What is this ‘human microbiota’, anyway?
How is it different from the 'human microbiome', or the 'commensal flora'?
The microbiota consists of all the microscopic things living in a particular place, so the ‘human microbiota’ is all the microbes found in and on people. (Click here for more details about what they are.) As with a lot of biology, the phrase isn’t absolutely precise. For example, living cells of soil-dwelling microbes will surely be found on and in people who have a lot of contact with the soil, even if those microbes are ‘transplants’ that can’t actually grow and divide in the body sites where they’re found – so are they part of the human microbiota or not? Fortunately, phrases like ‘human microbiota’ (and ‘skin microbiota’, ‘gut microbiota’, etc.) are generally useful, despite such ambiguity around the edges.
The term ‘microbiome’ has recently been used in two different ways. One definition is the same as ‘microbiota’, explained above. The other usage of ‘microbiome’ (the recent Human Microbiome Project used this definition) means not the living organisms, but rather all the genetic information of all the microbes that live in a particular place. Since a ‘genome’ refers to all the genetic information of an organism, and ‘metagenome’ means all the genomes of the different types of organisms in an ecological community, this second meaning of ‘microbiome’ could be expressed as ‘microbial metagenome’. (See Elio Schaecter's poll on his Small Things Considered blog on the definition of ‘microbiome’.) On this website, we tend to use ‘microbiota’ to mean a community of microbes, and ‘metagenome’ to refer to the genetic information of a community.
The ‘commensal flora’ is an older term used for the human gut microbiota, but the term is misleading in two ways: 1) the microbes of the gut microbiota aren’t plants, and 2) they aren’t all commensals, which implies they get a benefit from being associated with a host without either helping or hurting the host. The majority of the gut microbiota are probably mutualists (at least most of the time), meaning that they benefit the host, and a small fraction are pathogens or parasites (at least sometimes), meaning that they can harm the host. Practically, these can be tough distinctions to make, since a microbe generally has multiple effects, as well as having different effects at different times and places. Thus, the overall balance between benefit and harm for a particular microbial type may depend a lot on the context, but it's pretty clear that for most of us, most of our microbiota is helping us, most of the time.
How is it different from the 'human microbiome', or the 'commensal flora'?
The microbiota consists of all the microscopic things living in a particular place, so the ‘human microbiota’ is all the microbes found in and on people. (Click here for more details about what they are.) As with a lot of biology, the phrase isn’t absolutely precise. For example, living cells of soil-dwelling microbes will surely be found on and in people who have a lot of contact with the soil, even if those microbes are ‘transplants’ that can’t actually grow and divide in the body sites where they’re found – so are they part of the human microbiota or not? Fortunately, phrases like ‘human microbiota’ (and ‘skin microbiota’, ‘gut microbiota’, etc.) are generally useful, despite such ambiguity around the edges.
The term ‘microbiome’ has recently been used in two different ways. One definition is the same as ‘microbiota’, explained above. The other usage of ‘microbiome’ (the recent Human Microbiome Project used this definition) means not the living organisms, but rather all the genetic information of all the microbes that live in a particular place. Since a ‘genome’ refers to all the genetic information of an organism, and ‘metagenome’ means all the genomes of the different types of organisms in an ecological community, this second meaning of ‘microbiome’ could be expressed as ‘microbial metagenome’. (See Elio Schaecter's poll on his Small Things Considered blog on the definition of ‘microbiome’.) On this website, we tend to use ‘microbiota’ to mean a community of microbes, and ‘metagenome’ to refer to the genetic information of a community.
The ‘commensal flora’ is an older term used for the human gut microbiota, but the term is misleading in two ways: 1) the microbes of the gut microbiota aren’t plants, and 2) they aren’t all commensals, which implies they get a benefit from being associated with a host without either helping or hurting the host. The majority of the gut microbiota are probably mutualists (at least most of the time), meaning that they benefit the host, and a small fraction are pathogens or parasites (at least sometimes), meaning that they can harm the host. Practically, these can be tough distinctions to make, since a microbe generally has multiple effects, as well as having different effects at different times and places. Thus, the overall balance between benefit and harm for a particular microbial type may depend a lot on the context, but it's pretty clear that for most of us, most of our microbiota is helping us, most of the time.