Diel Mouse Gut Study (HF/LF diet)

16S V4-V5 region amplicons from mouse gut samples. Mice were fed on low fat (LF) or high fat (HF) diets. Samples were taken from feces, the cecum, and the ileum in replicate mice over a 24hr period. A second, similar experiment was performed over 48 hrs (see files with 48hrs in the name). Amplicons were sequenced in the forward direction only. The barcode sequences are in a seperate file (labeled 'I1'). The files with the forward amplicon reads have 'R1' in their names. Sequence files are in FASTQ format. A mapping file (containing barcodes an sample metadata) is included for the 24hr data set, and for the 48hr data (seperately).<br><b>File Processing Instructions:</b><br>After downloading and decompressing the fastq files in this repository, you can use the commands below to re-assemble the forward read fastq and index fastq files for each sequencing run:<br><br>For sequencing run starting with '48hrs_exp1_'<br>cat 48hrs_exp1_R1_a.fastq 48hrs_exp1_R1_b.fastq 48hrs_exp1_R1_c.fastq 48hrs_exp1_R1_d.fastq 48hrs_exp1_R1_e.fastq &gt; 48hrs_exp1_R1.fastq<br><br>cat 48hrs_exp1_I1_a.fastq 48hrs_exp1_I1_b.fastq &gt; 48hrs_exp1_I1.fastq<br><br>For sequencing run starting with '48hrs_exp2_'<br><br>cat 48hrs_exp2_R1_a.fastq 48hrs_exp2_R1_b.fastq 48hrs_exp2_R1_c.fastq 48hrs_exp2_R1_d.fastq 48hrs_exp2_R1_e.fastq 48hrs_exp2_R1_f.fastq 48hrs_exp2_R1_g.fastq &gt; 48hrs_exp2_R1.fastq<br><br>cat 48hrs_exp2_I1_a.fastq 48hrs_exp2_I1_b.fastq &gt; 48hrs_exp2_I1.fastq<br><br>For sequencing run starting with 'Undetermined_S0_L001_'<br><br>cat Undetermined_S0_L001_R1_001_a.fastq Undetermined_S0_L001_R1_001_b.fastq Undetermined_S0_L001_R1_001_c.fastq Undetermined_S0_L001_R1_001_d.fastq Undetermined_S0_L001_R1_001_e.fastq &gt; Undetermined_S0_L001_R1_001.fastq<br><br>Here are the read and index file pairs (note, that we only used the forward reads):<br><br> 48hrs_exp1_R1.fastq and 48hrs_exp1_I1.fastq<br><br> 48hrs_exp2_R1.fastq and 48hrs_exp2_I1.fastq<br><br>Undetermined_S0_L001_R1_001.fastq and Undetermined_S0_L001_I1_001.fastq<br><br>The mapping file with '48hrs' in the name can be used to demultiplex the two 48hrs sequencing runs. The other run can be demultiplexed with the second mapping file. <b>Project Abstract:</b> Diet-induced obesity (DIO) is rapidly becoming a global health problem, particularly as Westernization of emerging nations continues. Currently, one third of adult Americans are considered obese and, if current trends continue, &gt;90% of US citizens are predicted to be affected by 2050. However, efforts to fight this epidemic have not yet produced sound solutions for prevention or treatment. Our studies reveal a balanced and chronobiological relationship between food consumption, daily variation in gut microbial evenness and function, basomedial hypothalamic circadian clock (CC) gene expression, and key hepatic metabolic regulatory networks, including CC and nuclear receptors (NR), that is essential for metabolic homeostasis. “Western” diets high in saturated fats dramatically alter diurnal variation in microbial composition and function, which in turn lead to uncoupling of the hepatic CC and NR networks from central CC control in ways that offset the timing and types of regulatory factors directing metabolic function. These signals include microbial metabolites such as short chain fatty acids (SCFAs) and hydrogen sulfide (H2S) that can directly regulate or disrupt metabolic networks of the hepatocyte. Our study therefore provides insights into the complex and dynamic relationships between diet, gut microbes, and the host that are critical for maintenance of health. Perturbations of this constellation of processes, in this case by diet-induced dysbiosis and its metabolomic signaling, can potentially promote metabolic imbalances and disease. This knowledge opens up many possibilities for novel therapeutic and interventional strategies to treat and prevent DIO, ranging from the manipulation of gut microbial function to pharmacological targeting of host pathways to restore metabolic balance.