If I do your research for you, do I get academic credit?
Here's a paper from Nature about the recent discovery that there are three major types of microbiome (think blood type, but for your gut flora):
And a NYT article that explains it:
It may not be a scholarly resource per say, but Melissa's presentation at the Ancestral Health Symposium was very comprehensive and interesting, and she cites several scholarly resources: http://huntgatherlove.com/content/ancestral-health-symposium-talk
I am guessing Melissa herself would have plenty of scholarly resources about this subject, so hopefully she answers this.
Probably very complicated and very dependent on things like environment and diet - even some suggestion that carbohydrate metabolism might also be implicated: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0024585 Remember also that our gut microbiome is also interactive with our immune system and the little known gut virome: http://gutness-gracious-me.blogspot.com/2011/09/gut-virome.html
Here's a fascinating paper about how humans and H.pylori bacteria evolved together http://www.nature.com/hdy/journal/v98/n6/full/6800977a.html.
Here's another one about how the Bacteroides division of bacteria evolved to live in our gut https://docs.google.com/viewer?a=v&q=cache:aBfGPeo54jIJ:gordonlab.wustl.edu/PublicationPDFs/373_XuPLoS07.pdf+&hl=en&gl=us&pid=bl&srcid=ADGEESjKgvg-nnpJrtGZjclwz7DMyM6MoIDjgaz8W1iEzoB3pxJw3hKa8WMztXr0yqO27paX8erGudI2Zajvmpz6Vdeq-eE0fry8ndZgWqHVK7sKGMmddbuQ3N7rBxNalP8MFsQHVc6b&sig=AHIEtbTCD-Qoi_hSrmU7okjW-y00FDxpuQ.
Also, another fascinating article about how people in Japan have bacteria that evolved to breakdown sushi but we don't http://www.npr.org/templates/story/story.php?storyId=125675700.
I'm sure there's a lot more where that came from, this is a topic has a lot to be written about.
Baby, antibiotics and probiotics 3 Answers