Abstract
Next-generation sequencing (NGS) has been widely applied to the identification of microbiome in body fluids. The methodology of 16S rRNA amplicon sequencing is simple, fast, and cost-effective. It overcomes the problem that some microorganisms cannot be isolated or cultured. Low abundant bacteria can also be amplified and sequenced, but the resolution of classification can hardly reach species or sub-species level; moreover, this methodology is mainly used to identify bacterial populations, and other microorganisms like viruses or fungi cannot be sequenced. On the other hand, the microbiome profiling obtained by shotgun metagenomic sequencing is more comprehensive with better resolution, and more accurate classification can be expected due to higher coverage of genomic sequences from microorganisms. By combining the capture-based method with metagenomic sequencing, we can further enrich and detect low abundant microorganisms and identify the viral integration sites in host gDNA at once.
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References
Brestoff JR, Artis D (2013) Commensal bacteria at the interface of host metabolism and the immune system. Nat Immunol 14(7):676–684. https://doi.org/10.1038/ni.2640
Greenblum S, Turnbaugh PJ, Borenstein E (2012) Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease. Proc Natl Acad Sci U S A 109(2):594–599. https://doi.org/10.1073/pnas.1116053109
Belkaid Y, Hand Timothy W (2014) Role of the microbiota in immunity and inflammation. Cell 157(1):121–141. https://doi.org/10.1016/j.cell.2014.03.011
Araldi RP, Sant’Ana TA, Módolo DG, de Melo TC, Spadacci-Morena DD, de Cassia Stocco R, Cerutti JM, de Souza EB (2018) The human papillomavirus (HPV)-related cancer biology: an overview. Biomed Pharmacother 106:1537–1556. https://doi.org/10.1016/j.biopha.2018.06.149
Tsilimigras MCB, Fodor A, Jobin C (2017) Carcinogenesis and therapeutics: the microbiota perspective. Nat Microbiol 2(3):17008. https://doi.org/10.1038/nmicrobiol.2017.8
Zhang L, Richards A, Barrasa MA-O, Hughes SA-O, Young RA-O, Jaenisch R (2021) Reverse-transcribed SARS-CoV-2 RNA can integrate into the genome of cultured human cells and can be expressed in patient-derived tissues. Proc Natl Acad Sci U S A 118:e2105968118. https://doi.org/10.1073/pnas.2105968118
Xia Y, Liu Y, Deng M, Xi R (2019) Detecting virus integration sites based on multiple related sequencing data by VirTect. BMC Med Genet 12:19
Bousali M, Karamitros T (2022) Hepatitis B virus integration into transcriptionally active loci and HBV-associated hepatocellular carcinoma. Microorganisms 10(2):253
Woo PCY, Teng JLL, Yeung JMY, Tse H, Lau SKP, Yuen K-Y (2011) Automated identification of medically important bacteria by 16S rRNA gene sequencing using a novel comprehensive database, 16SpathDB. J Clin Microbiol 49(5):1799–1809. https://doi.org/10.1128/JCM.02350-10
Lao H-Y, Ng TT-L, Wong RY-L, Wong CS-T, Lee L-K, Wong DS-H, Chan CT-M, Jim SH-C, Leung JS-L, Lo HW-H, Wong IT-F, Yau MC-Y, Lam JY-W, Wu AK-L, Siu GK-H, Richter SS (2022) The clinical utility of two high-throughput 16S rRNA gene sequencing workflows for taxonomic assignment of unidentifiable bacterial pathogens in matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 60(1):e01769–e01721. https://doi.org/10.1128/JCM.01769-21
Lane DJ (1991) 16S/23S rRNA Sequencing. In: Nucleic acid techniques in bacterial systematics. Wiley
Jovel J, Patterson J, Wang W, Hotte N, O’Keefe S, Mitchel T, Perry T, Kao D, Mason AL, Madsen KL, Wong GK-S (2016) Characterization of the gut microbiome using 16S or shotgun metagenomics. Front Microbiol 7:459. https://doi.org/10.3389/fmicb.2016.00459
Chandrani P, Kulkarni V, Iyer P, Upadhyay P, Chaubal R, Das P, Mulherkar R, Singh R, Dutt A (2015) NGS-based approach to determine the presence of HPV and their sites of integration in human cancer genome. Br J Cancer 112(12):1958–1965. https://doi.org/10.1038/bjc.2015.121
Yang W, Liu Y, Dong R, Liu J, Lang J, Yang J, Wang W, Li J, Meng B, Tian G (2020) Accurate detection of HPV integration sites in cervical cancer samples using the Nanopore MinION sequencer without error correction. Front Genet 11:660. https://doi.org/10.3389/fgene.2020.00660
Quan L, Dong R, Yang W, Chen L, Lang J, Liu J, Song Y, Ma S, Yang J, Wang W, Meng B, Tian G (2019) Simultaneous detection and comprehensive analysis of HPV and microbiome status of a cervical liquid-based cytology sample using Nanopore MinION sequencing. Sci Rep 9(1):19337. https://doi.org/10.1038/s41598-019-55843-y
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Ji, X., Ni, S., Tian, G., Zhang, L., Wang, W. (2023). Detection of Microorganisms in Body Fluid Samples. In: Huang, T., Yang, J., Tian, G. (eds) Liquid Biopsies. Methods in Molecular Biology, vol 2695. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3346-5_5
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DOI: https://doi.org/10.1007/978-1-0716-3346-5_5
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