Metabolome-Informed Microbiome Analysis Refines Metadata Classifications and Reveals Unexpected Medication Transfer in Captive Cheetahs

MSystems
Julia M GauglitzPieter C Dorrestein

Abstract

Even high-quality collection and reporting of study metadata in microbiome studies can lead to various forms of inadvertently missing or mischaracterized information that can alter the interpretation or outcome of the studies, especially with nonmodel organisms. Metabolomic profiling of fecal microbiome samples can provide empirical insight into unanticipated confounding factors that are not possible to obtain even from detailed care records. We illustrate this point using data from cheetahs from the San Diego Zoo Safari Park. The metabolomic characterization indicated that one cheetah had to be moved from the non-antibiotic-exposed group to the antibiotic-exposed group. The detection of the antibiotic in this second cheetah was likely due to grooming interactions with the cheetah that was administered antibiotics. Similarly, because transit time for stool is variable, fecal samples within the first few days of antibiotic prescription do not all contain detected antibiotics, and the microbiome is not yet affected. These insights significantly altered the way the samples were grouped for analysis (antibiotic versus no antibiotic) and the subsequent understanding of the effect of the antibiotics on the cheetah microbiome. Metabol...Continue Reading

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Citations

Apr 17, 2021·Scientific Reports·Mihir Mongia, Hosein Mohimani
Jul 11, 2021·Science·Eran Blacher
Sep 24, 2021·Nature Reviews. Microbiology·Anelize BauermeisterPieter C Dorrestein

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Methods Mentioned

BETA
biopsy

Software Mentioned

MassIVE
SHOGUN
Songbird
MZmine2
Metabolomics
Qemistree
mzMINE
Bowtie
Qurro
QIIME

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