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Kusumawaty D, Augustine SMN, Aryani A, Effendi Y, Emran TB, Tallei TE. Configuration of gut bacterial community profile and their potential functionality in the digestive tract of the wild and cultivated Indonesian shortfin elver-phase eels ( Anguilla bicolor bicolor McClelland, 1844). 3 Biotech 2023; 13:153. [PMID: 37131968 PMCID: PMC10148933 DOI: 10.1007/s13205-023-03561-8] [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: 06/21/2022] [Accepted: 04/15/2023] [Indexed: 05/04/2023] Open
Abstract
This study aimed to explore the bacteria present in the digestive tracts of wild and cultivated Indonesian shortfin eel during the elver phase. The eel has high export potential due to its vitamin and micronutrient content, but slow growth and vulnerability to collapse in farm conditions hinder its cultivation. The microbiota in the eel's digestive tract is crucial for its health, particularly during the elver phase. This study used Next Generation Sequencing to analyze the community structure and diversity of bacteria in the eels' digestive tracts, focusing on the V3-V4 regions of the 16S rRNA gene. Mothur software was used for data analysis and PAST v.3.26 was used to calculate alpha diversity. The results showed that Proteobacteria (64.18%) and Firmicutes (33.55%) were the predominant phyla in the digestive tract of cultivated eels, while Bacteroidetes (54.16%), Firmicutes (14.71%), and Fusobacteria (10.56%) were predominant in wild eels. The most prevalent genera in cultivated and wild elver were Plesiomonas and Cetobacterium, respectively. The microbiota in the digestive tract of cultivated eels was diverse despite uneven distribution. The KEGG database analysis revealed that the primary function of the microbiome was to facilitate the eel's absorption of nutrients by contributing significantly to the metabolism of carbohydrates and amino acids. This study's findings can aid in assessing eel health and improving eel farming conditions.
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Affiliation(s)
- Diah Kusumawaty
- Department of Biology, Faculty of Mathematics and Natural Sciences Education, Universitas Pendidikan Indonesia, Bandung, 40154 Indonesia
| | - Stella Melbournita Noor Augustine
- Department of Biology, Faculty of Mathematics and Natural Sciences Education, Universitas Pendidikan Indonesia, Bandung, 40154 Indonesia
| | - Any Aryani
- Department of Biology, Faculty of Mathematics and Natural Sciences Education, Universitas Pendidikan Indonesia, Bandung, 40154 Indonesia
| | - Yunus Effendi
- Department of Biology, Faculty of Science and Technology, Al-Azhar Indonesia University, Jakarta, 12110 Indonesia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381 Bangladesh
| | - Trina Ekawati Tallei
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado, 95115 North Sulawesi Indonesia
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Singh A, Ambaru B, Bandsode V, Ahmed N. Panomics to decode virulence and fitness in Gram-negative bacteria. Front Cell Infect Microbiol 2022; 12:1061596. [PMID: 36478674 PMCID: PMC9719987 DOI: 10.3389/fcimb.2022.1061596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 10/26/2022] [Indexed: 11/22/2022] Open
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Gollapalli P, Tamizh Selvan G, Santoshkumar HS, Ballamoole KK. Functional insights of antibiotic resistance mechanism in Helicobacter pylori: Driven by gene interaction network and centrality-based nodes essentiality analysis. Microb Pathog 2022; 171:105737. [PMID: 36038087 DOI: 10.1016/j.micpath.2022.105737] [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: 07/12/2022] [Revised: 08/05/2022] [Accepted: 08/19/2022] [Indexed: 11/29/2022]
Abstract
Increased antibiotic resistance in Helicobacter pylori (H. pylori), a major human pathogen, constitutes a substantial threat to human health. Understanding the pathophysiology and development of antibiotic resistance can aid our battle with the infections caused by H. pylori. The aim of this study is to discover the high-impact key regulatory mechanisms and genes involved in antimicrobial drug resistance (AMR). In this study, we constructed a functional gene interaction network by integrating multiple sources of data related to antibiotic resistant genes (number-77) from H. pylori. The gene interaction network was assortative, with a hierarchical, scale-free topology enriched in a variety of gene ontology (GO) categories and KEGG pathways. Using an iterative clustering methodology, we identified a number of communities in the AMR gene network that comprised nine genes (sodB, groEL, gyrA, recA, polA, tuf, infB, rpsJ, and gyrB) that were present at the deepest level and hence were key regulators of AMR. Further, an antibiotic-resistant gene network-based centrality analysis revealed superoxide dismutase (sodB) as a bottleneck node in the network. Our findings suggested that sodB is critically enriched in the cellular response to oxidative stress, removal of superoxide radicals, cellular oxidant detoxification processes, cellular component biogenesis, response to reactive oxygen species, urea metabolic process, nitrogen cycle metabolic process and reactive oxygen species metabolic process. We demonstrated how the sodB, which are involved in the response to reactive oxygen species, urea metabolic process, nitrogen cycle metabolic process, reactive oxygen species metabolic process, regulated by Fur gene/proteins, claim a major authority over regulation and signal propagation in the AMR.
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Affiliation(s)
- Pavan Gollapalli
- Center for Bioinformatics and Biostatistics, Nitte (Deemed to Be University), Mangalore, 575018, Karnataka, India; Central Research Laboratory, K. S. Hegde Medical Academy, Nitte (Deemed to be University), Mangalore, 575018, Karnataka, India.
| | - G Tamizh Selvan
- Central Research Laboratory, K. S. Hegde Medical Academy, Nitte (Deemed to be University), Mangalore, 575018, Karnataka, India
| | - H S Santoshkumar
- Department of Biotechnology and Bioinformatics, Jnana Sahyadri Campus, Kuvempu University, Shankaraghatta, 577451, Shivamogga, Karnataka, India
| | - Krishna Kumar Ballamoole
- Nitte (Deemed to be University), Division of Infectious Diseases, Nitte University Centre for Science Education and Research (NUCSER), Paneer Campus, Deralakatte, Mangaluru, Karnataka, 575018, India
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Porphyromonas gingivalis resistance and virulence: An integrated functional network analysis. Gene 2022; 839:146734. [PMID: 35835406 DOI: 10.1016/j.gene.2022.146734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/23/2022] [Accepted: 07/08/2022] [Indexed: 11/23/2022]
Abstract
BACKGROUND The gram-negative bacteria Porphyromonas gingivalis (PG) is the most prevalent cause of periodontal diseases and multidrug-resistant (MDR) infections. Periodontitis and MDR infections are severe due to PG's ability to efflux antimicrobial and virulence factors. This gives rise to colonisation, biofilm development, evasion, and modulation of the host defence system. Despite extensive studies on the MDR efflux pump in other pathogens, little is known about the efflux pump and its association with the virulence factor in PG. Prolonged infection of PG leads to complete loss of teeth and other systemic diseases. This necessitates the development of new therapeutic interventions to prevent and control MDR. OBJECTIVE The study aims to identify the most indispensable proteins that regulate both resistance and virulence in PG, which could therefore be used as a target to fight against the MDR threat to antibiotics. METHODS We have adopted a hierarchical network-based approach to construct a protein interaction network. Firstly, individual networks of four major efflux pump proteins and two virulence regulatory proteins were constructed, followed by integrating them into one. The relationship between proteins was investigated using a combination of centrality scores, k-core network decomposition, and functional annotation, to computationally identify the indispensable proteins. RESULTS Our study identified four topologically significant genes, PG_0538, PG_0539, PG_0285, and PG_1797, as potential pharmacological targets. PG_0539 and PG_1797 were identified to have significant associations between the efflux pump and virulence genes. This type of underpinning research may help in narrowing the drug spectrum used for treating periodontal diseases, and may also be exploited to look into antibiotic resistance and pathogenicity in bacteria other than PG.
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Sherif MM, Elkhatib WF, Khalaf WS, Elleboudy NS, Abdelaziz NA. Multidrug Resistant Acinetobacter baumannii Biofilms: Evaluation of Phenotypic-Genotypic Association and Susceptibility to Cinnamic and Gallic Acids. Front Microbiol 2021; 12:716627. [PMID: 34650528 PMCID: PMC8508616 DOI: 10.3389/fmicb.2021.716627] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/17/2021] [Indexed: 11/20/2022] Open
Abstract
Acinetobacter baumannii armed with multidrug resistance (MDR) and biofilm-forming ability is increasingly recognized as an alarming pathogen. A deeper comprehension of the correlation between these two armories is required in circumventing its infections. This study examined the biofilm-forming ability of the isolates by crystal violet staining and the antibiotic susceptibility by broth microdilution method. The genetic basis of the MDR and biofilm-forming phenotypes was screened by polymerase chain reaction. The antimicrobial activities of cinnamic and gallic acids against planktonic cells and biofilms of A. baumannii were investigated, and the findings were confirmed with scanning electron microscopy (SEM). Among 90 A. baumannii isolates, 69 (76.6%) were MDR, and all were biofilm formers; they were classified into weak (12.2%), moderate (53.3%), and strong (34.5%) biofilm formers. Our results underlined a significant association between MDR and enhanced biofilm formation. Genotypically, the presence of blaVIM and blaOXA–23 genes along with biofilm-related genes (ompA, bap, and csuE) was statistically associated with the biofilm-forming abilities. Impressively, both gallic and cinnamic acids could significantly reduce the MDR A. baumannii biofilms with variable degrees dependent on the phenotype–genotype characteristics of the tested isolates. The current findings may possess future therapeutic impact through augmenting antimicrobial arsenal against life-threatening infections with MDR A. baumannii biofilms.
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Affiliation(s)
- Mahmoud M Sherif
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ahram Canadian University, 6th of October City, Egypt
| | - Walid F Elkhatib
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt.,Department of Microbiology and Immunology, Faculty of Pharmacy, Galala University, Al Galala, Egypt
| | - Wafaa S Khalaf
- Department of Microbiology and Immunology, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Nooran S Elleboudy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Neveen A Abdelaziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ahram Canadian University, 6th of October City, Egypt
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Kumar S, Anwer R, Azzi A. Virulence Potential and Treatment Options of Multidrug-Resistant (MDR) Acinetobacter baumannii. Microorganisms 2021; 9:microorganisms9102104. [PMID: 34683425 PMCID: PMC8541637 DOI: 10.3390/microorganisms9102104] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/18/2021] [Accepted: 09/21/2021] [Indexed: 12/12/2022] Open
Abstract
Acinetobacter baumannii is an opportunistic pathogen which is undoubtedly known for a high rate of morbidity and mortality in hospital-acquired infections. A. baumannii causes life-threatening infections, including; ventilator-associated pneumonia (VAP), meningitis, bacteremia, and wound and urinary tract infections (UTI). In 2017, the World Health Organization listed A. baumannii as a priority-1 pathogen. The prevalence of A. baumannii infections and outbreaks emphasizes the direct need for the use of effective therapeutic agents for treating such infections. Available antimicrobials, such as; carbapenems, tigecycline, and colistins have insufficient effectiveness due to the appearance of multidrug-resistant strains, accentuating the need for alternative and novel therapeutic remedies. To understand and overcome this menace, the knowledge of recent discoveries on the virulence factors of A. baumannii is needed. Herein, we summarized the role of various virulence factors, including; outer membrane proteins, efflux pumps, biofilm, penicillin-binding proteins, and siderophores/iron acquisition systems. We reviewed the recent scientific literature on different A. baumannii virulence factors and the effective antimicrobial agents for the treatment and management of bacterial infections.
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Affiliation(s)
- Sunil Kumar
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to Be University), Mullana, Ambala 133207, India;
| | - Razique Anwer
- Department of Pathology, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 13317-4233, Saudi Arabia;
| | - Arezki Azzi
- Department of Biochemistry, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 13317-4233, Saudi Arabia
- Correspondence:
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