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Old 10-12-2017, 02:57 PM   #1
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Default Fecal pellet does not contain E. coli

I isolated DNA from a mouse fecal pellet from the large intestine using the QIAamp DNA Stool Mini Kit. We readily detected enterobacteriaceae using specific primers and qPCR but upon sequencing there was very little detection of enterobacteriaceae. I also tried to qPCR for E.coli but there essentially no amplification. We should really expect to see plenty of enterobacteriaceae/E. coli because the treatment we are using (DSS) has been shown to increase these populations.

Is it possible that the fecal pellet did not contain any enterobacteriaceae/E. coli especially after DSS treatment?

Could the enterobacteriaceae/E. coli populations have been nearly all localized to the mucosal surface of the large intestine?

Is it common to not detect any enterobacteriaceae/E. coli in a mouse fecal pellet?

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Old 10-16-2017, 04:24 AM   #2
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Was this just from one mouse? Have you looked into the possibility of other intestinal enterobacteriaceae? I work with mice/16s sequencing too and although we often find E.coli it's definitely not a given that it'll show up.
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