Paleo Gut Used To Study Evolutionary History

Biologists have began to study gut bacteria in order to study the evolutionary history of mammals. This was done in hopes of following gut bacteria all the way back to the to carnivorous creatures 100 million years ago. Gut bacteria is considered microbes, and they have been found to be co-evolving with humans for a long time. They have been found to train our immune systems to fight pathogens and guide development of intestines. Andrew Moeller, a Fellow in UC Berkeley's Museum of Vertebrate Zoology, decided to study feces of different species. Moeller and a couple colleagues obtained feces from gorrillas, chimpanzees, bonobos, and people. Then they isolated and amplified the DNA of bacteria in order to study it. They found three families of bacteria that composed about 20% of the human gut. The bacteria found are Bacteroidaceae, Bifidobacteriaceae, and Lachnospiraceae. Lachnospiraceae was found to be transferred between host species due to their ability to grow spores and survive outside of a host. Bacteroidaceae and Bifodobacteriaceae were found in both the apes and humans, with more diversity in the ape species. 
Their study concluded: 

"Once we calibrated the molecular clock, we were able to date the split of human and chimp bacteria at around 5.3 million years ago, and the human-gorilla gut bacteria split at around 15.6 million years ago, which are roughly in line with what we know from fossil and genomic data of the hosts," Moeller said. "It is one more line of evidence that gut bacteria have cospeciated with humans."

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2649005/

Bacteria and Circadian Rhythms

Researchers from the Argonne National Library and the University of Chicago recently conducted a study concerning microbes that reside in mammalian stomachs and intestines that appear to have an affect on circadian rhythms.  Previous research has verified the relationship between metabolism and circadian rhythms, so it is not outrageous to assume that the microorganisms that aid in our digestion can also have an affect on how our bodies handle day and night cycles.  There is evidence that these bacteria also have an affect on allergies, mental health, and weight.

Using mice to conduct the experiment, researchers found that mice with the natural set of microbes (the control) exhibited normal daily microbial cycles, which were defined as having different species flourishing during different parts of the day and producing different compounds.  The compounds, in turn, facilitate the expression of circadian clock genes in the liver.  Another set of mice were given a high fat diet, which reduced the variation in microbial cycle, so less compounds were produced and the mice quickly gained weight.  This, researchers hypothesize, is because too much fat changes the natural compounds microbes produce.  A new set of mice, the “germ fee” mice, displayed a disrupted circadian cycle as well, however without the weight gain.  This demonstrates the possibility of a strong bond between bacteria and the regulation of circadian rhythms.  Understanding the microscopic organisms that reside in us can give us valuable insight into our dietary needs and circadian rhythms.  The researchers hope to continue their exploration of what other diets trigger these responses.