The human gastroinstestinal tract microbiota in health – current knowledge summary
DOI:
https://doi.org/10.12775/JEHS.2022.12.10.005Keywords
human microbiota, gut microbiota, gastrointestinal tract microbiota, health, homeostasis, gut health, metagenomic studies, 16S rRNA sequencingAbstract
The health of the human body is influenced by many external and internal factors, but one of the most important of them is the rich microbiota of the human body. The number of microorganism cells inhabiting the human body exceeds the number of cells that make up the human body. Several different ecosystems coexist in the human body, incl. microbiota of the skin, eye, respiratory tract, urogenital tract and gastrointestinal tract. The composition of microbiota in various parts of the human body, as well as in various parts of a given system or organ, differs significantly from one another. Detailed knowledge of the composition of the human microbiota, as well as its functions for the host organism, is a starting point for further considerations on the meaning of dysbiosis, i.e. changes in the composition of the microbiota, for changing the functioning of the microbiota-host relationship and the development of disease states. It seems that further scientific research on this topic will lead to the recognition of microbiota as a marker and diagnostic tool, and possibly a past therapeutic target for some diseases. This publication attempts to organize and summarize basic information on the human gastrointestinal tract microbiota (GIT microbiota) in health.
References
Panasiuk, A. (2019). Kowalińska J. Mikrobiota przewodu pokarmowego. Wydawnictwo Lekarskie PZWL, Warszawa.
D’Argenio, V., & Salvatore, F. (2015). The role of the gut microbiome in the healthy adult status. Clinica chimica acta, 451, 97-102.
Van den Akker, C. H. P., van Goudoever, J. B., Szajewska, H., Embleton, N. D., Hojsak, I., Reid, D., & Shamir, R. (2018). ESPGHAN working Group for Probiotics, Prebiotics & Committee on nutrition. Probiotics for preterm infants: a strain-specific systematic review and network meta-analysis. J Pediatr Gastroenterol Nutr, 67(1), 103-22.
Turnbaugh, P. J., Ley, R. E., Hamady, M., Fraser-Liggett, C. M., Knight, R., & Gordon, J. I. (2007). The human microbiome project. Nature, 449(7164), 804-810.
Panasiuk, A. (2018). Choroby infekcyjne przewodu pokarmowego. Wydawnictwo Lekarskie PZWL.
Yamashita, T. (2017). Intestinal immunity and gut microbiota in atherogenesis. Journal of atherosclerosis and thrombosis, 24(2), 110-119.
Yamashita, Y., & Takeshita, T. (2017). The oral microbiome and human health. Journal of oral science, 59(2), 201-206.
Walsh, C. J., Guinane, C. M., O’Toole, P. W., & Cotter, P. D. (2014). Beneficial modulation of the gut microbiota. FEBS letters, 588(22), 4120-4130.
Palmer, C., Bik, E. M., DiGiulio, D. B., Relman, D. A., & Brown, P. O. (2007). Development of the human infant intestinal microbiota. PLoS biology, 5(7), e177.
Koenig, J. E., Spor, A., Scalfone, N., Fricker, A. D., Stombaugh, J., Knight, R., ... & Ley, R. E. (2011). Succession of microbial consortia in the developing infant gut microbiome. Proceedings of the National Academy of Sciences, 108(supplement_1), 4578-4585.
Sharon, I., Morowitz, M. J., Thomas, B. C., Costello, E. K., Relman, D. A., & Banfield, J. F. (2013). Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization. Genome research, 23(1), 111-120.
Stewart, C. J., Marrs, E. C., Nelson, A., Lanyon, C., Perry, J. D., Embleton, N. D., ... & Berrington, J. E. (2013). Development of the preterm gut microbiome in twins at risk of necrotising enterocolitis and sepsis. PloS one, 8(8), e73465.
Turnbaugh, P. J., & Gordon, J. I. (2009). The core gut microbiome, energy balance and obesity. The Journal of physiology, 587(17), 4153-4158.
Flint, H. J., Scott, K. P., Duncan, S. H., Louis, P., & Forano, E. (2012). Microbial degradation of complex carbohydrates in the gut. Gut microbes, 3(4), 289-306.
Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., ... & Wang, J. (2010). A human gut microbial gene catalogue established by metagenomic sequencing. nature, 464(7285), 59-65.
Sekirov, I., Russell, S. L., Antunes, L. C. M., & Finlay, B. B. (2010). Gut microbiota in health and disease. Physiological reviews.
Cryan, J. F., & O’Mahony, S. M. (2011). The microbiome‐gut‐brain axis: from bowel to behavior. Neurogastroenterology & Motility, 23(3), 187-192.
O'Hara, A. M., & Shanahan, F. (2006). The gut flora as a forgotten organ. EMBO reports, 7(7), 688-693.
Abubucker, S., Segata, N., Goll, J., Schubert, A. M., Izard, J., Cantarel, B. L., ... & Huttenhower, C. (2012). Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS computational biology, 8(6), e1002358.
Walker, A. W., Duncan, S. H., Louis, P., & Flint, H. J. (2014). Phylogeny, culturing, and metagenomics of the human gut microbiota. Trends in microbiology, 22(5), 267-274.
Li, L., Mendis, N., Trigui, H., Oliver, J. D., & Faucher, S. P. (2014). The importance of the viable but non-culturable state in human bacterial pathogens. Frontiers in microbiology, 5, 258.
A framework for human microbiome research. nature, 2012, 486.7402: 215-221.
Gevers, D., Knight, R., Petrosino, J. F., Huang, K., McGuire, A. L., Birren, B. W., ... & Huttenhower, C. (2012). The Human Microbiome Project: a community resource for the healthy human microbiome.
Morgan, J. L., Darling, A. E., & Eisen, J. A. (2010). Metagenomic sequencing of an in vitro-simulated microbial community. PloS one, 5(4), e10209.
Woese, C. R., Fox, G. E., Zablen, L., Uchida, T., Bonen, L., Pechman, K., ... & Stahl, D. (1975). Conservation of primary structure in 16S ribosomal RNA. Nature, 254(5495), 83-86.
Jumpstart Consortium Human Microbiome Project Data Generation Working Group. (2012). Evaluation of 16S rDNA-based community profiling for human microbiome research. PloS one, 7(6), e39315.
Lee, C. K., Herbold, C. W., Polson, S. W., Wommack, K. E., Williamson, S. J., McDonald, I. R., & Cary, S. C. (2012). Groundtruthing next-gen sequencing for microbial ecology–biases and errors in community structure estimates from PCR amplicon pyrosequencing.
Giannoukos, G., Ciulla, D. M., Huang, K., Haas, B. J., Izard, J., Levin, J. Z., ... & Gnirke, A. (2012). Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes. Genome biology, 13(3), 1-13.
Morgan, X. C., & Huttenhower, C. (2014). Meta'omic analytic techniques for studying the intestinal microbiome. Gastroenterology, 146(6), 1437-1448.
Logares, R., Haverkamp, T. H., Kumar, S., Lanzén, A., Nederbragt, A. J., Quince, C., & Kauserud, H. (2012). Environmental microbiology through the lens of high-throughput DNA sequencing: synopsis of current platforms and bioinformatics approaches. Journal of microbiological methods, 91(1), 106-113.
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., ... & Knight, R. (2010). QIIME allows analysis of high-throughput community sequencing data. Nature methods, 7(5), 335-336.
Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., ... & Weber, C. F. (2009). Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and environmental microbiology, 75(23), 7537-7541.
Meyer, F., Paarmann, D., D'Souza, M., Olson, R., Glass, E. M., Kubal, M., ... & Edwards, R. (2008). The metagenomics RAST server–a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC bioinformatics, 9(1), 1-8.
Větrovský, T., & Baldrian, P. (2013). The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses. PloS one, 8(2), e57923.
Brady, A., & Salzberg, S. L. (2009). Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nature methods, 6(9), 673-676.
Boisvert, S., Raymond, F., Godzaridis, É., Laviolette, F., & Corbeil, J. (2012). Ray Meta: scalable de novo metagenome assembly and profiling. Genome biology, 13(12), 1-13.
Segata, N., Börnigen, D., Morgan, X. C., & Huttenhower, C. (2013). PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nature communications, 4(1), 1-11.
Leimena, M. M., Ramiro-Garcia, J., Davids, M., van den Bogert, B., Smidt, H., Smid, E. J., ... & Kleerebezem, M. (2013). A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets. BMC genomics, 14(1), 1-14.
Trapnell, C., Roberts, A., Goff, L., Pertea, G., Kim, D., Kelley, D. R., ... & Pachter, L. (2012). Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature protocols, 7(3), 562-578.
Mandlik, A., Livny, J., Robins, W. P., Ritchie, J. M., Mekalanos, J. J., & Waldor, M. K. (2011). RNA-Seq-based monitoring of infection-linked changes in Vibrio cholerae gene expression. Cell host & microbe, 10(2), 165-174.
Yoo, Y. J., Perinpanayagam, H., Oh, S., Kim, A. R., Han, S. H., & Kum, K. Y. (2019). Endodontic biofilms: contemporary and future treatment options. Restorative dentistry & endodontics, 44(1).
Lim, Y., Totsika, M., Morrison, M., & Punyadeera, C. (2017). Oral microbiome: a new biomarker reservoir for oral and oropharyngeal cancers. Theranostics, 7(17), 4313.
Marsh, P. D. (2018). In sickness and in health—what does the oral microbiome mean to us? An ecological perspective. Advances in dental research, 29(1), 60-65.
Verma, D., Garg, P. K., & Dubey, A. K. (2018). Insights into the human oral microbiome. Archives of microbiology, 200(4), 525-540.
Baker, J. L., Bor, B., Agnello, M., Shi, W., & He, X. (2017). Ecology of the oral microbiome: beyond bacteria. Trends in microbiology, 25(5), 362-374.
Sultan, A. S., Kong, E. F., Rizk, A. M., & Jabra-Rizk, M. A. (2018). The oral microbiome: A Lesson in coexistence. PLoS pathogens, 14(1), e1006719.
Di Pilato, V., Freschi, G., Ringressi, M. N., Pallecchi, L., Rossolini, G. M., & Bechi, P. (2016). The esophageal microbiota in health and disease. Annals of the New York Academy of Sciences, 1381(1), 21-33.
Wurm, P., Dörner, E., Kremer, C., Spranger, J., Maddox, C., Halwachs, B., ... & Fricke, W. F. (2018). Qualitative and quantitative DNA-and RNA-based analysis of the bacterial stomach microbiota in humans, mice, and gerbils. Msystems, 3(6), e00262-18.
Yu, G., Torres, J., Hu, N., Medrano-Guzman, R., Herrera-Goepfert, R., Humphrys, M. S., ... & Goldstein, A. M. (2017). Molecular characterization of the human stomach microbiota in gastric cancer patients. Frontiers in cellular and infection microbiology, 7, 302.
Freedberg, D. E., Lebwohl, B., & Abrams, J. A. (2014). The impact of proton pump inhibitors on the human gastrointestinal microbiome. Clinics in laboratory medicine, 34(4), 771-785.
Walker, M. M., & Talley, N. J. (2014). bacteria and pathogenesis of disease in the upper gastrointestinal tract–beyond the era of Helicobacter pylori. Alimentary pharmacology & therapeutics, 39(8), 767-779.
Dias-Jácome, E., Libânio, D., Borges-Canha, M., Galaghar, A., & Pimentel-Nunes, P. (2016). Gastric microbiota and carcinogenesis: the role of non-Helicobacter pylori bacteria: a systematic review. Revista Española de Enfermedades Digestivas, 108(9), 530-540.
Marteau, P., Lepage, P., Mangin, I., Suau, A., Dore, J., Pochart, P., & Seksik, P. (2004). Gut flora and inflammatory bowel disease. Alimentary pharmacology & therapeutics, 20, 18-23.
Swidsinski, A., Loening-Baucke, V., Kirsch, S., & Doerffel, Y. (2010). Functional biostructure of colonic microbiota (central fermenting area, germinal stock area and separating mucus layer) in healthy subjects and patients with diarrhea treated with Saccharomyces boulardii. Gastroentérologie clinique et biologique, 34, S79-S92.
Zhernakova, A., Kurilshikov, A., Bonder, M. J., Tigchelaar, E. F., Schirmer, M., Vatanen, T., ... & Fu, J. (2016). Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science, 352(6285), 565-569.
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