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Al Meslamani AZ, Sobrino I, de la Fuente J. Machine learning in infectious diseases: potential applications and limitations. Ann Med 2024; 56:2362869. [PMID: 38853633 PMCID: PMC11168216 DOI: 10.1080/07853890.2024.2362869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/02/2024] [Indexed: 06/11/2024] Open
Abstract
Infectious diseases are a major threat for human and animal health worldwide. Artificial Intelligence (AI) combined algorithms including Machine Learning and Big Data analytics have emerged as a potential solution to analyse diverse datasets and face challenges posed by infectious diseases. In this commentary we explore the potential applications and limitations of ML to management of infectious disease. It explores challenges in key areas such as outbreak prediction, pathogen identification, drug discovery, and personalized medicine. We propose potential solutions to mitigate these hurdles and applications of ML to identify biomolecules for effective treatment and prevention of infectious diseases. In addition to use of ML for management of infectious diseases, potential applications are based on catastrophic evolution events for the identification of biomolecular targets to reduce risks for infectious diseases and vaccinomics for discovery and characterization of vaccine protective antigens using intelligent Big Data analytics techniques. These considerations set a foundation for developing effective strategies for managing infectious diseases in the future.
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Affiliation(s)
- Ahmad Z. Al Meslamani
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi, United Arab Emirates
| | - Isidro Sobrino
- SaBio, Instituto de Investigación en Recursos Cinegéticos (IREC), Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Castilla-La Mancha (UCLM)-Junta de Comunidades de Castilla-La Mancha (JCCM), Ciudad Real, Spain
| | - José de la Fuente
- SaBio, Instituto de Investigación en Recursos Cinegéticos (IREC), Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Castilla-La Mancha (UCLM)-Junta de Comunidades de Castilla-La Mancha (JCCM), Ciudad Real, Spain
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, OK State University, Stillwater, Oklahoma, USA
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2
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Pham VHT, Kim J, Chang S. A Valuable Source of Promising Extremophiles in Microbial Plastic Degradation. Polymers (Basel) 2024; 16:2109. [PMID: 39125136 PMCID: PMC11314448 DOI: 10.3390/polym16152109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/01/2024] [Accepted: 07/22/2024] [Indexed: 08/12/2024] Open
Abstract
Plastics have accumulated in open environments, such as oceans, rivers, and land, for centuries, but their effect has been of concern for only decades. Plastic pollution is a global challenge at the forefront of public awareness worldwide due to its negative effects on ecological systems, animals, human health, and national economies. Therefore, interest has increased regarding specific circular economies for the development of plastic production and the investigation of green technologies for plastic degradation after use on an appropriate timescale. Moreover, biodegradable plastics have been found to contain potential new hazards compared with conventional plastics due to the physicochemical properties of the polymers involved. Recently, plastic biodegradation was defined as microbial conversion using functional microorganisms and their enzymatic systems. This is a promising strategy for depolymerizing organic components into carbon dioxide, methane, water, new biomass, and other higher value bioproducts under both oxic and anoxic conditions. This study reviews microplastic pollution, the negative consequences of plastic use, and the current technologies used for plastic degradation and biodegradation mediated by microorganisms with their drawbacks; in particular, the important and questionable role of extremophilic multi-enzyme-producing bacteria in synergistic systems of plastic decomposition is discussed. This study emphasizes the key points for enhancing the plastic degradation process using extremophiles, such as cell hydrophobicity, amyloid protein, and other relevant factors. Bioprospecting for novel mechanisms with unknown information about the bioproducts produced during the plastic degradation process is also mentioned in this review with the significant goals of CO2 evolution and increasing H2/CH4 production in the future. Based on the potential factors that were analyzed, there may be new ideas for in vitro isolation techniques for unculturable/multiple-enzyme-producing bacteria and extremophiles from various polluted environments.
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Affiliation(s)
- Van Hong Thi Pham
- Department of Environmental Energy Engineering, College of Creative Engineering, Kyonggi University, Suwon 16227, Republic of Korea;
- Department of Life Science, College of Natural Science, Kyonggi University, Suwon 16227, Republic of Korea
| | - Jaisoo Kim
- Department of Life Science, College of Natural Science, Kyonggi University, Suwon 16227, Republic of Korea
| | - Soonwoong Chang
- Department of Environmental Energy Engineering, College of Creative Engineering, Kyonggi University, Suwon 16227, Republic of Korea;
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3
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Xu Q, Ali S, Afzal M, Nizami AS, Han S, Dar MA, Zhu D. Advancements in bacterial chemotaxis: Utilizing the navigational intelligence of bacteria and its practical applications. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172967. [PMID: 38705297 DOI: 10.1016/j.scitotenv.2024.172967] [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: 02/15/2024] [Revised: 04/06/2024] [Accepted: 05/01/2024] [Indexed: 05/07/2024]
Abstract
The fascinating world of microscopic life unveils a captivating spectacle as bacteria effortlessly maneuver through their surroundings with astonishing accuracy, guided by the intricate mechanism of chemotaxis. This review explores the complex mechanisms behind this behavior, analyzing the flagellum as the driving force and unraveling the intricate signaling pathways that govern its movement. We delve into the hidden costs and benefits of this intricate skill, analyzing its potential to propagate antibiotic resistance gene while shedding light on its vital role in plant colonization and beneficial symbiosis. We explore the realm of human intervention, considering strategies to manipulate bacterial chemotaxis for various applications, including nutrient cycling, algal bloom and biofilm formation. This review explores the wide range of applications for bacterial capabilities, from targeted drug delivery in medicine to bioremediation and disease control in the environment. Ultimately, through unraveling the intricacies of bacterial movement, we can enhance our comprehension of the intricate web of life on our planet. This knowledge opens up avenues for progress in fields such as medicine, agriculture, and environmental conservation.
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Affiliation(s)
- Qi Xu
- International Joint Laboratory on Synthetic Biology and Biomass Biorefinery, Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Shehbaz Ali
- International Joint Laboratory on Synthetic Biology and Biomass Biorefinery, Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, PR China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, PR China
| | - Muhammad Afzal
- Soil & Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Abdul-Sattar Nizami
- Sustainable Development Study Centre, Government College University, Lahore 54000, Pakistan
| | - Song Han
- Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, PR China
| | - Mudasir A Dar
- International Joint Laboratory on Synthetic Biology and Biomass Biorefinery, Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Daochen Zhu
- International Joint Laboratory on Synthetic Biology and Biomass Biorefinery, Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, PR China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, PR China.
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Wang X, Qiu C, Chen C, Gao C, Wei W, Song W, Wu J, Liu L, Chen X. Metabolic Engineering of Escherichia coli for High-Level Production of l-Phenylalanine. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:11029-11040. [PMID: 38699920 DOI: 10.1021/acs.jafc.4c01563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
l-Phenylalanine (l-Phe) is widely used in the food and pharmaceutical industries. However, the biosynthesis of l-Phe using Escherichia coli remains challenging due to its lower tolerance to high concentration of l-Phe. In this study, to efficiently synthesize l-Phe, the l-Phe biosynthetic pathway was reconstructed by expressing the heterologous genes aroK1, aroL1, and pheA1, along with the native genes aroA, aroC, and tyrB in the shikimate-producing strain E. coli SA09, resulting in the engineered strain E. coli PHE03. Subsequently, adaptive evolution was conducted on E. coli PHE03 to enhance its tolerance to high concentrations of l-Phe, resulting in the strain E. coli PHE04, which reduced the cell mortality to 36.2% after 48 h of fermentation. To elucidate the potential mechanisms, transcriptional profiling was conducted, revealing MarA, a DNA-binding transcriptional dual regulator, as playing a crucial role in enhancing cell membrane integrity and fluidity for improving cell tolerance to high concentrations of l-Phe. Finally, the titer, yield, and productivity of l-Phe with E. coli PHE05 overexpressing marA were increased to 80.48 g/L, 0.27 g/g glucose, and 1.68 g/L/h in a 5-L fed-batch fermentation, respectively.
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Affiliation(s)
- Xiaoge Wang
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Chong Qiu
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Chenghu Chen
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Wanqing Wei
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xiulai Chen
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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Wang YC, Mao Y, Fu HM, Wang J, Weng X, Liu ZH, Xu XW, Yan P, Fang F, Guo JS, Shen Y, Chen YP. New insights into functional divergence and adaptive evolution of uncultured bacteria in anammox community by complete genome-centric analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171530. [PMID: 38453092 DOI: 10.1016/j.scitotenv.2024.171530] [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: 09/26/2023] [Revised: 11/13/2023] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
Anaerobic ammonium-oxidation (anammox) bacteria play a crucial role in global nitrogen cycling and wastewater nitrogen removal, but they share symbiotic relationships with various other microorganisms. Functional divergence and adaptive evolution of uncultured bacteria in anammox community remain underexplored. Although shotgun metagenomics based on short reads has been widely used in anammox research, metagenome-assembled genomes (MAGs) are often discontinuous and highly contaminated, which limits in-depth analyses of anammox communities. Here, for the first time, we performed Pacific Biosciences high-fidelity (HiFi) long-read sequencing on the anammox granule sludge sample from a lab-scale bioreactor, and obtained 30 accurate and complete metagenome-assembled genomes (cMAGs). These cMAGs were obtained by selecting high-quality circular contigs from initial assemblies of long reads generated by HiFi sequencing, eliminating the need for Illumina short reads, binning, and reassembly. One new anammox species affiliated with Candidatus Jettenia and three species affiliated with novel families were found in this anammox community. cMAG-centric analysis revealed functional divergence in general and nitrogen metabolism among the anammox community members, and they might adopt a cross-feeding strategy in organic matter, cofactors, and vitamins. Furthermore, we identified 63 mobile genetic elements (MGEs) and 50 putative horizontal gene transfer (HGT) events within these cMAGs. The results suggest that HGT events and MGEs related to phage and integration or excision, particularly transposons containing tnpA in anammox bacteria, might play important roles in the adaptive evolution of this anammox community. The cMAGs generated in the present study could be used to establish of a comprehensive database for anammox bacteria and associated microorganisms. These findings highlight the advantages of HiFi sequencing for the studies of complex mixed cultures and advance the understanding of anammox communities.
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Affiliation(s)
- Yi-Cheng Wang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Yanping Mao
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518071, Guangdong, China
| | - Hui-Min Fu
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China; National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing 400067, China
| | - Jin Wang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Xun Weng
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Zi-Hao Liu
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Xiao-Wei Xu
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Peng Yan
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Fang Fang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Jin-Song Guo
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Yu Shen
- National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing 400067, China
| | - You-Peng Chen
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China.
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6
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Kamel M, Aleya S, Alsubih M, Aleya L. Microbiome Dynamics: A Paradigm Shift in Combatting Infectious Diseases. J Pers Med 2024; 14:217. [PMID: 38392650 PMCID: PMC10890469 DOI: 10.3390/jpm14020217] [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: 12/26/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/24/2024] Open
Abstract
Infectious diseases have long posed a significant threat to global health and require constant innovation in treatment approaches. However, recent groundbreaking research has shed light on a previously overlooked player in the pathogenesis of disease-the human microbiome. This review article addresses the intricate relationship between the microbiome and infectious diseases and unravels its role as a crucial mediator of host-pathogen interactions. We explore the remarkable potential of harnessing this dynamic ecosystem to develop innovative treatment strategies that could revolutionize the management of infectious diseases. By exploring the latest advances and emerging trends, this review aims to provide a new perspective on combating infectious diseases by targeting the microbiome.
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Affiliation(s)
- Mohamed Kamel
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza 11221, Egypt
| | - Sami Aleya
- Faculty of Medecine, Université de Bourgogne Franche-Comté, Hauts-du-Chazal, 25030 Besançon, France
| | - Majed Alsubih
- Department of Civil Engineering, King Khalid University, Guraiger, Abha 62529, Saudi Arabia
| | - Lotfi Aleya
- Laboratoire de Chrono-Environnement, Université de Bourgogne Franche-Comté, UMR CNRS 6249, La Bouloie, 25030 Besançon, France
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Barros ALAN, Silva VC, Ribeiro-Junior AF, Cardoso MG, Costa SR, Moraes CB, Barbosa CG, Coleone AP, Simões RP, Cabral WF, Falcão RM, Vasconcelos AG, Rocha JA, Arcanjo DDR, Batagin-Neto A, Borges TKS, Gonçalves J, Brand GD, Freitas-Junior LHG, Eaton P, Marani M, Kato MJ, Plácido A, Leite JRSA. Antiviral Action against SARS-CoV-2 of a Synthetic Peptide Based on a Novel Defensin Present in the Transcriptome of the Fire Salamander ( Salamandra salamandra). Pharmaceutics 2024; 16:190. [PMID: 38399250 PMCID: PMC10892092 DOI: 10.3390/pharmaceutics16020190] [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: 12/14/2023] [Revised: 01/19/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
The potential emergence of zoonotic diseases has raised significant concerns, particularly in light of the recent pandemic, emphasizing the urgent need for scientific preparedness. The bioprospection and characterization of new molecules are strategically relevant to the research and development of innovative drugs for viral and bacterial treatment and disease management. Amphibian species possess a diverse array of compounds, including antimicrobial peptides. This study identified the first bioactive peptide from Salamandra salamandra in a transcriptome analysis. The synthetic peptide sequence, which belongs to the defensin family, was characterized through MALDI TOF/TOF mass spectrometry. Molecular docking assays hypothesized the interaction between the identified peptide and the active binding site of the spike WT RBD/hACE2 complex. Although additional studies are required, the preliminary evaluation of the antiviral potential of synthetic SS-I was conducted through an in vitro cell-based SARS-CoV-2 infection assay. Additionally, the cytotoxic and hemolytic effects of the synthesized peptide were assessed. These preliminary findings highlighted the potential of SS-I as a chemical scaffold for drug development against COVID-19, hindering viral infection. The peptide demonstrated hemolytic activity while not exhibiting cytotoxicity at the antiviral concentration.
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Affiliation(s)
- Ana Luisa A N Barros
- Núcleo de Pesquisa em Morfologia e Imunologia Aplicada, NuPMIA, Faculdade de Medicina, Universidade de Brasília, UnB, Brasília 70910-900, DF, Brazil
- Programa de Pós-graduação em Medicina Tropical, PGMT, Faculdade de Medicina, Universidade de Brasília, UnB, Brasília 70910-900, DF, Brazil
| | - Vladimir C Silva
- Laboratório de Vigilância Genômica e Biologia Molecular-Fundação Oswaldo Cruz Piauí, Teresina 64001-350, PI, Brazil
| | - Atvaldo F Ribeiro-Junior
- Núcleo de Pesquisa em Morfologia e Imunologia Aplicada, NuPMIA, Faculdade de Medicina, Universidade de Brasília, UnB, Brasília 70910-900, DF, Brazil
| | - Miguel G Cardoso
- Núcleo de Pesquisa em Morfologia e Imunologia Aplicada, NuPMIA, Faculdade de Medicina, Universidade de Brasília, UnB, Brasília 70910-900, DF, Brazil
- imed.ULisboa-Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, 1649-003 Lisbon, Portugal
| | - Samuel R Costa
- Instituto de Química, IQ, Universidade de Brasília, UnB, Brasília 70910-900, DF, Brazil
| | - Carolina B Moraes
- Department of Pharmaceutical Sciences, Federal University of São Paulo, Diadema 09913-030, SP, Brazil
| | - Cecília G Barbosa
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, São Paulo 05508-000, SP, Brazil
| | - Alex P Coleone
- Programa de Pós-Graduação em Ciência e Tecnologia de Materiais (POSMAT), School of Sciences, São Paulo State University (UNESP), Bauru 17033-360, SP, Brazil
| | - Rafael P Simões
- School of Agriculture, Department of Bioprocess and Biotechnology, São Paulo State University (UNESP), Botucatu 18618-689, SP, Brazil
| | - Wanessa F Cabral
- Núcleo de Pesquisa em Morfologia e Imunologia Aplicada, NuPMIA, Faculdade de Medicina, Universidade de Brasília, UnB, Brasília 70910-900, DF, Brazil
| | - Raul M Falcão
- Bioinformatics Postgraduate Program, Metrópole Digital Institute, Federal University of Rio Grande do Norte, Natal 59078-900, RN, Brazil
| | - Andreanne G Vasconcelos
- Núcleo de Pesquisa em Morfologia e Imunologia Aplicada, NuPMIA, Faculdade de Medicina, Universidade de Brasília, UnB, Brasília 70910-900, DF, Brazil
- People&Science Pesquisa Desenvolvimento e Inovação LTDA, Centro de Desenvolvimento Tecnológico (CDT), Universidade de Brasília, UnB, Brasília 70910-900, DF, Brazil
| | - Jefferson A Rocha
- Campus São Bernardo, Universidade Federal do Maranhão, UFMA, São Bernardo 65550-000, MA, Brazil
| | - Daniel D R Arcanjo
- Department of Biophysics and Physiology, Federal University of Piauí, Teresina 64049-550, PI, Brazil
| | - Augusto Batagin-Neto
- Programa de Pós-Graduação em Ciência e Tecnologia de Materiais (POSMAT), School of Sciences, São Paulo State University (UNESP), Bauru 17033-360, SP, Brazil
- Institute of Sciences and Engineering, São Paulo State University (UNESP), Itapeva 18409-010, SP, Brazil
| | - Tatiana Karla S Borges
- Núcleo de Pesquisa em Morfologia e Imunologia Aplicada, NuPMIA, Faculdade de Medicina, Universidade de Brasília, UnB, Brasília 70910-900, DF, Brazil
| | - João Gonçalves
- imed.ULisboa-Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, 1649-003 Lisbon, Portugal
| | - Guilherme D Brand
- Instituto de Química, IQ, Universidade de Brasília, UnB, Brasília 70910-900, DF, Brazil
| | - Lucio H G Freitas-Junior
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, São Paulo 05508-000, SP, Brazil
| | - Peter Eaton
- Laboratório Associado para a Química Verde/Rede de Química e Tecnologia (LAQV/REQUIMTE), Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
- School of Chemistry, The Bridge, University of Lincoln, Lincoln LN6 7EL, UK
| | - Mariela Marani
- IPEEC-CONICET, Consejo Nacional de Investigaciones Científicas y Técnicas, Puerto Madryn 9120, Argentina
| | - Massuo J Kato
- Instituto de Química (IQ), Universidade de São Paulo (USP), São Paulo 05508-900, SP, Brazil
| | - Alexandra Plácido
- Laboratório Associado para a Química Verde/Rede de Química e Tecnologia (LAQV/REQUIMTE), Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - José Roberto S A Leite
- Núcleo de Pesquisa em Morfologia e Imunologia Aplicada, NuPMIA, Faculdade de Medicina, Universidade de Brasília, UnB, Brasília 70910-900, DF, Brazil
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Contente D, Díaz-Formoso L, Feito J, Hernández PE, Muñoz-Atienza E, Borrero J, Poeta P, Cintas LM. Genomic and Functional Evaluation of Two Lacticaseibacillus paracasei and Two Lactiplantibacillus plantarum Strains, Isolated from a Rearing Tank of Rotifers ( Brachionus plicatilis), as Probiotics for Aquaculture. Genes (Basel) 2024; 15:64. [PMID: 38254954 PMCID: PMC10815930 DOI: 10.3390/genes15010064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/21/2023] [Accepted: 12/30/2023] [Indexed: 01/24/2024] Open
Abstract
Aquaculture plays a crucial role in meeting the increasing global demand for food and protein sources. However, its expansion is followed by increasing challenges, such as infectious disease outbreaks and antibiotic misuse. The present study focuses on the genetic and functional analyses of two Lacticaseibacillus paracasei (BF3 and RT4) and two Lactiplantibacillus plantarum (BF12 and WT12) strains isolated from a rotifer cultivation tank used for turbot larviculture. Whole-genome sequencing (WGS) and bioinformatics analyses confirmed their probiotic potential, the absence of transferable antibiotic resistance genes, and the absence of virulence and pathogenicity factors. Bacteriocin mining identified a gene cluster encoding six plantaricins, suggesting their role in the antimicrobial activity exerted by these strains. In vitro cell-free protein synthesis (IV-CFPS) analyses was used to evaluate the expression of the plantaricin genes. The in vitro-synthesized class IIb (two-peptide bacteriocins) plantaricin E/F (PlnE/F) exerted antimicrobial activity against three indicator microorganisms, including the well-known ichthyopathogen Lactococcus garvieae. Furthermore, MALDI-TOF MS on colonies detected the presence of a major peptide that matches the dimeric form of plantaricins E (PlnE) and F (PlnF). This study emphasizes the importance of genome sequencing and bioinformatic analysis for evaluating aquaculture probiotic candidates. Moreover, it provides valuable insights into their genetic features and antimicrobial mechanisms, paving the way for their application as probiotics in larviculture, which is a major bottleneck in aquaculture.
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Affiliation(s)
- Diogo Contente
- Grupo de Seguridad y Calidad de los Alimentos por Bacterias Lácticas, Bacteriocinas y Probióticos (SEGABALBP), Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain; (D.C.); (L.D.-F.); (P.E.H.); (E.M.-A.); (J.B.); (L.M.C.)
| | - Lara Díaz-Formoso
- Grupo de Seguridad y Calidad de los Alimentos por Bacterias Lácticas, Bacteriocinas y Probióticos (SEGABALBP), Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain; (D.C.); (L.D.-F.); (P.E.H.); (E.M.-A.); (J.B.); (L.M.C.)
| | - Javier Feito
- Grupo de Seguridad y Calidad de los Alimentos por Bacterias Lácticas, Bacteriocinas y Probióticos (SEGABALBP), Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain; (D.C.); (L.D.-F.); (P.E.H.); (E.M.-A.); (J.B.); (L.M.C.)
| | - Pablo E. Hernández
- Grupo de Seguridad y Calidad de los Alimentos por Bacterias Lácticas, Bacteriocinas y Probióticos (SEGABALBP), Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain; (D.C.); (L.D.-F.); (P.E.H.); (E.M.-A.); (J.B.); (L.M.C.)
| | - Estefanía Muñoz-Atienza
- Grupo de Seguridad y Calidad de los Alimentos por Bacterias Lácticas, Bacteriocinas y Probióticos (SEGABALBP), Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain; (D.C.); (L.D.-F.); (P.E.H.); (E.M.-A.); (J.B.); (L.M.C.)
| | - Juan Borrero
- Grupo de Seguridad y Calidad de los Alimentos por Bacterias Lácticas, Bacteriocinas y Probióticos (SEGABALBP), Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain; (D.C.); (L.D.-F.); (P.E.H.); (E.M.-A.); (J.B.); (L.M.C.)
| | - Patrícia Poeta
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal;
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
| | - Luis M. Cintas
- Grupo de Seguridad y Calidad de los Alimentos por Bacterias Lácticas, Bacteriocinas y Probióticos (SEGABALBP), Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain; (D.C.); (L.D.-F.); (P.E.H.); (E.M.-A.); (J.B.); (L.M.C.)
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9
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Lu S, Hao J, Yang H, Chen M, Lian J, Chen Y, Brown RW, Jones DL, Wan Z, Wang W, Chang W, Wu D. Earthworms mediate the influence of polyethylene (PE) and polylactic acid (PLA) microplastics on soil bacterial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:166959. [PMID: 37696400 DOI: 10.1016/j.scitotenv.2023.166959] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/25/2023] [Accepted: 09/08/2023] [Indexed: 09/13/2023]
Abstract
There is a growing body of evidence that suggests that both biodegradable and conventional (non-degradable) microplastics (MP) are hazardous to soil health by affecting the delivery of key ecological functions such as litter decomposition, nutrient cycling and water retention. Specifically, soil fauna may be harmed by the presence of MPs while also being involved in their disintegration, degradation, migration and transfer in soil. Therefore, a comprehensive understanding of the interactions between MPs and soil fauna is essential. Here, we conducted a 120-day soil microcosm experiment applying polyethylene (PE) and polylactic acid (PLA), in the absence/presence of the earthworm Eisenia nordenskioldi to estimate the relative singular and combined impact of MPs and earthworms on the soil bacterial community. Our findings revealed contrasting effects of PE and PLA on the composition and diversity of soil bacteria. All treatments affected the community and network structure of the soil bacterial community. Compared to the control (no MPs or earthworms), PE decreased bacterial alpha diversity, while PLA increased it. Patescibacteria were found to be significantly abundant in the PE group whereas Actinobacteria and Gemmatimonadetes were more abundant in PE, and PLA and earthworms groups. The presence of earthworms appeared to mediate the impact of PE/PLA on soil bacteria, potentially through bacterial consumption or by altering soil properties (e.g., pH, aeration, C availability). Earthworm presence also appeared to promote the chemical aging of PLA. Collectively, our results provide novel insights into the soil-fauna-driven impact of degradable/nondegradable MPs exposure on the long-term environmental risks associated with soil microorganisms.
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Affiliation(s)
- Siyuan Lu
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun, Jilin 130117, China
| | - Jiahua Hao
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun, Jilin 130117, China
| | - Hao Yang
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun, Jilin 130117, China
| | - Mengya Chen
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun, Jilin 130117, China
| | - Jiapan Lian
- Ministry of Education (MOE) Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yalan Chen
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Robert W Brown
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Davey L Jones
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Zhuoma Wan
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun, Jilin 130117, China
| | - Wei Wang
- Key Laboratory of Preparation and Applications of Environmental Friendly Materials, Ministry of Education, Jilin Normal University, Changchun 130103, China
| | - Wenjin Chang
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun, Jilin 130117, China
| | - Donghui Wu
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun, Jilin 130117, China; Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; Jilin Songnen Grassland Ecosystem National Observation and Research Station, Northeast Normal University, Changchun 130024, China; Key Laboratory of Vegetation Ecology, Ministry of Education, Northeast Normal University, Changchun 130024, China; Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China.
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10
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Michael CK, Lianou DT, Tsilipounidaki K, Gougoulis DA, Giannoulis T, Vasileiou NGC, Mavrogianni VS, Petinaki E, Fthenakis GC. Recovery of Staphylococci from Teatcups in Milking Parlours in Goat Herds in Greece: Prevalence, Identification, Biofilm Formation, Patterns of Antibiotic Susceptibility, Predictors for Isolation. Antibiotics (Basel) 2023; 12:1428. [PMID: 37760724 PMCID: PMC10525802 DOI: 10.3390/antibiotics12091428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/31/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
The objectives of this work are (a) to describe staphylococci on the teatcups of milking parlours in goat farms and identify predictors for the presence of staphylococcal isolates on the teatcups, (b) to evaluate relationships with total bacterial counts and somatic cell counts in bulk-tank milk, and (c) to establish patterns of susceptibility to antibiotics for the staphylococcal isolates and identify predictors for the recovery of resistant isolates. In a cross-sectional study of 66 goat farms across Greece, swab samples were collected from 303 teatcups (upper and lower part) for staphylococcal recovery, identification, and assessment of biofilm formation. Details regarding health management on the farms (including conditions in the milking parlour) and the socio-demographic characteristics of farmers were collected by means of a structured questionnaire. A total of 87 contaminated teatcups (28.7%) were found on 35 goat farms (53.0%). Staphylococci were more frequently recovered from the upper than the lower part of teatcups: 73 versus 43 teatcups, respectively. After identification, 67 staphylococcal isolates (i.e., excluding similar isolates) were recovered from the teatcups; Staphylococcus aureus, Staphylococcus capitis, and Staphylococcus equorum predominated. Of these isolates, 82.1% were biofilm-forming. In multivariable analysis, the annual incidence of clinical mastitis in the herd emerged as the only significant factor associated with the isolation of staphylococci from the teatcups. Of the 67 isolates, 23 (34.3%) were resistant to at least one antibiotic, and 14 (22.4%) were multi-resistant. Resistance was found most commonly against penicillin and ampicillin (22.4% of isolates), fosfomycin (17.9%), clindamycin (14.9%), erythromycin, and tetracycline (13.4%). In multivariable analysis, the annual incidence of clinical mastitis in the herd and the use of detergent for parlour cleaning emerged as significant factors associated with the isolation of staphylococci resistant to antibiotics.
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Affiliation(s)
| | - Daphne T. Lianou
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece (D.T.L.)
| | | | | | | | | | | | - Efthymia Petinaki
- Department of Microbiology, University Hospital of Larissa, 41110 Larissa, Greece
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11
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Zhou Z, Gu J, Wang Y. Editorial: Evolutionary mechanisms of infectious diseases, volume II. Front Microbiol 2023; 14:1192566. [PMID: 37077239 PMCID: PMC10106751 DOI: 10.3389/fmicb.2023.1192566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 04/05/2023] Open
Affiliation(s)
- Zhan Zhou
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- *Correspondence: Zhan Zhou
| | - Jianying Gu
- Department of Biology, College of Staten Island, City University of New York, Staten Island, New York, NY, United States
- Jianying Gu
| | - Yufeng Wang
- Department of Molecular Microbiology Immunology, South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX, United States
- Yufeng Wang
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12
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Niu L, Chen Y, Li Y, Wang Y, Shen J, Wang L, Zhang W, Zhang H, Zhao B. Diversity, abundance and distribution characteristics of potential polyethylene and polypropylene microplastic degradation bacterial communities in the urban river. WATER RESEARCH 2023; 232:119704. [PMID: 36764109 DOI: 10.1016/j.watres.2023.119704] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/28/2022] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Carbon chain microplastics, polyethylene (PE), and polypropylene (PP) are the main types of refractory organics. Compared to heterochain microplastics, PE/PP degrading bacterial community and their distribution characteristics in natural rivers are unclear. In this study, the field in situ experiment and indoor enrichment experiment with PE/PP resin as only carbon sources were conducted for a total period of 1150 days. The microbial degradation of pure PE/PP resin was determined by SEM, FTIR, CLSM, GC-MS, and GPC. The Chao 1 index and Invsimpson index of the bacterial community significantly reduced after a series of incubation, demonstrating that the bacterial community was selectively enriched. Empirical core PE/PP degrading bacteria (C-bacteria) and resuscitated PE/PP degrading bacteria (R-bacteria) were screened based on the variation of the abundance of OTUs, and co-occurrence analysis displayed that C-bacteria presented higher betweenness centrality than R-bacteria. The higher abundance and diversity of R-bacteria in biofilms suggest the presence of many rare or low abundance bacteria in natural rivers that may be potential PE/PP degrading bacteria or PE/PP degrading bacteria to be activated, while the lower abundance and diversity of C-bacteria support the slow degradation rate of PE and PP in waters. Compared to the isolated and indicatory PE/PP degrading bacterial genera, the C-bacteria OTUs or genera enriched in this study displayed higher richness and abundance. Enriched PE/PP degrading bacteria occurred in all sampled sites of the Qinhuai River with higher abundance and standard betweenness centrality in sediments (averaging 0.01354 and 0.44421, respectively) than those in overlying water (averaging 0.00536 and 0.17571, respectively), while the highest abundance of degrading bacteria presented in the eutrophic sediments. Inorganic nitrogen was determined to be significantly correlated with the distribution of PE/PP degrading bacteria in sediments via redundancy analysis. This study provides a new perspective on the natural degradation potential of carbon chain microplastics by microbial communities in rivers.
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Affiliation(s)
- Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, PR China
| | - Yamei Chen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, PR China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, PR China.
| | - Yingjie Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, PR China
| | - Jiayan Shen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, PR China
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, PR China
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, PR China
| | - Huanjun Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, PR China
| | - Bo Zhao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, PR China
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13
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Sun L, Cheng L, Fu H, Wang R, Gu Y, Qiu Y, Sun K, Xu H, Lei P. A strategy for nitrogen conversion in aquaculture water based on poly-γ-glutamic acid synthesis. Int J Biol Macromol 2023; 229:1036-1043. [PMID: 36603727 DOI: 10.1016/j.ijbiomac.2022.12.314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023]
Abstract
Ammonia and nitrite are nitrogenous pollutants in aquaculture effluents, which pose a major threat to the health of aquatic animals. In this study, we developed a nitrogen conversion strategy based on synthesis of poly-γ-glutamic acid (γ-PGA) by Bacillus subtilis NX-2. The nitrogen removal efficiency of NX-2 was closely related to synthesizing γ-PGA, and was positively correlated with the inoculum level. The degradation rates of ammonia nitrogen and nitrite at 104 CFU/mL were 84.42 % and 62.56 %, respectively. Through adaptive laboratory evolution (ALE) experiment, we obtained a strain named ALE 5 M with ammonia degradation rate of 98.03 % and nitrite of 93.62 % at the inoculum level of 104 CFU/mL. Transcriptome analysis showed that the strain was more likely to produce γ-PGA after ALE. By enzyme activity and qPCR analysis, we confirmed that ALE 5 M degraded ammonia nitrogen through γ-PGA synthesis, which provided a new way for nitrogen removal in aquaculture water.
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Affiliation(s)
- Liang Sun
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Lifangyu Cheng
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Heng Fu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Rui Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Yian Gu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Yibin Qiu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Ke Sun
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Hong Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Peng Lei
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China.
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14
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Traglia GM, Pasteran F, Escalante J, Nishimura B, Tuttobene MR, Subils T, Nuñez MR, Rivollier MG, Corso A, Tolmasky ME, Ramirez MS. Genomic Comparative Analysis of Two Multi-Drug Resistance (MDR) Acinetobacter baumannii Clinical Strains Assigned to International Clonal Lineage II Recovered Pre- and Post-COVID-19 Pandemic. BIOLOGY 2023; 12:358. [PMID: 36979049 PMCID: PMC10045941 DOI: 10.3390/biology12030358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/09/2023] [Accepted: 02/23/2023] [Indexed: 02/26/2023]
Abstract
BACKGROUND After the emergence of COVID-19, numerous cases of A. baumannii/SARS-CoV-2 co-infection were reported. Whether the co-infecting A. baumannii strains have distinctive characteristics remains unknown. METHODS AND RESULTS A. baumannii AMA_NO was isolated in 2021 from a patient with COVID-19. AMA166 was isolated from a mini-BAL used on a patient with pneumonia in 2016. Both genomes were similar, but they possessed 337 (AMA_NO) and 93 (AMA166) unique genes that were associated with biofilm formation, flagellar assembly, antibiotic resistance, secretion systems, and other functions. The antibiotic resistance genes were found within mobile genetic elements. While both strains harbored the carbapenemase-coding gene blaOXA-23, only the strain AMA_NO carried blaNDM-1. Representative functions coded for by virulence genes are the synthesis of the outer core of lipooligosaccharide (OCL5), biosynthesis and export of the capsular polysaccharide (KL2 cluster), high-efficiency iron uptake systems (acinetobactin and baumannoferrin), adherence, and quorum sensing. A comparative phylogenetic analysis including 239 additional sequence type (ST) 2 representative genomes showed high similarity to A. baumannii ABBL141. Since the degree of similarity that was observed between A. baumannii AMA_NO and AMA166 is higher than that found among other ST2 strains, we propose that they derive from a unique background based on core-genome phylogeny and comparative genome analysis. CONCLUSIONS Acquisition or shedding of specific genes could increase the ability of A. baumannii to infect patients with COVID-19.
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Affiliation(s)
- German Matias Traglia
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la Republica, Montevideo 11200, Uruguay
| | - Fernando Pasteran
- National Regional Reference Laboratory for Antimicrobial Resistance (NRL), Servicio Antimicrobianos, Instituto Nacional de Enfermedades Infecciosas, ANLIS Dr. Carlos G. Malbrán, Buenos Aires 1282, Argentina
| | - Jenny Escalante
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA
| | - Brent Nishimura
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA
| | - Marisel R. Tuttobene
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario 2000, Argentina
| | - Tomás Subils
- Instituto de Procesos Biotecnológicos y Químicos de Rosario (IPROBYQ, CONICET-UNR), Rosario 2000, Argentina
| | - Maria Rosa Nuñez
- Laboratorio de Microbiología, Hospital Provincial Neuquén Dr. Castro Rendón, Neuquén 8300, Argentina
| | | | - Alejandra Corso
- National Regional Reference Laboratory for Antimicrobial Resistance (NRL), Servicio Antimicrobianos, Instituto Nacional de Enfermedades Infecciosas, ANLIS Dr. Carlos G. Malbrán, Buenos Aires 1282, Argentina
| | - Marcelo E. Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA
| | - Maria Soledad Ramirez
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA
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15
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Fang L, Feng X, Liu D, Han Z, Liu M, Hao X, Cao Y. 大肠杆菌合成中链脂肪酸研究进展. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2022-0290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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