Hard to tell at a glance whether this "Hygiene Hypothesis" is legitimate science, or wishful thinking on the part of the journalist who wrote the book. I'm leaning towards being rather sceptical.

It's not bunk. http://en.wikipedia.org/wiki/Hygiene_hypothesis

Some studies have shown parasites improve the symptoms of certain chronic illnesses, such as Inflammatory Bowel Diseases. Fecal transplantation has also been used to treat chronic digestive ailments. http://en.wikipedia.org/wiki/Fecal_bacteriotherapy

You could do the absolute minimum of due diligence and check if there is a Wikipedia article:

http://en.wikipedia.org/wiki/Hygiene_hypothesis

It's been extensively studied by epidemiologists and immunologists. There is some experimental evidence to support the theory.

Oh, big whoop, some experimental evidence, huh! There's a Wikipedia article about the subject, so that blesses the contents of this book now, does it?

The premise, the logic stands on its own. We coevolve with other organisms and bacteria, not in a vacuum. So wether there is hard evidence for this or that, regardless it’s an interesting field of study right now and many are looking into it. Sometimes before you have evidence, you need a hypothesis.

I didn't say anything about the book, I haven't read it. You questioned whether the hygiene hypothesis was a real hypothesis.

According to my very casual glance at the evidence, it appears to be a hypothesis being actively debated by scientists. I'm not sure what else you might want for a hypothesis to be 'scientifically legitimate'.

thanks for the article