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Chakravarty K, Gaur S, Kumar R, Jha NK, Gupta PK. Exploring the Multifaceted Therapeutic Potential of Probiotics: A Review of Current Insights and Applications. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10328-x. [PMID: 39069588 DOI: 10.1007/s12602-024-10328-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2024] [Indexed: 07/30/2024]
Abstract
The interplay between human health and the microbiome has gained extensive attention, with probiotics emerging as pivotal therapeutic agents due to their vast potential in treating various health issues. As significant modulators of the gut microbiota, probiotics are crucial in maintaining intestinal homeostasis and enhancing the synthesis of short-chain fatty acids. Despite extensive research over the past decades, there remains an urgent need for a comprehensive and detailed review that encapsulates probiotics' latest insights and applications. This review focusses on the multifaceted roles of probiotics in promoting health and preventing disease, highlighting the complex mechanisms through which these beneficial bacteria influence both gut flora and the human body at large. This paper also explores probiotics' neurological and gastrointestinal applications, focussing on their significant impact on the gut-brain axis and their therapeutic potential in a broad spectrum of pathological conditions. Current innovations in probiotic formulations, mainly focusing on integrating genomics and biotechnological advancements, have also been comprehensively discussed herein. This paper also critically examines the regulatory landscape that governs probiotic use, ensuring safety and efficacy in clinical and dietary settings. By presenting a comprehensive overview of recent studies and emerging trends, this review aims to illuminate probiotics' extensive therapeutic capabilities, leading to future research and clinical applications. However, besides extensive research, further advanced explorations into probiotic interactions and mechanisms will be essential for developing more targeted and effective therapeutic strategies, potentially revolutionizing health care practices for consumers.
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Affiliation(s)
- Kashyapi Chakravarty
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, Uttar Pradesh, 201309, India
| | - Smriti Gaur
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, Uttar Pradesh, 201309, India.
| | - Rohit Kumar
- Centre for Development of Biomaterials and Department of Life Sciences, Sharda School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, 201310, India
| | - Niraj Kumar Jha
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, 201310, India
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, 602105, India
- School of Bioengineering & Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
- Centre of Research Impact and Outcome, Chitkara University, Rajpura, Punjab, 140401, India
| | - Piyush Kumar Gupta
- Centre for Development of Biomaterials and Department of Life Sciences, Sharda School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, 201310, India.
- Department of Biotechnology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand, 248002, India.
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2
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Kulshrestha S, Narad P, Singh B, Pai SS, Vijayaraghavan P, Tandon A, Gupta P, Modi D, Sengupta A. Biomarker Identification for Preterm Birth Susceptibility: Vaginal Microbiome Meta-Analysis Using Systems Biology and Machine Learning Approaches. Am J Reprod Immunol 2024; 92:e13905. [PMID: 39033501 DOI: 10.1111/aji.13905] [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: 04/02/2024] [Revised: 06/25/2024] [Accepted: 07/03/2024] [Indexed: 07/23/2024] Open
Abstract
PROBLEM The vaginal microbiome has a substantial role in the occurrence of preterm birth (PTB), which contributes substantially to neonatal mortality worldwide. However, current bioinformatics approaches mostly concentrate on the taxonomic classification and functional profiling of the microbiome, limiting their abilities to elucidate the complex factors that contribute to PTB. METHOD OF STUDY A total of 3757 vaginal microbiome 16S rRNA samples were obtained from five publicly available datasets. The samples were divided into two categories based on pregnancy outcome: preterm birth (PTB) (N = 966) and term birth (N = 2791). Additionally, the samples were further categorized based on the participants' race and trimester. The 16S rRNA reads were subjected to taxonomic classification and functional profiling using the Parallel-META 3 software in Ubuntu environment. The obtained abundances were analyzed using an integrated systems biology and machine learning approach to determine the key microbes, pathways, and genes that contribute to PTB. The resulting features were further subjected to statistical analysis to identify the top nine features with the greatest effect sizes. RESULTS We identified nine significant features, namely Shuttleworthia, Megasphaera, Sneathia, proximal tubule bicarbonate reclamation pathway, systemic lupus erythematosus pathway, transcription machinery pathway, lepA gene, pepX gene, and rpoD gene. Their abundance variations were observed through the trimesters. CONCLUSIONS Vaginal infections caused by Shuttleworthia, Megasphaera, and Sneathia and altered small metabolite biosynthesis pathways such as lipopolysaccharide folate and retinal may increase the susceptibility to PTB. The identified organisms, genes, pathways, and their networks may be specifically targeted for the treatment of bacterial infections that increase PTB risk.
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Affiliation(s)
- Sudeepti Kulshrestha
- Systems Biology and Data Analytics Research Lab, Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | - Priyanka Narad
- Division of Biomedical Informatics (BMI), Indian Council of Medical Research, Ansari Nagar, New Delhi, India
| | - Brojen Singh
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Somnath S Pai
- Amity Institute of Virology & Immunology, Amity University, Noida, Uttar Pradesh, India
| | - Pooja Vijayaraghavan
- Anti-mycotic Drug Susceptibility Laboratory, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | - Ansh Tandon
- Systems Biology and Data Analytics Research Lab, Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | - Payal Gupta
- Systems Biology and Data Analytics Research Lab, Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | - Deepak Modi
- Molecular and Cellular Biology Laboratory, National Institute for Research in Reproductive and Child Health, Mumbai, Maharashtra, India
| | - Abhishek Sengupta
- Systems Biology and Data Analytics Research Lab, Centre for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
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3
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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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4
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Kodera SM, Das P, Gilbert JA, Lutz HL. Conceptual strategies for characterizing interactions in microbial communities. iScience 2022; 25:103775. [PMID: 35146390 PMCID: PMC8819398 DOI: 10.1016/j.isci.2022.103775] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Understanding the sets of inter- and intraspecies interactions in microbial communities is a fundamental goal of microbial ecology. However, the study and quantification of microbial interactions pose several challenges owing to their complexity, dynamic nature, and the sheer number of unique interactions within a typical community. To overcome such challenges, microbial ecologists must rely on various approaches to distill the system of study to a functional and conceptualizable level, allowing for a practical understanding of microbial interactions in both simplified and complex systems. This review broadly addresses the role of several conceptual approaches available for the microbial ecologist’s arsenal, examines specific tools used to accomplish such approaches, and describes how the assumptions, expectations, and philosophies underlying these tools change across scales of complexity.
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Affiliation(s)
- Sho M Kodera
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA
| | - Promi Das
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA.,Department of Pediatrics, University of California San Diego, La Jolla, CA 92161, USA
| | - Jack A Gilbert
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA.,Department of Pediatrics, University of California San Diego, La Jolla, CA 92161, USA
| | - Holly L Lutz
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA.,Department of Pediatrics, University of California San Diego, La Jolla, CA 92161, USA.,Negaunee Integrative Collections Center, Field Museum of Natural History, Chicago, IL 60605, USA
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5
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Jones GB, Bryant A, Wright J. Democratizing Global Health Care Through Scalable Emergent (Beyond the Mobile) Wireless Technologies. JMIR BIOMEDICAL ENGINEERING 2022; 7:e31079. [PMID: 38875689 PMCID: PMC11041427 DOI: 10.2196/31079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/22/2021] [Accepted: 12/20/2021] [Indexed: 01/17/2023] Open
Abstract
Advances in mobile phone technologies coupled with the availability of modern wireless networks are beginning to have a marked impact on digital health through the growing array of apps and connected devices. That said, limited deployment outside of developed nations will require additional approaches to collectively reach the 8 billion people on earth. Another consideration for development of digital health centered around mobile devices lies in the need for pairing steps, firmware updates, and a variety of user inputs, which can increase friction for the patient. An alternate, so-called Beyond the Mobile approach where medicaments, devices, and health services communicate directly to the cloud offers an attractive means to expand and fully realize our connected health utopia. In addition to offering highly personalized experiences, such approaches could address cost, security, and convenience concerns associated with smartphone-based systems, translating to improved engagement and adherence rates among patients. Furthermore, connecting these Internet of Medical Things instruments through next-generation networks offers the potential to reach patients with acute needs in nonurban regions of developing nations. Herein, we outline how deployment of Beyond the Mobile technologies through low-power wide-area networks could offer a scalable means to democratize digital health and contribute to improved patient outcomes globally.
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Affiliation(s)
- Graham B Jones
- Technical Research and Development, Novartis Pharmaceuticals, East Hanover, NJ, United States
| | - Andrew Bryant
- Technical Research and Development, Novartis AG, Basel, Switzerland
| | - Justin Wright
- Global Drug Development Connected Health, Novartis Pharmaceuticals, East Hanover, NJ, United States
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6
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Advances in Microbiome-Derived Solutions and Methodologies Are Founding a New Era in Skin Health and Care. Pathogens 2022; 11:pathogens11020121. [PMID: 35215065 PMCID: PMC8879973 DOI: 10.3390/pathogens11020121] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 12/04/2022] Open
Abstract
The microbiome, as a community of microorganisms and their structural elements, genomes, metabolites/signal molecules, has been shown to play an important role in human health, with significant beneficial applications for gut health. Skin microbiome has emerged as a new field with high potential to develop disruptive solutions to manage skin health and disease. Despite an incomplete toolbox for skin microbiome analyses, much progress has been made towards functional dissection of microbiomes and host-microbiome interactions. A standardized and robust investigation of the skin microbiome is necessary to provide accurate microbial information and set the base for a successful translation of innovations in the dermo-cosmetic field. This review provides an overview of how the landscape of skin microbiome research has evolved from method development (multi-omics/data-based analytical approaches) to the discovery and development of novel microbiome-derived ingredients. Moreover, it provides a summary of the latest findings on interactions between the microbiomes (gut and skin) and skin health/disease. Solutions derived from these two paths are used to develop novel microbiome-based ingredients or solutions acting on skin homeostasis are proposed. The most promising skin and gut-derived microbiome interventional strategies are presented, along with regulatory, safety, industrial, and technical challenges related to a successful translation of these microbiome-based concepts/technologies in the dermo-cosmetic industry.
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7
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Hao X, Li P, Wu S, Tan J. Association of the Cervical Microbiota With Pregnancy Outcome in a Subfertile Population Undergoing In Vitro Fertilization: A Case-Control Study. Front Cell Infect Microbiol 2021; 11:654202. [PMID: 34631595 PMCID: PMC8495128 DOI: 10.3389/fcimb.2021.654202] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 09/10/2021] [Indexed: 01/13/2023] Open
Abstract
The microorganisms of the reproductive tract have been implicated to affect in vitro fertilization (IVF) outcomes. However, studies on the reproductive tract microbiota of infertile women are limited and the correlation between cervical microbiota and IVF outcome remains elusive. This study aimed to characterize the cervical microbiota of IVF patients undergoing embryo transfer (ET) and assess associations between the cervical microbiota and pregnancy outcomes while exploring the underlying contributing factors. We launched a nested case-control study of 100 patients with two fresh or frozen-thawed cleavage embryos transferred per IVF cycle. Cervical swabs were collected on the day of ET and divided into four groups according to clinical pregnancy outcomes. Variable regions 3 and 4 (V3-V4) of the 16S rRNA gene were amplified and sequenced on the Illumina MiSeq platform. In fresh IVF-ET cycles, the clinical pregnancy group (FP, n = 25) demonstrated higher α diversity (P = 0.0078) than the non-pregnancy group (FN, n = 26). Analysis of similarity (ANOSIM) revealed a significant difference in β diversity between the two groups (R = 0.242, P = 0.001). In frozen-thawed ET cycles, though not significant, similar higher α diversity was found in the clinical pregnancy group (TP, n = 27) compared to the non-pregnancy group (TN, n = 22) and ANOSIM analysis showed a significant difference between the two groups (R = 0.062, P = 0.045). For patients in fresh IVF-ET groups, Lactobacillus, Akkermansia, Desulfovibrio, Atopobium, and Gardnerella showed differentially abundance between pregnant and non-pregnant women and they accounted for the largest share of all taxa investigated. Among them, Lactobacillus was negatively correlated with the other genera and positively correlated with serum estradiol levels. Logistic regression analysis suggested that the composition of the cervical microbiota on the day of ET was associated with the clinical pregnancy in fresh IVF-ET cycles (P = 0.030). Our results indicate that cervical microbiota composition has an impact on the outcome of assisted reproductive therapy.
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Affiliation(s)
- Xinyao Hao
- Center of Reproductive Medicine, Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.,Key Laboratory of Reproductive Dysfunction Disease and Fertility Remodeling of Liaoning Province, Shenyang, China
| | - Pingping Li
- Center of Reproductive Medicine, Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.,Key Laboratory of Reproductive Dysfunction Disease and Fertility Remodeling of Liaoning Province, Shenyang, China
| | - Shanshan Wu
- Center of Reproductive Medicine, Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.,Key Laboratory of Reproductive Dysfunction Disease and Fertility Remodeling of Liaoning Province, Shenyang, China
| | - Jichun Tan
- Center of Reproductive Medicine, Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.,Key Laboratory of Reproductive Dysfunction Disease and Fertility Remodeling of Liaoning Province, Shenyang, China
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8
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Ding C, Yu Y, Zhou Q. Bacterial Vaginosis: Effects on reproduction and its therapeutics. J Gynecol Obstet Hum Reprod 2021; 50:102174. [PMID: 34087449 DOI: 10.1016/j.jogoh.2021.102174] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/10/2021] [Accepted: 05/28/2021] [Indexed: 01/11/2023]
Abstract
Bacterial Vaginosis (BV) is the most common vaginal infection. A large amount of evidence shows that the anatomical scope of BV's pathogenic effect is far beyond the lower reproductive tract. BV is closely related to adverse reproductive outcomes, which may be due to the infection of the vaginal flora ascending to the upper genital tract. In addition, the incidence of BV is relatively high in infertile women. The vaginal microbiome also plays an important role in women's health and diseases. For most women, the normal vaginal microbiota is dominated by Lactobacillus, which can maintain a healthy vaginal environment by producing lactic acid, H2O2 and bacteriocin, etc. BV is characterized by the imbalanced vaginal flora. It changes the acidic environment that is normally dominated by Lactobacillus, and causes an overgrowth of anaerobic and facultative anaerobic bacteria such as Gardnerella vaginalis and Atopobium vaginae. Studies have shown that bacterial infections in the vagina can spread to upper genital tract and cause adverse fertility outcome. Therefore, early diagnosis and therapeutics of symptomatic BV is helpful to improve the outcome of poor fertility.
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Affiliation(s)
- Chuanfeng Ding
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China; Department of Reproductive Immunology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Yongsheng Yu
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Qian Zhou
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China; Department of Reproductive Immunology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China.
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9
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Gut microbiome modulates Drosophila aggression through octopamine signaling. Nat Commun 2021; 12:2698. [PMID: 33976215 PMCID: PMC8113466 DOI: 10.1038/s41467-021-23041-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 04/13/2021] [Indexed: 02/07/2023] Open
Abstract
Gut microbiome profoundly affects many aspects of host physiology and behaviors. Here we report that gut microbiome modulates aggressive behaviors in Drosophila. We found that germ-free males showed substantial decrease in inter-male aggression, which could be rescued by microbial re-colonization. These germ-free males are not as competitive as wild-type males for mating with females, although they displayed regular levels of locomotor and courtship behaviors. We further found that Drosophila microbiome interacted with diet during a critical developmental period for the proper expression of octopamine and manifestation of aggression in adult males. These findings provide insights into how gut microbiome modulates specific host behaviors through interaction with diet during development. The gut microbiome regulates behaviour in a number of species. Here the authors show that depletion of the gut microbiome in Drosophila reduced aggressive behaviour, in an octopamine-dependent manner.
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10
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Kiousi DE, Rathosi M, Tsifintaris M, Chondrou P, Galanis A. Pro-biomics: Omics Technologies To Unravel the Role of Probiotics in Health and Disease. Adv Nutr 2021; 12:1802-1820. [PMID: 33626128 PMCID: PMC8483974 DOI: 10.1093/advances/nmab014] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/29/2020] [Accepted: 01/26/2021] [Indexed: 12/11/2022] Open
Abstract
The comprehensive characterization of probiotic action has flourished during the past few decades, alongside the evolution of high-throughput, multiomics platforms. The integration of these platforms into probiotic animal and human studies has provided valuable insights into the holistic effects of probiotic supplementation on intestinal and extraintestinal diseases. Indeed, these methodologies have informed about global molecular changes induced in the host and residing commensals at multiple levels, providing a bulk of metagenomic, transcriptomic, proteomic, and metabolomic data. The meaningful interpretation of generated data remains a challenge; however, the maturation of the field of systems biology and artificial intelligence has supported analysis of results. In this review article, we present current literature on the use of multiomics approaches in probiotic studies, we discuss current trends in probiotic research, and examine the possibility of tailor-made probiotic supplementation. Lastly, we delve deeper into newer technologies that have been developed in the last few years, such as single-cell multiomics analyses, and provide future directions for the maximization of probiotic efficacy.
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Affiliation(s)
- Despoina Eugenia Kiousi
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Marina Rathosi
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Margaritis Tsifintaris
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Pelagia Chondrou
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
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11
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Uriarte-Navarrete I, Hernández-Lemus E, de Anda-Jáuregui G. Gene-Microbiome Co-expression Networks in Colon Cancer. Front Genet 2021; 12:617505. [PMID: 33659025 PMCID: PMC7917223 DOI: 10.3389/fgene.2021.617505] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/22/2021] [Indexed: 12/27/2022] Open
Abstract
It is known that cancer onset and development arise from complex, multi-factorial phenomena spanning from the molecular, functional, micro-environmental, and cellular up to the tissular and organismal levels. Important advances have been made in the systematic analysis of the molecular (mostly genomic and transcriptomic) within large studies of high throughput data such as The Cancer Genome Atlas collaboration. However, the role of the microbiome in the induction of biological changes needed to reach these pathological states remains to be explored, largely because of scarce experimental data. In recent work a non-standard bioinformatics strategy was used to indirectly quantify microbial abundance from TCGA RNA-seq data, allowing the evaluation of the microbiome in well-characterized cancer patients, thus opening the way to studies incorporating the molecular and microbiome dimensions altogether. In this work, we used such recently described approaches for the quantification of microbial species alongside with gene expression. With this, we will reconstruct bipartite networks linking microbial abundance and gene expression in the context of colon cancer, by resorting to network reconstruction based on measures from information theory. The rationale is that microbial communities may induce biological changes important for the cancerous state. We analyzed changes in microbiome-gene interactions in the context of early (stages I and II) and late (stages III and IV) colon cancer, studied changes in network descriptors, and identify key discriminating features for early and late stage colon cancer. We found that early stage bipartite network is associated with the establishment of structural features in the tumor cells, whereas late stage is related to more advance signaling and metabolic features. This functional divergence thus arise as a consequence of changes in the organization of the corresponding gene-microorganism co-expression networks.
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Affiliation(s)
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Guillermo de Anda-Jáuregui
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Conacyt Research Chairs, National Council on Science and Technology, Mexico City, Mexico
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12
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Kumbale CM, Davis JD, Voit EO. Models for Personalized Medicine. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11349-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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13
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McBrayer DN, Cameron CD, Tal-Gan Y. Development and utilization of peptide-based quorum sensing modulators in Gram-positive bacteria. Org Biomol Chem 2020; 18:7273-7290. [PMID: 32914160 PMCID: PMC7530124 DOI: 10.1039/d0ob01421d] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Quorum sensing (QS) is a mechanism by which bacteria regulate cell density-dependent group behaviors. Gram-positive bacteria generally rely on auto-inducing peptide (AIP)-based QS signaling to regulate their group behaviors. To develop synthetic modulators of these behaviors, the natural peptide needs to be identified and its structure-activity relationships (SARs) with its cognate receptor (either membrane-bound or cytosolic) need to be understood. SAR information allows for the rational design of peptides or peptide mimics with enhanced characteristics, which in turn can be utilized in studies to understand species-specific QS mechanisms and as lead scaffolds for the development of therapeutic candidates that target QS. In this review, we discuss recent work associated with the approaches used towards forwarding each of these steps in Gram-positive bacteria, with a focus on species that have received less attention.
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Affiliation(s)
- Dominic N McBrayer
- Department of Chemistry, SUNY New Paltz, 1 Hawk Drive, New Paltz, NY 12561, USA. and Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, NV 89557, USA.
| | - Crissey D Cameron
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, NV 89557, USA.
| | - Yftah Tal-Gan
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, NV 89557, USA.
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14
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Abdelsalam NA, Ramadan AT, ElRakaiby MT, Aziz RK. Toxicomicrobiomics: The Human Microbiome vs. Pharmaceutical, Dietary, and Environmental Xenobiotics. Front Pharmacol 2020; 11:390. [PMID: 32372951 PMCID: PMC7179069 DOI: 10.3389/fphar.2020.00390] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 03/16/2020] [Indexed: 12/13/2022] Open
Abstract
The harmful impact of xenobiotics on the environment and human health is being more widely recognized; yet, inter- and intraindividual genetic variations among humans modulate the extent of harm, mostly through modulating the outcome of xenobiotic metabolism and detoxification. As the Human Genome Project revealed that host genetic, epigenetic, and regulatory variations could not sufficiently explain the complexity of interindividual variability in xenobiotics metabolism, its sequel, the Human Microbiome Project, is investigating how this variability may be influenced by human-associated microbial communities. Xenobiotic-microbiome relationships are mutual and dynamic. Not only does the human microbiome have a direct metabolizing potential on xenobiotics, but it can also influence the expression of the host metabolizing genes and the activity of host enzymes. On the other hand, xenobiotics may alter the microbiome composition, leading to a state of dysbiosis, which is linked to multiple diseases and adverse health outcomes, including increased toxicity of some xenobiotics. Toxicomicrobiomics studies these mutual influences between the ever-changing microbiome cloud and xenobiotics of various origins, with emphasis on their fate and toxicity, as well the various classes of microbial xenobiotic-modifying enzymes. This review article discusses classic and recent findings in toxicomicrobiomics, with examples of interactions between gut, skin, urogenital, and oral microbiomes with pharmaceutical, food-derived, and environmental xenobiotics. The current state and future prospects of toxicomicrobiomic research are discussed, and the tools and strategies for performing such studies are thoroughly and critically compared.
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Affiliation(s)
| | - Ahmed Tarek Ramadan
- The Center for Genome and Microbiome Research, Cairo University, Cairo, Egypt
| | - Marwa Tarek ElRakaiby
- The Center for Genome and Microbiome Research, Cairo University, Cairo, Egypt.,Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Ramy Karam Aziz
- The Center for Genome and Microbiome Research, Cairo University, Cairo, Egypt.,Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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15
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Peñalver Bernabé B, Maki PM, Dowty SM, Salas M, Cralle L, Shah Z, Gilbert JA. Precision medicine in perinatal depression in light of the human microbiome. Psychopharmacology (Berl) 2020; 237:915-941. [PMID: 32065252 DOI: 10.1007/s00213-019-05436-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 12/11/2019] [Indexed: 12/17/2022]
Abstract
Perinatal depression is the most common complication of pregnancy and affects the mother, fetus, and infant. Recent preclinical studies and a limited number of clinical studies have suggested an influence of the gut microbiome on the onset and course of mental health disorders. In this review, we examine the current state of knowledge regarding genetics, epigenetics, heritability, and neuro-immuno-endocrine systems biology in perinatal mood disorders, with a particular focus on the interaction between these factors and the gut microbiome, which is mediated via the gut-brain axis. We also provide an overview of experimental and analytical methods that are currently available to researchers interested in elucidating the influence of the gut microbiome on mental health disorders during pregnancy and postpartum.
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Affiliation(s)
- Beatriz Peñalver Bernabé
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, United States.
| | - Pauline M Maki
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA
- Department of Psychology, University of Illinois at Chicago, Chicago, IL, USA
- Department of Obstetrics and Gynecology, University of Illinois at Chicago, Chicago, IL, USA
| | - Shannon M Dowty
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA
| | - Mariana Salas
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, United States
| | - Lauren Cralle
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Zainab Shah
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA
| | - Jack A Gilbert
- Scripts Oceanographic Institute, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
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16
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Chowdhury S, Fong SS. Computational Modeling of the Human Microbiome. Microorganisms 2020; 8:microorganisms8020197. [PMID: 32023941 PMCID: PMC7074762 DOI: 10.3390/microorganisms8020197] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/23/2020] [Accepted: 01/27/2020] [Indexed: 12/20/2022] Open
Abstract
The impact of microorganisms on human health has long been acknowledged and studied, but recent advances in research methodologies have enabled a new systems-level perspective on the collections of microorganisms associated with humans, the human microbiome. Large-scale collaborative efforts such as the NIH Human Microbiome Project have sought to kick-start research on the human microbiome by providing foundational information on microbial composition based upon specific sites across the human body. Here, we focus on the four main anatomical sites of the human microbiome: gut, oral, skin, and vaginal, and provide information on site-specific background, experimental data, and computational modeling. Each of the site-specific microbiomes has unique organisms and phenomena associated with them; there are also high-level commonalities. By providing an overview of different human microbiome sites, we hope to provide a perspective where detailed, site-specific research is needed to understand causal phenomena that impact human health, but there is equally a need for more generalized methodology improvements that would benefit all human microbiome research.
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Affiliation(s)
- Shomeek Chowdhury
- Integrative Life Sciences, Virginia Commonwealth University, 1000 West Cary Street, Richmond, VA 23284 USA;
| | - Stephen S. Fong
- Chemical and Life Science Engineering, Virginia Commonwealth University, 601 West Main Street, Richmond, VA 23284, USA
- Correspondence:
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17
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Man B, Koenig MD, Bernabe BP, Nagelli U, Tussing-Humphreys L. The Role of the Gut Microbiota in the Prevention and Management of Gestational Diabetes Mellitus: Are We There Yet? J Perinat Neonatal Nurs 2020; 34:195-198. [PMID: 32697535 PMCID: PMC7384246 DOI: 10.1097/jpn.0000000000000497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Current nonpharmacological approaches, including diet and exercise interventions, for preventing and treating gestational diabetes mellitus are effective for less than 50% of women. Recent evidence suggests that the gut microbiome is integrally involved in maternal glucose homeostasis. Changes to the composition and metabolic behavior of the gut microbiota may play a role in the development and persistence of gestational diabetes mellitus. Thus, there is growing interest in targeting the maternal gut microbiome for preventing and managing pregnancy-related diseases including gestational diabetes mellitus. Future progress may come from a systems biology approach to elucidate the role of the gut microbiota in maternal glucose homeostasis.
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Affiliation(s)
- Bernice Man
- Departments of Medicine, Division of Academic Internal Medicine and Geriatrics (Drs Man and Tussing-Humphreys), Bioengineering, College of Medicine (Dr Bernabe), and Psychiatry, College of Medicine (Ms Nagelli), University of Illinois at Chicago; and Department of Women, Children, and Family Health Science, College of Nursing, University of Illinois at Chicago (Dr Koenig)
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18
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Yadav M, Shukla P. Recent systems biology approaches for probiotics use in health aspects: a review. 3 Biotech 2019; 9:448. [PMID: 31763126 PMCID: PMC6848287 DOI: 10.1007/s13205-019-1980-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 10/29/2019] [Indexed: 12/19/2022] Open
Abstract
The market of probiotics is growing dynamically for the food and supplements, which provides better health to an individual. Probiotics are used as dietary management for diseases, but it varies between regions and persons. Systems biology can help in resolving the strain specificity of probiotics by studying their genome level organization. In this review, we have compiled facets of systems biology and next-generation omics methods such as metagenomics, proteomics and metabolomics. These tools are crucial for the optimization of the metabolic processes in probiotics and hence, their use for human health. The limitations and challenges associated with the development of probiotics involve their stability and function in different individuals. Systems biology facilitates emerging metabolic engineering approaches to improve probiotics strain for their broader application. This review provides comprehensive and updated knowledge of engineered probiotics as therapeutics and various challenges in the development of engineered probiotics.
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Affiliation(s)
- Monika Yadav
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001 India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001 India
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19
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Effect of the vaginal microbiome on the pregnancy rate in women receiving assisted reproductive treatment. J Assist Reprod Genet 2019; 36:2111-2119. [PMID: 31446545 DOI: 10.1007/s10815-019-01564-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 08/09/2019] [Indexed: 12/20/2022] Open
Abstract
PURPOSE To investigate if the vaginal microbiome influences the IVF outcome. METHODS Thirty-one patients undergoing assisted reproductive treatment (ART) with own or donated gametes and with cryotransfer of a single euploid blastocyst were recruited for this cohort study. Two vaginal samples were taken during the embryo transfer procedure, just before transferring the embryo. The V3 V4 region of 16S rRNA was used to analyze the vaginal microbiome, and the bioinformatic analysis was performed using QIIME2, Bioconductor Phyloseq, and MicrobiomeAnalyst packages. Alpha diversity was compared between groups according to the result of the pregnancy test. RESULTS Fourteen (45.2%) patients did not and seventeen (54.8 %) did achieve pregnancy under ART. A greater index of alpha diversity was found in patients who did not achieve pregnancy comparing to those who did, although this difference was not significant (p = 0.088). In the analysis of beta diversity, no statistically significant differences were observed between groups established as per the pregnancy status. Samples from women who achieved pregnancy showed a greater presence of Lactobacillus spp. The cluster analysis identified two main clusters: the first encompassed the genera Lactobacillus, Gardnerella, Clostridium, Staphylococcus, and Dialister, and the second included all other genera. Women who achieved pregnancy were mainly detected microorganisms from the first cluster. CONCLUSIONS The vaginal microbiome can influence the results of ART. The profiles dominated by Lactobacillus were associated with the achievement of pregnancy, and there was a relationship between the stability of the vaginal microbiome and the achievement of pregnancy.
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20
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Alonso SG, de la Torre Díez I, Zapiraín BG. Predictive, Personalized, Preventive and Participatory (4P) Medicine Applied to Telemedicine and eHealth in the Literature. J Med Syst 2019; 43:140. [PMID: 30976942 DOI: 10.1007/s10916-019-1279-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/05/2019] [Indexed: 10/27/2022]
Abstract
The main objective of this work is to provide a review of existing research work into predictive, personalized, preventive and participatory medicine in telemedicine and ehealth. The academic databases used for searches are IEEE Xplore, PubMed, Science Direct, Web of Science and ResearchGate, taking into account publication dates from 2010 up to the present day. These databases cover the greatest amount of information on scientific texts in multidisciplinary fields, from engineering to medicine. Various search criteria were established, such as ("Predictive" OR "Personalized" OR "Preventive" OR "Participatory") AND "Medicine" AND ("eHealth" OR "Telemedicine") selecting the articles of most interest. A total of 184 publications about predictive, personalized, preventive and participatory (4P) medicine in telemedicine and ehealth were found, of which 48 were identified as relevant. Many of the publications found show how the P4 medicine is being developed in the world and the benefits it provides for patients with different illnesses. After the revision that was undertaken, it can be said that P4 medicine is a vital factor for the improvement of medical services. It is hoped that one of the main contributions of this study is to provide an insight into how P4 medicine in telemedicine and ehealth is being applied, as well as proposing outlines for the future that contribute to the improvement of prevention and prediction of illnesses.
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Affiliation(s)
- Susel Góngora Alonso
- Department of Signal Theory and Communications, and Telematics Engineering, University of Valladolid, Paseo de Belén, 15, 47011, Valladolid, Spain
| | - Isabel de la Torre Díez
- Department of Signal Theory and Communications, and Telematics Engineering, University of Valladolid, Paseo de Belén, 15, 47011, Valladolid, Spain.
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21
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Dugas LR, Bernabé BP, Priyadarshini M, Fei N, Park SJ, Brown L, Plange-Rhule J, Nelson D, Toh EC, Gao X, Dong Q, Sun J, Kliethermes S, Gottel N, Luke A, Gilbert JA, Layden BT. Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women. Sci Rep 2018; 8:17135. [PMID: 30459320 PMCID: PMC6244201 DOI: 10.1038/s41598-018-35230-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 10/28/2018] [Indexed: 02/07/2023] Open
Abstract
We compared the gut microbial populations in 100 women, from rural Ghana and urban US [50% lean (BMI < 25 kg/m2) and 50% obese (BMI ≥ 30 kg/m2)] to examine the ecological co-occurrence network topology of the gut microbiota as well as the relationship of short chain fatty acids (SCFAs) with obesity. Ghanaians consumed significantly more dietary fiber, had greater microbial alpha-diversity, different beta-diversity, and had a greater concentration of total fecal SCFAs (p-value < 0.002). Lean Ghanaians had significantly greater network density, connectivity and stability than either obese Ghanaians, or lean and obese US participants (false discovery rate (FDR) corrected p-value ≤ 0.01). Bacteroides uniformis was significantly more abundant in lean women, irrespective of country (FDR corrected p < 0.001), while lean Ghanaians had a significantly greater proportion of Ruminococcus callidus, Prevotella copri, and Escherichia coli, and smaller proportions of Lachnospiraceae, Bacteroides and Parabacteroides. Lean Ghanaians had a significantly greater abundance of predicted microbial genes that catalyzed the production of butyric acid via the fermentation of pyruvate or branched amino-acids, while obese Ghanaians and US women (irrespective of BMI) had a significantly greater abundance of predicted microbial genes that encoded for enzymes associated with the fermentation of amino-acids such as alanine, aspartate, lysine and glutamate. Similar to lean Ghanaian women, mice humanized with stool from the lean Ghanaian participant had a significantly lower abundance of family Lachnospiraceae and genus Bacteroides and Parabacteroides, and were resistant to obesity following 6-weeks of high fat feeding (p-value < 0.01). Obesity-resistant mice also showed increased intestinal transcriptional expression of the free fatty acid (Ffa) receptor Ffa2, in spite of similar fecal SCFAs concentrations. We demonstrate that the association between obesity resistance and increased predicted ecological connectivity and stability of the lean Ghanaian microbiota, as well as increased local SCFA receptor level, provides evidence of the importance of robust gut ecologic network in obesity.
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Affiliation(s)
- Lara R Dugas
- Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA.
| | | | - Medha Priyadarshini
- Division of Endocrinology, Diabetes, and Metabolism, University of Illinois at Chicago, Chicago, IL, USA
| | - Na Fei
- Microbiome Center, Department of Surgery, University of Chicago, Chicago, IL, USA
| | - Seo Jin Park
- Department of Microbiology-Immunology, Northwestern University, Chicago, Illinois, USA
| | - Laquita Brown
- Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | | | - David Nelson
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, USA
| | - Evelyn C Toh
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, USA
| | - Xiang Gao
- Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Qunfeng Dong
- Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Jun Sun
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Stephanie Kliethermes
- Department of Orthopedics and Rehabilitation, University of Wisconsin School of Medicine and Public Health, Wisconsin, USA
| | - Neil Gottel
- Microbiome Center, Department of Surgery, University of Chicago, Chicago, IL, USA
| | - Amy Luke
- Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Jack A Gilbert
- Microbiome Center, Department of Surgery, University of Chicago, Chicago, IL, USA
| | - Brian T Layden
- Division of Endocrinology, Diabetes, and Metabolism, University of Illinois at Chicago, Chicago, IL, USA.,Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois, USA
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22
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Aziz RK, Hegazy SM, Yasser R, Rizkallah MR, ElRakaiby MT. Drug pharmacomicrobiomics and toxicomicrobiomics: from scattered reports to systematic studies of drug-microbiome interactions. Expert Opin Drug Metab Toxicol 2018; 14:1043-1055. [PMID: 30269615 DOI: 10.1080/17425255.2018.1530216] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Pharmacomicrobiomics and toxicomicrobiomics study how variations within the human microbiome (the combination of human-associated microbial communities and their genomes) affect drug disposition, action, and toxicity. These emerging fields, interconnecting microbiology, bioinformatics, systems pharmacology, and toxicology, complement pharmacogenomics and toxicogenomics, expanding the scope of precision medicine. Areas covered: This article reviews some of the most recently reported pharmacomicrobiomic and toxicomicrobiomic interactions. Examples include the impact of the human gut microbiota on cardiovascular drugs, natural products, and chemotherapeutic agents, including immune checkpoint inhibitors. Although the gut microbiota has been the most extensively studied, some key drug-microbiome interactions involve vaginal, intratumoral, and environmental bacteria, and are briefly discussed here. Additionally, computational resources, moving the field from cataloging to predicting interactions, are introduced. Expert opinion: The rapid pace of discovery triggered by the Human Microbiome Project is moving pharmacomicrobiomic research from scattered observations to systematic studies focusing on screening microbiome variants against different drug classes. Better representation of all human populations will improve such studies by avoiding sampling bias, and the integration of multiomic studies with designed experiments will allow establishing causation. In the near future, pharmacomicrobiomic testing is expected to be a key step in screening novel drugs and designing precision therapeutics.
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Affiliation(s)
- Ramy K Aziz
- a Department of Microbiology and Immunology, Faculty of Pharmacy , Cairo University , Cairo , Egypt
| | - Shaimaa M Hegazy
- b Undergraduate program, Faculty of Pharmacy , Cairo University , Cairo , Egypt
| | - Reem Yasser
- b Undergraduate program, Faculty of Pharmacy , Cairo University , Cairo , Egypt
| | - Mariam R Rizkallah
- c Department of Biometry and Data Management , Leibniz Institute for Prevention Research and Epidemiology - BIPS , Bremen , Germany
| | - Marwa T ElRakaiby
- a Department of Microbiology and Immunology, Faculty of Pharmacy , Cairo University , Cairo , Egypt
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