1
|
Kamath S, Stringer AM, Prestidge CA, Joyce P. Targeting the gut microbiome to control drug pharmacomicrobiomics: the next frontier in oral drug delivery. Expert Opin Drug Deliv 2023; 20:1315-1331. [PMID: 37405390 DOI: 10.1080/17425247.2023.2233900] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/04/2023] [Indexed: 07/06/2023]
Abstract
INTRODUCTION The trillions of microorganisms that comprise the gut microbiome form dynamic bidirectional interactions with orally administered drugs and host health. These relationships can alter all aspects of drug pharmacokinetics and pharmacodynamics (PK/PD); thus, there is a desire to control these interactions to maximize therapeutic efficacy. Attempts to modulate drug-gut microbiome interactions have spurred advancements within the field of 'pharmacomicrobiomics' and are poised to become the next frontier of oral drug delivery. AREAS COVERED This review details the bidirectional interactions that exist between oral drugs and the gut microbiome, with clinically relevant case examples outlining a clear motive for controlling pharmacomicrobiomic interactions. Specific focus is attributed to novel and advanced strategies that have demonstrated success in mediating drug-gut microbiome interactions. EXPERT OPINION Co-administration of gut-active supplements (e.g. pro- and pre-biotics), innovative drug delivery vehicles, and strategic polypharmacy serve as the most promising and clinically viable approaches for controlling pharmacomicrobiomic interactions. Targeting the gut microbiome through these strategies presents new opportunities for improving therapeutic efficacy by precisely mediating PK/PD, while mitigating metabolic disturbances caused by drug-induced gut dysbiosis. However, successfully translating preclinical potential into clinical outcomes relies on overcoming key challenges related to interindividual variability in microbiome composition and study design parameters.
Collapse
Affiliation(s)
- Srinivas Kamath
- UniSa Clinical & Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Andrea M Stringer
- UniSa Clinical & Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Clive A Prestidge
- UniSa Clinical & Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Paul Joyce
- UniSa Clinical & Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| |
Collapse
|
2
|
Habteweld HA, Asfaw T. Novel Dietary Approach with Probiotics, Prebiotics, and Synbiotics to Mitigate Antimicrobial Resistance and Subsequent Out Marketplace of Antimicrobial Agents: A Review. Infect Drug Resist 2023; 16:3191-3211. [PMID: 37249957 PMCID: PMC10224695 DOI: 10.2147/idr.s413416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/16/2023] [Indexed: 05/31/2023] Open
Abstract
Antimicrobial resistance (AMR) is a significant public health concern worldwide. The continuous use and misuse of antimicrobial agents have led to the emergence and spread of resistant strains of bacteria, which can cause severe infections that are difficult to treat. One of the reasons for the constant development of new antimicrobial agents is the need to overcome the resistance that has developed against existing drugs. However, this approach is not sustainable in the long term, as bacteria can quickly develop resistance to new drugs as well. Additionally, the development of new drugs is costly and time-consuming, and there is no guarantee that new drugs will be effective or safe. An alternative approach to combat AMR is to focus on improving the body's natural defenses against infections by using probiotics, prebiotics, and synbiotics, which are helpful to restore and maintain a healthy balance of bacteria in the body. Probiotics are live microorganisms that can be consumed as food or supplements to promote gut health and improve the body's natural defenses against infections. Prebiotics are non-digestible fibers that stimulate the growth of beneficial bacteria in the gut, while synbiotics are a combination of probiotics and prebiotics that work together to improve gut health. By promoting a healthy balance of bacteria in the body, these can help to reduce the risk of infections and the need for antimicrobial agents. Additionally, these approaches are generally safe and well tolerated, and they do not contribute to the development of AMR. In conclusion, the continuous development of new antimicrobial agents is not a sustainable approach to combat AMR. Instead, alternative approaches such as probiotics, prebiotics, and synbiotics should be considered as they can help to promote a healthy balance of bacteria in the body and reduce the need for antibiotics.
Collapse
Affiliation(s)
| | - Tsegahun Asfaw
- Department of Medical Laboratory Science, Debre Berhan University, Debre Berhan, Ethiopia
| |
Collapse
|
3
|
Maki KA, Wolff B, Varuzza L, Green SJ, Barb JJ. Multi-amplicon microbiome data analysis pipelines for mixed orientation sequences using QIIME2: Assessing reference database, variable region and pre-processing bias in classification of mock bacterial community samples. PLoS One 2023; 18:e0280293. [PMID: 36638095 PMCID: PMC9838852 DOI: 10.1371/journal.pone.0280293] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/24/2022] [Indexed: 01/14/2023] Open
Abstract
Microbiome research relies on next-generation sequencing and on downstream data analysis workflows. Several manufacturers have introduced multi-amplicon kits for microbiome characterization, improving speciation, but present unique challenges for analysis. The goal of this methodology study was to develop two analysis pipelines specific to mixed-orientation reads from multi-hypervariable (V) region amplicons. A secondary aim was to assess agreement with expected abundance, considering database and variable region. Mock community sequence data (n = 41) generated using the Ion16S™ Metagenomics Kit and Ion Torrent Sequencing Platform were analyzed using two workflows. Amplicons from V2, V3, V4, V6-7, V8 and V9 were deconvoluted using a specialized plugin based on CutPrimers. A separate workflow using Cutadapt is also presented. Three reference databases (Ribosomal Database Project, Greengenes and Silva) were used for taxonomic assignment. Bray-Curtis, Euclidean and Jensen-Shannon distance measures were used to evaluate overall annotation consistency, and specific taxon agreement was determined by calculating the ratio of observed to expected relative abundance. Reads that mapped to regions V2-V9 varied for both CutPrimers and Cutadapt-based methods. Within the CutPrimers-based pipeline, V3 amplicons had the best agreement with the expected distribution, tested using global distance measures, while V9 amplicons had the worst agreement. Accurate taxonomic annotation varied by genus-level taxon and V region analyzed. For the first time, we present a microbiome analysis pipeline that employs a specialized plugin to allow microbiome researchers to separate multi-amplicon data from the Ion16S Metagenomics Kit into V-specific reads. We also present an additional analysis workflow, modified for Ion Torrent mixed orientation reads. Overall, the global agreement of amplicons with the expected mock community abundances differed across V regions and reference databases. Benchmarking data should be referenced when planning a microbiome study to consider these biases related to sequencing and data analysis for multi-amplicon sequencing kits.
Collapse
Affiliation(s)
- Katherine A. Maki
- Translational Biobehavioral and Health Disparities Branch, Clinical Center, National Institutes of Health, Bethesda, MD, United States of America
| | - Brian Wolff
- National Institute of Nursing Research, National Institutes of Health, Bethesda, MD, United States of America
| | | | - Stefan J. Green
- Genomics and Microbiome Core Facility, Rush University, Chicago, IL, United States of America
| | - Jennifer J. Barb
- Translational Biobehavioral and Health Disparities Branch, Clinical Center, National Institutes of Health, Bethesda, MD, United States of America
- * E-mail:
| |
Collapse
|
4
|
Stepanova N, Akulenko I, Serhiichuk T, Dovbynchuk T, Savchenko S, Tolstanova G. Synbiotic supplementation and oxalate homeostasis in rats: focus on microbiota oxalate-degrading activity. Urolithiasis 2022; 50:249-258. [PMID: 35129638 DOI: 10.1007/s00240-022-01312-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 01/22/2022] [Indexed: 01/08/2023]
Abstract
The present study aimed (i) to evaluate whether ceftriaxone treatment could affect not only intestinal oxalate-degrading bacteria number but also their total activity to degrade oxalate and influence oxalate homeostasis in rats, (ii) and to estimate the ability of commercially available inulin-contained synbiotic to restore fecal oxalate-degrading activity and ceftriaxone-induced disruption of oxalate homeostasis in rats. Twenty-eight female Wistar rats (200-300 g) were randomly divided into four groups (n = 7). Group 1 was treated with vehicle sterile water (0.1 ml, i.m., 14 days); Group 2 received synbiotic (30 mg/kg, per os, 14 days); Group 3 was treated with ceftriaxone (300 mg/kg, i.m., 7 days); Group 4 was supplemented with ceftriaxone and synbiotic. Oxalate-degrading bacteria number and their total activity, urinary and plasma oxalate concentrations were measured on days 1 and 57 after the treatment withdrawal. The redoximetric titration with KMnO4 was adopted to evaluate the total oxalate-degrading activity in highly selective Oxalate Medium. Ceftriaxone treatment reduced total fecal oxalate-degrading activity independently on oxalate-degrading bacteria number and increased urinary and plasma oxalate concentrations. The synbiotic had higher oxalate-degrading activity vs probiotics and was able to restore fecal oxalate-degrading activity and significantly decrease urinary oxalate excretion in antibiotic-treated rats. Total fecal oxalate-degrading activity but not oxalate-degrading bacteria number should be thoroughly examined in the future to develop predictive diagnostics methods, targeted prevention and personalized treatment in kidney stone disease. Synbiotic supplementation had a beneficial effect on the total oxalate-degrading activity of gut microbiota, which resulted in decreased UOx excretion in rats.
Collapse
Affiliation(s)
- Natalia Stepanova
- State Institution, Institute of Nephrology of the National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine.
| | - Iryna Akulenko
- Taras Shevchenko National University of Kyiv, Kyiv, Ukraine.,Department of Clinical Medicine, ESC "Institute of Biology and Medicine", Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Tetyana Serhiichuk
- Taras Shevchenko National University of Kyiv, Kyiv, Ukraine.,Department of Microbiology and Immunology, ESC "Institute of Biology and Medicine", Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Taisa Dovbynchuk
- Taras Shevchenko National University of Kyiv, Kyiv, Ukraine.,Department of Biology, ESC "Institute of Biology and Medicine", Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Svitlana Savchenko
- State Institution, Institute of Nephrology of the National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine
| | | |
Collapse
|
5
|
Huang M, Li S, He Y, Lin C, Sun Y, Li M, Zheng R, Xu R, Lin P, Ke X. Modulation of gastrointestinal bacterial in chronic atrophic gastritis model rats by Chinese and west medicine intervention. Microb Cell Fact 2021; 20:31. [PMID: 33530970 PMCID: PMC7852297 DOI: 10.1186/s12934-021-01525-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 01/21/2021] [Indexed: 11/17/2022] Open
Abstract
Chronic atrophic gastritis (CAG) is well-known related with multiple pathogenic factors and normally therapies comprised by western or Chinese medicines. The present study was designed to identify the bacterial community characterized by 16S rRNA amplicon sequencing and determine the modulate affection of bacterial composition response western and Chinese medicine Qinghuayin (QHY) as well as antibiotic on model rats. The result shown the overall structure alteration of bacterial appeared under medicine intervened, antibiotic caused a marked depletion in bacterial diversity and richness. The enrichments of Firmicutes (85.1-90.7%) in antibiotic-free converts into Bacteroidetes (30.7-34.6%) in antibiotic-added model rat were demonstrated. Firmicutes as the most dominant phylum in antibiotic-free treatments and significantly decreased till 21.9-68.5% in antibiotic-added treatments. Especially QHY-treated rats showed highest RA of Firmicutes (90.7%) and the amelioration of CAG using QHY attributed by beneficial bacterial enrichment, especially Ruminococcus, Lactobacillus and Bifidobacterium. In addition, alpha and beta diversity analysis also demonstrated the clear dispersion and aggregation that revealed the alteration and steady of bacterial community structures. In summary, QHY has potential application value in the treatment of CAG, which attributed to close relation with the modulatory of internal bacterial communities.
Collapse
Affiliation(s)
- Minghan Huang
- Department of Gastroenterology, The Second People's Hospital affiliated to Fujian University of Traditional Chinese Medicine, Fuzhou, 350003, China
| | - Sihan Li
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
| | - Youcheng He
- Department of Gastroenterology, The Second People's Hospital affiliated to Fujian University of Traditional Chinese Medicine, Fuzhou, 350003, China
| | - Cuili Lin
- Department of Gastroenterology, The Second People's Hospital affiliated to Fujian University of Traditional Chinese Medicine, Fuzhou, 350003, China
| | - Yueming Sun
- Department of Gastroenterology, The Second People's Hospital affiliated to Fujian University of Traditional Chinese Medicine, Fuzhou, 350003, China
| | - Mingzhu Li
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Rong Zheng
- Department of Gastroenterology, The Second People's Hospital affiliated to Fujian University of Traditional Chinese Medicine, Fuzhou, 350003, China
| | - Ruoying Xu
- Department of Gastroenterology, The Second People's Hospital affiliated to Fujian University of Traditional Chinese Medicine, Fuzhou, 350003, China
| | - Ping Lin
- Department of Gastroenterology, The Second People's Hospital affiliated to Fujian University of Traditional Chinese Medicine, Fuzhou, 350003, China.
| | - Xiao Ke
- Department of Gastroenterology, The Second People's Hospital affiliated to Fujian University of Traditional Chinese Medicine, Fuzhou, 350003, China.
| |
Collapse
|
6
|
Cai X, Deng L, Ma X, Guo Y, Feng Z, Liu M, Guan Y, Huang Y, Deng J, Li H, Sang H, Liu F, Yang X. Altered diversity and composition of gut microbiota in Wilson's disease. Sci Rep 2020; 10:21825. [PMID: 33311635 PMCID: PMC7732847 DOI: 10.1038/s41598-020-78988-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 12/02/2020] [Indexed: 02/06/2023] Open
Abstract
Wilson's disease (WD) is an autosomal recessive inherited disorder of chronic copper toxicosis with high mortality and disability. Recent evidence suggests a correlation between dysbiosis in gut microbiome and multiple diseases such as genetic and metabolic disease. However, the impact of intestinal microbiota polymorphism in WD have not been fully elaborated and need to be explore for seeking some microbiota benefit for WD patients. In this study, the 16S rRNA sequencing was performed on fecal samples from 14 patients with WD and was compared to the results from 16 healthy individuals. The diversity and composition of the gut microbiome in the WD group were significantly lower than those in healthy individuals. The WD group presented unique richness of Gemellaceae, Pseudomonadaceae and Spirochaetaceae at family level, which were hardly detected in healthy controls. The WD group had a markedly lower abundance of Actinobacteria, Firmicutes and Verrucomicrobia, and a higher abundance of Bacteroidetes, Proteobacteria, Cyanobacteria and Fusobacteria than that in healthy individuals. The Firmicutes to Bacteroidetes ratio in the WD group was significantly lower than that of healthy control. In addition, the functional profile of the gut microbiome from WD patients showed a lower abundance of bacterial groups involved in the host immune and metabolism associated systems pathways such as transcription factors and ABC-type transporters, compared to healthy individuals. These results implied dysbiosis of gut microbiota may be influenced by the host metabolic disorders of WD, which may provide a new understanding of the pathogenesis and new possible therapeutic targets for WD.
Collapse
Affiliation(s)
- Xiangsheng Cai
- Clinical Laboratory, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080, People's Republic of China.
- Department of Medical Laboratory, Guangdong Pharmaceutical University, Guangzhou, 510080, People's Republic of China.
- Center for Medical Experiments, University of Chinese Academy of Science-Shenzhen Hospital, Shenzhen, 518106, People's Republic of China.
| | - Lin Deng
- Department of Dermatology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, People's Republic of China
| | - Xiaogui Ma
- Clinical Laboratory, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080, People's Republic of China
| | - Yusheng Guo
- Department of Medical Laboratory, Guangdong Pharmaceutical University, Guangzhou, 510080, People's Republic of China
| | - Zhiting Feng
- Department of Pathology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080, People's Republic of China
| | - Minqi Liu
- Department of Medical Laboratory, Guangdong Pharmaceutical University, Guangzhou, 510080, People's Republic of China
| | - Yubin Guan
- Clinical Laboratory, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080, People's Republic of China
| | - Yanting Huang
- Clinical Laboratory, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080, People's Republic of China
| | - Jianxin Deng
- Department of Endocrinology, Shenzhen Second People's Hospital, Health Science Center of Shenzhen University, Shenzhen, 518035, People's Republic of China
| | - Hongwei Li
- Institute of Biotherapy, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Hong Sang
- Nanjing School of Clinical Medicine, Southern Medical University, Jinling Hospital, Nanjing, 210002, People's Republic of China
| | - Fang Liu
- Institute of Biotherapy, Southern Medical University, Guangzhou, 510515, People's Republic of China.
| | - Xiaorong Yang
- Clinical Laboratory, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080, People's Republic of China.
| |
Collapse
|