The Gut Microbiome and Human Health: Insights from Recent Research

Authors

  • Semir Bechir Suheil GAOUAR Applied genetics in agronomy, ecology and public health laboratory, Tlemcen, Algeria

DOI:

https://doi.org/10.46325/gabj.v9i1.431

Keywords:

Gut Microbiome, Human Health, Investigation Techniques, Physiological Impact, Psychological Impact, Immunological Impact, Genetic and Epigenetic Influence, Ethnic Differences, Environmental Factors, Nutrition, Medication, Microbiome Evolution, Obesity

Abstract

The gut microbiome, a complex community of microorganisms residing in the human gastrointestinal tract, plays a crucial role in maintaining overall health. This review explores recent advancements in the investigation of the gut microbiome, highlighting cutting-edge techniques such as metagenomics, metatranscriptomics, metabolomics, single-cell sequencing, and bioinformatics. We discuss the evolution of the human gut microbiome, examining historical perspectives and the influence of lifestyle changes, as well as differences between ancient and modern human microbiomes. This review delves into the physiological impacts of the gut microbiome on digestive, metabolic, and cardiovascular health, emphasizing its significant role in these areas. Special attention is given to the connection between the gut microbiome and obesity, detailing mechanisms, research findings, and potential interventions. Furthermore, we explore the psychological impacts through the gut-brain axis and its influence on mental health. Immunological impacts are also covered, focusing on the microbiome's role in immune system modulation and its link to autoimmune diseases. The genetic and epigenetic influences of the microbiome on host genetics and gene expression are analyzed, along with ethnic differences in microbial composition driven by genetic and environmental factors. Environmental influences such as diet, geography, lifestyle, pollutants, and the effects of medication and antibiotics on the gut microbiota are discussed. The review concludes with an exploration of therapeutic potentials, including probiotics, prebiotics, fecal microbiota transplantation (FMT), and personalized medicine based on microbiome profiles. This comprehensive review aims to summarize key findings, highlight the implications for future research and clinical practice, and underscore the significance of the gut microbiome in human health.

References

Adler, C. J., Dobney, K., Weyrich, L. S., Kaidonis, J., Walker, A. W., Haak, W., ... & Cooper, A. (2013). Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions. Nature genetics, 45(4), 450-455.

Alam, M. T., Amos, G. C., Murphy, A. R., Murch, S., Wellington, E. M., & Arasaradnam, R. P. (2020). Microbial imbalance in inflammatory bowel disease patients at different taxonomic levels. Gut pathogens, 12, 1-8.

Almeida, A., Mitchell, A. L., Boland, M., Forster, S. C., Gloor, G. B., Tarkowska, A., ... & Finn, R. D. (2019). A new genomic blueprint of the human gut microbiota. Nature, 568 (7753), 499-504.

Al-Mustanjid, M., Mahmud, S. H., Royel, M. R. I., Rahman, M. H., Islam, T., Rahman, M. R., & Moni, M. A. (2020). Detection of molecular signatures and pathways shared in inflammatory bowel disease and colorectal cancer: a bioinformatics and systems biology approach. Genomics, 112(5), 3416-3426.

Alpino, G. D. C. Á., Pereira-Sol, G. A., Dias, M. D. M. E., Aguiar, A. S. D., & Peluzio, M. D. C. G. (2024). Beneficial effects of butyrate on brain functions: a view of epigenetic. Critical Reviews in Food Science and Nutrition, 64(12), 3961-3970.

Alzahrani, H., & Fernstad, S. (2023). An investigation into various visualization tools for complex biological networks. Information Visualization, 22(4), 323-339.

Amabebe, E., Robert, F. O., Agbalalah, T., & Orubu, E. S. (2020). Microbial dysbiosis-induced obesity: role of gut microbiota in homoeostasis of energy metabolism. British Journal of Nutrition, 123(10), 1127-1137.

Amarasinghe, S. L., Su, S., Dong, X., Zappia, L., Ritchie, M. E., & Gouil, Q. (2020). Opportunities and challenges in long-read sequencing data analysis. Genome biology, 21(1), 30.

Arıkan, M., & Muth, T. (2023). Integrated multi-omics analyses of microbial communities: a review of the current state and future directions. Molecular Omics.

Armour, C. R., Nayfach, S., Pollard, K. S., & Sharpton, T. J. (2019). A metagenomic meta-analysis reveals functional signatures of health and disease in the human gut microbiome. MSystems, 4(4), 10-1128.

Arnone, D., Chabot, C., Heba, A. C., Kökten, T., Caron, B., Hansmannel, F., ... & Peyrin-Biroulet, L. (2022). Sugars and gastrointestinal health. Clinical Gastroenterology and Hepatology, 20(9), 1912-1924.

Aron-Wisnewsky, J., Warmbrunn, M. V., Nieuwdorp, M., & Clément, K. (2021). Metabolism and metabolic disorders and the microbiome: the intestinal microbiota associated with obesity, lipid metabolism, and metabolic health—pathophysiology and therapeutic strategies. Gastroenterology, 160(2), 573-599.

Aziz, T., Khan, A. A., Tzora, A., Voidarou, C., & Skoufos, I. (2023). Dietary implications of the bidirectional relationship between the gut microflora and inflammatory diseases with special emphasis on irritable bowel disease: current and future perspective. Nutrients, 15(13), 2956.

Bashiardes, S., Zilberman-Schapira, G., & Elinav, E. (2016). Use of metatranscriptomics in microbiome research. Bioinformatics and biology insights, 10, BBI-S34610.

Beghini, F., McIver, L. J., Blanco-Míguez, A., Dubois, L., Asnicar, F., Maharjan, S., ... & Segata, N. (2021). Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. elife, 10, e65088.

Belkaid, Y., & Hand, T. W. (2014). Role of the microbiota in immunity and inflammation. Cell, 157(1), 121-141.

Belkaid, Y., & Harrison, O. J. (2017). Homeostatic immunity and the microbiota. Immunity, 46(4), 562-576.

Bischoff, S. C., Nguyen, N. K., Seethaler, B., Beisner, J., Kügler, P., & Stefan, T. (2022). Gut microbiota patterns predicting long-term weight loss success in individuals with obesity undergoing nonsurgical therapy. Nutrients, 14(15), 3182.

Blaak, E. E., Canfora, E. E., Theis, S., Frost, G., Groen, A. K., Mithieux, G., ... & Verbeke, K. (2020). Short chain fatty acids in human gut and metabolic health. Beneficial microbes, 11(5), 411-455.

Blaser, M. J., & Falkow, S. (2009). What are the consequences of the disappearing human microbiota? Nature Reviews Microbiology, 7(12), 887-894.

Blaser, M. J. (2016). Antibiotic use and its consequences for the normal microbiome. Science, 352(6285), 544-545.

Bode, L. (2012). Human milk oligosaccharides: Every baby needs a sugar mama. Glycobiology, 22(9), 1147-1162.

Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114-2120.

Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., ... & Caporaso, J. G. (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature biotechnology, 37(8), 852-857.

Bongaerts, M., Bonte, R., Demirdas, S., Jacobs, E. H., Oussoren, E., van der Ploeg, A. T., ... & Ruijter, G. J. (2020). Using out-of-batch reference populations to improve untargeted metabolomics for screening inborn errors of metabolism. Metabolites, 11(1), 8.

Borrello, K., Lim, U., Park, S. Y., Monroe, K. R., Maskarinec, G., Boushey, C. J., ... & Lampe, J. W. (2022). Dietary intake mediates ethnic differences in gut microbial composition. Nutrients, 14(3), 660.

Bray, N. L., Pimentel, H., Melsted, P., & Pachter, L. (2016). Near-optimal probabilistic RNA-seq quantification. Nature Biotechnology, 34(5), 525-527.

Brown, C. T., Olm, M. R., Thomas, B. C., & Banfield, J. F. (2016). Measurement of bacterial replication rates in microbial communities. Nature biotechnology, 34(12), 1256-1263.

Canani, R. B., Di Costanzo, M., Leone, L., Pedata, M., Meli, R., & Calignano, A. (2011). Potential beneficial effects of butyrate in intestinal and extraintestinal diseases. World journal of gastroenterology: WJG, 17(12), 1519.

Cani, P. D., Amar, J., Iglesias, M. A., Poggi, M., Knauf, C., Bastelica, D., ... & Burcelin, R. (2007). Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes, 56(7), 1761-1772.

Cani, P. D., & Delzenne, N. M. (2008). The gut microbiome as a therapeutic target. Pharmacological Research, 61(2), 103-113.

Cammarota, G., Ianiro, G., Tilg, H., Rajilić-Stojanović, M., Kump, P., Satokari, R., ... & Gasbarrini, A. (2017). European consensus conference on faecal microbiota transplantation in clinical practice. Gut, 66(4), 569-580.

Carlessi, A. S., Borba, L. A., Zugno, A. I., Quevedo, J., & Réus, G. Z. (2021). Gut microbiota–brain axis in depression: The role of neuroinflammation. European Journal of Neuroscience, 53(1), 222-235.

Cheng, M., Cao, L., & Ning, K. (2019). Microbiome big-data mining and applications using single-cell technologies and metagenomics approaches toward precision medicine. Frontiers in Genetics, 10, 972.

Chen, Y., Ma, C., Liu, L., He, J., Zhu, C., Zheng, F., ... & Dai, Y. (2021). Analysis of gut microbiota and metabolites in patients with rheumatoid arthritis and identification of potential biomarkers. Aging (Albany NY), 13(20), 23689.

Chen, Y., Xu, J., & Chen, Y. (2021). Regulation of neurotransmitters by the gut microbiota and effects on cognition in neurological disorders. Nutrients, 13(6), 2099.

Choi, H., Rao, M. C., & Chang, E. B. (2021). Gut microbiota as a transducer of dietary cues to regulate host circadian rhythms and metabolism. Nature Reviews Gastroenterology & Hepatology, 18(10), 679-689.

Chu, X., Zhang, B., Koeken, V. A., Gupta, M. K., & Li, Y. (2021). Multi-omics approaches in immunological research. Frontiers in Immunology, 12, 668045.

Chudzik, A., Orzyłowska, A., Rola, R., & Stanisz, G. J. (2021). Probiotics, prebiotics and postbiotics on mitigation of depression symptoms: modulation of the brain–gut–microbiome axis. Biomolecules, 11(7), 1000.

Clemente, J. C., Pehrsson, E. C., Blaser, M. J., Sandhu, K., Gao, Z., Wang, B., ... & Dominguez-Bello, M. G. (2015). The microbiome of uncontacted Amerindians. Science advances, 1(3), e1500183.

Cockburn, D. W., & Koropatkin, N. M. (2016). Polysaccharide degradation by the intestinal microbiota and its influence on human health and disease. Journal of molecular biology, 428(16), 3230-3252.

Conlon, M. A., & Bird, A. R. (2014). The impact of diet and lifestyle on gut microbiota and human health. Nutrients, 7(1), 17-44.

Conte, M. I., Fuentes-Trillo, A., & Conde, C. D. (2024). Opportunities and tradeoffs in single-cell transcriptomic technologies. Trends in Genetics.

Crothers, J. W., Chu, N. D., Nguyen, L. T. T., Phillips, M., Collins, C., Fortner, K., ... & Moses, P. L. (2021). Daily, oral FMT for long-term maintenance therapy in ulcerative colitis: results of a single-center, prospective, randomized pilot study. BMC gastroenterology, 21, 1-16.

Cryan, J. F., & Dinan, T. G. (2012). Mind-altering microorganisms: The impact of the gut microbiota on brain and behaviour. Nature Reviews Neuroscience, 13(10), 701-712.

Cryan, J. F., & Dinan, T. G. (2017). Brain-gut-microbiota axis - mood, metabolism, and behaviour. Nature Reviews Gastroenterology & Hepatology, 14(2), 69-70.

Dai, Z., Ramesh, V., & Locasale, J. W. (2020). The evolving metabolic landscape of chromatin biology and epigenetics. Nature Reviews Genetics, 21(12), 737-753.

Dalby, M. J. (2023). Questioning the foundations of the gut microbiota and obesity.

Dar, D., Dar, N., Cai, L., & Newman, D. K. (2021). Spatial transcriptomics of planktonic and sessile bacterial populations at single-cell resolution. Science, 373(6556), eabi4882.

Davis, J. J., Wattam, A. R., Aziz, R. K., Brettin, T., Butler, R., Butler, R. M., ... & Stevens, R. (2020). The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities. Nucleic acids research, 48(D1), D606-D612.

Deris Zayeri, Z., Parsi, A., Shahrabi, S., Kargar, M., Davari, N., & Saki, N. (2023). Epigenetic and metabolic reprogramming in inflammatory bowel diseases: diagnostic and prognostic biomarkers in colorectal cancer. Cancer Cell International, 23(1), 264.

Philosophical Transactions of the Royal Society B, 378(1888), 20220221.

Deschasaux, M., Huybrechts, I., Murphy, N., Julia, C., Hercberg, S., Srour, B., ... & Touvier, M. (2018). Nutritional quality of food as represented by the FSAm-NPS nutrient profiling system underlying the Nutri-Score label and cancer risk in Europe: Results from the EPIC prospective cohort study. PLoS medicine, 15(9), e1002651.

Dinan, T. G., & Cryan, J. F. (2017). Gut-brain axis in 2016: Brain-gut-microbiota axis - mood, metabolism and behaviour. Nature Reviews Gastroenterology & Hepatology, 14(2), 69-70.

Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., ... & Gingeras, T. R. (2013). STAR: ultrafast universal RNA-seq aligner. Bioinformatics, 29(1), 15-21.

Dominguez-Bello, M. G., Costello, E. K., Contreras, M., Magris, M., Hidalgo, G., Fierer, N., & Knight, R. (2010). Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proceedings of the National Academy of Sciences, 107(26), 11971-11975.

Duan, M., Wang, Y., Zhang, Q., Zou, R., Guo, M., & Zheng, H. (2021). Characteristics of gut microbiota in people with obesity. Plos one, 16(8), e0255446.

Dunn, W. B., Broadhurst, D., Begley, P., Zelena, E., Francis-McIntyre, S., Anderson, N., ... & Human Serum Metabolome (HUSERMET) Consortium. (2011). Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry. Nature protocols, 6(7), 1060-1083.

Edler, D., Klein, J., Antonelli, A., & Silvestro, D. (2021). raxmlGUI 2.0: a graphical interface and toolkit for phylogenetic analyses using RAxML. Methods in ecology and evolution, 12(2), 373-377.

Eicher, T. P., & Mohajeri, M. H. (2022). Overlapping mechanisms of action of brain-active bacteria and bacterial metabolites in the pathogenesis of common brain diseases. Nutrients, 14(13), 2661.

Einarsson, K., Ericsson, S., Ewerth, S., Reihner, E., Rudling, M., Ståhlberg, D., & Angelin, B. (1991). Bile acid sequestrants: mechanisms of action on bile acid and cholesterol metabolism. European journal of clinical pharmacology, 40(Suppl 1), S53-S58.

Emwas, A. H., Roy, R., McKay, R. T., Tenori, L., Saccenti, E., Gowda, G. N., ... & Wishart, D. S. (2019). NMR spectroscopy for metabolomics research. Metabolites, 9(7), 123.

Ervin, S. M., Li, H., Lim, L., Roberts, L. R., Liang, X., Mani, S., & Redinbo, M. R. (2019). Gut microbial β-glucuronidases reactivate estrogens as components of the estrobolome that reactivate estrogens. Journal of Biological Chemistry, 294(49), 18586-18599.

Escalas, A., Hale, L., Voordeckers, J. W., Yang, Y., Firestone, M. K., Alvarez‐Cohen, L., & Zhou, J. (2019). Microbial functional diversity: from concepts to applications. Ecology and Evolution, 9(20), 12000-12016.

Espina, V., Heiby, M., Pierobon, M., & Liotta, L. A. (2007). Laser capture microdissection technology. Expert review of molecular diagnostics, 7(5), 647-657.

Fan, L., Ren, J., Chen, Y., Wang, Y., Guo, Z., Bu, P., ... & Cai, J. (2022). Effect of fecal microbiota transplantation on primary hypertension and the underlying mechanism of gut microbiome restoration: protocol of a randomized, blinded, placebo-controlled study. Trials, 23(1), 178.

Fan, Y., & Pedersen, O. (2021). Gut microbiota in human metabolic health and disease. Nature Reviews Microbiology, 19(1), 55-71.

Fragiadakis, G. K., Smits, S. A., Sonnenburg, E. D., Van Treuren, W., Reid, G., Knight, R., ... & Sonnenburg, J. L. (2019). Links between environment, diet, and the hunter-gatherer microbiome. Gut Microbes, 10(2), 216-227.

Fuentes-Trillo, A., Monzó, C., Manzano, I., Santiso-Bellón, C., Andrade, J. D. S. R. D., Gozalbo-Rovira, R., ... & Chaves, F. J. (2021). Benchmarking different approaches for norovirus genome assembly in metagenome samples. BMC genomics, 22, 1-12.

Fukuda, K., Ogawa, M., Taniguchi, H., & Saito, M. (2016). Molecular approaches to studying microbial communities: targeting the 16S ribosomal RNA gene. Journal of UOEH, 38(3), 223-232.

Gasaly, N., De Vos, P., & Hermoso, M. A. (2021). Impact of bacterial metabolites on gut barrier function and host immunity: a focus on bacterial metabolism and its relevance for intestinal inflammation. Frontiers in immunology, 12, 658354.

Ghosh, S., & Pramanik, S. (2021). Structural diversity, functional aspects and future therapeutic applications of human gut microbiome. Archives of microbiology, 203(9), 5281-5308.

Gomaa, E. Z. (2020). Human gut microbiota/microbiome in health and diseases: a review. Antonie Van Leeuwenhoek, 113(12), 2019-2040.

Gou, H. Z., Zhang, Y. L., Ren, L. F., Li, Z. J., & Zhang, L. (2022). How do intestinal probiotics restore the intestinal barrier?. Frontiers in microbiology, 13, 929346.

Gray, I. D., Kross, A. R., Renfrew, M. E., & Wood, P. (2020). Precision medicine in lifestyle medicine: the way of the future?. American Journal of Lifestyle Medicine, 14(2), 169-186.

Graw, S., Chappell, K., Washam, C. L., Gies, A., Bird, J., Robeson, M. S., & Byrum, S. D. (2021). Multi-omics data integration considerations and study design for biological systems and disease. Molecular omics, 17(2), 170-185.

Green, M., Arora, K., & Prakash, S. (2020). Microbial medicine: prebiotic and probiotic functional foods to target obesity and metabolic syndrome. International journal of molecular sciences, 21(8), 2890.

Groussin, M., Mazel, F., & Alm, E. J. (2020). Co-evolution and co-speciation of host-gut bacteria systems. Cell Host & Microbe, 28(1), 12-22.

Gupta, V. K., Paul, S., & Dutta, C. (2017). Geography, ethnicity or subsistence-specific variations in human microbiome composition and diversity. Frontiers in microbiology, 8, 1162.

Haarhuis, J. E., Kardinaal, A., & Kortman, G. A. M. (2022). Probiotics, prebiotics and postbiotics for better sleep quality: A narrative review. Beneficial Microbes, 13(3), 169-182.

He, F. F., & Li, Y. M. (2020). Role of gut microbiota in the development of insulin resistance and the mechanism underlying polycystic ovary syndrome: a review. Journal of ovarian research, 13(1), 73.

He, S., Li, H., Yu, Z., Zhang, F., Liang, S., Liu, H., ... & Lü, M. (2021). The gut microbiome and sex hormone-related diseases. Frontiers in microbiology, 12, 711137.

Hillesheim, E., & Brennan, L. (2023). Distinct patterns of personalised dietary advice delivered by a metabotype framework similarly improve dietary quality and metabolic health parameters: secondary analysis of a randomised controlled trial. Frontiers in Nutrition, 10, 1282741.

Huang, K., Xu, Y., Feng, T., Lan, H., Ling, F., Xiang, H., & Liu, Q. (2024). The Advancement and Application of the Single-Cell Transcriptome in Biological and Medical Research. Biology, 13(6), 451.

Hussain, T., Murtaza, G., Kalhoro, D. H., Kalhoro, M. S., Metwally, E., Chughtai, M. I., ... & Khan, S. A. (2021). Relationship between gut microbiota and host-metabolism: Emphasis on hormones related to reproductive function. Animal Nutrition, 7(1), 1-10.

Iablokov, S. N., Klimenko, N. S., Efimova, D. A., Shashkova, T., Novichkov, P. S., Rodionov, D. A., & Tyakht, A. V. (2021). Metabolic phenotypes as potential biomarkers for linking gut microbiome with inflammatory bowel diseases. Frontiers in Molecular Biosciences, 7, 603740.

Iversen, K. N., Dicksved, J., Zoki, C., Fristedt, R., Pelve, E. A., Langton, M., & Landberg, R. (2022). The effects of high fiber rye, compared to refined wheat, on gut microbiota composition, plasma short chain fatty acids, and implications for weight loss and metabolic risk factors (the RyeWeight Study). Nutrients, 14(8), 1669.

Jiang, Y., Wu, R., Zhang, W., Xin, F., & Jiang, M. (2023). Construction of stable microbial consortia for effective biochemical synthesis. Trends in Biotechnology, 41(11), 1430-1441.

Ji-Chao, Z. H. O. U., & Zhang, X. W. (2019). Akkermansia muciniphila: a promising target for the therapy of metabolic syndrome and related diseases. Chinese journal of natural medicines, 17(11), 835-841.

Keegan, K. P., Glass, E. M., & Meyer, F. (2016). MG-RAST, a metagenomics service for analysis of microbial community structure and function. Microbial environmental genomics (MEG), 207-233.

Keerthi, T. R., Narayanan, R., Sreelekshmi, K., & Honey Chandran, C. (2021). Immunity and gut microbiome: role of probiotics and prebiotics. Probiotic Bacteria and Postbiotic Metabolites: Role in Animal and Human Health, 61-83.

Keklik, G. (2023). Understanding evolutionary relationships and analysis methods through mega software. INTERNATIONAL JOURNAL OF NEW HORIZONS IN THE SCIENCES, 83-90.

Khan, M. F., & Wang, H. (2020). Environmental exposures and autoimmune diseases: contribution of gut microbiome. Frontiers in immunology, 10, 3094.

Kim, C. H. (2021). Control of lymphocyte functions by gut microbiota-derived short-chain fatty acids. Cellular & molecular immunology, 18(5), 1161-1171.

Kurilshikov, A., Medina-Gomez, C., Bacigalupe, R., Radjabzadeh, D., Wang, J., Demirkan, A., & Zhernakova, A. (2021). Large-scale association analyses identify host factors influencing human gut microbiome composition. Nature genetics, 53(2), 156-165.

Kviatcovsky, D., Zheng, D., & Elinav, E. (2021). Gut microbiome and its potential link to personalized nutrition. Current opinion in physiology, 22, 100439.

Lenti, M. V., Rugge, M., Lahner, E., Miceli, E., Toh, B. H., Genta, R. M., ... & Di Sabatino, A. (2020). Autoimmune gastritis. Nature Reviews Disease Primers, 6(1), 56.

Li, F., Ye, J., Shao, C., & Zhong, B. (2021). Compositional alterations of gut microbiota in nonalcoholic fatty liver disease patients: A systematic review and Meta-analysis. Lipids in Health and Disease, 20, 1-12.

Li, H., He, J., & Jia, W. (2016). The influence of gut microbiota on drug metabolism and toxicity. Expert opinion on drug metabolism & toxicology, 12(1), 31-40.

Li, H., Hsieh, K., Wong, P. K., Mach, K. E., Liao, J. C., & Wang, T. H. (2023). Single-cell pathogen diagnostics for combating antibiotic resistance. Nature Reviews Methods Primers, 3(1), 6.

Liu, P., Wang, Y., Yang, G., Zhang, Q., Meng, L., Xin, Y., & Jiang, X. (2021). The role of short-chain fatty acids in intestinal barrier function, inflammation, oxidative stress, and colonic carcinogenesis. Pharmacological research, 165, 105420.

Liu, X., Liu, Y., Liu, J., Zhang, H., Shan, C., Guo, Y., ... & Tang, M. (2024). Correlation between the gut microbiome and neurodegenerative diseases: a review of metagenomics evidence. Neural Regeneration Research, 19(4), 833-845.

Long, N., Qiao, Y., Xu, Z., Tu, J., & Lu, Z. (2020). Recent advances and application in whole‐genome multiple displacement amplification. Quantitative Biology, 8(4), 279-294.

Lu, J., Rincon, N., Wood, D. E., Breitwieser, F. P., Pockrandt, C., Langmead, B., ... & Steinegger, M. (2022). Metagenome analysis using the Kraken software suite. Nature protocols, 17(12), 2815-2839.

Lucarelli, G., Loizzo, D., Ferro, M., Rutigliano, M., Vartolomei, M. D., Cantiello, F., ... & Battaglia, M. (2019). Metabolomic profiling for the identification of novel diagnostic markers and therapeutic targets in prostate cancer: An update. Expert Review of Molecular Diagnostics, 19(5), 377-387.

Magne, F., Gotteland, M., Gauthier, L., Zazueta, A., Pesoa, S., Navarrete, P., & Balamurugan, R. (2020). The firmicutes/bacteroidetes ratio: a relevant marker of gut dysbiosis in obese patients?. Nutrients, 12(5), 1474.

Maranga, M., Szczerbiak, P., Bezshapkin, V., Gligorijevic, V., Chandler, C., Bonneau, R., ... & Kosciolek, T. (2023). Comprehensive functional annotation of metagenomes and microbial genomes using a deep learning-based method. Msystems, 8(2), e01178-22.

Margoob, M., Kouser, S., & Jan, N. (2024). Serotonin: The Link between Gut Microbiome and Brain. In Serotonin-Neurotransmitter and Hormone of Brain, Bowels and Blood. IntechOpen.

Matchado, M. S., Lauber, M., Reitmeier, S., Kacprowski, T., Baumbach, J., Haller, D., & List, M. (2021). Network analysis methods for studying microbial communities: A mini review. Computational and structural biotechnology journal, 19, 2687-2698.

May, K. S., & Den Hartigh, L. J. (2021). Modulation of adipocyte metabolism by microbial short-chain fatty acids. Nutrients, 13(10), 3666.

McElhinney, J. M., Catacutan, M. K., Mawart, A., Hasan, A., & Dias, J. (2022). Interfacing machine learning and microbial omics: a promising means to address environmental challenges. Frontiers in Microbiology, 13, 851450.

Medjaoui, I., Rahmani, B., Talhi, M., Mahammi, F. Z., Moghtit, F. Z., Mehtar, N., & Gaouar, S. B. S. (2016). Isolation and Characterization of Lactic Acid Bacteria from Human Milk and Newborn Feces. Journal of Pure & Applied Microbiology, 10(4).

Mitrea, L., Nemeş, S. A., Szabo, K., Teleky, B. E., & Vodnar, D. C. (2022). Guts imbalance imbalances the brain: a review of gut microbiota association with neurological and psychiatric disorders. Frontiers in medicine, 9, 813204.

Miyauchi, E., Shimokawa, C., Steimle, A., Desai, M. S., & Ohno, H. (2023). The impact of the gut microbiome on extra-intestinal autoimmune diseases. Nature Reviews Immunology, 23(1), 9-23.

Molinero, N., Ruiz, L., Sánchez, B., Margolles, A., & Delgado, S. (2019). Intestinal bacteria interplay with bile and cholesterol metabolism: implications on host physiology. Frontiers in physiology, 10, 185.

Molska, M., Mruczyk, K., Cisek-Woźniak, A., Prokopowicz, W., Szydełko, P., Jakuszewska, Z., ... & Trocholepsza, M. (2024). The Influence of Intestinal Microbiota on BDNF Levels. Nutrients, 16(17), 2891.

Moszak, M., Szulińska, M., & Bogdański, P. (2020). You are what you eat—the relationship between diet, microbiota, and metabolic disorders—a review. Nutrients, 12(4), 1096.

Mukherjee, A., D’Ugo, E., Giuseppetti, R., Magurano, F., & Cotter, P. D. (2023). Metagenomic approaches for understanding microbial communities in contaminated environments: Bioinformatic tools, case studies and future outlook. In Metagenomics to bioremediation (pp. 103-156). Academic Press.

Musazadeh, V., Zarezadeh, M., Faghfouri, A. H., Keramati, M., Jamilian, P., Jamilian, P., ... & Farnam, A. (2023). Probiotics as an effective therapeutic approach in alleviating depression symptoms: an umbrella meta-analysis. Critical Reviews in Food Science and Nutrition, 63(26), 8292-8300.

Musich, R., Cadle-Davidson, L., & Osier, M. V. (2021). Comparison of short-read sequence aligners indicates strengths and weaknesses for biologists to consider. Frontiers in Plant Science, 12, 657240.

Nguyen, T. M., Shafi, A., Nguyen, T., & Draghici, S. (2019). Identifying significantly impacted pathways: a comprehensive review and assessment. Genome biology, 20, 1-15.

Ojala, T., Häkkinen, A. E., Kankuri, E., & Kankainen, M. (2023). Current concepts, advances, and challenges in deciphering the human microbiota with metatranscriptomics. Trends in Genetics, 39(9), 686-702.

Olsson, L. M., Boulund, F., Nilsson, S., Khan, M. T., Gummesson, A., Fagerberg, L., ... & Bäckhed, F. (2022). Dynamics of the normal gut microbiota: a longitudinal one-year population study in Sweden. Cell host & microbe, 30(5), 726-739.

O'Riordan, K. J., Collins, M. K., Moloney, G. M., Knox, E. G., Aburto, M. R., Fülling, C., ... & Cryan, J. F. (2022). Short chain fatty acids: microbial metabolites for gut-brain axis signalling. Molecular and Cellular Endocrinology, 546, 111572.

Palma, A. (2024). Unveiling microglial heterogeneity from single-cell transcriptomics in neurodegenerative diseases. bioRxiv, 2024-08.

Payling, L., Fraser, K., Loveday, S. M., Sims, I., Roy, N., & McNabb, W. (2020). The effects of carbohydrate structure on the composition and functionality of the human gut microbiota. Trends in Food Science & Technology, 97, 233-248.

Peredo-Lovillo, A., Romero-Luna, H. E., & Jiménez-Fernández, M. (2020). Health promoting microbial metabolites produced by gut microbiota after prebiotics metabolism. Food Research International, 136, 109473.

Pérez-Rubio, P., Lottaz, C., & Engelmann, J. C. (2019). FastqPuri: high-performance preprocessing of RNA-seq data. BMC bioinformatics, 20, 1-11.

Pham, V. T., Dold, S., Rehman, A., Bird, J. K., & Steinert, R. E. (2021). Vitamins, the gut microbiome and gastrointestinal health in humans. Nutrition Research, 95, 35-53.

Rani, K., Kaur, G., & Ali, S. A. (2023). Probiotic-prebiotic therapeutic potential: a new horizon of microbial biotherapy to reduce female reproductive complications. PharmaNutrition, 24, 100342.

Rebersek, M. (2021). Gut microbiome and its role in colorectal cancer. BMC cancer, 21(1), 1325.

Reichart, N. J., Jay, Z. J., Krukenberg, V., Parker, A. E., Spietz, R. L., & Hatzenpichler, R. (2020). Activity-based cell sorting reveals responses of uncultured archaea and bacteria to substrate amendment. The ISME journal, 14(11), 2851-2861.

Rezende, E. S. V., Lima, G. C., & Naves, M. M. V. (2021). Dietary fibers as beneficial microbiota modulators: A proposed classification by prebiotic categories. Nutrition, 89, 111217.

Rifkin, R. F., Vikram, S., Ramond, J. B., Rey-Iglesia, A., Brand, T. B., Porraz, G., & Hansen, A. J. (2020). Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the ‘ancestral’sub-Saharan African intestinal microbiome. Microbiome, 8, 1-23.

Roopashree, K. M., & Naik, D. (2019). Advanced method of secondary metabolite extraction and quality analysis. Journal of Pharmacognosy and Phytochemistry, 8(3), 1829-1842.

Roy, S., & Dhaneshwar, S. (2023). Role of prebiotics, probiotics, and synbiotics in management of inflammatory bowel disease: Current perspectives. World Journal of Gastroenterology, 29(14), 2078.

Ruan, W., Engevik, M. A., Spinler, J. K., & Versalovic, J. (2020). Healthy human gastrointestinal microbiome: composition and function after a decade of exploration. Digestive diseases and sciences, 65, 695-705.

Sánchez-Quinto, A., Cerqueda-García, D., Falcón, L. I., Gaona, O., Martínez-Correa, S., Nieto, J., & G-Santoyo, I. (2020). Gut microbiome in children from indigenous and urban communities in México: Different subsistence models, different microbiomes. Microorganisms, 8(10), 1592.

Sarkar, A., Yoo, J. Y., Valeria Ozorio Dutra, S., Morgan, K. H., & Groer, M. (2021). The association between early-life gut microbiota and long-term health and diseases. Journal of clinical medicine, 10(3), 459.

Schalla, M. A., & Stengel, A. (2020). Effects of microbiome changes on endocrine ghrelin signaling–A systematic review. Peptides, 133, 170388.

Seo, H., & Song, H. Y. (2024). Perspectives on Microbiome Therapeutics in Infectious Diseases: A Comprehensive Approach beyond Immunology and Microbiology.

Sequeira, J. C., Rocha, M., Alves, M. M., & Salvador, A. F. (2022). UPIMAPI, reCOGnizer and KEGG Charter: Bioinformatics tools for functional annotation and visualization of (meta)-omics datasets. Computational and Structural Biotechnology Journal, 20, 1798-1810.

Shaffer, J. P., Carpenter, C. S., Martino, C., Salido, R. A., Minich, J. J., Bryant, M., ... & Knight, R. (2022). A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities. Biotechniques, 73(1), 34-46.

Shaheen, W. A., Quraishi, M. N., & Iqbal, T. H. (2022). Gut microbiome and autoimmune disorders. Clinical and Experimental Immunology, 209(2), 161-174.

Silva, R., Padovani, K., Góes, F., & Alves, R. (2021). geneRFinder: gene finding in distinct metagenomic data complexities. BMC bioinformatics, 22, 1-17.

Singh, R., Zogg, H., Wei, L., Bartlett, A., Ghoshal, U. C., Rajender, S., & Ro, S. (2021). Gut microbial dysbiosis in the pathogenesis of gastrointestinal dysmotility and metabolic disorders. Journal of neurogastroenterology and motility, 27(1), 19.

Sisk-Hackworth, L., Kelley, S. T., & Thackray, V. G. (2023). Sex, puberty, and the gut microbiome. Reproduction, 165(2), R61-R74.

Snigdha, S., Ha, K., Tsai, P., Dinan, T. G., Bartos, J. D., & Shahid, M. (2022). Probiotics: Potential novel therapeutics for microbiota-gut-brain axis dysfunction across gender and lifespan. Pharmacology & Therapeutics, 231, 107978.

Stark, R., Grzelak, M., & Hadfield, J. (2019). RNA sequencing: the teenage years. Nature Reviews Genetics, 20(11), 631-656.

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.

Subramanian, I., Verma, S., Kumar, S., Jere, A., & Anamika, K. (2020). Multi-omics data integration, interpretation, and its application. Bioinformatics and biology insights, 14, 1177932219899051.

Sun, Y., Zuo, T., Cheung, C. P., Gu, W., Wan, Y., Zhang, F., ... & Miao, Y. (2021). Population-level configurations of gut mycobiome across 6 ethnicities in urban and rural China. Gastroenterology, 160(1), 272-286.

Tan, S., Santolaya, J. L., Wright, T. F., Liu, Q., Fujikawa, T., Chi, S., ... & Burstein, E. (2024). Interaction between the gut microbiota and colonic enteroendocrine cells regulates host metabolism. Nature Metabolism, 1-16.

Thomson, C. A., Morgan, S. C., Ohland, C., & McCoy, K. D. (2022). From germ-free to wild: modulating microbiome complexity to understand mucosal immunology. Mucosal Immunology, 15(6), 1085-1094.

Ting, N. L. N., Lau, H. C. H., & Yu, J. (2022). Cancer pharmacomicrobiomics: targeting microbiota to optimise cancer therapy outcomes. Gut, 71(7), 1412-1425.

Toya, T., Corban, M. T., Marrietta, E., Horwath, I. E., Lerman, L. O., Murray, J. A., & Lerman, A. (2020). Coronary artery disease is associated with an altered gut microbiome composition. PloS one, 15(1), e0227147.

Uddin, T. M., Chakraborty, A. J., Khusro, A., Zidan, B. R. M., Mitra, S., Emran, T. B., ... & Koirala, N. (2021). Antibiotic resistance in microbes: History, mechanisms, therapeutic strategies and future prospects. Journal of infection and public health, 14(12), 1750-1766.

Um, C. Y., Peters, B. A., Choi, H. S., Oberstein, P., Beggs, D. B., Usyk, M., ... & Ahn, J. (2023). Grain, gluten, and dietary fiber intake influence gut microbial diversity: data from the food and microbiome longitudinal investigation. Cancer Research Communications, 3(1), 43-53.

Vallianou, N., Stratigou, T., Christodoulatos, G. S., Tsigalou, C., & Dalamaga, M. (2020). Probiotics, prebiotics, synbiotics, postbiotics, and obesity: current evidence, controversies, and perspectives. Current obesity reports, 9, 179-192.

Van der Hee, B., & Wells, J. M. (2021). Microbial regulation of host physiology by short-chain fatty acids. Trends in Microbiology, 29(8), 700-712.

Venneri, M. A., Franceschini, E., Sciarra, F., Rosato, E., D’ettorre, G., & Lenzi, A. (2022). Human genital tracts microbiota: dysbiosis crucial for infertility. Journal of Endocrinological Investigation, 45(6), 1151-1160.

Wang, B., Kong, Q., Li, X., Zhao, J., Zhang, H., Chen, W., & Wang, G. (2020). A high-fat diet increases gut microbiota biodiversity and energy expenditure due to nutrient difference. Nutrients, 12(10), 3197.

Wang, N., Chen, L., Yi, K., Zhang, B., Li, C., & Zhou, X. (2024). The effects of microbiota on reproductive health: A review. Critical Reviews in Food Science and Nutrition, 64(6), 1486-1507.

Wensel, C. R., Pluznick, J. L., Salzberg, S. L., & Sears, C. L. (2022). Next-generation sequencing: insights to advance clinical investigations of the microbiome. The Journal of clinical investigation, 132(7).

Wishart, D. S., Feunang, Y. D., Marcu, A., Guo, A. C., Liang, K., Vázquez-Fresno, R., ... & Scalbert, A. (2018). HMDB 4.0: the human metabolome database for 2018. Nucleic acids research, 46(D1), D608-D617.

Williams, N., Vella, R., Zhou, Y., Gao, H., Mass, K., Townsel, C., ... & Luo, G. (2022). Investigating the origin of the fetal gut and placenta microbiome in twins. The Journal of Maternal-Fetal & Neonatal Medicine, 35(25), 7025-7035.

Witkowski, M., Weeks, T. L., & Hazen, S. L. (2020). Gut microbiota and cardiovascular disease. Circulation research, 127(4), 553-570.

Wu, H., & Chiou, J. (2021). Potential benefits of probiotics and prebiotics for coronary heart disease and stroke. Nutrients, 13(8), 2878.

Xu, T., Wu, X., Liu, J., Sun, J., Wang, X., Fan, G., ... & Zhang, Y. (2022). The regulatory roles of dietary fibers on host health via gut microbiota-derived short chain fatty acids. Current Opinion in Pharmacology, 62, 36-42.

Yang, C., Chowdhury, D., Zhang, Z., Cheung, W. K., Lu, A., Bian, Z., & Zhang, L. (2021). A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data. Computational and Structural Biotechnology Journal, 19, 6301-6314.

Yang, Q., Liang, Q., Balakrishnan, B., Belobrajdic, D. P., Feng, Q. J., & Zhang, W. (2020). Role of dietary nutrients in the modulation of gut microbiota: a narrative review. Nutrients, 12(2), 381.

Yoo, J. Y., Groer, M., Dutra, S. V. O., Sarkar, A., & McSkimming, D. I. (2020). Gut microbiota and immune system interactions. Microorganisms, 8(10), 1587.

Yousefi, B., Melograna, F., Galazzo, G., van Best, N., Mommers, M., Penders, J., ... & Van Steen, K. (2023). Capturing the dynamics of microbial interactions through individual-specific networks. Frontiers in microbiology, 14, 1170391.

Yu, Y., Wen, H., Li, S., Cao, H., Li, X., Ma, Z., ... & Huang, S. (2022). Emerging microfluidic technologies for microbiome research. Frontiers in Microbiology, 13, 906979.

Zeki, Ö. C., Eylem, C. C., Reçber, T., Kır, S., & Nemutlu, E. (2020). Integration of GC–MS and LC–MS for untargeted metabolomics profiling. Journal of Pharmaceutical and Biomedical Analysis, 190, 113509.

Zhang, Y., Chen, H., Lu, M., Cai, J., Lu, B., Luo, C., & Dai, M. (2022). Habitual diet pattern associations with gut microbiome diversity and composition: results from a Chinese adult cohort. Nutrients, 14(13), 2639.

Zhang, W., Qu, W., Wang, H., & Yan, H. (2021). Antidepressants fluoxetine and amitriptyline induce alterations in intestinal microbiota and gut microbiome function in rats exposed to chronic unpredictable mild stress. Translational psychiatry, 11(1), 131.

Zhang, Z. H., Jhaveri, D. J., Marshall, V. M., Bauer, D. C., Edson, J., Narayanan, R. K. & Zhao, Q. Y. (2014). A comparative study of techniques for differential expression analysis on RNA-Seq data. PloS one, 9(8), e103207.

Zheng, D., Liwinski, T., & Elinav, E. (2020). Interaction between microbiota and immunity in health and disease. Cell research, 30(6), 492-506.

Zikou, E., Koliaki, C., & Makrilakis, K. (2024). The Role of Fecal Microbiota Transplantation (FMT) in the Management of Metabolic Diseases in Humans: A Narrative Review. Biomedicines, 12(8), 1871.

Downloads

Published

01/13/2025

How to Cite

GAOUAR, S. B. S. (2025). The Gut Microbiome and Human Health: Insights from Recent Research. Genetics & Biodiversity Journal, 9(1). https://doi.org/10.46325/gabj.v9i1.431

Issue

Section

Review Article

Most read articles by the same author(s)

1 2 3 4 5 6 > >>