Effects of short photoperiod and carbohydrate consumption on sleep, liver steatosis, and the gut microbiome in diurnal grass rats

# SAD rats: Effects of short photoperiod and carbohydrate consumption on sleep, liver steatosis, and the gut microbiome in diurnal grass rats --- ## General Info Dataset contains 4 zipped files, corresponding to data used for analysis. AnimalData.zip contains data files (in .csv format) to analyze data corresponding to animal weights, fat pad data, liver steatosis data, and phase 1 and phase 2 animal metadata. ConsumptionData.zip contains all data (in .csv format) necessary for analyze sucrose/water consumption stats. microBiome.zip contains data files (in .csv, .qza, and .txt format) necessary to analyze fecal/intestine microBiome data. sleepData.zip contains all data to analyze sleep data obtained from the piezo system. We used a 2x2 experimental design, with animals subjected to either a short (4h Light: 20h Dark [4:20 LD]) or neutral (12:12 LD) photoperiod and provided with either access to 8% sucrose or only water. Room temperatures were always maintained at 22°C. Grass rats were given ad libitum food (Prolab RMH 2000 5P06 rodent chow from PMINutrition International, St. Louis, Missouri, USA) and ad libitum water access from a water bottle. Every three days, slip cages and bottles were changed, and animals were weighed. Prior to the experiment, animals were co-housed with littermates on a neutral photoperiod (lights on: 05:00-17:00). Animals were then moved into individual cages and provided two weeks to acclimate to their experimental rooms prior to altering photoperiod. After acclimation, we kept 23 rats (11 males, 12 females) on this neutral photoperiod, and shifted 22 rats (10 males, 12 females) to the short photoperiod treatment (lights on: 09:00-13:00). Four weeks later, half of the animals were given a second bottle with sucrose solution whereas the other half were given a second bottle of water. At the end of the experiment, animals were euthanized (using CO2), weighed, fat pads were extracted and weighed, liver samples were taken, and fecal pellets were extracted from the large intestine. Liver samples were fixed in 10% buffered formalin, trimmed, and then stained with a hematoxylin & eosin (H&E) stain. Fecal samples from the large intestine were immediately frozen on dry ice and then stored at -80°C for further analyses. Fecal samples were also collected directly from animal tubs (Trial 2 only) for microbiome analyses immediately prior to photoperiod treatment (0 weeks), after 4 weeks of photoperiod treatment, and at the end of the experiment after 7 weeks of photoperiod treatment and 3 weeks of sucrose treatment. ## Description of the data and file structure All data filenames are referenced in the appropriate code (upload on github: ) Data files: ### AnimalData: Data in this folder are used to calculate animals weight data, fat pad data, liver steatosis data. Folder has metadata files to correlate animals to other experimental information. Animal_weights_forMassChange.csv Chamber_Animal_IDs_Sex_bothPhases.csv Fat_pads.csv Merged_Liver.csv Meta_litter_parents.csv metadata.csv \--Information relevant for Chamber_Animal_IDs_Sex_bothPhases.csv: Number of variables: 23 Number of rows: 47 Variable list: GrassRat_ID - Unique animal identifier Phase - specifies if animals were in phase 1 or phase 2 of the experiment Chamber - Chamber room animals were located Sex - male (M) or female (F) Photoperiod - Photoperiod treatment animals were subjected too, Short or Long Sugar_conc - Sugar concentration animals were given in bottle; 0 - no sugar, 0.02 - 2% sugar concentration, 0.04 - 4% sugar concentration, 0.06 - 6% sugar concentration, 0.08 - 8% sugar concentration Sugar - Animals were under No sugar (0 sugar_conc) or High sugar (0.08 sugar_conc) treatment Parent_Sire - Unique ID of animals biological father Parent_Dame - Unique ID of animals biological mother\ ParentPair - Animals were obtained from 4 parental pairs (1- pair 1, 2- pair 2, 3 - pair 3, 4 - pair 4) Litter - Litter that animal belonged to. AgeAtDeath_days - Age in days (from birth (0), to death) animals died Percent_liver_fat - Percent area of liver occupied by fat (NA values indicate no measurement taken) Weight g - Weight of animals (in grams) and time of death Fat_pad_wt_g - Weight of fat pad (in grams) and time of death DOB_Day - Day of birth DOB_Month - Month of birth\ DOB_Year - Year of birth DOB_MMDDYYYY - combined date of birth (mm/dd/yyyy) DOD_Day - Day of death DOD_Month - Month of death DOD_Year - Year of death DOD_MMDDYYYY - combined date of death (mm/dd/yyyy) \--Information relevant for Animal_weights_forMassChange.csv: Number of variables: 20 Number of rows: 45 Variable list: Individual - Unique animal identifier Litter - Litter that animal belonged to. Room - Room identifier animals were kept in Sugar - Animals were under No sugar (0 sugar_conc) or High sugar (0.08 sugar_conc) treatment Photoperiod - Photoperiod treatment animals were subjected too, Short or Long Group - Specify if animals were under short photoperiod and high or low sugar (ShortHigh or ShortNone) or long photoperiod and high or low sugar (NeutralHigh or NeutralNone) DOB_Day - Day of birth DOB_Month - Month of birth\ DOB_Year - Year of birth\ DOB - Date of birth (mm/dd/yyyy) Euthanized_date - Date (mm/dd/yyyy) animals were euthanized Age_death - Age (in days) at death Chamber - Chamber room animals were located Weight_start - Weight (in grams) at start of experiment under Short or Neutral/Long photoperiods Weight_2wk - Weight (in grams) after 2 weeks under Short or Neutral/Long photoperiods Weight_presugar - Weight (in grams) under Short or Neutral/Long photoperiods prior to recieving high or no sugar. Weight_euthanasia - Weight (in grams) at time of euthanasia under ShortNone, ShortHigh, NeutralHigh, or NeutralNone treatments pct_2wk - Percent change in body weight after 2 weeks under Short or Neutral/Long photoperiods pct_presugar - Percent change in body weight prior to switching to recieveing suagr treatments pct_euthanasia - Percent change in body weight at time of euthanasia \--Information relevant for Fat_pads.csv: Number of variables: 6 Number of rows: 46 Variable list: Individual - Unique animal identifier Treatment - Animals under different photoperiod treatments (Short or Neutral/Long) Sex - male (M) or female (F) Weight g - Animal body weight (in grams) at time of euthanasia\ Fat_pad_wt_g - Fat pad weight (in grams) at time of euthanasia Sugar - Animals were under high sugar yreatment (Y) or no sugar treatment (N) \--Information relevant for Merged_liver.csv: Number of variables: 33 Number of rows: 70 Variable list: ID - Unique animal ID Phase_Slide_Casette_Region - Animals phase (1 or 2), slide number, cassette number tissue is mounted in, region of liver imaged\ Slice - .tif formats of prior Phase_Slide_Cassette_Region Count - Count (number) of steatosis idetified in liver TotalArea - Area that the count occupied AverageSize - Average size (mm) of liver steatosis PercentArea - Percent area that the liver steatosis occupied in the image Mean - Slide - slide number Casette - cassette number tissue is mounted in Region - region of liver imaged Slide_Casette_Region - slide number_cassette number tissue is mounted in_region of liver imaged Size - size range in an image Size_units - units of the image size range, inches square (in2) or micrometer (um2) Cropped - Image cropped (Y) or not cropped (N) Distance_calibrated - Was image dstance calibrated (Y) or not (N) Circularity - Range of image particle circularity between polygon shape (0.5)to a perfect circle (1.0) ColorThreshold - ImageJ color threshold value X - Specifies manual thresholding AutoThresholdWas - Auto color threshold value specified by ImageJ Use - Was authotheshold value used (Y) or not used (N) Microsteatosis_0min_4max - Range of microsteatosis from not present (0) to very present (4) Checked_With_Original Image verification check (Y) Phase - Animals in epxeriment Phase 1 (1) or phase 2 (2) Comments - Imager comments CropArea - Crop area used (value) or not used (NA) NecropsyID - Necropsy identifier Chamber - Chamber animals was housed in (1-24) Photoperiod - Animals under Neutral/Long or Short experimental photoperiod Sugar - Animals were under No sugar (0 sugar_conc) or High sugar (0.08 sugar_conc) treatment AgeAtDeath_days - Age (in days) at death Sugar_conc - No sugar (0 sugar_conc) or High sugar (0.08 sugar_conc) treatment PhotoSugar - Specify if animals were under short photoperiod and high or low sugar (ShortHigh or ShortNone) or long photoperiod and high or low sugar (NeutralHigh or NeutralNone) \--Information relevant for Meta_litter_parents.csv: Number of variables: 13 Number of rows: 47 Variable list: GrassRat_ID - Unique animal ID Parent_Sire - Unique ID of animals biological father Parent_Dame - Unique ID of animals biological mother\ ParentPair - Animals were obtained from 4 parental pairs (1- pair 1, 2- pair 2, 3 - pair 3, 4 - pair 4) Litter - Litter that animal belonged to. AgeAtDeath_days - Age in days (from birth (0), to death) animals died Percent_liver_fat - Percent area of liver occupied by fat (NA values indicate no measurement taken) Phase - specifies if animals were in phase 1 or phase 2 of the experiment Chamber - Chamber room animals were located Sex - male (M) or female (F) Photoperiod - Photoperiod treatment animals were subjected too, Short or Long Sugar_conc - Sugar concentration animals were given in bottle; 0 - no sugar, 0.02 - 2% sugar concentration, 0.04 - 4% sugar concentration, 0.06 - 6% sugar concentration, 0.08 - 8% sugar concentration Sugar - Animals were under No sugar (0 sugar_conc) or High sugar (0.08 sugar_conc) treatment \--Information relevant for metadata.csv: Number of variables: 25 Number of rows: 161 Variable list: SampleID - Unique animal identifier for microbiome analysis Type - Tissue type taken, Int: Intestine sample; Fecal: Fecal sample Daylength - Photoperiod treatment, Normal/Long or Short Sample - Sample identifier A, B, C or D Experimental.Trial - Treatment animals were under. 2wk acclim: 2 weeks of acclimation to Neutral/Long photoperiod; 4wk photoperiod: 4 weeks under Neutral/Long or Short photoperiods; 0% HCS: animals recieving no sugar solution; 8% HCS: animals recieving 8% sugar solution. NA specify animals not under any specific experimental trial and are disregarded in downstream analysis. GrassRat_ID - Unique animal identifier Trial - Which phase animals were in, 1 or 2 Sex - male (M) or female (F) Sucrose - Animals given sugar (yes) or not (no) Sugar_conc - Sugar concentration animals were given in bottle; 0 - no sugar, 0.08 - 8% sugar concentration Photoperiod - Animals under Neutral/Long or Short photoperiod Chamber - What experimental chamber animals were in Plate - PCR plate identifier (A or B) PCRRow - What row of the PCR plate sample was in PCRCol - What column of the PCR plate sample was in TrialA - Which phase animals were in, 1 or 2 LightDay - Numeric for if animals were under Neutral/Long photoperiod (12) or Short photoperiod (4) TubeID - Microcentrifuge tube ID samples were in Parent_Sire - Unique ID of animals biological father Parent_Dame - Unique ID of animals biological mother\ ParentPair - Animals were obtained from 4 parental pairs (1- pair 1, 2- pair 2, 3 - pair 3, 4 - pair 4) Litter - Litter that animal belonged to. AgeAtDeath_days - Age in days (from birth (0), to death) animals died Percent_liver_fat - Percent area of liver occupied by fat (NA values indicate no measurement taken) ### ConsumptionData: Data files in this folder are used to calculate sugar consumption data across the various experimental treatments and phases. The sleep data is included in this folder to calculate the time spent asleep while animals were on high (8%) sucrose during the second phase of the experiment. Phase2_8%sucrose_12Aug2019_long.csv Phase2_8%sucrose_12Aug2019_short.csv Phase2_8%sucrose_21Aug2019_short.csv Phase2_8%sucrose_30Aug2019_short.csv SucroseTest.csv SugarConcTest_weights_05Feb2020.csv \--Information relevant for Phase2_8%sucrose_12Aug2019_long.csv, Phase2_8%sucrose_12Aug2019_short.csv, Phase2_8%sucrose_21Aug2019_short.csv, and Phase2_8%sucrose_30Aug2019_short.csv: Number of variables: 18, 50 or 60 Number of rows: 23 Variable list; these are common variable names shared across the files, and only differ by the numeric at the end, which corresponds to the day/night, i.e., PERCENTSLEEPTOT1 and PERCENTSLEEPTOT2 correspond to percentage sleep for day/night or day/night 2: MOUSE_ID - Unique animals identifier TESTDATE - Date of when sleep data is recored (mm/dd/yyyy) PERCENTSLEEPTOT - Total percentage of time spent asleep PERCENTSLEEPNIGHT - Percentage of time spent asleep during the night\ PERCENTSLEEPDAY - Percentage of time spent asleep during the day\ BOUTLENGTHTOT - Total percentage of sleep bouts across day and night BOUTLENGTHNITE - Total percentage of sleep bouts across the night BOUTLENGTHDAY - Total percentage of sleep bouts across the day DIURNAL WAKE RATIO - Ratio of time awake versus asleep during the active period PEAKACT - Maximum peak amplitude value across the day and night \--Information relevant for SucroseTest.csv, SugarConcTest_weights_05Feb2020.csv, SugarConcTest_weights.xlsx; All share the same variables. Primary difference between the five is SucroseTest.csv and is cleaned to contain sugar consumption information for animals under high (8%) or no (0%) sugar solution; SugarConcTest_weights_05Feb2020.csv and SugarConcTest_weights.xlsx are identifical, except SugarConcTest_weights.xlsx contain formulas in cells for calculations of sugar/water solutions consumed during the experiment: Number of variables: 30 Number of rows: 1182 Variable list: IndivSugarDay - Unique animals ID, sugar treatment: 0 - no sugar, 0.02 - 2% sugar concentration, 0.04 - 4% sugar concentration, 0.06 - 6% sugar concentration, 0.08 - 8% sugar concentration, and days since treatment start. Day - Day of the month Month - Numerical month Year - Year Date - day, month, year (ddmmyyyy) DaySinceStart - Day since start of expoeriment\ Time - Time of day bottle measurement was taken (hhmm) Indiv - Unique animal identifier Chamber - Chamber ID animals were in Pre_test - specify if animals were in a Pre-Test period (Pre), prior to receiving a sugar solution (Test) Treatment - Photoperiod animals were under Neutral/Long or Short DopamineStage - Animals under no treatment (NA), a pre treatment period (Pre), high sugar solution (HCS), low dopamine concentraion (DopLO2) or high dopamine concentration (DopHI2) Animal_wt_g - Animals weight (in grams) at time of sugar measurement on the 3rd day of treatment Sex - male (M) or female (F) Sugar_conc - Sugar concentration animals were given in bottle; 0 - no sugar, 0.02 - 2% sugar concentration, 0.04 - 4% sugar concentration, 0.06 - 6% sugar concentration, 0.08 - 8% Sugar_ConcDay - Days under a given sugar concentration treatment Sugar_Total1_g - Weight (in grams) of bottle number 1\ Sugar_Total2_g - Weight (in grams) of bottle number 2 Fed_sugarsoln_g - Weight (in grams) of difference bottle 2 versus bottle 1 consumption Fed_sugarsoln_g_perday - Weight (in grams) of solution consumed accounting for how many days animals have been under the treatment (Fed_sugarsoln_g/Sugar_ConcDay)\ Sugar_mmt_good - Did bottle 1 or 2 spill (Y) or not spill (N) Water_ConcDay - Days under a given sugar concentration treatment Water_Total1_g - Weight (in grams) of bottle number 1\ Water_Total2_g - Weight (in grams) of bottle number 2 Fed_water_g - Weight (in grams) of difference bottle 2 versus bottle 1 consumption Fed_water_g_perday - Weight (in grams) of solution consumed accounting for how many days animals have been under the treatment (Fed_water_g/Water_ConcDay) Consumed - Consumption of bottle 1 versus bottle 2 (Fed_sugarsoln_g/(Fed_sugarsoln_g + Fed_water_g)) Water_mmt_good - Did bottle 1 or 2 spill (Y) or not spill (N) Initials - Initial of researcher who checked animals and weighed bottle Comments - Researcher comments ### SleepData Files in folder are used to calculate percent hourly sleep for animals under a 2 week acclimation period, 4 weeks under a photoperiod treatment, or 3 weeks under a no sgar or high sugar solution. 2WeekAcclimation_26Mar2019_longTime.csv 4WeekPhotoperiod_08Apr2019_long.csv 4WeekPhotoperiod_08Apr2019_short.csv 4WeekPhotoperiod_15Apr2019_dailySS_combinedTime.csv 4WeekPhotoperiod_24Apr2019_combined_with_sub_day.csv 4WeekPhotoperiod_24Apr2019_long.csv 4WeekPhotoperiod_24Apr2019_short.csv 4WeekPhotoperiod_24Apr2019SleepBout_MeanSB.csv Chamber_Animal_IDs_Sex_bothPhases.csv Chamber_Animal_IDs.csv DailySleepBothPhases_FINAL.csv HighSucrose_29May2019_combined_with_sub_day.csv HighSucrose_29May2019_PercentHourlySleep_processed.csv HighSucrose_29May2019SleepBout_MeanSB_processed.csv HourlySleepBouts_PrePostSugar.csv LowSucrose_andTest_07May2019_combined_with_sub_day.csv Phase2_2WeekAcclimation_19Jun2019_long.csv Phase2_4WeekPhotoperiod_03Jul2019_combined.csv Phase2_4WeekPhotoperiod_22Jul2019_combined_with_sub_day.csv Phase2_4WeekPhotoperiod_22Jul2019_combined.csv Phase2_4WeekPhotoperiod_22Jul2019SleepBout_MeanSB.csv Phase2_8%sucrose_12Aug2019_long.csv Phase2_8%sucrose_12Aug2019_short.csv Phase2_8%sucrose_21Aug2019_combined_with_sub_day.csv Phase2_8%sucrose_21Aug2019_long.csv Phase2_8%sucrose_21Aug2019_PercentHourlySleep_processed.csv Phase2_8%sucrose_21Aug2019_short.csv Phase2_8%sucrose_21Aug2019SleepBout_MeanSB.csv Phase2_8%sucrose_30Aug2019_long.csv Phase2_8%sucrose_30Aug2019_short.csv Phase2_LowSucroseTest_03Aug2019_combined_with_sub_day.csv \--Information relevant for 2WeekAcclimation_26Mar2019_longTime.csv, 4WeekPhotoperiod_08Apr2019_long.csv, 4WeekPhotoperiod_08Apr2019_short.csv, 4WeekPhotoperiod_15Apr2019_dailySS_combinedTime.csv, 4WeekPhotoperiod_24Apr2019_combined_with_sub_day.csv, 4WeekPhotoperiod_24Apr2019_long.csv, 4WeekPhotoperiod_24Apr2019_short.csv, 4WeekPhotoperiod_24Apr2019SleepBout_MeanSB.csv, HighSucrose_29May2019_combined_with_sub_day.csv, LowSucrose_andTest_07May2019_combined_with_sub_day.csv, Phase2_2WeekAcclimation_19Jun2019_long.csv, Phase2_4WeekPhotoperiod_03Jul2019_combined.csv, Phase2_4WeekPhotoperiod_22Jul2019_combined_with_sub_day.csv, Phase2_4WeekPhotoperiod_22Jul2019_combined.csv, Phase2_8%sucrose_12Aug2019_long.csv, Phase2_8%sucrose_12Aug2019_short.csv, Phase2_8%sucrose_21Aug2019_combined_with_sub_day.csv, Phase2_8%sucrose_21Aug2019_long.csv, Phase2_8%sucrose_21Aug2019_short.csv,Phase2_8%sucrose_30Aug2019_long.csv, Phase2_8%sucrose_30Aug2019_short.csv, Phase2_LowSucroseTest_03Aug2019_combined_with_sub_day.csv Variable list; these are common variable names shared across the files, and only differ by the numeric at the end, which corresponds to the day/night, i.e., PERCENTSLEEPTOT1 and PERCENTSLEEPTOT2 correspond to percentage sleep for day/night or day/night 2: MOUSE_ID - Unique animals identifier TESTDATE - Date of when sleep data is recored (mm/dd/yyyy) PERCENTSLEEPTOT - Total percentage of time spent asleep PERCENTSLEEPNIGHT - Percentage of time spent asleep during the night\ PERCENTSLEEPDAY - Percentage of time spent asleep during the day\ BOUTLENGTHTOT - Total percentage of sleep bouts across day and night BOUTLENGTHNITE - Total percentage of sleep bouts across the night BOUTLENGTHDAY - Total percentage of sleep bouts across the day DIURNAL WAKE RATIO - Ratio of time awake versus asleep during the active period PEAKACT - Maximum peak amplitude value across the day and night \--Information relevant fo Chamber_Animal_IDs_Sex_bothPhases.csv Number of variables: 18 Number of rows: 47 Variable list: GrassRat_ID - Unique animal identifier Phase - specifies if animals were in phase 1 or phase 2 of the experiment Chamber - Chamber room animals were located Sex - male (M) or female (F) Photoperiod - Photoperiod treatment animals were subjected too, Short or Long Sugar_conc - Sugar concentration animals were given in bottle; 0 - no sugar, 0.02 - 2% sugar concentration, 0.04 - 4% sugar concentration, 0.06 - 6% sugar concentration, 0.08 - 8% sugar concentration Sugar - Animals were under No sugar (0 sugar_conc) or High sugar (0.08 sugar_conc) treatment Parent_Sire - Unique ID of animals biological father Parent_Dame - Unique ID of animals biological mother\ ParentPair - Animals were obtained from 4 parental pairs (1- pair 1, 2- pair 2, 3 - pair 3, 4 - pair 4) Litter - Litter that animal belonged to. AgeAtDeath_days - Age in days (from birth (0), to death) animals died Percent_liver_fat - Percent area of liver occupied by fat (NA values indicate no measurement taken) Weight g - Weight of animals (in grams) and time of death Fat_pad_wt_g - Weight of fat pad (in grams) and time of death DOB_Day - Day of birth DOB_Month - Month of birth\ DOB_Year - Year of birth DOB_MMDDYYYY - combined date of birth (mm/dd/yyyy) DOD_Day - Day of death DOD_Month - Month of death DOD_Year - Year of death DOD_MMDDYYYY - combined date of death (mm/dd/yyyy) \--Information relevant to Chamber_Animal_IDs.csv Number of variables: 6 Number of rows: 25 Variable list: GrassRat_ID - Unique animal identifier Phase - specifies if animals were in phase 1 or phase 2 of the experiment Chamber - Chamber room animals were located Sex - male (M) or female (F) Photoperiod - Photoperiod treatment animals were subjected too, Short or Long Sugar_conc - Sugar concentration animals were given in bottle; 0 - no sugar, 0.02 - 2% sugar concentration, 0.04 - 4% sugar concentration, 0.06 - 6% sugar concentration, 0.08 - 8% sugar concentration Sugar - Animals were under No sugar (0 sugar_conc) or High sugar (0.08 sugar_conc) treatment \--Information relevant to 4WeekPhotoperiod_24Apr2019SleepBout_MeanSB.csv, HighSucrose_29May2019_PercentHourlySleep_processed.csv, HighSucrose_29May2019SleepBout_MeanSB_processed.csv, Phase2_4WeekPhotoperiod_22Jul2019SleepBout_MeanSB.csv, Phase2_8%sucrose_21Aug2019_PercentHourlySleep_processed.csv, Phase2_8%sucrose_21Aug2019SleepBout_MeanSB.csv Variable list; all files contain values from piezoelectric sleep system measuring either avergae sleep bouts (i.e., MeanSB.csv) or percently hourly sleep (i.e., PercentHourlySleep-processed.csv): Date - Date and time of when sleeo data is collected by piezo system (mm/dd/yyyy hh:mm) Following columns specify an animals ID with corresponding values generated by piezoelectric system. ### MicroBiome Folder contains data files for microbiome statistics and generating PCOA plots combined_otu_tax.tsv GRP_20191213.metadata_AS.csv GRP_20191213.metadata.csv GRP_20191213.rarefied-class-feature-table.csv Meta_litter_parents.csv metadata_cut_for_shannon.csv metadata.csv otu_matrix.csv otu_table.txt shannon_vector.qza taxonomy.csv taxonomy.tsv tree.nwk unweighted_unifrac_pcoa_results.qza \--Information relevant to GRP_20191213.metadata_AS.csv and GRP_20191213.metadata.csv Number of variables: 19 Number of rows: 193 Variable list: SampleID - Unique animal identifier for microbiome analysis Type - Tissue type taken, Int: Intestine sample; Fecal: Fecal sample Daylength - Photoperiod treatment, Normal/Long or Short Sample - Sample identifier A, B, C or D Experimental.Trial - Treatment animals were under. 2wk acclim: 2 weeks of acclimation to Neutral/Long photoperiod; 4wk photoperiod: 4 weeks under Neutral/Long or Short photoperiods; 0% HCS: animals recieving no sugar solution; 8% HCS: animals recieving 8% sugar solution. NA specify animals not under any specific experimental trial and are disregarded in downstream analysis. GrassRat_ID - Unique animal identifier Trial - Which phase animals were in, 1 or 2 Sex - male (M) or female (F) Sucrose - Animals given sugar (yes) or not (no) Sugar_conc - Sugar concentration animals were given in bottle; 0 - no sugar, 0.08 - 8% sugar concentration Photoperiod - Animals under Neutral/Long or Short photoperiod Chamber - What experimental chamber animals were in Plate - PCR plate identifier (A or B) PCRRow - What row of the PCR plate sample was in PCRCol - What column of the PCR plate sample was in TrialA - Which phase animals were in, 1 or 2 LightDay - Numeric for if animals were under Neutral/Long photoperiod (12) or Short photoperiod (4) TubeID - Microcentrifuge tube ID samples were in \--Information relevant to GRP_20191213.rarefied-class-feature-table.csv Number of variables: 19 Number of rows: 193 Variable list: OTU_ID - Contains concatenated identifier of a microbiome group, phylum, class, order, family, and genus\ D0 - column specifying microbiota group D1 - column specifying microbiota phylum D2 - column specifying microbiota class\ D3 - column specifying microbiota order\ D4 - column specifying microbiota family\ D5 - column specifying microbiota genus The rest of the columns specify the animals ID and corresponding sequencing readcounts for the prior columns \--Information relevant to Meta_litter_parents.csv Number of variables: 13 Number of rows: 47 Variable list: GrassRat_ID - Unique animal identifier Parent_Sire - Unique ID of animals biological father Parent_Dame - Unique ID of animals biological mother\ ParentPair - Animals were obtained from 4 parental pairs (1- pair 1, 2- pair 2, 3 - pair 3, 4 - pair 4) Litter - Litter that animal belonged to. AgeAtDeath_days - Age in days (from birth (0), to death) animals died Percent_liver_fat - Percent area of liver occupied by fat (NA values indicate no measurement taken) Phase - specifies if animals were in phase 1 or phase 2 of the experiment Chamber - Chamber room animals were located Sex - male (M) or female (F) Photoperiod - Photoperiod treatment animals were subjected too, Short or Long Sugar_conc - Sugar concentration animals were given in bottle; 0 - no sugar, 0.02 - 2% sugar concentration, 0.04 - 4% sugar concentration, 0.06 - 6% sugar concentration, 0.08 - 8% sugar concentration Sugar - Animals were under No sugar (0 sugar_conc) or High sugar (0.08 sugar_conc) treatment \--Information relevant to metadata_cut_for_shannon.csv and metadata.csv Number of variables: 25 Number of rows: 159 Variable list: SampleID - Unique animal identifier for microbiome analysis Type - Tissue type taken, Int: Intestine sample; Fecal: Fecal sample Daylength - Photoperiod treatment, Normal/Long or Short Sample - Sample identifier A, B, C or D Experimental.Trial - Treatment animals were under. 2wk acclim: 2 weeks of acclimation to Neutral/Long photoperiod; 4wk photoperiod: 4 weeks under Neutral/Long or Short photoperiods; 0% HCS: animals recieving no sugar solution; 8% HCS: animals recieving 8% sugar solution. NA specify animals not under any specific experimental trial and are disregarded in downstream analysis. GrassRat_ID - Unique animal identifier Trial - Which phase animals were in, 1 or 2 Sex - male (M) or female (F) Sucrose - Animals given sugar (yes) or not (no) Sugar_conc - Sugar concentration animals were given in bottle; 0 - no sugar, 0.08 - 8% sugar concentration Photoperiod - Animals under Neutral/Long or Short photoperiod Chamber - What experimental chamber animals were in Plate - PCR plate identifier (A or B) PCRRow - What row of the PCR plate sample was in PCRCol - What column of the PCR plate sample was in TrialA - Which phase animals were in, 1 or 2 LightDay - Numeric for if animals were under Neutral/Long photoperiod (12) or Short photoperiod (4) TubeID - Microcentrifuge tube ID samples were in Parent_Sire - Unique ID of animals biological father Parent_Dame - Unique ID of animals biological mother\ ParentPair - Animals were obtained from 4 parental pairs (1- pair 1, 2- pair 2, 3 - pair 3, 4 - pair 4) Litter - Litter that animal belonged to. AgeAtDeath_days - Age in days (from birth (0), to death) animals died Percent_liver_fat - Percent area of liver occupied by fat (NA values indicate no measurement taken) \--Information relevant to out_matrix.csv and otu_table.tsv Number of variables: 161 Number of rows: 1711 Variable list: OTUID - Unique identifier corresponding to the microbiota group, phylum, class, order, family, and genus\ The following columns contain microbiota readcount data for each sample \--Information relevant to taxonomy.csv and taxonomy.tsv Number of variables: 3 Number of rows: 1711 Variable list: OTUID - Unique identifier corresponding to the microbiota group, phylum, class, order, family, and genus\ Taxon - Contains concatenated character identifier of a microbiome group, phylum, class, order, family, and genus\ Confidence - Confidence value in placement of sample to the OTUID \--Information relevant to shannon_vector.qza and unweighted_unifrac_pcoa_results.qza Files are in zipped qza format containing experimental metadata and shannon entropy values for all samples (shannon_vector.qza) and PCOA eigenvalues for generating PCOA plot. Data file access: qza files can be unzipped with Archive Utility on Mac (and the analogous software on Windows). Contents: Unzipped shannon_vector.qza and unweighted_unifrac_pcoa_results.qza files contain checksums.md5 file from sequencing, an alpha diversity file in .tsv format, and a metadata.yaml file for appropriate downstream analysis in R. Files can be read into R using the read_qza() as part of the qiime2R package. \--Information relevant to tree.nwk Newick file to visualize tree network from microbiota sequencing data, and for phylogenetic analysis using UniFrac package in R. Contents: Files are non-readable for humans but can be viewed with a text editor (in Mac or Windows) in Newick format, where parenthesis and commas represent graph-theoretical trees with edge lengths. Files can be read into R using the read_tree() function as part of the phyloseq package. ## Code/Software All uploaded data in Dryad is compatible for use with Excel and R.