Metagenomics as a Diagnostic Method for Identifying Microbiota Profiles in Diarrhea Cases
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https://doi.org/10.59188/eduvest.v6i2.52490##semicolon##
Metagenomics##common.commaListSeparator## 16S rRNA##common.commaListSeparator## Shotgun Sequencing##common.commaListSeparator## Gut Microbiota##common.commaListSeparator## Diarrhea DiagnosisAbstrakt
Diarrhea remains a major global health issue and is one of the leading causes of morbidity and mortality, especially in children. Changes in the composition of gut microbiota are strongly associated with the occurrence of diarrhea, particularly due to infections caused by pathogenic microorganisms. Conventional diagnostic techniques, such as culture, still have limitations in detecting diverse and unculturable microbes. Metagenomics offers a comprehensive diagnostic solution by analyzing the entire genetic material directly from stool samples using sequencing-based approaches. This review discusses two metagenomic strategies—16S rRNA sequencing and whole-genome shotgun metagenomic sequencing—based on studies conducted in India and Peru. The 16S rRNA approach enables the identification of bacterial community structure and dysbiosis in diarrhea cases, while shotgun metagenomics provides higher resolution for detecting pathogenic species, including Campylobacter spp., and co-infections that are often missed by standard methods. Both techniques demonstrate significant advantages in detecting microbiota diversity, identifying novel pathogens, and uncovering antimicrobial resistance profiles. Therefore, metagenomics represents a promising diagnostic tool for improving the accuracy of diarrhea detection and supporting public health interventions in endemic regions.
##submission.citations##
Chakravorty, S., Helb, D., Burday, M., Connell, N., & Alland, D. (2007). A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. Journal of Microbiological Methods, 69(2), 330. https://doi.org/10.1016/J.MIMET.2007.02.005
Chen, J., Wan, C. M., & Gong, S. T. (2018). Chinese clinical practice guidelines for acute infectious diarrhea in children. World Journal of Pediatrics, 14(5), 429–436. https://doi.org/10.1007/S12519-018-0190-2
De, R., Mukhopadhyay, A. K., & Dutta, S. (2020). Metagenomic analysis of gut microbiome and resistome of diarrheal fecal samples from Kolkata, India. Gut Pathogens, 12(1), 1–48. https://doi.org/10.1186/S13099-020-00371-8
Field, M. (2003). Intestinal ion transport and the pathophysiology of diarrhea. Journal of Clinical Investigation, 111(7), 931. https://doi.org/10.1172/JCI18326
Handelsman, J. (2004). Metagenomics: Application of genomics to uncultured microorganisms. Microbiology and Molecular Biology Reviews, 68(4), 669–685. https://doi.org/10.1128/MMBR.68.4.669-685.2004
Heyman, M. B. (2006). Lactose intolerance in infants, children, and adolescents. Pediatrics, 118(3), 1279–1286. https://doi.org/10.1542/PEDS.2006-1721
Indonesia, K. K. R. (2021). Profil Kesehatan Indonesia 2020. Kementrian Kesehatan Republik Indonesia, 139.
Janda, J. M., & Abbott, S. L. (2007). 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory. Journal of Clinical Microbiology, 45(9), 2761–2764. https://doi.org/10.1128/JCM.01228-07
Keusch, G. T., Fontaine, O., & Bhargava, A. (2006). Diarrheal diseases. https://www.ncbi.nlm.nih.gov/books/NBK11764/
Miller, R. R., Montoya, V., Gardy, J. L., Patrick, D. M., & Tang, P. (2013). Metagenomics for pathogen detection in public health. Genome Medicine, 5(9). https://doi.org/10.1186/GM485
Norman, J. M., Handley, S. A., & Virgin, H. W. (2014). Kingdom-agnostic metagenomics and the importance of complete characterization of enteric microbial communities. Gastroenterology, 146(6), 1459–1469. https://doi.org/10.1053/J.GASTRO.2014.02.001
Odamaki, T., Kato, K., & Sugahara, H. (2016). Age-related changes in gut microbiota composition from newborn to centenarian: A cross-sectional study. BMC Microbiology, 16(1), 1–12. https://doi.org/10.1186/S12866-016-0708-5
Organization, W. H. (2017). Diarrhoeal disease. https://www.who.int/news-room/fact-sheets/detail/diarrhoeal-disease
Parker, C. T., Schiaffino, F., & Huynh, S. (2022). Shotgun metagenomics of fecal samples from children in Peru reveals frequent complex co-infections. PLoS Neglected Tropical Diseases, 16(10). https://doi.org/10.1371/JOURNAL.PNTD.0010815
Patel, M. M., Glass, R., Desai, R., Tate, J. E., & Parashar, U. D. (2012). Fulfilling the promise of rotavirus vaccines: How far have we come since licensure? The Lancet Infectious Diseases, 12(7), 561–570. https://doi.org/10.1016/S1473-3099(12)70029-4
Quince, C., Walker, A. W., Simpson, J. T., Loman, N. J., & Segata, N. (2017). Shotgun metagenomics, from sampling to analysis. Nature Biotechnology, 35(9), 833–844. https://doi.org/10.1038/NBT.3935
Schloss, P. D., & Handelsman, J. (2004). Status of the microbial census. Microbiology and Molecular Biology Reviews, 68(4), 686–691. https://doi.org/10.1128/MMBR.68.4.686-691.2004
Sharpton, T. J. (2014). An introduction to the analysis of shotgun metagenomic data. Frontiers in Plant Science, 5. https://doi.org/10.3389/FPLS.2014.00209
Walker, C. L. F., & Black, R. E. (2010). Diarrhoea morbidity and mortality in older children, adolescents, and adults. Epidemiology and Infection, 138(9), 1215–1226. https://doi.org/10.1017/S0950268810000592
Wenzl, H. H. (2012). Diarrhea in chronic inflammatory bowel diseases. Gastroenterology Clinics of North America, 41(3), 651–675. https://doi.org/10.1016/J.GTC.2012.06.006
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