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The article is titled "Microbes maketh man". Where did you get this title from?

This isn't a revolution in thinking about the human body, we've known for quite sometime of the bacterial soup that helps us digest and procedures like “Stool transplants” are controversial at best, unhealthy at worst.

Very interesting. The idea of human a human superorganism as a host to a variety of specialized and essential symbiotic bacteria should appeal to the Unixers in the audience.

The following quote is unrelated, but talk about counter-intuitive:

"This bacterium, which causes life-threatening distension of the gut in some people who have been treated with antibiotics and thus had their microbiomes disrupted, is a bane of hospitals. It kills 14,000 people a year in America alone. But recent experiments have shown it can be eliminated by introducing, as an enema, the faeces of a healthy individual."

Thanks for the quote, here's bitcookie #8635 for you
Are these microbes limited to the stomach or to be found over the entire body and brain?
Almost every part of the human body directly exposed to the environment is covered with microbes: the skin, the gut lining, your mouth, your nasal passage, etc. Only a small part isn't (as I recall your eyes are sterile). I don't have proper citation for this, but AFAIK if you disrupt the microbial balance on these surfaces it might result in health-related problems. So in a way, yes, we need them to live healthy.

Other parts have to be kept sterile. Your brain, your heart, your lymph nodes, are some examples. When these parts gets infected, you get sick.

On another note, microbes are fantastic creatures. The earth is covered in them and they've been around much longer than us. They can live off a myriad of different substances and even without the sun.

Yay microbes :p!

This idea is almost always expressed in terms of number of cells: some 90% of "our" cells are not human. But what about mass? What fraction of "our" mass consists of human cells vs. nonhuman cells?