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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, 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; however, the term human metagenome has the same meaning.
Gut microbiota, gut microbiome, or gut flora are the microorganisms, including bacteria, archaea, fungi, and viruses, that live in the digestive tracts of animals. The gastrointestinal metagenome is the aggregate of all the genomes of the gut microbiota. The gut is the main location of the human microbiome. The gut microbiota has broad impacts, including effects on colonization, resistance to pathogens, maintaining the intestinal epithelium, metabolizing dietary and pharmaceutical compounds, controlling immune function, and even behavior through the gut–brain axis.
Skin flora, also called skin microbiota, refers to microbiota that reside on the skin, typically human skin.
The Human Microbiome Project (HMP) was a United States National Institutes of Health (NIH) research initiative to improve understanding of the microbiota involved in human health and disease. Launched in 2007, the first phase (HMP1) focused on identifying and characterizing human microbiota. The second phase, known as the Integrative Human Microbiome Project (iHMP) launched in 2014 with the aim of generating resources to characterize the microbiome and elucidating the roles of microbes in health and disease states. The program received $170 million in funding by the NIH Common Fund from 2007 to 2016.
Microbiota are the range of microorganisms that may be commensal, mutualistic, or pathogenic found in and on all multicellular organisms, including plants. Microbiota include bacteria, archaea, protists, fungi, and viruses, and have been found to be crucial for immunologic, hormonal, and metabolic homeostasis of their host.
Bacterial phyla constitute the major lineages of the domain Bacteria. While the exact definition of a bacterial phylum is debated, a popular definition is that a bacterial phylum is a monophyletic lineage of bacteria whose 16S rRNA genes share a pairwise sequence identity of ~75% or less with those of the members of other bacterial phyla.
Microbial phylogenetics is the study of the manner in which various groups of microorganisms are genetically related. This helps to trace their evolution. To study these relationships biologists rely on comparative genomics, as physiology and comparative anatomy are not possible methods.
A microbiome is the community of microorganisms that can usually be found living together in any given habitat. It was defined more precisely in 1988 by Whipps et al. as "a characteristic microbial community occupying a reasonably well-defined habitat which has distinct physio-chemical properties. The term thus not only refers to the microorganisms involved but also encompasses their theatre of activity". In 2020, an international panel of experts published the outcome of their discussions on the definition of the microbiome. They proposed a definition of the microbiome based on a revival of the "compact, clear, and comprehensive description of the term" as originally provided by Whipps et al., but supplemented with two explanatory paragraphs. The first explanatory paragraph pronounces the dynamic character of the microbiome, and the second explanatory paragraph clearly separates the term microbiota from the term microbiome.
Metatranscriptomics is the set of techniques used to study gene expression of microbes within natural environments, i.e., the metatranscriptome.
The uterine microbiome refers to the community of commensal, nonpathogenic microorganisms—including bacteria, viruses, and yeasts/fungi—present in a healthy uterus, as well as in the amniotic fluid and endometrium. These microorganisms coexist in a specific environment within the uterus, playing a vital role in maintaining reproductive health. In the past, the uterus was believed to be a sterile environment, free of any microbial life. Recent advancements in microbiological research, particularly the improvement of 16S rRNA gene sequencing techniques, have challenged this long-held belief. These advanced techniques have made it possible to detect bacteria and other microorganisms present in very low numbers. Using this procedure that allows the detection of bacteria that cannot be cultured outside the body, studies of microbiota present in the uterus are expected to increase.
Microbiomes of the built environment is a field of inquiry into the communities of microorganisms that live in human constructed environments like houses, cars and water pipes. It is also sometimes referred to as microbiology of the built environment.
Hologenomics is the omics study of hologenomes. A hologenome is the whole set of genomes of a holobiont, an organism together with all co-habitating microbes, other life forms, and viruses. While the term hologenome originated from the hologenome theory of evolution, which postulates that natural selection occurs on the holobiont level, hologenomics uses an integrative framework to investigate interactions between the host and its associated species. Examples include gut microbe or viral genomes linked to human or animal genomes for host-microbe interaction research. Hologenomics approaches have also been used to explain genetic diversity in the microbial communities of marine sponges.
Pharmacomicrobiomics, proposed by Prof. Marco Candela for the ERC-2009-StG project call, and publicly coined for the first time in 2010 by Rizkallah et al., is defined as the effect of microbiome variations on drug disposition, action, and toxicity. Pharmacomicrobiomics is concerned with the interaction between xenobiotics, or foreign compounds, and the gut microbiome. It is estimated that over 100 trillion prokaryotes representing more than 1000 species reside in the gut. Within the gut, microbes help modulate developmental, immunological and nutrition host functions. The aggregate genome of microbes extends the metabolic capabilities of humans, allowing them to capture nutrients from diverse sources. Namely, through the secretion of enzymes that assist in the metabolism of chemicals foreign to the body, modification of liver and intestinal enzymes, and modulation of the expression of human metabolic genes, microbes can significantly impact the ingestion of xenobiotics.
Halomonas meridiana is a bacterial species discovered in 1990 in the hypersaline lakes of Vestfold Hills, Antarctica.
TM7x, also known as Nanosynbacter lyticus type strain TM7x HMT 952. is a phylotype of one of the most enigmatic phyla, Candidatus Saccharibacteria, formerly candidate phylum TM7. It is the only member of the candidate phylum that has been cultivated successfully from the human oral cavity, and stably maintained in vitro. and serves as a crucial paradigm. of the newly described Candidate Phyla Radiation (CPR). The cultivated oral taxon is designated as Saccharibacteria oral taxon TM7x. TM7x has a unique lifestyle in comparison to other bacteria that are associated with humans. It is an obligate epibiont parasite, or an "epiparasite", growing on the surface of its host bacterial species Actinomyces odontolyticus subspecies actinosynbacter strain XH001, which is referred to as the "basibiont". Actinomyces species are one of the early microbial colonizers in the oral cavity. Together, they exhibit parasitic epibiont symbiosis.
Culturomics is the high-throughput cell culture of bacteria that aims to comprehensively identify strains or species in samples obtained from tissues such as the human gut or from the environment. This approach was conceived as an alternative, complementary method to metagenomics, which relies on the presence of homologous sequences to identify new bacteria. Due to the limited phylogenetic information available on bacteria, metagenomic data generally contains large amounts of "microbial dark matter", sequences of unknown origin. Culturomics provides some of the missing gaps with the added advantage of enabling the functional study of the generated cultures. Its main drawback is that many bacterial species remain effectively uncultivable until their growth conditions are better understood. Therefore, optimization of the culturomics approach has been done by improving culture conditions.
A. Murat Eren (Meren) is a computer scientist known for his work on microbial ecology and developing novel, open-source, computational tools for analysis of large data sets.
Ornithobacterium is a genus of Gram-negative, microaerophilic, rod-shaped bacteria from the family Weeksellaceae. It comprises two known species, O. hominis and O. rhinotracheale. Both species inhabit the respiratory tract: O. hominis is found in the human nasopharynx and O. rhinotracheale in the trachea of wild and domesticated birds
Bile salt hydrolases (BSH) are microbial enzymes that deconjugate primary bile acids. They catalyze the first step of bile acid metabolism and maintain the bile acid pool for further modification by the microbiota. BSH enzymes play a role in a range of host and microbe functions including host physiology, immunity, and protection from pathogens.
The poultry microbiome is an understudied, yet extremely impactful part of the poultry industry. Poultry is defined as any avian species used for production purposes such as food or down feathers. The United States consumes more poultry, specifically broiler meat, than any other type of protein. Worldwide, poultry makes up 33% of consumed meat. This makes poultry extremely valuable and the impact of the poultry microbiome on health and production even more valuable. Antonie van Leeuwenhoek was the first to notice microbes inside animals through stool samples giving light to further research into the gut microbiome. His discovery lead to the ever evolving study of the microbiota and microbiome. The microbiota is the entirety of living organisms including bacteria, viruses, fungi, and archaea in an environment. The microbiome is the combination of the microbiota and the additional activities in that system including metabolites and chemicals in a habitat. Much of the work done to characterize the poultry microbiome has been accomplished over the past decade and was done through the use of 16s rRNA sequencing.
References
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- ↑ Kwambana-Adams, B. (2017). "Rapid replacement by non-vaccine pneumococcal serotypes may mitigate the impact of the pneumococcal conjugate vaccine on nasopharyngeal bacterial ecology". Scientific Reports. 7 (1): 8127. Bibcode:2017NatSR...7.8127K. doi:10.1038/s41598-017-08717-0. PMC 5557800 . PMID 28811633.
- ↑ Vonaesch, P. (2018). "Stunted childhood growth is associated with decompartmentalization of the gastrointestinal tract and overgrowth of oropharyngeal taxa". Proc Natl Acad Sci USA. 115 (36): E8489–E8498. Bibcode:2018PNAS..115E8489V. doi: 10.1073/pnas.1806573115 . PMC 6130352 . PMID 30126990.
- ↑ Feazel, L.M. (2015). "Effects of Vaccination with 10-Valent Pneumococcal Non-Typeable Haemophilus influenza Protein D Conjugate Vaccine (PHiD-CV) on the Nasopharyngeal Microbiome of Kenyan Toddlers". PLOS ONE. 10 (6): e0128064. Bibcode:2015PLoSO..1028064F. doi: 10.1371/journal.pone.0128064 . PMC 4471099 . PMID 26083474.
- ↑ Salter, S.J. (2017). "A longitudinal study of the infant nasopharyngeal microbiota: The effects of age, illness and antibiotic use in a cohort of South East Asian children". PLOS Neglected Tropical Diseases. 11 (10): e0005975. doi: 10.1371/journal.pntd.0005975 . PMC 5638608 . PMID 28968382.
- ↑ Clemente, J.C. (2015). "The microbiome of uncontacted Amerindians". Science Advances. 1 (3): e1500183. Bibcode:2015SciA....1E0183C. doi:10.1126/sciadv.1500183. PMC 4517851 . PMID 26229982.
- ↑ Marsh, R.L. (2016). "The microbiota in bronchoalveolar lavage from young children with chronic lung disease includes taxa present in both the oropharynx and nasopharynx". Microbiome. 4 (1): 37. doi: 10.1186/s40168-016-0182-1 . PMC 4936249 . PMID 27388563.
- ↑ Boelsen, L.K. (2019). "The association between pneumococcal vaccination, ethnicity, and the nasopharyngeal microbiota of children in Fiji". Microbiome. 7 (1): 106. doi: 10.1186/s40168-019-0716-4 . PMC 6636143 . PMID 31311598.
- ↑ "Reference sequence for Ca. O. hominis strain OH-22803, 16S rRNA gene". www.ncbi.nlm.nih.gov. 29 August 2018.
- ↑ Lawrence, K.A. (2019). "Method for culturing Candidatus Ornithobacterium hominis". Journal of Microbial Methods. 159: 157–160. doi:10.1016/j.mimet.2019.03.006. PMID 30871998. S2CID 78093117.