I was amazed to see that antibiotics weren't mentioned in the abstract as a cause of lost diversity.
Decreased Diversity of Bacteria Microbiome in Gut Associated Colorectal Cancer http://www.sciencedaily.com/releases/2013/12/131206163051.htm



Our data demonstrate that the loss of bacterial diversity under antibiotic selection is highly associated with the development of pneumonia in ventilated patients colonized with P. aeruginosa.
Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa.http://www.ncbi.nlm.nih.gov/pubmed/17409203

"...dramatic shifts were observed one week after antibiotic treatment with reduced bacterial diversity in all treated subjects"
Short-Term Antibiotic Treatment Has Differing Long-Term Impacts on the Human Throat and Gut Microbiomehttp://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0009836

"lean people are likely to have a more diverse community of gut flora compared to obese individuals...bacteria-killing antibiotics may be playing a role in predisposing some people to being fat."
Antibiotics that reduce gut bacteria linked to obesityhttp://www.independent.co.uk/news/science/antibiotics-that-reduce-gut-bacteria-linked-to-obesity-2278042.html

"Exposure to broad spectrum antibiotics, such as cephalosporins, causes marked shifts in bacterial community structure, including decreased numbers, reduced diversity, changes in membership and changes in evenness"
Modulation of Post-Antibiotic Bacterial Community Reassembly and Host Response by Candida albicans
http://www.nature.com/srep/2013/130712/srep02191/full/srep02191.html


Oxytetracycline Treatment Reduces Bacterial Diversity of Intestinal Microbiota of Atlantic Salmonhttp://www.ncbi.nlm.nih.gov/pubmed/18942594