology, Trinity College Dublin, Ireland
| | - Stephen Galvin
- Department of Psychiatry, Trinity College, Dublin, Ireland
| | - Vishnu Pradeep
- Department of Psychiatry, Trinity College, Dublin, Ireland
- Tallaght University Hospital, Dublin, Ireland
| | - John F. Cryan
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Veronica O'Keane
- Department of Psychiatry, Trinity College, Dublin, Ireland
- Tallaght University Hospital, Dublin, Ireland
- Trinity College Institute of Neuroscience, Ireland
| | - Timothy G. Dinan
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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42
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Zhang H, Sanidad KZ, Zhang J, Wang G, Zhang R, Hu C, Lin Y, Haggerty TD, Parsonnet J, Zheng Y, Zhang G, Cai Z. Microbiota-mediated reactivation of triclosan oxidative metabolites in colon tissues. JOURNAL OF HAZARDOUS MATERIALS 2023; 445:130509. [PMID: 36463744 PMCID: PMC10187939 DOI: 10.1016/j.jhazmat.2022.130509] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 11/18/2022] [Accepted: 11/26/2022] [Indexed: 05/18/2023]
Abstract
Triclosan (TCS) is a widespread antimicrobial agent that is associated with many adverse health outcomes. Its gut toxicity has been attributed to the molecular modifications mediated by commensal microbes, but microbial transformations of TCS derivatives in the gut lumen are still largely unknown. Aromatic hydroxylation is the predominant oxidative metabolism of TCS that linked to its toxicological effects in host tissues. Here, we aimed to reveal the biological fates of hydroxyl-TCS (OH-TCS) in the colon, where intestinal microbes mainly reside. Unlike the profiles generated via host metabolism, OH-TCS species remain unconjugated in human stools from a cohort study. Through tracking molecular compositions in mouse intestinal tract, elevated abundance of free-form OH-TCS while reduced abundance of conjugated forms was observed in the colon digesta and mucosa. Using antibiotic-treated and germ-free mice, as well as in vitro approaches, we demonstrate that gut microbiota-encoded enzymes efficiently convert glucuronide/sulfate-conjugated OH-TCS, which are generated from host metabolism, back to their bioactive free-forms in colon tissues. Thus, host-gut microbiota metabolic interactions of TCS derivatives were proposed. These results shed light on the crucial roles of microbial metabolism in TCS toxicity, and highlight the importance of incorporating gut microbial transformations in health risk assessment of environmental chemicals.
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Affiliation(s)
- Hongna Zhang
- Department of Occupational and Environmental Health, School of Public Health, Qingdao University, Qingdao 266071, China; State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, China
| | - Katherine Z Sanidad
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA
| | - Jianan Zhang
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA
| | - Guangqiang Wang
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA; School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Rong Zhang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, China
| | - Chengchen Hu
- Department of Occupational and Environmental Health, School of Public Health, Qingdao University, Qingdao 266071, China
| | - Yongfeng Lin
- Department of Occupational and Environmental Health, School of Public Health, Qingdao University, Qingdao 266071, China
| | - Thomas D Haggerty
- Department of Medicine and Department of Health Research and Policy, Stanford University, Stanford, CA 94305, USA
| | - Julie Parsonnet
- Department of Medicine and Department of Health Research and Policy, Stanford University, Stanford, CA 94305, USA
| | - Yuxin Zheng
- Department of Occupational and Environmental Health, School of Public Health, Qingdao University, Qingdao 266071, China
| | - Guodong Zhang
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA; Department of Food Science and Technology, National University of Singapore, Singapore.
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, China.
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Tian B, Liu J. Smart stimuli-responsive chitosan hydrogel for drug delivery: A review. Int J Biol Macromol 2023; 235:123902. [PMID: 36871689 DOI: 10.1016/j.ijbiomac.2023.123902] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/21/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023]
Abstract
Smart stimuli-responsive materials can respond to different signals (pH, temperature, light, electricity, etc.), and they have become a hot research topic for drug delivery. As a polysaccharide polymer with excellent biocompatibility, chitosan can be obtained from diverse natural sources. Chitosan hydrogels with different stimuli-response capabilities are widely applied in the drug delivery field. This review highlights and discusses the research progress on chitosan hydrogels concerning their stimuli-responsive capabilities. The feature of various stimuli-responsive kinds of hydrogels is outlined, and their potential use of drug delivery is summarized. Furthermore, the questions and future development chances of stimuli-responsive chitosan hydrogels are analyzed by comparing the current published literature, and the directions for the intelligent development of chitosan hydrogels are discussed.
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Affiliation(s)
- Bingren Tian
- Institute of Medical Sciences, General Hospital of Ningxia Medical University, Yinchuan 750004, Ningxia, China; Key Laboratory of Ningxia Stem Cell and Regenerative Medicine, General Hospital of Ningxia Medical University, Yinchuan 750004, Ningxia, China.
| | - Jiayue Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, Macau SAR, China.
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44
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Malwe AS, Srivastava GN, Sharma VK. GutBug: A Tool for Prediction of Human Gut Bacteria Mediated Biotransformation of Biotic and Xenobiotic Molecules Using Machine Learning. J Mol Biol 2023. [DOI: 10.1016/j.jmb.2023.168056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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45
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Xu F, Xie Q, Kuang W, Dong Z. Interactions Between Antidepressants and Intestinal Microbiota. Neurotherapeutics 2023; 20:359-371. [PMID: 36881351 PMCID: PMC10121977 DOI: 10.1007/s13311-023-01362-8] [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] [Accepted: 02/27/2023] [Indexed: 03/08/2023] Open
Abstract
The microbiota-gut-brain axis has been shown to influence human health and diseases, including depression. The interactions between drugs and intestinal microbiota are complex and highly relevant to treat diseases. Studies have shown an interaction between antidepressants and intestinal microbiota. Antidepressants may alter the abundance and composition of intestinal microbiota, which are closely related to the treatment outcomes of depression. Intestinal microbiota can influence the metabolism of antidepressants to change their availability (e.g., tryptophan can be metabolized to kynurenine by intestinal microbiota) and regulate their absorption by affecting intestinal permeability. In addition, the permeability of the blood-brain barrier can be altered by intestinal microbiota, influencing antidepressants to reach the central nervous system. Bioaccumulation is also a type of drug-microbiota interaction, which means bacteria accumulate drugs without biotransformation. These findings imply that it is important to consider intestinal microbiota when evaluating antidepressant therapy regimens and that intestinal microbiota can be a potential target for depression treatment.
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Affiliation(s)
- Feiyu Xu
- West China School of Medicine, Sichuan University, Chengdu, 610041, China
| | - Qinglian Xie
- Department of Outpatient, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Weihong Kuang
- Mental Health Center of West China Hospital, Sichuan University, Chengdu, 610041, China
- Department of Psychiatry and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zaiquan Dong
- Mental Health Center of West China Hospital, Sichuan University, Chengdu, 610041, China.
- Department of Psychiatry and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China.
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46
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Fang D, Xu T, Sun J, Shi J, Li F, Yin Y, Wang Z, Liu Y. Nicotinamide Mononucleotide Ameliorates Sleep Deprivation-Induced Gut Microbiota Dysbiosis and Restores Colonization Resistance against Intestinal Infections. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2207170. [PMID: 36698264 PMCID: PMC10037695 DOI: 10.1002/advs.202207170] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Indexed: 06/12/2023]
Abstract
Gut microbiota-mediated colonization resistance (CR) is crucial in protecting the host from intestinal infections. Sleep deprivation (SD) is an important contributor in the disturbances of intestinal homeostasis. However, whether and how SD affects host CR remains largely unknown. Here, it is shown that SD impairs intestinal CR in mice, whereas nicotinamide mononucleotide (NMN) supplementation restores it. Microbial diversity and metabolomic analyses suggest that gut microbiota and metabolite profiles in SD-treated mice are highly shaped, whereas NMN reprograms these differences. Specifically, the altered gut microbiota in SD mice further incurs the disorder of secondary bile acids pool accompanied by a decrease in deoxycholic acid (DCA). Conversely, NMN supplementation retakes the potential benefits of DCA, which is associated with specific gut microbiota involved in primary bile acids metabolic flux. In animal models of infection, DCA is effective in preventing and treating bacterial infections when used alone or in combination with antibiotics. Mechanistically, DCA alone disrupts membrane permeability and aggravates oxidative damage, thereby reducing intestinal pathogen burden. Meanwhile, exogenous DCA promotes antibiotic accumulation and destroys oxidant-antioxidant system, thus potentiating antibiotic efficacy. Overall, this work highlights the important roles of gut microbiota and bile acid metabolism in the maintenance of intestinal CR.
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Affiliation(s)
- Dan Fang
- College of Veterinary MedicineYangzhou UniversityYangzhou225009P. R. China
| | - Tianqi Xu
- College of Veterinary MedicineYangzhou UniversityYangzhou225009P. R. China
| | - Jingyi Sun
- College of Veterinary MedicineYangzhou UniversityYangzhou225009P. R. China
| | - Jingru Shi
- College of Veterinary MedicineYangzhou UniversityYangzhou225009P. R. China
| | - Fulei Li
- College of Veterinary MedicineYangzhou UniversityYangzhou225009P. R. China
| | - Yanqing Yin
- College of Veterinary MedicineYangzhou UniversityYangzhou225009P. R. China
| | - Zhiqiang Wang
- College of Veterinary MedicineYangzhou UniversityYangzhou225009P. R. China
- Jiangsu Co‐innovation Center for Prevention and Control of Important Animal Infectious Diseases and ZoonosesJoint International Research Laboratory of Agriculture and Agri‐Product Safety the Ministry of Education of ChinaYangzhou UniversityYangzhou225009P. R. China
- Institute of Comparative MedicineYangzhou UniversityYangzhou225009P. R. China
| | - Yuan Liu
- College of Veterinary MedicineYangzhou UniversityYangzhou225009P. R. China
- Jiangsu Co‐innovation Center for Prevention and Control of Important Animal Infectious Diseases and ZoonosesJoint International Research Laboratory of Agriculture and Agri‐Product Safety the Ministry of Education of ChinaYangzhou UniversityYangzhou225009P. R. China
- Institute of Comparative MedicineYangzhou UniversityYangzhou225009P. R. China
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47
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Fournier E, Leveque M, Ruiz P, Ratel J, Durif C, Chalancon S, Amiard F, Edely M, Bezirard V, Gaultier E, Lamas B, Houdeau E, Lagarde F, Engel E, Etienne-Mesmin L, Blanquet-Diot S, Mercier-Bonin M. Microplastics: What happens in the human digestive tract? First evidences in adults using in vitro gut models. JOURNAL OF HAZARDOUS MATERIALS 2023; 442:130010. [PMID: 36182891 DOI: 10.1016/j.jhazmat.2022.130010] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/08/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Microplastics (MPs) are ubiquitous in the environment and humans are inevitably exposed to them. However, the effects of MPs in the human digestive environment are largely unknown. The aim of our study was to investigate the impact of repeated exposure to polyethylene (PE) MPs on the human gut microbiota and intestinal barrier using, under adult conditions, the Mucosal Artificial Colon (M-ARCOL) model, coupled with a co-culture of intestinal epithelial and mucus-secreting cells. The composition of the luminal and mucosal gut microbiota was determined by 16S metabarcoding and microbial activities were characterized by gas, short chain fatty acid, volatolomic and AhR activity analyses. Gut barrier integrity was assessed via intestinal permeability, inflammation and mucin synthesis. First, exposure to PE MPs induced donor-dependent effects. Second, an increase in abundances of potentially harmful pathobionts, Desulfovibrionaceae and Enterobacteriaceae, and a decrease in beneficial bacteria such as Christensenellaceae and Akkermansiaceae were observed. These bacterial shifts were associated with changes in volatile organic compounds profiles, notably characterized by increased indole 3-methyl- production. Finally, no significant impact of PE MPs mediated by changes in gut microbial metabolites was reported on the intestinal barrier. Given these adverse effects of repeated ingestion of PE MPs on the human gut microbiota, studying at-risk populations like infants would be a valuable advance.
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Affiliation(s)
- Elora Fournier
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, F-63000 Clermont-Ferrand, France; Toxalim, Research Centre in Food Toxicology, INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, F-31000 Toulouse, France
| | - Mathilde Leveque
- Toxalim, Research Centre in Food Toxicology, INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, F-31000 Toulouse, France
| | - Philippe Ruiz
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, F-63000 Clermont-Ferrand, France
| | - Jeremy Ratel
- INRAE, UR QuaPA, F-63122 Saint-Genès-Champanelle, France
| | - Claude Durif
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, F-63000 Clermont-Ferrand, France
| | - Sandrine Chalancon
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, F-63000 Clermont-Ferrand, France
| | - Frederic Amiard
- Le Mans Université, IMMM UMR-CNRS 6283, Avenue Olivier Messiaen, F-72085, Le Mans Cedex 9, France
| | - Mathieu Edely
- Le Mans Université, IMMM UMR-CNRS 6283, Avenue Olivier Messiaen, F-72085, Le Mans Cedex 9, France
| | - Valerie Bezirard
- Toxalim, Research Centre in Food Toxicology, INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, F-31000 Toulouse, France
| | - Eric Gaultier
- Toxalim, Research Centre in Food Toxicology, INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, F-31000 Toulouse, France
| | - Bruno Lamas
- Toxalim, Research Centre in Food Toxicology, INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, F-31000 Toulouse, France
| | - Eric Houdeau
- Toxalim, Research Centre in Food Toxicology, INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, F-31000 Toulouse, France
| | - Fabienne Lagarde
- Le Mans Université, IMMM UMR-CNRS 6283, Avenue Olivier Messiaen, F-72085, Le Mans Cedex 9, France
| | - Erwan Engel
- INRAE, UR QuaPA, F-63122 Saint-Genès-Champanelle, France
| | - Lucie Etienne-Mesmin
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, F-63000 Clermont-Ferrand, France
| | | | - Muriel Mercier-Bonin
- Toxalim, Research Centre in Food Toxicology, INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, F-31000 Toulouse, France.
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48
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Yang Y, Guo X, Xu T, Yin D. Effects of carbamazepine on gut microbiota, ARGs and intestinal health in zebrafish. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 249:114473. [PMID: 38321688 DOI: 10.1016/j.ecoenv.2022.114473] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 12/18/2022] [Accepted: 12/23/2022] [Indexed: 02/08/2024]
Abstract
Carbamazepine (CBZ) in the aquatic environment is recognized as a potential threat to aquatic organisms and public health. However, the response of organism intestinal health, resistome, microbiota, and their relationship after CBZ exposure has been rarely reported. This study aimed to explore the impacts of CBZ on gut microbiota, antibiotic resistance genes (ARGs) and the expression of intestinal health related genes as well as their interaction using the zebrafish model. 16 S ribosomal RNA sequencing indicated CBZ altered the composition of gut microbiota. Using high-throughput quantitative polymerase chain reaction (HT-qPCR), we found the number and abundance of ARGs were impacted by CBZ levels and exposure duration. We also observed the upregulated expression of the pro-inflammatory gene IL6 and downregulated expression of toll-like receptor gene TLR2 and intestinal barrier gene TJP2a at different exposure times. Correlation analyses revealed that Geobacillus, Rhodococcus, Ralstonia, Delftia, Luteolibacter and Escherichia-Shigella might be the main bacterial genera carrying ARGs. Meanwhile, Cetobacterium and Aeromonas could be the dominant bacteria affecting intestinal health related genes. Our results could contribute to understanding the health risks of CBZ to the intestinal microecology of aquatic animals.
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Affiliation(s)
- Yiting Yang
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
| | - Xueping Guo
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
| | - Ting Xu
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
| | - Daqiang Yin
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
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49
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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.
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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
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50
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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.
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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
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