Human microbiome
The human microbiome is the aggregate of all
The human body hosts many microorganisms, with approximately the same
During early life, the establishment of a diverse and balanced human microbiota plays a critical role in shaping an individual's long-term health.[7] 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.[8] There are several beneficial species of bacteria and potential probiotics present in breast milk.[9] 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.[10] 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.[11]
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.[2] It reached a milestone in 2012 when it published its initial results.[12]
Terminology
million years ago) |
Though widely known as flora or microflora, this is a
Relative numbers
The number of
Study
The problem of elucidating the human microbiome is essentially identifying the members of a microbial community, which includes bacteria, eukaryotes, and viruses.
Aside from simply elucidating the composition of the human microbiome, one of the major questions involving the human microbiome is whether there is a "core", that is, whether there is a subset of the community that is shared among most humans.[23][24] If there is a core, then it would be possible to associate certain community compositions with disease states, which is one of the goals of the HMP. It is known that the human microbiome (such as the gut microbiota) is highly variable both within a single subject and among different individuals, a phenomenon which is also observed in mice.[4]
On 13 June 2012, a major milestone of the HMP was announced by the
Analysis after the processing
The statistical analysis is essential to validate the obtained results (
Once a metagenome is assembled, it is possible to infer the functional potential of the microbiome. The computational challenges for this type of analysis are greater than for single genomes, because usually metagenomes assemblers have poorer quality, and many recovered
Marker gene analysis
It is a technique that exploits
Marker gene analysis can be influenced by the primer choice; in this kind of analysis, it is desirable to use a well-validated protocol (such as the one used in the
Another important step in the analysis is to assign a taxonomic name to microbial sequences in the data. This can be done using machine learning approaches that can reach an accuracy at genus-level of about 80%. Other popular analysis packages provide support for taxonomic classification using exact matches to reference databases and should provide greater specificity, but poor sensitivity. Unclassified microorganism should be further checked for organelle sequences.[30]
Phylogenetic analysis
Many methods that exploit phylogenetic inference use the 16SRNA gene for Archea and Bacteria and the 18SRNA gene for Eukaryotes. Phylogenetic comparative methods (PCS) are based on the comparison of multiple traits among microorganisms; the principle is: the closely they are related, the higher number of traits they share. Usually PCS are coupled with phylogenetic generalized least square (PGLS) or other statistical analysis to get more significant results. Ancestral state reconstruction is used in microbiome studies to impute trait values for taxa whose traits are unknown. This is commonly performed with PICRUSt, which relies on available databases. Phylogenetic variables are chosen by researchers according to the type of study: through the selection of some variables with significant biological informations, it is possible to reduce the dimension of the data to analyse.[31]
Phylogenetic aware distance is usually performed with
Ecological Network analysis
Microbial communities develop in a very complex dynamic which can be viewed and analyzed as an ecosystem. The ecological interactions between microbes govern its change, equilibrium and stability, and can be represented by a population dynamic model.[32] The ongoing study of ecological features of the microbiome is growing rapidly and allows to understand the fundamental properties of the microbiome. Understanding the underlying rules of microbial community could help with treating diseases related to unstable microbial communities. A very basic question is if different humans, who share different microbial communities, have the same underlying microbial dynamics.[33] Increasing evidence and indications have found that the dynamics is indeed universal.[34] This question is a basic step that will allow scientists to develop treatment strategies, based on the complex dynamics of human microbial communities. There are more important properties on which considerations should be taken into account for developing interventions strategies for controlling the human microbial dynamics.[35] Controlling the microbial communities could result in solving very bad and harmful diseases.
Types
Bacteria
Populations of microbes (such as
The Human Microbiome Project found that individuals host thousands of bacterial types, different body sites having their own distinctive communities. Skin and vaginal sites showed smaller diversity than the mouth and gut, these showing the greatest richness. The bacterial makeup for a given site on a body varies from person to person, not only in type, but also in abundance. Bacteria of the same species found throughout the mouth are of multiple subtypes, preferring to inhabit distinctly different locations in the mouth. Even the enterotypes in the human gut, previously thought to be well understood, are from a broad spectrum of communities with blurred taxon boundaries.[37][38]
It is estimated that 500 to 1,000
A number of types of bacteria, such as Actinomyces viscosus and A. naeslundii, live in the mouth, where they are part of a sticky substance called plaque. If this is not removed by brushing, it hardens into calculus (also called tartar). The same bacteria also secrete acids that dissolve tooth enamel, causing tooth decay.[citation needed]
The vaginal microflora consist mostly of various lactobacillus species. It was long thought that the most common of these species was Lactobacillus acidophilus, but it has later been shown that L. iners is in fact most common, followed by L. crispatus. Other lactobacilli found in the vagina are L. jensenii, L. delbruekii and L. gasseri. Disturbance of the vaginal flora can lead to infections such as bacterial vaginosis and candiadiasis.[40]
Archaea
Archaea are present in the human gut, but, in contrast to the enormous variety of bacteria in this organ, the numbers of archaeal species are much more limited.[41] The dominant group are the methanogens, particularly Methanobrevibacter smithii and Methanosphaera stadtmanae.[42] However, colonization by methanogens is variable, and only about 50% of humans have easily detectable populations of these organisms.[43]
As of 2007, no clear examples of archaeal pathogens were known,[44][45] although a relationship has been proposed between the presence of some methanogens and human periodontal disease.[46] Methane-dominant small intestinal bacterial overgrowth (SIBO) is also predominently caused by methanogens, and Methanobrevibacter smithii in particular.[47]
Fungi
Fungi, in particular
Viruses
Viruses, especially bacterial viruses (bacteriophages), colonize various body sites. These colonized sites include the skin,[54] gut,[55] lungs,[56] and oral cavity.[57] Virus communities have been associated with some diseases, and do not simply reflect the bacterial communities.[58][59][60]
In January 2024, biologists reported the discovery of "
Anatomical areas
Skin
A study of 20 skin sites on each of ten healthy humans found 205 identified genera in 19 bacterial phyla, with most sequences assigned to four phyla: Actinomycetota (51.8%), Bacillota (24.4%), Pseudomonadota (16.5%), and Bacteroidota (6.3%).[63] A large number of fungal genera are present on healthy human skin, with some variability by region of the body; however, during pathological conditions, certain genera tend to dominate in the affected region.[48] For example, Malassezia is dominant in atopic dermatitis and Acremonium is dominant on dandruff-affected scalps.[48]
The skin acts as a barrier to deter the invasion of pathogenic microbes. The human skin contains microbes that reside either in or on the skin and can be residential or transient. Resident microorganism types vary in relation to skin type on the human body. A majority of microbes reside on superficial cells on the skin or prefer to associate with glands. These glands such as oil or sweat glands provide the microbes with water, amino acids, and fatty acids. In addition, resident bacteria that associated with oil glands are often Gram-positive and can be pathogenic.[2]
Conjunctiva
A small number of bacteria and fungi are normally present in the
Gastrointestinal tract
Tryptophan metabolism by
human gastrointestinal microbiota ( ) |
In humans, the composition of the gastrointestinal microbiome is established during birth.
The relationship between some
The composition of human gut microbiota changes over time, when the diet changes, and as overall health changes.
Urethra and bladder
The genitourinary system appears to have a microbiota,[75][76] which is an unexpected finding in light of the long-standing use of standard clinical microbiological culture methods to detect bacteria in urine when people show signs of a urinary tract infection; it is common for these tests to show no bacteria present.[77] It appears that common culture methods do not detect many kinds of bacteria and other microorganisms that are normally present.[77] As of 2017, sequencing methods were used to identify these microorganisms to determine if there are differences in microbiota between people with urinary tract problems and those who are healthy.[75][76][78] To properly assess the microbiome of the bladder as opposed to the genitourinary system, the urine specimen should be collected directly from the bladder, which is often done with a catheter.[79]
Vagina
Vaginal microbiota refers to those species and genera that colonize the vagina. These organisms play an important role in protecting against infections and maintaining vaginal health.
Fungal genera that have been detected in the vagina include Candida, Pichia, Eurotium, Alternaria, Rhodotorula, and Cladosporium, among others.[48]
Placenta
Until recently the placenta was considered to be a sterile organ but commensal, nonpathogenic bacterial species and genera have been identified that reside in the placental tissue.[86][87][88] However, the existence of a microbiome in the placenta is controversial as criticized in several researches. So called "placental microbiome" is likely derived from contamination of regents because low-biomass samples are easily contaminated.[89][90][91]
Uterus
Until recently, the upper reproductive tract of women was considered to be a sterile environment. A variety of microorganisms inhabit the uterus of healthy, asymptomatic women of reproductive age. The microbiome of the uterus differs significantly from that of the vagina and gastrointestinal tract.[92]
Oral cavity
The environment present in the human mouth allows the growth of characteristic microorganisms found there. It provides a source of water and nutrients, as well as a moderate temperature.[2] Resident microbes of the mouth adhere to the teeth and gums to resist mechanical flushing from the mouth to stomach where acid-sensitive microbes are destroyed by hydrochloric acid.[2][50]
Anaerobic bacteria in the oral cavity include:
Bacteria accumulate on both the hard and soft oral tissues in biofilm allowing them to adhere and strive in the oral environment while protected from the environmental factors and antimicrobial agents.[94] Saliva plays a key biofilm homeostatic role allowing recolonization of bacteria for formation and controlling growth by detaching biofilm buildup.[95] It also provides a means of nutrients and temperature regulation. The location of the biofilm determines the type of exposed nutrients it receives.[96]
Oral bacteria have evolved mechanisms to sense their environment and evade or modify the host. However, a highly efficient innate host defense system constantly monitors the bacterial colonization and prevents bacterial invasion of local tissues. A dynamic equilibrium exists between dental plaque bacteria and the innate host defense system.[97]
This dynamic between host oral cavity and oral microbes plays a key role in health and disease as it provides entry into the body.[98]
A healthy equilibrium presents a symbiotic relationship where oral microbes limit growth and adherence of pathogens while the host provides an environment for them to flourish.
Persistent proper oral hygiene is the primary method for preventing oral and systemic disease.[98] It reduces the density of biofilm and overgrowth of potential pathogenic bacteria resulting in disease.[96] However, proper oral hygiene may not be enough as the oral microbiome, genetics, and changes to immune response play a factor in developing chronic infections.[96] Use of antibiotics could treat already spreading infection but ineffective against bacteria within biofilms.[96]
Nasal cavity
The healthy nasal microbiome is dominated by Corynebacterium, and Staphylococcus. The mucosal microbiome plays a critical role in modulating viral infection.[99]
Lung
Much like the oral cavity, the upper and lower respiratory system possess mechanical deterrents to remove microbes. Goblet cells produce mucous which traps microbes and moves them out of the respiratory system via continuously moving ciliated epithelial cells.[2] In addition, a bactericidal effect is generated by nasal mucus which contains the enzyme lysozyme.[2] The upper and lower respiratory tract appears to have its own set of microbiota.[100] Pulmonary bacterial microbiota belong to 9 major bacterial genera: Prevotella, Sphingomonas, Pseudomonas, Acinetobacter, Fusobacterium, Megasphaera, Veillonella, Staphylococcus, and Streptococcus. Some of the bacteria considered "normal biota" in the respiratory tract can cause serious disease especially in immunocompromised individuals; these include Streptococcus pyogenes, Haemophilus influenzae, Streptococcus pneumoniae, Neisseria meningitidis, and Staphylococcus aureus.[citation needed] Fungal genera that compose the pulmonary mycobiome include Candida, Malassezia, Neosartorya, Saccharomyces, and Aspergillus, among others.[48]
Unusual distributions of bacterial and fungal genera in the respiratory tract is observed in people with cystic fibrosis.[48][101] Their bacterial flora often contains antibiotic-resistant and slow-growing bacteria, and the frequency of these pathogens changes in relation to age.[101]
Biliary tract
Traditionally the biliary tract has been considered to be normally sterile, and the presence of microorganisms in bile is a marker of pathological process. This assumption was confirmed by failure in allocation of bacterial strains from the normal bile duct. Papers began emerging in 2013 showing that the normal biliary microbiota is a separate functional layer which protects a biliary tract from colonization by exogenous microorganisms.[102]
Disease and death
Human bodies rely on the innumerable bacterial genes as the source of essential nutrients.[103] Both metagenomic and epidemiological studies indicate vital roles for the human microbiome in preventing a wide range of diseases, from type 2 diabetes and obesity to inflammatory bowel disease, Parkinson's disease, and even mental health conditions like depression.[104] A symbiotic relationship between the gut microbiota and different bacteria may influence an individual's immune response.[105] Metabolites generated by gut microbes appear to be causative factors in type 2 diabetes.[106] Although in its infancy, microbiome-based treatment is also showing promise, most notably for treating drug-resistant C. difficile[dead link] infection[107] and in diabetes treatment.[108]
Clostridioides difficile infection
An overwhelming presence of the bacteria, C. difficile, leads to an infection of the gastrointestinal tract, normally associated to dysbiosis with the microbiota believed to have been caused by the administration of antibiotics. Use of antibiotics eradicates the beneficial gut flora within the gastrointestinal tract, which normally prevents pathogenic bacteria from establishing dominance.[109] Traditional treatment for C. difficile infections includes an additional regime of antibiotics, however, efficacy rates average between 20 and 30%.[110] Recognizing the importance of healthy gut bacteria, researchers turned to a procedure known as fecal microbiota transplant (FMT), where patients experiencing gastrointestinal diseases, such as C. difficile infection (CDI), receive fecal content from a healthy individual in hopes of restoring a normal functioning intestinal microbiota.[111] Fecal microbiota transplant is approximately 85–90% effective in people with CDI for whom antibiotics have not worked or in whom the disease recurs following antibiotics.[112][113] Most people with CDI recover with one FMT treatment.[114][109][115]
Cancer
Although cancer is generally a disease of host genetics and environmental factors, microorganisms are implicated in some 20% of human cancers.
The microbiota may affect carcinogenesis in three broad ways: (i) altering the balance of tumor cell proliferation and death, (ii) regulating immune system function, and (iii) influencing metabolism of host-produced factors, foods and pharmaceuticals.
Concerning the relationship of immune function and development of inflammation, mucosal surface barriers are subject to environmental risks and must rapidly repair to maintain homeostasis. Compromised host or microbiota resiliency also reduce resistance to malignancy, possibly inducing inflammation and cancer. Once barriers are breached, microbes can elicit proinflammatory or immunosuppressive programs through various pathways.[116] For example, cancer-associated microbes appear to activate NF-κΒ signaling within the tumor microenvironment. Other pattern recognition receptors, such as nucleotide-binding oligomerization domain–like receptor (NLR) family members NOD-2, NLRP3, NLRP6 and NLRP12, may play a role in mediating colorectal cancer.[116] Likewise Helicobacter pylori appears to increase the risk of gastric cancer, due to its driving a chronic inflammatory response in the stomach.[116][117]
Inflammatory bowel disease
Inflammatory bowel disease consists of two different diseases: ulcerative colitis and Crohn's disease and both of these diseases present with disruptions in the gut microbiota (also known as dysbiosis). This dysbiosis presents itself in the form of decreased microbial diversity in the gut,[118][119] and is correlated to defects in host genes that changes the innate immune response in individuals.[118]
Human immunodeficiency virus
The
Vaginal microbiota plays a role in the infectivity of HIV, with an increased risk of infection and transmission when the woman has
Gut microbiome of centenarians
Humans who are 100 years old or older, called centenarians, have a distinct gut microbiome. This microbiome is characteristically enriched in microorganisms that are able to synthesize novel secondary bile acids.[122] These secondary bile acids include various isoforms of lithocholic acid that may contribute to healthy aging.[122]
Death
With death, the microbiome of the living body collapses and a different composition of microorganisms named necrobiome establishes itself as an important active constituent of the complex physical decomposition process. Its predictable changes over time are thought to be useful to help determine the time of death.[123][124]
Environmental health
Studies in 2009 questioned whether the decline in
Changes, modulation and transmission
can change the human microbiome across various anatomical systems or regions such as skin and gut.Person-to-person transmission
The human microbiome is transmitted between a
Research
Migration
Cellulose digestion
A 2024 study suggests that
See also
Bibliography
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External links
- The Secret World Inside You Exhibit 2015–2016, American Museum of Natural History
- FAQ: Human Microbiome, January 2014 American Society For Microbiology