Metagenomic Analysis of Intestinal Microbiota Derived from Stool Samples of Third-Trimester Pregnant Women
Abstract
Background: The human gut microbiota plays a unique role in metabolism, immunity, and nutrient absorption. Various studies on the gut microbiota have identified a link between changes in bacterial abundance in the gut known as dysbiosis (imbalance) and the pathogenesis of certain disorders. It is known that an imbalance in the ratio of the phyla Firmicutes and Bacteroidetes has been associated with various chronic diseases, including inflammatory bowel disease and metabolic disorders. The Firmicutes/Bacteroidetes (F/B) ratio is a measure used to assess gut microbiota composition, which is believed to play a significant role in intestinal health and metabolism. Studies suggest that a higher F/B ratio is often associated with obesity and other metabolic conditions. Objective: This study aims to carry out metagenomic analysis of third-trimester pregnant women's faecal samples to predict degenerative diseases using third-generation whole genome sequencing, namely PromethION nanopore technology. Method: Nanopore Technology: DNA sequencing of faecal samples from pregnant women in the third trimester was performed using the Oxford Nanopore Technology (ONT) device based on the Ligation Sequencing gDNA - Native Barcoding Kit 24 V14 and following its guidelines. Result: Based on the quality and quantity of total DNA reads from 20 stool samples from pregnant women, only 4 samples were continued for analysis (1A, 2A, 3A and 4A). The results of the abundance of intestinal microbiota based on the most abundant phylum are Proteobacteria, Bacteriodetes, and Firmicutes. Conclusion: Meanwhile, based on species abundance, it shows that Prevotella copri (phylum Bacteriodetes) is abundant in samples 2A, 3A and 4A, while in sample 1A the most abundant species is Succinivirio dextrinosolvens (phylum Proteobacteria). Bacteroidetes are a group of Gram-negative bacteria that are often found to increase in individuals with type 2 diabetes and obesity
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Amir, M., Brown, J. A., Rager, S. L., Sanidad, K. Z., Ananthanarayanan, A., & Zeng, M. Y. (2020). Maternal microbiome and infections in pregnancy. Microorganisms, 8(12), 1–21. https://doi.org/10.3390/microorganisms8121996
Breitwieser FP, Salzberg SL. 2016. Pavian: Interactive analysis of metagenomics data for microbiome studies and pathogen identification. Bioinformatics. 36(4):1303–1304.doi:10.1093/bioinformatics/btz715.
Fite, M. B., Tura, A. K., Yadeta, T. A., Oljira, L., & Roba, K. T. (2022). Prevalence and determinants of dietary practices among pregnant women in eastern Ethiopia. BMC Nutrition, 1–10. https://doi.org/10.1186/s40795-021-00494-4
Gotama, D., Wardhana, M., Santoso, A., & Sissy, S. (2021). Mikrobiota usus pada dermatitis atopik. Intisari Sains Medis, 12(2), 718–722. https://doi.org/10.15562/ism.v12i2.994
Hasibuan, F. E. B., & Kolondam, B. J. (2017). Interaksi Antara Mikrobiota Usus Dan Sistem Kekebalan Tubuh Manusia. Jurnal Ilmiah Sains, 17(1), 35. https://doi.org/10.35799/jis.17.1.2017.15221
Hudson, I., Pedro-suvorov, P., & Kocak, S. (2024). applied sciences Random Forest Spatial-Temporal and State Space Models to Assess the Impact of Bushfire-Induced Aerosol Events on Ozone Depletion in Australia.
Hunt, J. M. (2010). Shiga toxin-producing escherichia coli (STEC). Clinics in Laboratory Medicine, 30(1), 21–45. https://doi.org/10.1016/j.cll.2009.11.001
Kamaruddin, M. (2023). Genotyphing & Karakterisasi Molekuler Spesies Trichomonad di Indonesia Dalam Pencegahan Penyakit Zoonosis. Deepublish, Yogyakarta.
Kamaruddin, M., Triananinsi, N., Sampara, N., Sumarni, S., Minarti, M., Maya. (2020). Karakterisasi DNA Mikrobiota Usus Bayi pada Persalinan Normal yang diberi ASI dan Susu Formula. Media Kesehat. Masy. Indones. 16(1):116.doi:10.30597/mkmi.v16i1.9050.
Kamaruddin, M., Tokoro, M., Rahman, M. M., Arayama, S., Hidayati, A. P., Syafruddin, D., Asih, P. B., Yoshikawa, H., & Kawahara, E. (2014). Molecular characterization of various trichomonad species isolated from humans and related mammals in Indonesia. The Korean journal of parasitology, 52(5), 471–478.
https://doi.org/10.3347/kjp.2014.52.5.471
Koliada, A., Syzenko, G., Moseiko, V., Budovska, L., Puchkov, K., Perederiy, V., Gavalko, Y., Dorofeyev, A., Romanenko, M., Tkach, S., et al. (2017). Association between body mass index and Firmicutes/Bacteroidetes ratio in an adult Ukrainian population. BMC Microbiol. 17(120):1–6.doi:10.1186/s12866-017-1027-1.
Kusharyati DF, Rovik A, Ryandini D, Pramono H. 2020. Bifidobacterium longum , a Predominant Bifidobacterium in Early-life Infant Potentially Used as Probiotic. J. Biol. Biol. Educ. 12(3):378–383.
Lange-Enyedi, N. T., Németh, P., Borsodi, A. K., Spötl, C., & Makk, J. (2024). Calcium carbonate precipitating extremophilic bacteria in an Alpine ice cave. Scientific Reports, 14(1), 1–15. https://doi.org/10.1038/s41598-024-53131-y
Logor NT, Manoppo JIC, Tatura SNN. (2021). Gambaran Mikrobiota Usus dan Konsistensi Tinja pada Bayi Sehat Usia 0-6 Bulan yang Mendapat ASI dan Susu Formula. J. Biomedik. 13(2):207.
Man AWC, Zhou Y, Xia N, Li H. (2020). Involvement of gut microbiota, microbial metabolites and interaction with polyphenol in host immunometabolism. Nutrients. 12(10):1–29.
Morimoto T, Kobayashi T, Kakiuchi T, Esaki M, Tsukamoto M, Yoshihara T, Hirata H, Yabuki S, Mawatari M. 2023. Gut-spine axis: a possible correlation between gut microbiota and spinal degenerative diseases. Front. Microbiol. 14(October):1–15.
Minarti, M., Triananinsi, N., Nurqalbi, N., Sumarni, S., & Kamaruddin, M. (2020). Metagenomic Diversity of Gut Microbiota of Gestational Diabetes Mellitus of Pregnant Women. Biomedika, 13(1), 1-8. https://doi.org/https://doi.org/10.31001/biomedika.v13i1.747
Naithani, N., Atal, A. T., Tilak, T. V. S. V. G. K., Vasudevan, B., Misra, P., & Sinha, S. (2021). Precision medicine: Uses and challenges. Medical Journal Armed Forces India, 77(3), 258–265. https://doi.org/10.1016/j.mjafi.2021.06.020.
Narayan Biswal, B., Narayan Das, S., Kumar Das, B., & Rath, R. (2017). Alteration of cellular metabolism in cancer cells and its therapeutic. Journal of Oral and Maxillofacial Pathology, 21(3), 244–251. https://doi.org/10.4103/jomfp.JOMFP.
Nuriel-Ohayon, M., Neuman, H., & Koren, O. (2016). Microbial changes during pregnancy, birth, and infancy. Frontiers in Microbiology, 7(JUL), 1–13. https://doi.org/10.3389/fmicb.2016.01031.
Petersen, L. M., Martin, I. W., Moschetti, W. E., Kershaw, C. M., & Tsongalis, G. J. (2020). crossm Third-Generation Sequencing in the Clinical Laboratory : Sequencing. December 2019, 1–10.
Perxachs, J. M., & Real, J. M. F. (2019). Exploration of the microbiota and metabolites within body fluids could pinpoint novel disease mechanisms. The Febs Journal, 287(8239097), 856–865. https://doi.org/10.1111/febs.15130.
Pratama, R. B., Berawi, K. N., & Islamy, N. (2021). Mikrobiota Usus dan Osteoartritis. Jurnal Ilmu Medis Indonesia, 1(1), 1–6. https://doi.org/10.35912/jimi.v1i1.279.
Selle A, Brosseau C, Dijk W, Duval A, Bouchaud G, Rousseaux A, Bruneau A, Cherbuy C, Mariadassou M, Cariou V, et al. (2022). Prebiotic Supplementation During Gestation Induces a Tolerogenic Environment and a Protective Microbiota in Offspring Mitigating Food Allergy. Front. Immunol. 12:745535.doi:10.3389/fimmu.2021.745535.
Simone, N. Di, Ortiz, A. S., Specchia, M., Tersigni, C., Villa, P., Gasbarrini, A., Scambia, G., & Ippolito, S. D. (2020). Recent Insights on the Maternal Microbiota : Impact on Pregnancy Outcomes. 11(October), 1–9. https://doi.org/10.3389/fimmu.2020.528202.
Sajdel-Sulkowska, E. M. (2023). The Impact of Maternal Gut Microbiota during Pregnancy on Fetal Gut–Brain Axis Development and Life-Long Health Outcomes. Microorganisms, 11(9). https://doi.org/10.3390/microorganisms11092199
Sinha, T., Brushett, S., Prins, J., & Zhernakova, A. (2023). The maternal gut microbiome during pregnancy and its role in maternal and infant health. Current Opinion in Microbiology, 74, 102309. https://doi.org/10.1016/j.mib.2023.102309
Song, Z., & Liu, H. (2023). The investigation of the association of pregnancy weight gain on maternal and neonatal gut microbiota composition and abundance using 16sRNA sequencing. BMC Pregnancy and Childbirth, 4, 1–12. https://doi.org/10.1186/s12884-022-05289-4
Stojanov, S., Berlec, A., & Štrukelj, B. (2020). The Influence of Probiotics on the Firmicutes/Bacteroidetes Ratio in the Treatment of Obesity and Inflammatory Bowel disease. Microorganisms, 8(11), 1715. https://doi.org/10.3390/microorganisms8111715
Sun C, Zhou X, Guo T, Meng J. (2023). The immune role of the intestinal microbiome in knee osteoarthritis. Front. Immunol. 14(June):1–18.
Tu, X., Duan, C., Lin, B., Li, K., Gao, J., Yan, H., Wang, K., & Zhao, Z. (2022b). Characteristics of the gut microbiota in pregnant women with fetal growth restriction. BMC Pregnancy and Childbirth, 22(1), 1–8. https://doi.org/10.1186/s12884-022-04635-w
Venegas, D. P., De La Fuente, M. K., Landskron, G., González, M. J., Quera, R., Dijkstra, G., Harmsen, H. J. M., Faber, K. N., & Hermoso, M. A. (2019). Short chain fatty acids (SCFAs)mediated gut epithelial and immune regulation and its relevance for inflammatory bowel diseases. Frontiers in Immunology, 10(MAR). https://doi.org/10.3389/fimmu.2019.00277
Yang, H., Guo, R., Li, S., Liang, F., Tian, C., Zhao, X., Long, Y., Liu, F., Jiang, M., Zhang, Y., Ma, J., Peng, M., Zhang, S., Ye, W., Gan, Q., Zeng, F., Mao, S., Liang, Q., Ma, X., … Zhu, C. (2020). Systematic analysis of gut microbiota in pregnant women and its correlations with individual heterogeneity. Npj Biofilms and Microbiomes, 6(1), 1–12. https://doi.org/10.1038/s41522-020-00142-y.
Yang, P., Lu, T., Liang, X., Huang, T., Wu, L., He, Z., Xiao, X., & Fan, S. (2024). The influence of placenta microbiota of normal term pregnant women on immune regulation during pregnancy. BMC Pregnancy and Childbirth, 1–11. https://doi.org/10.1186/s12884-024-06353-x.
Woodall CA, McGeoch LJ, Hay AD, Hammond A. 2022. Respiratory tract infections and gut microbiome modifications: A systematic review. PLoS One. 17(1 January):1–20.doi:10.1371/journal.pone.0262057.
DOI: http://dx.doi.org/10.30742/jikw.v14i1.4173
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