What is the human microbiota made of?
Viruses, bacteria, archaea, fungi, and other single-celled and multicellular eukaryotes. Some of those terms may be unfamiliar, so let’s unpack that last sentence.
You probably know that viruses can’t replicate by themselves. Basically, viruses are tiny packets of genetic information with a way to get inside of some type of cell; the virus genes then use the replication machinery of the cell they invaded to make more viruses. Of course there are human viruses in the human microbiota, but they’re usually outnumbered by the viruses of the bacteria that belong to the human microbiota. (Viruses of bacteria are called bacteriophages.)
Bacteria are the most familiar component of the human microbiota, both in terms of public awareness and in our scientific knowledge. Bacteria are structurally simple, single-celled organisms that are generally much smaller than animal cells. In their biochemistry and metabolism, however, some types of bacteria (with only a few thousand genes) can be more versatile in carrying out certain functions than animals that have much more genetic information. (This has important practical consequences…vertebrate animals, including humans, depend on the biochemical abilities of their gut bacteria to help digest their food and to synthesize various useful chemicals, ranging from vitamins to neurotransmitters.) Across the whole spectrum of all the types of bacteria that exist, the range of bacterial biochemical abilities is truly staggering.
Archaea are single-celled organisms that are bacteria-like in size and structural simplicity; in fact, they were thought to be just some unusual kinds of bacteria until a few decades ago. However, Archaea are a deep evolutionary lineage, separate from Bacteria and Eukaryotes. (Between them, these three lineages comprise all known cellular life. By the way, when the words are capitalized they refer to the name of an evolutionary lineage, but they aren’t capitalized when used to describe a type of cell.) The archaeal cells of the human microbiota are almost all of only one type, a striking contrast compared to the thousands of bacterial types in the human microbiota. This predominant archaeal type in the human gut is a methanogen, which means it obtains energy by combining hydrogen with carbon to make methane. Methanogenesis is an uncommon trait that seems to have evolved only once: of all known life forms, it is found only within a single lineage of microbes within the Archaea.
Fungi are the predominant form of eukaryotic microbe in the human microbiota, but they aren’t as abundant or diverse as the bacteria of the human microbiota. Eukaryotes are the deep evolutionary division that includes not only fungi, but also animals, plants, red and brown algae, and other less familiar (and mostly single-celled) organisms. The non-fungal eukaryotes of the human microbiota include some nasty unicellular pathogens like giardia and amoebas, and various types of worms (i.e., animals) that at some stages of their life are microscopic, even if they eventually grow to a visible size. (Should these be considered members of the microbiota? More ambiguity…)
For the most part, our current research into the dynamics of the human microbiota (like most other studies of the human microbiota) will focus on the bacterial component, but we’ll be able to examine the archaea and fungal components using the same or similar techniques.
Viruses, bacteria, archaea, fungi, and other single-celled and multicellular eukaryotes. Some of those terms may be unfamiliar, so let’s unpack that last sentence.
You probably know that viruses can’t replicate by themselves. Basically, viruses are tiny packets of genetic information with a way to get inside of some type of cell; the virus genes then use the replication machinery of the cell they invaded to make more viruses. Of course there are human viruses in the human microbiota, but they’re usually outnumbered by the viruses of the bacteria that belong to the human microbiota. (Viruses of bacteria are called bacteriophages.)
Bacteria are the most familiar component of the human microbiota, both in terms of public awareness and in our scientific knowledge. Bacteria are structurally simple, single-celled organisms that are generally much smaller than animal cells. In their biochemistry and metabolism, however, some types of bacteria (with only a few thousand genes) can be more versatile in carrying out certain functions than animals that have much more genetic information. (This has important practical consequences…vertebrate animals, including humans, depend on the biochemical abilities of their gut bacteria to help digest their food and to synthesize various useful chemicals, ranging from vitamins to neurotransmitters.) Across the whole spectrum of all the types of bacteria that exist, the range of bacterial biochemical abilities is truly staggering.
Archaea are single-celled organisms that are bacteria-like in size and structural simplicity; in fact, they were thought to be just some unusual kinds of bacteria until a few decades ago. However, Archaea are a deep evolutionary lineage, separate from Bacteria and Eukaryotes. (Between them, these three lineages comprise all known cellular life. By the way, when the words are capitalized they refer to the name of an evolutionary lineage, but they aren’t capitalized when used to describe a type of cell.) The archaeal cells of the human microbiota are almost all of only one type, a striking contrast compared to the thousands of bacterial types in the human microbiota. This predominant archaeal type in the human gut is a methanogen, which means it obtains energy by combining hydrogen with carbon to make methane. Methanogenesis is an uncommon trait that seems to have evolved only once: of all known life forms, it is found only within a single lineage of microbes within the Archaea.
Fungi are the predominant form of eukaryotic microbe in the human microbiota, but they aren’t as abundant or diverse as the bacteria of the human microbiota. Eukaryotes are the deep evolutionary division that includes not only fungi, but also animals, plants, red and brown algae, and other less familiar (and mostly single-celled) organisms. The non-fungal eukaryotes of the human microbiota include some nasty unicellular pathogens like giardia and amoebas, and various types of worms (i.e., animals) that at some stages of their life are microscopic, even if they eventually grow to a visible size. (Should these be considered members of the microbiota? More ambiguity…)
For the most part, our current research into the dynamics of the human microbiota (like most other studies of the human microbiota) will focus on the bacterial component, but we’ll be able to examine the archaea and fungal components using the same or similar techniques.