For other uses, see Microbiota (disambiguation).
Depiction of the human skin and bacteria that predominate

A microbiota is "the ecological community of commensal, symbiotic and pathogenic microorganisms that literally share our body space".[1][2] Joshua Lederberg coined the term, emphasising the importance of microorganisms inhabiting the human body in health and disease. Many scientific articles distinguish microbiome and microbiota to describe either the collective genomes of the microorganisms that reside in an environmental niche or the microorganisms themselves, respectively.[3][4][5] However, by the original definitions, these terms are largely synonymous.

The microbes being discussed generally do not cause disease unless they grow abnormally nonpathogenic organisms; they exist in harmony and symbiotically with their hosts.[6] The microbiome and host may have emerged as a unit by the process of integration.[7]


All plants and animals, from protists to humans, live in close association with microbial organisms (see for example the human microbiome). Up until relatively recently, however, biologists have defined the interactions of plants and animals with the microbial world mostly in the context of disease states and of a relatively small number of symbiotic case studies. Organisms do not live in isolation, but have evolved in the context of complex communities. A number of advances have driven a change in the perception of microbiomes, including:

Increasingly, biologists have come to appreciate that microbes make up an important part of an organism's phenotype, far beyond the occasional symbiotic case study.[8]

Pierre-Joseph van Beneden (1809-1894), a Belgian professor at the University of Louvain, developed the concept of commensalism during the nineteenth century. In his 1875 publication Animal Parasites and Messmates, Van Beneden presented 264 examples of commensalism. His conception was widely accepted by his contemporaries and commensalism has continued to be used as a concept right up to the present day: microbiome is clearly linked to commensalism.[9]

Microbiota by host

There is a strengthening consensus among evolutionary biologists that one should not separate an organism's genes from the context of its resident microbes.


Main article: Human microbiome

The human microbiota includes bacteria, fungi, and archaea. Micro-animals which live on the human body are excluded. The human microbiome refers to their genomes.[10]

Humans are colonized by many microorganisms; the traditional estimate was that humans live with ten times more non-human cells than human cells; more recent estimates have lowered that to 3:1 and even to approximately the same number; all the numbers are estimates.[11][12][13][14] Regardless of the exact number, the microbiota that colonize humans have not merely a commensal (a non-harmful coexistence), but rather a mutualistic relationship with their human hosts.[10]:700[15] Some of these organisms perform tasks that are known to be useful for the human host; for most, the role is not well understood. Those that are expected to be present, and that under normal circumstances do not cause disease, are deemed normal flora or normal microbiota.[10]

The Human Microbiome Project 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.[10] It reached a milestone in 2012 when it published initial results.[16]

Non-human animals

A chytrid-infected frog (see Chytridiomycosis)


Light micrograph of a cross section of a coralloid root of a cycad, showing the layer that hosts symbiotic cyanobacteria

Immune system

The symbiotic relationship between a mammalian host and its microbiota has a significant impact on shaping the host's immune system.[33] In many animals, the immune system and microbiota engage in "cross-talk", exchanging chemical signals. This allows the immune system to recognize the types of bacteria that are harmful to the host and combat them, while allowing the helpful bacteria to carry out their functions; in turn, the microbiota influence immune reactivity and targeting.[34] Bacteria can be transferred from mother to child through direct contact and after birth, or through indirect contact through eggs, coprophagy, and several other pathways.[35] As the infant microbiome is established, commensal bacteria quickly populate the gut, prompting a range of immune responses and "programming" the immune system with long-lasting effects.[34] This early colonization helps to establish the symbiotic microbiome inside the animal host early in its life.[33] The bacteria are also able to stimulate lymphoid tissue associated with the gut mucosa. This enables the tissue to produce antibodies for pathogens that may enter the gut.

It has been found that bacteria may also play a role in the activation of TLRs (toll-like receptors) in the intestines. TLRs are a type of PRR (pattern recognition receptor) used by host cells to help repair damage and recognize dangers to the host. This could be important in immune tolerance and autoimmune diseases. Pathogens could influence this symbiotic coexistence leading to immune dysregulation and susceptibility to diseases. This could provide new direction for managing immunological and metabolic diseases.[36]

Co-evolution of microbiota

Bleached branching coral (foreground) and normal branching coral (background). Keppel Islands, Great Barrier Reef

Organisms evolve within eco-systems so that the change of one organism affects the change of others. Co-evolution (also called "hologenome theory") proposes that an object of natural selection is not the individual organism, but the organism together with its associated organisms, includings its microbial communities.

Coral reefs. The hologenome theory originated in studies on coral reefs. Coral reefs are the largest structures created by living organisms, and contain abundant and highly complex microbial communities. Over the past several decades, major declines in coral populations have occurred. Climate change, water pollution and over-fishing are three stress factors that have been described as leading to disease susceptibility. Over twenty different coral diseases have been described, but of these, only a handful have had their causative agents isolated and characterized. Coral bleaching is the most serious of these diseases. In the Mediterranean Sea, the bleaching of Oculina patagonica was first described in 1994 and shortly determined to be due to infection by Vibrio shiloi. From 1994 to 2002, bacterial bleaching of O. patagonica occurred every summer in the eastern Mediterranean. Surprisingly, however, after 2003, O. patagonica in the eastern Mediterranean has been resistant to V. shiloi infection, although other diseases still cause bleaching. The surprise stems from the knowledge that corals are long lived, with lifespans on the order of decades,[37] and do not have adaptive immune systems. Their innate immune systems do not produce antibodies, and they should seemingly not be able to respond to new challenges except over evolutionary time scales. The puzzle of how corals managed to acquire resistance to a specific pathogen led Eugene Rosenberg and Ilana Zilber-Rosenberg to propose the Coral Probiotic Hypothesis. This hypothesis proposes that a dynamic relationship exists between corals and their symbiotic microbial communities. By altering its composition, this holobiont can adapt to changing environmental conditions far more rapidly than by genetic mutation and selection alone. Extrapolating this hypothesis of adaptation and evolution to other organisms, including higher plants and animals, led to the proposal of the Hologenome Theory of Evolution.[38]

The hologenome theory is still being debated.[39] A major criticism has been the claim that V. shiloi was misidentified as the causative agent of coral bleaching, and that its presence in bleached O. patagonica was simply that of opportunistic colonization.[40] If this is true, the basic observation leading to the theory would be invalid. Nevertheless, the theory has gained significant popularity as a way of explaining rapid changes in adaptation that cannot otherwise be explained by traditional mechanisms of natural selection. For those who accept the hologenome theory, the holobiont has become the principal unit of natural selection. On the other hand, it has been stated that the holobiont is the result of other step of integration that it is also observed at the cell (symbiogenesis, endosymbiosis) and genomic levels.[7]

Research methods

Targeted amplicon sequencing

Targeted amplicon sequencing relies on having some expectations about the composition of the community that is being studied. In target amplicon sequencing a phylogenetically informative marker is targeted for sequencing. Such a marker should be present in ideally all the expected organisms. It should also evolve in such a way that it is conserved enough that primers can target genes from a wide range of organisms while evolving quickly enough to allow for finer resolution at the taxonomic level. A common marker for human microbiome studies is the gene for bacterial 16S rRNA (i.e. "16S rDNA", the sequence of DNA which encodes the ribosomal RNA molecule).[41] Since ribosomes are present in all living organisms, using 16S rDNA allows for DNA to be amplified from many more organisms than if another marker were used. The 16S rDNA gene contains both slowly evolving regions and fast evolving regions; the former can be used to design broad primers while the latter allow for finer taxonomic distinction. However, species-level resolution is not typically possible using the 16S rDNA. Primer selection is an important step, as anything that cannot be targeted by the primer will not be amplified and thus will not be detected. Different sets of primers have been shown to amplify different taxonomic groups due to sequence variation.

Targeted studies of eukaryotic and viral communities are limited[42] and subject to the challenge of excluding host DNA from amplification and the reduced eukaryotic and viral biomass in the human microbiome.[43]

After the amplicons are sequenced, molecular phylogenetic methods are used to infer the composition of the microbial community. This is done by clustering the amplicons into operational taxonomic units (OTUs) and inferring phylogenetic relationships between the sequences. Due to the complexity of the data, distance measures such as UniFrac distances are usually defined between microbiome samples, and downstream multivariate methods are carried out on the distance matrices. An important point is that the scale of data is extensive, and further approaches must be taken to identify patterns from the available information. Tools used to analyze the data include VAMPS,[44] QIIME[45] and mothur.[46]

Metagenomic sequencing

Main article: Metagenomics

Metagenomics is also used extensively for studying microbial communities.[47][48][49] In metagenomic sequencing, DNA is recovered directly from environmental samples in an untargeted manner with the goal of obtaining an unbiased sample from all genes of all members of the community. Recent studies use shotgun Sanger sequencing or pyrosequencing to recover the sequences of the reads.[50] The reads can then be assembled into contigs. To determine the phylogenetic identity of a sequence, it is compared to available full genome sequences using methods such as BLAST. One drawback of this approach is that many members of microbial communities do not have a representative sequenced genome.[41]

Despite the fact that metagenomics is limited by the availability of reference sequences, one significant advantage of metagenomics over targeted amplicon sequencing is that metagenomics data can elucidate the functional potential of the community DNA.[51][52] Targeted gene surveys cannot do this as they only reveal the phylogenetic relationship between the same gene from different organisms. Functional analysis is done by comparing the recovered sequences to databases of metagenomic annotations such as KEGG. The metabolic pathways that these genes are involved in can then be predicted with tools such as MG-RAST,[53] CAMERA[54] and IMG/M.[55]

RNA and protein-based approaches

Metatranscriptomics studies have been performed to study the gene expression of microbial communities through methods such as the pyrosequencing of extracted RNA.[56] Structure based studies have also identified non-coding RNAs (ncRNAs) such as ribozymes from microbiota.[57] Metaproteomics is a new approach that studies the proteins expressed by microbiota, giving insight into its functional potential.[58]


The Human Microbiome Project (HMP) was a United States National Institutes of Health initiative with the goal of identifying and characterizing the microorganisms which are found in association with both healthy and diseased humans (their microbial flora).[59] Launched in 2008, it was a five-year project, best characterized as a feasibility study, with a total budget of $115 million. The ultimate goal of this and similar NIH-sponsored microbiome projects is to test how changes in the human microbiome are associated with human health or disease.[59]

The Earth Microbiome Project (EMP) is an initiative to collect natural samples and analyze the microbial community around the globe. Microbes are highly abundant, diverse and have an important role in the ecological system. Yet as of 2010, it was estimated that the total global environmental DNA sequencing effort had produced less than 1 percent of the total DNA found in a liter of seawater or a gram of soil,[60] and the specific interactions between microbes are largely unknown. The EMP aims to process as many as 200,000 samples in different biomes, generating a complete database of microbes on earth to characterize environments and ecosystems by microbial composition and interaction. Using these data, new ecological and evolutionary theories can be proposed and tested.[61]

The Brazilian Microbiome Project (BMP) aims to assemble a Brazilian Microbiome Consortium/Database. At present, many metagenomic projects underway in Brazil are widely known. Our goal is to co-ordinate and standardize these, together with future projects. This is the first attempt to collect and collate information about Brazilian microbial genetic and functional diversity in a systematic and holistic manner. New sequence data have been generated from samples collected in all Brazilian regions, however the success of the BMP depends on a massive collaborative effort of both the Brazilian and international scientific communities. Therefore, we invite all colleagues to participate in this project. There is no prioritization of specific taxonomic groups, studies could include any ecosystem, and all proposals and any help will be very welcome.


The DNA of the microbes that inhabit a person's human body can uniquely identify the person. A risk to violating a person's privacy may exist, if the person anonymously donated microbe DNA data, and the data could be used to identify the person and their medical condition, and if the person's identity were revealed.[62][63][64][65]

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