Tuesday, September 4, 2012

Microbiome Part 1

Note: This program first aired on September 1, 2012.

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.


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