1
|
Guo Z, Lei Y, Wang Q. Chinese expert consensus on standard technical specifications for a gut microecomics laboratory (Review). Exp Ther Med 2024; 28:403. [PMID: 39234587 PMCID: PMC11372251 DOI: 10.3892/etm.2024.12692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 07/11/2024] [Indexed: 09/06/2024] Open
Abstract
The intestinal microbiota is a complex ecosystem that not only affects various physiological functions, such as metabolism, inflammation and the immune response, but also has an important effect on the development of tumors and response to treatment. The detection of intestinal flora enables the timely identification of disease-related flora abnormalities, which has significant implications for both disease prevention and treatment. In the field of basic and clinical research targeting gut microbiome, there is a need to recognize and understand the laboratory assays for gut microbiomics. Currently, there is no unified standard for the experimental procedure, quality management and report interpretation of intestinal microbiome assay technology. In order to clarify the process, the Tumor and Microecology Committee of China Anti-Cancer Association and the Tumor and Microecology Committee of Hubei Provincial Immunology Society organized relevant experts to discuss and put forward the standard technical specifications for gut microecomics laboratories, which provides a basis for further in-depth research in the field of intestinal microecomics.
Collapse
Affiliation(s)
- Zhi Guo
- Department of Hematology, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, Guangdong 518052, P.R. China
- Institute of Infection, Immunology and Tumor Microenvironment, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Medical College, Wuhan University of Science and Technology, Wuhan, Hubei 430065, P.R. China
| | - Yumeng Lei
- Institute of Infection, Immunology and Tumor Microenvironment, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Medical College, Wuhan University of Science and Technology, Wuhan, Hubei 430065, P.R. China
| | - Qiang Wang
- Institute of Infection, Immunology and Tumor Microenvironment, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Medical College, Wuhan University of Science and Technology, Wuhan, Hubei 430065, P.R. China
| |
Collapse
|
2
|
Eltokhy MA, Saad BT, Eltayeb WN, Alshahrani MY, Radwan SMR, Aboshanab KM, Ashour MSE. Metagenomic nanopore sequencing for exploring the nature of antimicrobial metabolites of Bacillus haynesii. AMB Express 2024; 14:52. [PMID: 38704474 PMCID: PMC11069495 DOI: 10.1186/s13568-024-01701-8] [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: 01/16/2024] [Accepted: 04/08/2024] [Indexed: 05/06/2024] Open
Abstract
Multidrug-resistant (MDR) pathogens are a rising global health worry that imposes an urgent need for the discovery of novel antibiotics particularly those of natural origin. In this context, we aimed to use the metagenomic nanopore sequence analysis of soil microbiota coupled with the conventional phenotypic screening and genomic analysis for identifying the antimicrobial metabolites produced by promising soil isolate(s). In this study, whole metagenome analysis of the soil sample(s) was performed using MinION™ (Oxford Nanopore Technologies). Aligning and analysis of sequences for probable secondary metabolite gene clusters were extracted and analyzed using the antiSMASH version 2 and DeepBGC. Results of the metagenomic analysis showed the most abundant taxa were Bifidobacterium, Burkholderia, and Nocardiaceae (99.21%, followed by Sphingomonadaceae (82.03%) and B. haynesii (34%). Phenotypic screening of the respective soil samples has resulted in a promising Bacillus isolate that exhibited broad-spectrum antibacterial activities against various MDR pathogens. It was identified using microscopical, cultural, and molecular methods as Bacillus (B.) haynesii isolate MZ922052. The secondary metabolite gene analysis revealed the conservation of seven biosynthetic gene clusters of antibacterial metabolites namely, siderophore lichenicidin VK21-A1/A2 (95% identity), lichenysin (100%), fengycin (53%), terpenes (100%), bacteriocin (100%), Lasso peptide (95%) and bacillibactin (53%). In conclusion, metagenomic nanopore sequence analysis of soil samples coupled with conventional screening helped identify B. haynesii isolate MZ922052 harboring seven biosynthetic gene clusters of promising antimicrobial metabolites. This is the first report for identifying the bacteriocin, lichenysin, and fengycin biosynthetic gene clusters in B. haynesii MZ922052.
Collapse
Affiliation(s)
- Mohamed A Eltokhy
- Department of Microbiology, Faculty of Pharmacy, Misr International University (MIU), Cairo, 19648, Egypt
| | - Bishoy T Saad
- Department of Bioinformatics, HITS Solutions Co., Cairo, 11765, Egypt
| | - Wafaa N Eltayeb
- Department of Microbiology, Faculty of Pharmacy, Misr International University (MIU), Cairo, 19648, Egypt
| | - Mohammad Y Alshahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, P.O. Box 61413, Abha, 9088, Saudi Arabia
| | - Sahar M R Radwan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University (Girls), Organization of African Unity St., Cairo, 11651, Egypt
| | - Khaled M Aboshanab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Organization of African Unity St, Ain Shams University, Organization of African Unity St., Cairo, 11566, Egypt.
| | - Mohamed S E Ashour
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University (Boys), Cairo, 11651, Egypt
| |
Collapse
|
3
|
Helal AA, Saad BT, Saad MT, Mosaad GS, Aboshanab KM. Benchmarking long-read aligners and SV callers for structural variation detection in Oxford nanopore sequencing data. Sci Rep 2024; 14:6160. [PMID: 38486064 PMCID: PMC10940726 DOI: 10.1038/s41598-024-56604-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 03/08/2024] [Indexed: 03/18/2024] Open
Abstract
Structural variants (SVs) are one of the significant types of DNA mutations and are typically defined as larger-than-50-bp genomic alterations that include insertions, deletions, duplications, inversions, and translocations. These modifications can profoundly impact the phenotypic characteristics and contribute to disorders like cancer, response to treatment, and infections. Four long-read aligners and five SV callers have been evaluated using three Oxford Nanopore NGS human genome datasets in terms of precision, recall, and F1-score statistical metrics, depth of coverage, and speed of analysis. The best SV caller regarding recall, precision, and F1-score when matched with different aligners at different coverage levels tend to vary depending on the dataset and the specific SV types being analyzed. However, based on our findings, Sniffles and CuteSV tend to perform well across different aligners and coverage levels, followed by SVIM, PBSV, and SVDSS in the last place. The CuteSV caller has the highest average F1-score (82.51%) and recall (78.50%), and Sniffles has the highest average precision value (94.33%). Minimap2 as an aligner and Sniffles as an SV caller act as a strong base for the pipeline of SV calling because of their high speed and reasonable accomplishment. PBSV has a lower average F1-score, precision, and recall and may generate more false positives and overlook some actual SVs. Our results are valuable in the comprehensive evaluation of popular SV callers and aligners as they provide insight into the performance of several long-read aligners and SV callers and serve as a reference for researchers in selecting the most suitable tools for SV detection.
Collapse
Affiliation(s)
- Asmaa A Helal
- Department of Bioinformatics, HITS Solutions Co., Cairo, 11765, Egypt
| | - Bishoy T Saad
- Department of Bioinformatics, HITS Solutions Co., Cairo, 11765, Egypt.
| | - Mina T Saad
- Department of Bioinformatics, HITS Solutions Co., Cairo, 11765, Egypt
| | - Gamal S Mosaad
- Department of Bioinformatics, HITS Solutions Co., Cairo, 11765, Egypt
| | - Khaled M Aboshanab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Organization of African Unity St., Abassi, Cairo, 11566, Egypt.
| |
Collapse
|
4
|
Metagenomic nanopore sequencing versus conventional diagnosis for identification of the dieback pathogens of mango trees. Biotechniques 2022; 73:261-272. [DOI: 10.2144/btn-2022-0087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Dieback is one of the most dangerous fungal diseases affecting mango trees. In this study, nanopore metagenome sequencing of the root-soil samples and infected plant tissues was conducted to identify the fungal pathogens present. Soil analysis of the infected mango trees showed the abundance of the Dikarya subkingdom (59%) including Lasiodiplodia theobromae (15%), Alternaria alternata (6%), Ceratocystis huliohia and Colletotrichum gloeosporioides. Analysis of the infected plant tissues revealed the presence of A. alternata (34%). The data were deposited in the National Center of Biotechnology Information (PRJNA767267). In conclusion, nanopore metagenome sequencing analysis was a valuable tool to rapidly identify dieback-associated fungal pathogens.
Collapse
|
5
|
Evaluation of the Available Variant Calling Tools for Oxford Nanopore Sequencing in Breast Cancer. Genes (Basel) 2022; 13:genes13091583. [PMID: 36140751 PMCID: PMC9498802 DOI: 10.3390/genes13091583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 11/23/2022] Open
Abstract
The goal of biomarker testing, in the field of personalized medicine, is to guide treatments to achieve the best possible results for each patient. The accurate and reliable identification of everyone’s genome variants is essential for the success of clinical genomics, employing third-generation sequencing. Different variant calling techniques have been used and recommended by both Oxford Nanopore Technologies (ONT) and Nanopore communities. A thorough examination of the variant callers might give critical guidance for third-generation sequencing-based clinical genomics. In this study, two reference genome sample datasets (NA12878) and (NA24385) and the set of high-confidence variant calls provided by the Genome in a Bottle (GIAB) were used to allow the evaluation of the performance of six variant calling tools, including Human-SNP-wf, Clair3, Clair, NanoCaller, Longshot, and Medaka, as an integral step in the in-house variant detection workflow. Out of the six variant callers understudy, Clair3 and Human-SNP-wf that has Clair3 incorporated into it achieved the highest performance rates in comparison to the other variant callers. Evaluation of the results for the tool was expressed in terms of Precision, Recall, and F1-score using Hap.py tools for the comparison. In conclusion, our findings give important insights for identifying accurate variants from third-generation sequencing of personal genomes using different variant detection tools available for long-read sequencing.
Collapse
|
6
|
Eltokhy MA, Saad BT, Eltayeb WN, Yahia IS, Aboshanab KM, Ashour MSE. Exploring the Nature of the Antimicrobial Metabolites Produced by Paenibacillus ehimensis Soil Isolate MZ921932 Using a Metagenomic Nanopore Sequencing Coupled with LC-Mass Analysis. Antibiotics (Basel) 2021; 11:antibiotics11010012. [PMID: 35052889 PMCID: PMC8773065 DOI: 10.3390/antibiotics11010012] [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: 12/06/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 11/28/2022] Open
Abstract
The continuous emergence of multidrug-resistant (MDR) pathogens poses a global threat to public health. Accordingly, global efforts are continuously conducted to find new approaches to infection control by rapidly discovering antibiotics, particularly those that retain activities against MDR pathogens. In this study, metagenomic nanopore sequence analysis coupled with spectroscopic methods has been conducted for rapid exploring of the various active metabolites produced by Paenibacillus ehimensis soil isolate. Preliminary soil screening resulted in selection of a Gram-positive isolate identified via 16S ribosomal RNA gene sequencing as Paenibacillus ehimensis MZ921932. The isolate showed a broad range of activity against MDR Gram-positive, Gram-negative, and Candida spp. A metagenomics sequence analysis of the soil sample harboring Paenibacillus ehimensis isolate MZ921932 (NCBI GenBank accession PRJNA785410) revealed the presence of conserved biosynthetic gene clusters of petrobactin, tridecaptin, locillomycin (β-lactone), polymyxin, and macrobrevin (polyketides). The liquid chromatography/mass (LC/MS) analysis of the Paenibacillus ehimensis metabolites confirmed the presence of petrobactin, locillomycin, and macrobrevin. In conclusion, Paenibacillus ehimensis isolate MZ921932 is a promising rich source for broad spectrum antimicrobial metabolites. The metagenomic nanopore sequence analysis was a rapid, easy, and efficient method for the preliminary detection of the nature of the expected active metabolites. LC/MS spectral analysis was employed for further confirmation of the nature of the respective active metabolites.
Collapse
Affiliation(s)
- Mohamed A. Eltokhy
- Department of Microbiology, Faculty of Pharmacy, Misr International University (MIU), Cairo 19648, Egypt; (M.A.E.); (W.N.E.)
| | - Bishoy T. Saad
- Department of Bioinformatics, HITS Solutions Co., Cairo 11765, Egypt;
| | - Wafaa N. Eltayeb
- Department of Microbiology, Faculty of Pharmacy, Misr International University (MIU), Cairo 19648, Egypt; (M.A.E.); (W.N.E.)
| | - Ibrahim S. Yahia
- Laboratory of Nano-Smart Materials for Science and Technology (LNSMST), Department of Physics, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia;
- Research Center for Advanced Materials Science (RCAMS), King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
- Nanoscience Laboratory for Environmental and Biomedical Applications (NLEBA), Semiconductor Lab., Department of Physics, Faculty of Education, Ain Shams University, Roxy, Cairo 11757, Egypt
| | - Khaled M. Aboshanab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Organization of African Unity Str., Cairo 11566, Egypt
- Correspondence: ; Tel.: +20-010-075-82620; Fax: +20-202-240-51107
| | - Mohamed S. E. Ashour
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Cairo 11651, Egypt;
| |
Collapse
|