The microbiome: Our life in common with microorganisms

Fifth in a series of posts inspired by ten topics in ‘Insights of the Decade’ from the December 17, 2010 special issue of Science Magazine The topics are: Inflammation, climatology, tricks of light, alien planets, the microbiome, cell development, Martian water, the DNA time machine, cosmology and epigenetics. The original articles are now behind a paywall; they won’t be reproduced here, but their gist is present. I’ll try to put them in context and specifically within the Impact Areas of SciTechStory.

When I was a kid (a few decades ago), my parents took me to Yellowstone National Park (Wyoming, USA). I remember marveling at many things, not the least of which were the brilliant colors in and near the pools of very hot water – oranges, yellows, greens – in all hues. I wondered aloud what made the colors and I was told the common wisdom of the day that most of the colors were from minerals dissolved in the water, except maybe some green, which was from algae. There were probably a few biologists of the time who suspected the presence of bacteria in these pools, but it was generally agreed that bacteria couldn’t live in the heat of these waters.

The concept of the thermophile, heat loving microorganisms, was probably first used in 1879 and promptly put on the mental back-shelf by almost all biologists. While it was accepted that some forms of plant life (algae) could tolerate higher temperatures (between 60 and 80 degrees Celsius, 140-180 degrees Fahrenheit), it just didn’t seem likely that any form of animal life could survive. This ‘intuition’ was generally frozen into many scientists’ thinking in the form of a bias.

That bias persisted until research in the 1980’s and 90’s showed that not only could bacteria live – and thrive – in hot environments, but there were, in fact, such a thing as hyperthermophiles that could live in water up to and above the boiling point. Many of these microorganisms were highly specialized bacteria, and many more were from what is now recognized as a completely distinct domain of life – the Archaea. It is such creatures that produce the colorful bands around thermal pools in Yellowstone. These days, the study of such extremophiles, life in extreme conditions, is of enormous biological and even commercial importance.

In a similar vein, scientists have known since the 19th century that the human body contained bacteria. Mostly though, these bacteria were known as the cause of disease. It was assumed that they didn’t belong in the body. This intuition became frozen into common knowledge, a bias. Even when it was later shown that some bacteria lived inside the body, particularly in the gut and were probably part of the digestive system, the focus was still very much on dealing with the destructive bacterial invaders. In short, the bias continued to guide the accepted wisdom and most of the research effort.

Unbelievable as it might seem now, it wasn’t until the year 2000, when Nobelist Joshua Lederberg published in Science a broadside aimed at his fellow bacteriologists:

New strategies and tactics for countering pathogens will be uncovered by finding and exploiting innovations that evolved within other species in defense against infection. But our most sophisticated leap would be to drop the Manichaean view of microbes – “We good; they evil.” Microbes indeed have a knack for making us ill, killing us, and even recycling our remains to the geosphere. But in the long run microbes have a shared interest in their hosts’ survival: A dead host is a dead end for most invaders too. Domesticating the host is the better long-term strategy for pathogens.
[Source: From Science Magazine: Infectious History]

Even Lederberg couldn’t purge his language of the ‘pathogen’ view of microorganisms, but those who heeded his call for a more equanimous view of microbes in the human body soon began to discover that the reality called for a wholly different view. For example, as is now often cited, the human body contains far more cells of microbes than our own cells – by almost 10 to 1. There are at least 1,000 species living inside us, and most of them are symbiotic or at least commensal (one sided benefit). This vast community of mostly non-pathogenic microorganisms is now called the microbiome, an ecology inside us.

As you can imagine, with only ten years of research microbiologists have just begun to scratch the surface of this newly appreciated relationship between human and microbe. For example, while scientists knew that bacteria were involved with digestion, a 2004 study by a team working with Jeffrey Gordon at the Washington University School of Medicine (St. Louis, Missouri, USA) discovered that bacteria were essential partners in helping to break down the food we eat and to make metabolic use of it.

The microbiome is now linked to various aspects of human health, including the proper functioning of our immune system. It is also suspected that bacterial DNA may play an active role in our own DNA development. With each new study the links to bacteria within the body proliferate. This new view is even extending to diminish an even greater bias – the bias against viruses. A new term, the virome was coined to encompass the role that viruses have within the normal functioning of the body, as strange as that may seem.

Some of the practical impact of research into the microbiome and virome will be a better understanding of their benefits to the body – and how to keep it that way. Scientists are also learning that the microbiome is highly individualized; we can be identified as individuals by the denizens of our gut. These same fellow-travelers also identify our culture and genetic background. This has led research into areas of diet and body chemistry. In fact, the knowledge of the microbiome is leading research into fundamental metabolic pathways that were not even suspected ten years ago. This work will in time have an impact on cell biology, immune systems, and genetics.

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  1. [...] that you’re an ecosystem? Our bodies are host to trillions of microbes, with bacterial cells outnumbering our own 10 to 1. The highest concentration of bacteria is in the colon and small intestine, where food is broken [...]

  2. [...] you know that you’re an ecosystem? Our bodies are host to trillions of microbes, with bacterial cells outnumbering our own 10 to 1. The highest concentration of bacteria is in the colon and small intestine, where food is [...]

  3. [...] that you’re an ecosystem? Our bodies are host to trillions of microbes, with bacterial cells outnumbering our own 10 to 1. The highest concentration of bacteria is in the colon and small intestine, where food is broken [...]

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