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Kim C, Pongpanich M, Porntaveetus T. Unraveling metagenomics through long-read sequencing: a comprehensive review. J Transl Med 2024; 22:111. [PMID: 38282030 PMCID: PMC10823668 DOI: 10.1186/s12967-024-04917-1] [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: 10/15/2023] [Accepted: 01/21/2024] [Indexed: 01/30/2024] Open
Abstract
The study of microbial communities has undergone significant advancements, starting from the initial use of 16S rRNA sequencing to the adoption of shotgun metagenomics. However, a new era has emerged with the advent of long-read sequencing (LRS), which offers substantial improvements over its predecessor, short-read sequencing (SRS). LRS produces reads that are several kilobases long, enabling researchers to obtain more complete and contiguous genomic information, characterize structural variations, and study epigenetic modifications. The current leaders in LRS technologies are Pacific Biotechnologies (PacBio) and Oxford Nanopore Technologies (ONT), each offering a distinct set of advantages. This review covers the workflow of long-read metagenomics sequencing, including sample preparation (sample collection, sample extraction, and library preparation), sequencing, processing (quality control, assembly, and binning), and analysis (taxonomic annotation and functional annotation). Each section provides a concise outline of the key concept of the methodology, presenting the original concept as well as how it is challenged or modified in the context of LRS. Additionally, the section introduces a range of tools that are compatible with LRS and can be utilized to execute the LRS process. This review aims to present the workflow of metagenomics, highlight the transformative impact of LRS, and provide researchers with a selection of tools suitable for this task.
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Affiliation(s)
- Chankyung Kim
- Center of Excellence in Genomics and Precision Dentistry, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
- Graduate Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence for Cancer and Inflammation, Chulalongkorn University, Bangkok, Thailand
| | - Thantrira Porntaveetus
- Center of Excellence in Genomics and Precision Dentistry, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand.
- Graduate Program in Geriatric and Special Patients Care, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand.
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Dotto-Maurel A, Pelletier C, Morga B, Jacquot M, Faury N, Dégremont L, Bereszczynki M, Delmotte J, Escoubas JM, Chevignon G. Evaluation of tangential flow filtration coupled to long-read sequencing for ostreid herpesvirus type 1 genome assembly. Microb Genom 2022; 8:mgen000895. [PMID: 36355418 PMCID: PMC9836095 DOI: 10.1099/mgen.0.000895] [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] [Indexed: 11/12/2022] Open
Abstract
Whole-genome sequencing is widely used to better understand the transmission dynamics, the evolution and the emergence of new variants of viral pathogens. This can bring crucial information to stakeholders for disease management. Unfortunately, aquatic virus genomes are usually difficult to characterize because most of these viruses cannot be easily propagated in vitro. Developing methodologies for routine genome sequencing of aquatic viruses is timely given the ongoing threat of disease emergence. This is particularly true for pathogenic viruses infecting species of commercial interest that are widely exchanged between production basins or countries. For example, the ostreid herpesvirus type 1 (OsHV-1) is a Herpesvirus widely associated with mass mortality events of juvenile Pacific oyster Crassostrea gigas. Genomes of Herpesviruses are large and complex with long direct and inverted terminal repeats. In addition, OsHV-1 is unculturable. It therefore accumulates several features that make its genome sequencing and assembly challenging. To overcome these difficulties, we developed a tangential flow filtration (TFF) method to enrich OsHV-1 infective particles from infected host tissues. This virus purification allowed us to extract high molecular weight and high-quality viral DNA that was subjected to Illumina short-read and Nanopore long-read sequencing. Dedicated bioinformatic pipelines were developed to assemble complete OsHV-1 genomes with reads from both sequencing technologies. Nanopore sequencing allowed characterization of new structural variations and major viral isomers while having 99,98 % of nucleotide identity with the Illumina assembled genome. Our study shows that TFF-based purification method, coupled with Nanopore sequencing, is a promising approach to enable in field sequencing of unculturable aquatic DNA virus.
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Affiliation(s)
| | | | | | | | | | | | | | - Jean Delmotte
- IHPE, Univ. Montpellier, CNRS, Ifremer, UPVD, F-34095 Montpellier, France
| | - Jean-Michel Escoubas
- IHPE, Univ. Montpellier, CNRS, Ifremer, UPVD, F-34095 Montpellier, France,*Correspondence: Jean-Michel Escoubas,
| | - Germain Chevignon
- Ifremer, ASIM, F-17390 La Tremblade, France,*Correspondence: Germain Chevignon,
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Saranathan R, Asare E, Leung L, de Oliveira AP, Kaugars KE, Mulholland CV, Lukose R, Berney M, Jacobs WR. Capturing Structural Variants of Herpes Simplex Virus Genome in Full Length by Oxford Nanopore Sequencing. Microbiol Spectr 2022; 10:e0228522. [PMID: 36040163 PMCID: PMC9602439 DOI: 10.1128/spectrum.02285-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/10/2022] [Indexed: 01/04/2023] Open
Abstract
Genome sequencing and assembly of viral genomes within the Herpesviridae family, particularly herpes simplex virus (HSV), have been challenging due to the large size (~154 Kb), high GC content (68%), and nucleotide variations arising during replication. Oxford Nanopore Technology (ONT) has been successful in obtaining read lengths ranging from 100 Kb up to 2.3 Mb. We have optimized DNA extraction and sequencing with ONT to capture the whole genome of HSV-1 as a single read. Although previous studies described the presence of four different genome isomers of HSV, we provided the first report on capturing all four variants' full-length genome as single reads. These isomers were found to be present in almost equal proportion in the sequenced DNA preparation. IMPORTANCE With the advent of next-generation sequencing platforms, genome sequencing of viruses can be performed in a relatively shorter time frame in even the most austere conditions. Ultralong read sequencing platforms, such as Oxford Nanopore Technology (ONT), have made it possible to capture the full-length genome of DNA viruses as a single read. By optimizing ONT for this purpose, we captured the genome (~154 Kb) of a clinical strain of herpes simplex virus 1 (HSV-1). Additionally, we captured full-length sequences of the four isomers of lab-grown HSV-1 virus and were able to determine the frequency of each within the isogenic population. This method will open new directions in studying the significance of these isomers and their clinical relevance to HSV-1 infections. It will also improve basic studies on the recombination and replication of this virus.
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Affiliation(s)
- Rajagopalan Saranathan
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York City, New York, USA
| | - Emmanuel Asare
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York City, New York, USA
| | - Lawrence Leung
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York City, New York, USA
| | - Anna Paula de Oliveira
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York City, New York, USA
| | - Katherine E. Kaugars
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York City, New York, USA
| | - Claire V. Mulholland
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York City, New York, USA
| | - Regy Lukose
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York City, New York, USA
| | - Michael Berney
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York City, New York, USA
| | - William R. Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York City, New York, USA
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Chang W, Jiao X, Sui H, Goswami S, Sherman BT, Fromont C, Caravaca JM, Tran B, Imamichi T. Complete Genome Sequence of Herpes Simplex Virus 2 Strain G. Viruses 2022; 14:v14030536. [PMID: 35336943 PMCID: PMC8954253 DOI: 10.3390/v14030536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/22/2022] [Accepted: 03/03/2022] [Indexed: 12/13/2022] Open
Abstract
Herpes simplex virus type 2 (HSV-2) is a common causative agent of genital tract infections. Moreover, HSV-2 and HIV infection can mutually increase the risk of acquiring another virus infection. Due to the high GC content and highly repetitive regions in HSV-2 genomes, only the genomes of four strains have been completely sequenced (HG52, 333, SD90e, and MS). Strain G is commonly used for HSV-2 research, but only a partial genome sequence has been assembled with Illumina sequencing reads. In the current study, we de novo assembled and annotated the complete genome of strain G using PacBio long sequencing reads, which can span the repetitive regions, analyzed the ‘α’ sequence, which plays key roles in HSV-2 genome circulation, replication, cleavage, and packaging of progeny viral DNA, identified the packaging signals homologous to HSV-1 within the ‘α’ sequence, and determined both termini of the linear genome and cleavage site for the process of concatemeric HSV-2 DNA produced via rolling-circle replication. In addition, using Oxford Nanopore Technology sequencing reads, we visualized four HSV-2 genome isomers at the nucleotide level for the first time. Furthermore, the coding sequences of HSV-2 strain G have been compared with those of HG52, 333, and MS. Moreover, phylogenetic analysis of strain G and other diverse HSV-2 strains has been conducted to determine their evolutionary relationship. The results will aid clinical research and treatment development of HSV-2.
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Affiliation(s)
- Weizhong Chang
- Laboratory of Human Retrovirology and lmmunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (X.J.); (H.S.); (S.G.); (B.T.S.)
- Correspondence: (W.C.); (T.I.); Tel.: +1-(301)-846-6295 (W.C.); +1-(301)-846-5450 (T.I.)
| | - Xiaoli Jiao
- Laboratory of Human Retrovirology and lmmunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (X.J.); (H.S.); (S.G.); (B.T.S.)
| | - Hongyan Sui
- Laboratory of Human Retrovirology and lmmunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (X.J.); (H.S.); (S.G.); (B.T.S.)
| | - Suranjana Goswami
- Laboratory of Human Retrovirology and lmmunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (X.J.); (H.S.); (S.G.); (B.T.S.)
| | - Brad T. Sherman
- Laboratory of Human Retrovirology and lmmunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (X.J.); (H.S.); (S.G.); (B.T.S.)
| | - Caroline Fromont
- Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (C.F.); (J.M.C.); (B.T.)
| | - Juan Manuel Caravaca
- Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (C.F.); (J.M.C.); (B.T.)
| | - Bao Tran
- Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (C.F.); (J.M.C.); (B.T.)
| | - Tomozumi Imamichi
- Laboratory of Human Retrovirology and lmmunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (X.J.); (H.S.); (S.G.); (B.T.S.)
- Correspondence: (W.C.); (T.I.); Tel.: +1-(301)-846-6295 (W.C.); +1-(301)-846-5450 (T.I.)
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