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Parthasarathy A, Miranda RR, Bedore TJ, Watts LM, Mantravadi PK, Wong NH, Chu J, Adjei JA, Rana AP, Savka MA, Bulman ZP, Borrego EJ, Hudson AO. Interaction of Acinetobacter sp. RIT 592 induces the production of broad-spectrum antibiotics in Exiguobacterium sp. RIT 594. Front Pharmacol 2024; 15:1456027. [PMID: 39148551 PMCID: PMC11324575 DOI: 10.3389/fphar.2024.1456027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Accepted: 07/18/2024] [Indexed: 08/17/2024] Open
Abstract
Antimicrobial resistance (AMR) is one of the most alarming global public health challenges of the 21st century. Over 3 million antimicrobial-resistant infections occur in the United States annually, with nearly 50,000 cases being fatal. Innovations in drug discovery methods and platforms are crucial to identify novel antibiotics to combat AMR. We present the isolation and characterization of potentially novel antibiotic lead compounds produced by the cross-feeding of two rhizosphere bacteria, Acinetobacter sp. RIT 592 and Exiguobacterium sp. RIT 594. We used solid-phase extraction (SPE) followed by liquid chromatography (LC) to enrich antibiotic extracts and subsequently mass spectrometry (MS) analysis of collected fractions for compound structure identification and characterization. The MS data were processed through the Global Natural Product Social Molecular Networking (GNPS) database. The supernatant from RIT 592 induced RIT 594 to produce a cocktail of antimicrobial compounds active against Gram-positive and negative bacteria. The GNPS analysis indicated compounds with known antimicrobial activity in the bioactive samples, including oligopeptides and their derivatives. This work emphasizes the utility of microbial community-based platforms to discover novel clinically relevant secondary metabolites. Future work includes further structural characterization and antibiotic activity evaluation of the individual compounds against pathogenic multidrug-resistant (MDR) bacteria.
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Affiliation(s)
| | - Renata Rezende Miranda
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, NY, United States
| | - T J Bedore
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Lizabeth M Watts
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | | | - Narayan H Wong
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Jonathan Chu
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Joseph A Adjei
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Amisha P Rana
- Department of Pharmacy Practice, University of Illinois at Chicago, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States
| | - Michael A Savka
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Zackery P Bulman
- Department of Pharmacy Practice, University of Illinois at Chicago, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States
| | - Eli J Borrego
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - André O Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
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Mejías M, Madrid R, Díaz K, Gutiérrez-Cortés I, Pulgar R, Mandakovic D. The Impact of Environmental Gaseous Pollutants on the Cultivable Bacterial and Fungal Communities of the Aerobiome. Microorganisms 2024; 12:1103. [PMID: 38930485 PMCID: PMC11206153 DOI: 10.3390/microorganisms12061103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 06/28/2024] Open
Abstract
Understanding air microbial content, especially in highly polluted urban areas, is crucial for assessing its effect on human health and ecosystems. In this context, the impact of gaseous pollutants on the aerobiome remains inconclusive due to a lack of studies separating this factor from other contaminants or environmental factors. In this study, we aimed to experimentally assess the influence of contrasting concentrations of atmospheric gaseous pollutants as isolated variables on the composition of the aerobiome. Our study sites were contrasting Air Quality Index (AQI) sites of the Metropolitan Region of Chile, where nitric oxide (NO) was significantly lower at the low-AQI site than at the high-AQI site, while ozone (O3) was significantly higher. Cultivable aerobiome communities from the low-AQI site were exposed to their own pollutants or those from the high-AQI site and characterized using high-throughput sequencing (HTS), which allowed comparisons between the entire cultivable communities. The results showed increased alpha diversity in bacterial and fungal communities exposed to the high-AQI site compared to the low-AQI site. Beta diversity and compositional hierarchical clustering analyses revealed a clear separation based on NO and O3 concentrations. At the phylum level, four bacterial and three fungal phyla were identified, revealing an over-representation of Actinobacteriota and Basidiomycota in the samples transferred to the high-AQI site, while Proteobacteria were more abundant in the community maintained at the low-AQI site. At the functional level, bacterial imputed functions were over-represented only in samples maintained at the low-AQI site, while fungal functions were affected in both conditions. Overall, our results highlight the impact of NO and/or O3 on both taxonomic and functional compositions of the cultivable aerobiome. This study provides, for the first time, insights into the influence of contrasting pollutant gases on entire bacterial and fungal cultivable communities through a controlled environmental intervention.
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Affiliation(s)
- Madelaine Mejías
- GEMA Center for Genomics, Ecology and Environment, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago 8580745, Chile; (M.M.); (R.M.); (K.D.); (I.G.-C.)
- Programa de Doctorado en Ecología Integrativa, Universidad Mayor, Santiago 8580745, Chile
| | - Romina Madrid
- GEMA Center for Genomics, Ecology and Environment, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago 8580745, Chile; (M.M.); (R.M.); (K.D.); (I.G.-C.)
| | - Karina Díaz
- GEMA Center for Genomics, Ecology and Environment, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago 8580745, Chile; (M.M.); (R.M.); (K.D.); (I.G.-C.)
| | - Ignacio Gutiérrez-Cortés
- GEMA Center for Genomics, Ecology and Environment, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago 8580745, Chile; (M.M.); (R.M.); (K.D.); (I.G.-C.)
| | - Rodrigo Pulgar
- Laboratorio de Genómica y Genética de Interacciones Biológicas (LG2IB), Instituto de Nutrición y Tecnología de los Alimento, Universidad de Chile, Santiago 7830490, Chile
| | - Dinka Mandakovic
- GEMA Center for Genomics, Ecology and Environment, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago 8580745, Chile; (M.M.); (R.M.); (K.D.); (I.G.-C.)
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Song T, Hao Y, Wang M, Li T, Zhao C, Li J, Hou Y. Sophoridine manifests as a leading compound for anti-arrhythmia with multiple ion-channel blocking effects. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 112:154688. [PMID: 36738478 DOI: 10.1016/j.phymed.2023.154688] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/09/2023] [Accepted: 01/28/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Sophoridine (SR) has shown the potential to be an antiarrhythmic agent. However, SR's electrophysiological properties and druggability research are relatively inadequate, which limits the development of SR as an antiarrhythmic candidate. PURPOSE To facilitate the development process of SR as an antiarrhythmic candidate, we performed integrated studies on the electrophysiological properties of SR in vitro and ex vivo to gain more comprehensive insights into the multi-ion channel blocking effects of SR, which provided the foundation for the further drugability studies in antiarrhythmic and safety studies. Firstly, SR's electrophysiological properties and antiarrhythmic potentials were recorded and assessed at the cell and tissue levels by comprehensively integrating the patch clamp with the Electrical and Optical Mapping systems. Subsequently, the antiarrhythmic effects of SR were validated by aconitine and ouabain-induced arrhythmia in vivo. Finally, the safety of SR as an antiarrhythmic candidate compound was evaluated based on the guidelines of the Comprehensive in Vitro Proarrhythmia Assay (CiPA). STUDY DESIGN The antiarrhythmic effect of SR was evaluated at the in vitro, ex vivo, and in vivo levels. METHODS Isolated primary cardiomyocytes and stable cell lines were prepared to explore the electrophysiologic properties of being a multiple ion-channel blocker in vitro by whole-cell patch clamp. Using electrical and optical mapping, the negative chronotropic effect of SR was determined in langendorff-perfused rat or guinea-pig hearts.The antiarrhythmic activity of SR was assessed by the ex vivo tachyarrhythmia models induced by left coronary artery ligation (LCAL) and isoproterenol (ISO). Canonical models of aconitine and ouabain-induced arrhythmia were used to verify the antiarrhythmic effects in vivo. Finally, the pro-arrhythmic risk of SR was detected in Human-Induced Pluripotent Stem Cell-Derived Cardiomyocytes (hSCCMs) using a Microelectrode array (MEA). RESULTS Single-cell patch assay validated the multiple ion-channel blockers of SR in transient outward current potassium currents (Ito), l-type calcium currents (ICa-l), and rapid activation delayed rectifier potassium currents (IKr). SR ex vivo depressed heart rates (HR) and ventricular conduction velocity (CV) and prolonged Q-T intervals in a concentration-dependent manner. Consistent with the changes in HRs, SR extended the active time of hearts and increased the action potential duration measured at 90% repolarization (APD90). SR could also significantly lengthen the onset time and curtail the duration of spontaneous ventricular tachycardia (VT) in the ex vivo arrhythmic model induced by LCAL. Meanwhile, SR could also significantly upregulate the programmed electrical stimulation (PES) frequency after the ISO challenge in forming electrical alternans and re-entrant excitation. Furthermore, SR exerted antiarrhythmic effects in the tachyarrhythmia models induced by aconitine and ouabain in vivo. Notably, the pro-arrhythmic risk of SR was shallow for a moderate inhibition of the human ether-à-go-go-related gene (hERG) channel. Moreover, SR prolonged field potential duration (FPDc) of hSCCMs in a concentration-dependent manner without early after depolarization (EAD) and arrhythmia occurrence. CONCLUSION Our results indicated that SR manifested as a multiple ion-channel blocker in the electrophysiological properties and exerts antiarrhythmic effects ex vivo and in vivo. Meanwhile, due to the low pro-arrhythmic risk in the hERG inhibition assay and the induction of EAD, SR has great potential as a leading candidate in the treatment of ventricular tachyarrhythmia.
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Affiliation(s)
- Tao Song
- College of Integrated Chinese and Western Medicine, Hebei University of Chinese Medicine, Shijiazhuang 050035, China
| | - Yuanyuan Hao
- College of Integrated Chinese and Western Medicine, Hebei University of Chinese Medicine, Shijiazhuang 050035, China; New Drug Evaluation Center, Shijiazhuang Yiling Pharmaceutical Co., Ltd, Shijiazhuang 050035, China
| | - Mingye Wang
- College of Integrated Chinese and Western Medicine, Hebei University of Chinese Medicine, Shijiazhuang 050035, China
| | - Tongtong Li
- College of Integrated Chinese and Western Medicine, Hebei University of Chinese Medicine, Shijiazhuang 050035, China
| | - Chi Zhao
- Hebei Medical University, No. 361, East Zhongshan Road, Shijiazhuang, Hebei 050017, China
| | - Jiajia Li
- Department of Pharmacy, The Fourth Hospital of Shijiazhuang, No.16, the North of Tangu street, Shijiazhuang, Hebei 050031, China
| | - Yunlong Hou
- College of Integrated Chinese and Western Medicine, Hebei University of Chinese Medicine, Shijiazhuang 050035, China; New Drug Evaluation Center, Shijiazhuang Yiling Pharmaceutical Co., Ltd, Shijiazhuang 050035, China; Shijiazhuang Compound Traditional Chinese Medicine Technology Innovation Center, Shijiazhuang 050035, China.
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Moreira VA, Cravo-Laureau C, de Carvalho ACB, Baldy A, Bidone ED, Sabadini-Santos E, Duran R. Microbial indicators along a metallic contamination gradient in tropical coastal sediments. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130244. [PMID: 36327839 DOI: 10.1016/j.jhazmat.2022.130244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 10/03/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
The structure and diversity of microbial community inhabiting coastal sediments reflect the exposition to contaminants. Aiming to assess the changes in the microbiota from Sepetiba Bay (SB, Brazil) sediments, correlations between the 16S rRNA gene data (V4-V5 region), metal contamination factors (CF), and the ecological risk classification provided by the Quality Ratio (QR) index were considered. The results show that microbial diversity differs significantly between the less (SB external sector) and the most (SB internal sector) polluted sectors. Also, differences in the microbial community structure regarding the ecological risk classifications validated the QR index as a reliable tool to report the SB chronic contamination. Microbial indicator genera resistant to metals (Desulfatiglans, SEEP-SRB1, Spirochaeta 2, among others) presented mainly anaerobic metabolisms. These genera are related to the sulfate reducing and methanogenic metabolisms probably participating in the natural attenuation processes but also associated with greenhouse gas emissions. In contrast, microbial indicator genera sensitive to metals (Rubripirellula, Blastopirellula, Aquibacter, among others) presented mainly aerobic metabolisms. It is suggested that future works should investigate the metabolic functions to evaluate the influence of metallic contaminants on microbial community inhabiting SB sediment.
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Affiliation(s)
- Vanessa Almeida Moreira
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ 24020-150, Brazil; Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | | | - Angelo Cezar Borges de Carvalho
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ 24020-150, Brazil; Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Alice Baldy
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Edison Dausacker Bidone
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ 24020-150, Brazil
| | - Elisamara Sabadini-Santos
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ 24020-150, Brazil
| | - Robert Duran
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France.
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George DM, Ramadoss R, Mackey HR, Vincent AS. Comparative computational study to augment UbiA prenyltransferases inherent in purple photosynthetic bacteria cultured from mangrove microbial mats in Qatar for coenzyme Q 10 biosynthesis. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2022; 36:e00775. [PMID: 36404947 PMCID: PMC9672418 DOI: 10.1016/j.btre.2022.e00775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/31/2022] [Accepted: 11/11/2022] [Indexed: 11/15/2022]
Abstract
Coenzyme Q10 (CoQ10) is a powerful antioxidant with a myriad of applications in healthcare and cosmetic industries. The most effective route of CoQ10 production is microbial biosynthesis. In this study, four CoQ10 biosynthesizing purple photosynthetic bacteria: Rhodobacter blasticus, Rhodovulum adriaticum, Afifella pfennigii and Rhodovulum marinum, were identified using 16S rRNA sequencing of enriched microbial mat samples obtained from Purple Island mangroves (Qatar). The membrane bound enzyme 4-hydroxybenzoate octaprenyltransferase (UbiA) is pivotal for bacterial biosynthesis of CoQ10. The identified bacteria could be inducted as efficient industrial bio-synthesizers of CoQ10 by engineering their UbiA enzymes. Therefore, the mutation sites and substitution residues for potential functional enhancement were determined by comparative computational study. Two mutation sites were identified within the two conserved Asp-rich motifs, and the effect of proposed mutations in substrate binding affinity of the UbiA enzymes was assessed using multiple ligand simultaneous docking (MLSD) studies, as a groundwork for experimental studies.
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Affiliation(s)
- Drishya M. George
- College of Health and Life Sciences, Hamad bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Ramya Ramadoss
- Biological Sciences, Carnegie Mellon University Qatar, Doha, Qatar
| | - Hamish R. Mackey
- College of Health and Life Sciences, Hamad bin Khalifa University, Qatar Foundation, Doha, Qatar
- Division of Sustainable Development, College of Science and Engineering, Hamad bin Khalifa University, Qatar Foundation, Doha, Qatar
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Suyal DC, Joshi D, Kumar S, Bhatt P, Narayan A, Giri K, Singh M, Soni R, Kumar R, Yadav A, Devi R, Kaur T, Kour D, Yadav AN. Himalayan Microbiomes for Agro-environmental Sustainability: Current Perspectives and Future Challenges. MICROBIAL ECOLOGY 2022; 84:643-675. [PMID: 34647148 DOI: 10.1007/s00248-021-01849-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
The Himalayas are one of the most mystical, yet least studied terrains of the world. One of Earth's greatest multifaceted and diverse montane ecosystems is also one of the thirty-four global biodiversity hotspots of the world. These are supposed to have been uplifted about 60-70 million years ago and support, distinct environments, physiography, a variety of orogeny, and great biological diversity (plants, animals, and microbes). Microbes are the pioneer colonizer of the Himalayas that are involved in various bio-geological cycles and play various significant roles. The applications of Himalayan microbiomes inhabiting in lesser to greater Himalayas have been recognized. The researchers explored the applications of indigenous microbiomes in both agricultural and environmental sectors. In agriculture, microbiomes from Himalayan regions have been suggested as better biofertilizers and biopesticides for the crops growing at low temperature and mountainous areas as they help in the alleviation of cold stress and other biotic stresses. Along with alleviation of low temperature, Himalayan microbes also have the capability to enhance plant growth by availing the soluble form of nutrients like nitrogen, phosphorus, potassium, zinc, and iron. These microbes have been recognized for producing plant growth regulators (abscisic acid, auxin, cytokinin, ethylene, and gibberellins). These microbes have been reported for bioremediating the diverse pollutants (pesticides, heavy metals, and xenobiotics) for environmental sustainability. In the current perspectives, present review provides a detailed discussion on the ecology, biodiversity, and adaptive features of the native Himalayan microbiomes in view to achieve agro-environmental sustainability.
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Affiliation(s)
- Deep Chandra Suyal
- Department of Microbiology, Akal College of Basic Sciences, Eternal University, Sirmaur, Himachal Pradesh, India
| | - Divya Joshi
- Uttarakhand Pollution Control Board, Regional Office, Kashipur, Uttarakhand, India
| | - Saurabh Kumar
- Division of Crop Research, Research Complex for Eastern Region, Patna, Bihar, India
| | - Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
| | - Arun Narayan
- Forest Research Institute, Dehradun, 2480 06, India
| | - Krishna Giri
- Rain Forest Research Institute, Jorhat, 785 010, India
| | - Manali Singh
- Department of Biotechnology, Invertis Institute of Engineering and Technology (IIET), Invertis University, Bareilly, 243123, Uttar Pradesh, India
| | - Ravindra Soni
- Department of Agricultural Microbiology, College of Agriculture, Indira Gandhi Krishi Vishwa Vidyalaya, Raipur, Chhattisgarh, India
| | - Rakshak Kumar
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Ashok Yadav
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Rubee Devi
- Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India
| | - Tanvir Kaur
- Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India
| | - Divjot Kour
- Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India
| | - Ajar Nath Yadav
- Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India.
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