So, I've been designing a microbiome sequencing (MiSeq V3 600 cycle kit) experiment in different groups of mice.
I've been collecting fecal samples as pellets from the upper gut (cecum) as well as lower colon region from sacrificed mice. The samples are then snap frozen and kept at -80 degrees.
I assume each type of sample would result in a different microbiome sequence profile. However, I was wondering which type of sample was generally considered a more common one to be used in microbiome sequencing.
I've been doing some research in the literature but all the papers I've found don't really go into detail about fecal sample collection from sacrificed mice. Any advice would be much appreciated. Thanks!
Microbiota from different part of mice intestine do have difference. We always collect mice feces to extract DNA. The microbiota from pellets from lower colon region can also be considered the same as fecal microbiota. But the pellets from the cecum are more likely to be closely to ileum.
Depends what you wanted to see in your results. If you want to find out particular community composition from a particular region of gut, there is no other way than to "Cut-and-Get" from that region. However, if you are just interested in the fecal community composition, feces is a good way to go.
Yes to all the answers so far.. In addition quantities used in previous studies can be adopted