Human microbiome

Not to be confused with Microbiome.

Graphic depicting the human skin microbiota, with relative prevalences of various classes of bacteria

The human microbiome is the aggregate of all microbiota that reside on or within human tissues and biofluids along with the corresponding anatomical sites in which they reside,[1][2] including the gastrointestinal tract, skin, mammary glands, seminal fluid, uterus, ovarian follicles, lung, saliva, oral mucosa, conjunctiva, and the biliary tract. Types of human microbiota include bacteria, archaea, fungi, protists, and viruses. Though micro-animals can also live on the human body, they are typically excluded from this definition. In the context of genomics, the term human microbiome is sometimes used to refer to the collective genomes of resident microorganisms;[3] however, the term human metagenome has the same meaning.[1]

The human body hosts many microorganisms, with approximately the same order of magnitude of non-human cells as human cells.[4] Some microorganisms that humans host are commensal, meaning they co-exist without harming humans; others have a mutualistic relationship with their human hosts.[3]: 700 [5] Conversely, some non-pathogenic microorganisms can harm human hosts via the metabolites they produce, like trimethylamine, which the human body converts to trimethylamine N-oxide via FMO3-mediated oxidation.[6][7] Certain microorganisms perform tasks that are known to be useful to the human host, but the role of most of them is not well understood. Those that are expected to be present, and that under normal circumstances do not cause disease, are sometimes deemed normal flora or normal microbiota.[3]

During early life, the establishment of a diverse and balanced human microbiota plays a critical role in shaping an individual's long-term health.[8] Studies have shown that the composition of the gut microbiota during infancy is influenced by various factors, including mode of delivery, breastfeeding, and exposure to environmental factors.[9] There are several beneficial species of bacteria and potential probiotics present in breast milk.[10] Research has highlighted the beneficial effects of a healthy microbiota in early life, such as the promotion of immune system development, regulation of metabolism, and protection against pathogenic microorganisms.[11] Understanding the complex interplay between the human microbiota and early life health is crucial for developing interventions and strategies to support optimal microbiota development and improve overall health outcomes in individuals.[12]

The Human Microbiome Project (HMP) took on the project of sequencing the genome of the human microbiota, focusing particularly on the microbiota that normally inhabit the skin, mouth, nose, digestive tract, and vagina.[3] It reached a milestone in 2012 when it published its initial results.[13]

  1. ^ a b Marchesi JR, Ravel J (2015). "The vocabulary of microbiome research: a proposal". Microbiome. 3: 31. doi:10.1186/s40168-015-0094-5. PMC 4520061. PMID 26229597.
    Microbiome
    This term refers to the entire habitat, including the microorganisms (bacteria, archaea, lower and higher eurkaryotes, and viruses), their genomes (i.e., genes), and the surrounding environmental conditions. This definition is based on that of "biome," the biotic and abiotic factors of given environments. Others in the field limit the definition of microbiome to the collection of genes and genomes of members of a microbiota. It is argued that this is the definition of metagenome, which combined with the environment constitutes the microbiome.
  2. ^ Mousa, Walaa K.; Chehadeh, Fadia; Husband, Shannon (2022). "Recent Advances in Understanding the Structure and Function of the Human Microbiome". Frontiers in Microbiology. 13. doi:10.3389/fmicb.2022.825338. PMC 8851206. PMID 35185849.
  3. ^ a b c d Sherwood L, Willey J, Woolverton C (2013). Prescott's Microbiology (9th ed.). New York: McGraw Hill. pp. 713–721. ISBN 9780073402406. OCLC 886600661.
  4. ^ Sender R, Fuchs S, Milo R (January 2016). "Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans". Cell. 164 (3): 337–40. doi:10.1016/j.cell.2016.01.013. PMID 26824647.
  5. ^ Quigley EM (September 2013). "Gut bacteria in health and disease". Gastroenterology & Hepatology. 9 (9): 560–9. PMC 3983973. PMID 24729765.
  6. ^ Falony G, Vieira-Silva S, Raes J (2015). "Microbiology Meets Big Data: The Case of Gut Microbiota-Derived Trimethylamine". Annual Review of Microbiology. 69: 305–21. doi:10.1146/annurev-micro-091014-104422. PMID 26274026. we review literature on trimethylamine (TMA), a microbiota-generated metabolite linked to atherosclerosis development.
  7. ^ Gaci N, Borrel G, Tottey W, O'Toole PW, Brugère JF (November 2014). "Archaea and the human gut: new beginning of an old story". World Journal of Gastroenterology. 20 (43): 16062–78. doi:10.3748/wjg.v20.i43.16062. PMC 4239492. PMID 25473158. Trimethylamine is exclusively a microbiota-derived product of nutrients (lecithin, choline, TMAO, L-carnitine) from normal diet, from which seems originate two diseases, trimethylaminuria (or Fish-Odor Syndrome) and cardiovascular disease through the proatherogenic property of its oxidized liver-derived form.
  8. ^ Smith A, et al. (2019). "The role of the microbiota in the development of allergies and asthma." Current Allergy and Asthma Reports, 19(8), 38.
  9. ^ Jackson KD, et al. (2016). "Gut microbiota associations with common diseases and prescription medications in a population-based cohort." Nature Communications, 7, 11622.
  10. ^ Yi DY, Kim SY (September 2021). "Human Breast Milk Composition and Function in Human Health: From Nutritional Components to Microbiome and MicroRNAs". Nutrients. 13 (9): 3094. doi:10.3390/nu13093094. PMC 8471419. PMID 34578971.
  11. ^ Yatsunenko T, et al. (2012). "Human gut microbiome viewed across age and geography." Nature, 486(7402), 222-227.
  12. ^ Sjögren YM, et al. (2009). "Influence of early gut microbiota on the maturation of childhood mucosal and systemic immune responses." Clinical and Experimental Allergy, 39(12), 1842-1851.
  13. ^ "NIH Human Microbiome Project defines normal bacterial makeup of the body". NIH News. 13 June 2012.