Gut microbiota in the cecal content was analyzed as described in our previous report (4 (link)). Briefly, primers specific for 16S rRNA V4-V5 region (Forward: 515F: 5’-GTGYCAGCMGCCGCGGTAA - 3’ and Reverse: 806R: 5’-GGACTACHVGGGTWTCTAAT-3’) that contained Illumina 3’ adapter sequences, as well as a 12-bp barcode were used. Sequences were generated by an Illumina MiSeq DNA platform at Argonne National Laboratory and analyzed by the program Quantitative Insights Into Microbial Ecology (QIIME) (24 (link)). Operational Taxonomic Units (OTUs) were picked at 97% sequence identity using open reference OTU picking against the Greengenes database (25 (link)). Representative sequences were aligned via PyNAST, taxonomy assigned using the RDP Classifier, and a phylogenetic tree was built using FastTree.
Protocol detail
Gut Microbiome Profiling by 16S rRNA Sequencing
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16s rrna
Cecal
Gut microbiota
Primers
Corresponding Organization : University of Chicago
Other organizations : University of Tennessee Health Science Center
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Variable analysis
independent variables
- Primers specific for 16S rRNA V4-V5 region (Forward: 515F: 5'-GTGYCAGCMGCCGCGGTAA - 3' and Reverse: 806R: 5'-GGACTACHVGGGTWTCTAAT-3') that contained Illumina 3' adapter sequences, as well as a 12-bp barcode
- Gut microbiota in the cecal content
- Not explicitly mentioned
- No positive or negative controls were explicitly mentioned in the provided information.
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