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McCoubrey LE, Ferraro F, Seegobin N, Verin J, Alfassam HA, Awad A, Marzorati M, Verstrepen L, Ghyselinck J, De Munck J, De Medts J, Steppe E, De Vleeschhauwer V, De Rocker G, Droesbeke A, De Rijck M, Vanthoor S, Moens F, Siepmann J, Siepmann F, Gaisford S, Orlu M, Basit AW. Poly(D,l-lactide-co-glycolide) particles are metabolised by the gut microbiome and elevate short chain fatty acids. J Control Release 2024:S0168-3659(24)00192-5. [PMID: 38521168 DOI: 10.1016/j.jconrel.2024.03.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/17/2024] [Accepted: 03/20/2024] [Indexed: 03/25/2024]
Abstract
The production of short chain fatty acids (SCFAs) by the colonic microbiome has numerous benefits for human health, including maintenance of epithelial barrier function, suppression of colitis, and protection against carcinogenesis. Despite the therapeutic potential, there is currently no optimal approach for elevating the colonic microbiome's synthesis of SCFAs. In this study, poly(D,l-lactide-co-glycolide) (PLGA) was investigated for this application, as it was hypothesised that the colonic microbiota would metabolise PLGA to its lactate monomers, which would promote the resident microbiota's synthesis of SCFAs. Two grades of spray dried PLGA, alongside a lactate bolus control, were screened in an advanced model of the human colon, known as the M-SHIME® system. Whilst the high molecular weight (Mw) grade of PLGA was stable in the presence of the microbiota sourced from three healthy humans, the low Mw PLGA (PLGA 2) was found to be metabolised. This microbial degradation led to sustained release of lactate over 48 h and increased concentrations of the SCFAs propionate and butyrate. Further, microbial synthesis of harmful ammonium was significantly reduced compared to untreated controls. Interestingly, both types of PLGA was found to influence the composition of the luminal and mucosal microbiota in a donor-specific manner. An in vitro model of an inflamed colonic epithelium also showed the polymer to affect the expression of pro- and anti-inflammatory markers, such as interleukins 8 and 10. The findings of this study reveal PLGA's sensitivity to enzymatic metabolism in the gut, which could be harnessed for therapeutic elevation of colonic SCFAs.
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Affiliation(s)
- Laura E McCoubrey
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Fabiana Ferraro
- Univ. Lille, Inserm, CHU Lille, U1008, F-59000 Lille, France
| | - Nidhi Seegobin
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Jérémy Verin
- Univ. Lille, Inserm, CHU Lille, U1008, F-59000 Lille, France
| | - Haya A Alfassam
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom; Advanced Diagnostics and Therapeutics Institute, Health Sector, King Abdulaziz City for Science and Technology (KACST), 114422 Riyadh, Saudi Arabia
| | - Atheer Awad
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom; Department of Clinical, Pharmaceutical and Biological Sciences, University of Hertfordshire, College Lane, Hatfield AL10 9AB, United Kingdom
| | | | | | | | | | | | - Evi Steppe
- ProDigest BVB, Technologiepark 73, 9052 Ghent, Belgium
| | | | | | | | | | - Sara Vanthoor
- ProDigest BVB, Technologiepark 73, 9052 Ghent, Belgium
| | | | | | | | - Simon Gaisford
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Mine Orlu
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Abdul W Basit
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom.
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Zhang M, Yu B, Fang Q, Liu J, Xia Q, Ye K, Zhang D, Qiang Z, Pan X. Microbiome recognition of virulence-factor-governed interfacial mechanisms in antibiotic resistance and pathogenicity removal by functionalized microbubbles. Water Res 2023; 242:120224. [PMID: 37352673 DOI: 10.1016/j.watres.2023.120224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/24/2023] [Accepted: 06/12/2023] [Indexed: 06/25/2023]
Abstract
The frequent occurrence of epidemics around the world gives rise to increasing concerns of the pollution of pathogens and antibiotic resistant bacteria in water. This study investigated the impacts of virulence factors (VFs) on the removal of antibiotic resistant and pathogenic bacteria from municipal wastewater by ozone-free or ozone-encapsulated Fe(III)-coagulant-modified colloidal microbubbles (O3_free-CCMBs or O3-CCMBs). The highly interface-dependent process was initiated with cell-capture on the microbubble surface where the as-collected cells could be further inactivated with the bubble-released ozone and oxidative species if O3-CCMBs were used. The microbiome sequencing analyses denote that the O3_free-CCMB performance of antibiotic resistant and pathogenic bacteria removal was dependent on the virulence phenotypes related to cell-surface properties or structures. The adhesion-related VFs facilitated the effective attachment between cells and the coagulant-modified bubble-surface, which further enhanced cell inactivation by bubble-released ozone. On the contrary, the motility-related VFs might help cells to escape from the bubble capture by locomotion; however, this could be overcome by O3-CCMB-induced oxidative demolition of the movement structures. Besides, the microbubble performance was also impacted with the cell-membrane structure related to antibiotic resistance (i.e., efflux pumps) and the dissolved organic matter through promoting the surface-capture and decreasing the oxidation efficacy. The ozone-encapsulated microbubbles with surface functionalization are robust and promising tools in hampering antibiotic resistance and pathogenicity dissemination from wastewater to surface water environment; and awareness should be raised for the influence of virulence signatures on its performance.
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Affiliation(s)
- Ming Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Beilei Yu
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Qunkai Fang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jiayuan Liu
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Qiaoyun Xia
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Kun Ye
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Daoyong Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Zhimin Qiang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing 100085, China
| | - Xiangliang Pan
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China.
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Bağcı C, Albrecht B, Huson DH. MAIRA: Protein-based Analysis of MinION Reads on a Laptop. Methods Mol Biol 2023; 2649:223-234. [PMID: 37258865 DOI: 10.1007/978-1-0716-3072-3_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Third-generation sequencing technologies are being increasingly used in microbiome research and this has given rise to new challenges in computational microbiome analysis. Oxford Nanopore's MinION is a portable sequencer that streams data that can be basecalled on-the-fly. Here we give an introduction to the MAIRA software, which is designed to analyze MinION sequencing reads from a microbiome sample, as they are produced in real-time, on a laptop. The software processes reads in batches and updates the presented analysis after each batch. There are two analysis steps: First, protein alignments are calculated to determine which genera might be present in a sample. When strong evidence for a genus is found, then, in a second step, a more detailed analysis is performed by aligning the reads against the proteins of all species in the detected genus. The program presents a detailed analysis of species, antibiotic resistance genes, and virulence factors.
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Affiliation(s)
- Caner Bağcı
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany.
- International Max Planck Research School "From Molecules to Organisms", Max Planck Institute for Developmental Biology, Tübingen, Germany.
| | | | - Daniel H Huson
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany.
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Gong X, Zhao W, Lu G, Li Y. Using microbiome sequencing in hemoptysis children to avoid unnecessary transcatheter invasive therapy. Asian J Surg 2022; 45:1346-1349. [PMID: 35221190 DOI: 10.1016/j.asjsur.2022.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 02/11/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Xue Gong
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Wanling Zhao
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Guoyan Lu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Yifei Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
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Abstract
The oral microbiome has been implicated as a trigger for immune responsiveness in the oral cavity, particularly in the setting of the inflammatory disease periodontitis. The protocol presented here is aimed at characterizing the oral microbiome in murine models at steady state and during perturbations of immunity or physiology. Herein, we describe murine oral microbiome sampling procedures, processing of low biomass samples and subsequent microbiome characterization based on 16S rRNA gene sequencing.
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Affiliation(s)
- Loreto Abusleme
- Oral Immunity and Inflammation Unit, NIDCR, NIH, Bethesda, MD, USA
| | - Bo-Young Hong
- Division of Periodontology, Department of Oral Health and Diagnostic Sciences, UConn Health, Farmington, CT, USA
| | - Anilei Hoare
- Division of Periodontology, Department of Oral Health and Diagnostic Sciences, UConn Health, Farmington, CT, USA
| | - Joanne E Konkel
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.,Manchester Collaborative Centre for Inflammation Research (MCCIR), University of Manchester, Manchester, UK
| | - Patricia I Diaz
- Division of Periodontology, Department of Oral Health and Diagnostic Sciences, UConn Health, Farmington, CT, USA
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