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The microbiome is a hot topic in science media and research
circles right now. Google the term microbiome and you get thousands of relevant
hits. It is a new field because the techniques that enable us to identify
microbes are relatively new, like cheap and fast genetic sequencing.
Previously, many microbes were unable to be cultured in the lab, making them
impossible to identify let alone study. This is a field that is changing at an
incredible rate. We are going to spend some time with the microbiome so today I
want to cover the basics.
Biome is another word for ecosystem, the totality of an
abiotic environment and its living components, classically in a distinct
climatic region. Biome usually refers to the big picture; desert and rainforest
are textbook examples of biomes. The term microbiome refers to the biome or
ecosystem of microorganisms, wherever they are found. The human microbiome has
been in the news quite a bit lately, this refers to the human body as a biome
for microbes. Various Earth microbiome projects seek to identify the microbial
communities involved in the traditionally recognized climatic biomes (the
deserts, the rainforests). What we are learning from all this is that
microorganisms are everywhere, and are intimately involved with every important
cycle and function in our bodies and on Earth. It is not an overstatement to
say they are a really big deal.
So what are microorganisms? The term encompasses bacteria,
yeasts and other fungi, viruses, and microscopic plants and animals—really the
only qualification is to be microscopic. When we talk about microorganisms, we
generally think of bacteria as the dominant player, but keep in mind all those
other organisms as well. They will come back into our discussion later.
If you think back to your high school biology course, you
may remember a little bit about bacteria. They are single celled organisms that lack a
nuclear membrane. Knowing this may help you pass your SATs, but what does it
really mean? To start, the world is divided into two kinds of organisms,
prokaryotes and eukaryotes. Prokaryotes are organisms without any kind of
membrane bound organelles, the most important of which they don’t have is a
nucleus. Its as if in our bodies, our
organs weren’t distinctly delineated, and everything, including our brain, just
sloshed around loose inside us. They are almost always single celled, with a
chemically complex cell wall, and a loose tangle of DNA somewhere inside them,
as well as smaller loose bits of circular DNA. Eukaryotes are the opposite;
they are often large, and usually multicellular. They have many bound
organelles in their cells, to perform all kinds of metabolic functions, and
they have a true nucleus that houses their linear DNA. Just for the record, we
are eukaryotes.
Prokaryotes can be further divided into two groups, and
amazingly, they seem to be more distantly related to each other as we are from
either of them. The two groups are so different they each qualify as a separate
Domain of life, domain being the step above Kingdom in classical taxonomy. When
we lump everything that is alive together, Domain is the first level at which
things are sorted. Two of those domains are microscopic prokaryotes, the
Eubacteria and the Archea. Archea are often called “extremophiles”, they are
the organisms that live in hydrothermal vents, hot springs, hypersaline
solutions and other extremely hostile environments. The Eubacteria are
generally what we are referring to when we talk about “germs” or bacteria, and
as far as we know currently, are key players in the microbiomes of both our
bodies and our environments. In the interest of completeness, the third Domain
of life is the Eukaryota (the one that contains us and pretty much all the life
we can see with our own eyes).
We’ll be talking more about bacteria and other members of
the microbiome in the coming weeks as we explore the world that is not only all
around us, but inside us as well.
References:
The New York Times did several articles this summer about
the human microbiome and new research coming out regarding it. This is one: http://www.nytimes.com/2012/06/14/health/human-microbiome-project-decodes-our-100-trillion-good-bacteria.html?pagewanted=all
The L.A. Times did s similar series: articles.latimes.com/2012/jun/13/science/la-sci-bacteria-20120614
Interesting personal site from a fellow science nerd: http://microbes.org/
The National Institute of Health’s Human Microbiome project:
https://commonfund.nih.gov/hmp/
The Earth Microbiome project: http://www.earthmicrobiome.org/
The University of California Museum of Paleontology
maintains a fantastic website with excellent information about a range of
topics and links to other good external sites:
http://www.ucmp.berkeley.edu/bacteria/bacteriasy.html
The Tree of Life Web Project
is a terrific and growing web resources for learning about phylogenetic
relationships between groups of organisms. Highly recommended: http://tolweb.org/Life_on_Earth/1
