One thing thing that has always fascinated me is how we humans live in such harmony with bacteria throughout our bodies. We absolutley require these symbionts for our daily existence for nutrition, development, metabolism, pathogen resistence, and even the regulation of immune responses. In fact, microbes in our body outnumber human cells by at least a factor of ten (For a reference check here), which quite frankly is astounding.
I often chuckle when I see humans (read Americans) that are so obsessed with anti-bacterials and running to the doctor at the first sign of a cold to grab antibiotics, especially since many colds are viral in nature. Regardess, it has long been thought that common antibiotics like Ciproflaxin have mild to no effects on gut microbiota.
Two recent manuscripts in PLoS Biology and PLoS Genetics from Mitch Sogin's group at Woods Hole Marine Biological Laboratory and David Relman's group at Stanford challenge this hypothesis. These authors used a combination of massively parallel pyrosequencing and the more classical dideoxy Sanger sequencing technique to examine hypervariable regions from small subunit ribosomal RNA genes in the gut of humans before and after a 5-day course of treatment with Ciproflaxin. The surprising result was that 30% of the bacteria present were significantly affected by the treatment with large loss of gut microbial diversity. To a germaphobe that might sound like a good thing, but it is decidely not given the requirment of these guys for our lives. It should be noted that 4 weeks post treatment the vast majority of these microbes did recover.
In all the two groups identified conservatively 5,700 taxa from the stool samples, but suggest that there might be an order of magnitude more present. Those numbers blow me away. The authors also note that the human colon is one the most dense bacterial havens on the planet! Cool!
I invite you to read these articles and comment. I also think they would make good journal club fodder if you're looking for a paper to present. You can learn a lot about pyrosequencing and gut microbiota from reading these manuscripts.