Supplementary Data for "Sugar-rich foods exacerbate antibiotic-induced microbiome injury"

Data S1. Sequencing Data Accession Numbers and Metadata for Microbiome and Host Gene Expression Samples

This file contains five sheets detailing the sample identifiers, experimental metadata, and NCBI Sequence Read Archive (SRA) accession numbers for the study.

• Sheet 1: Human 16S rRNA Amplicon Sequencing. A mapping of sample IDs to their corresponding SRA accession numbers for human microbiome amplicon data.

• Sheet 2: Human Shotgun Metagenomics. Detailed mapping for human shotgun sequencing samples, including sample IDs, patient IDs (PID), and corresponding SRA, BioProject, and BioSample accession numbers.

• Sheet 3: Mouse 16S rRNA Amplicon Sequencing. Metadata for mouse microbiome amplicon samples, including sample IDs, experiment numbers, collection timepoints (day), mouse identifiers, and specific antibiotic and diet treatments.

• Sheet 4: Mouse Shallow Shotgun Metagenomics. Comprehensive metadata for mouse shallow shotgun sequencing, listing sample IDs, timepoints, treatments and SRA accession numbers.

• Sheet 5: Mouse RNA-seq. Metadata for host transcriptomic profiling (RNA-seq) of mouse large intestine epithelium, including mouse IDs, gavage and diet treatments, and corresponding accession numbers.

Data S2. Detailed Nutritional Intake Data for Anonymized Patients (filename: 152_combined_DTB.csv)

This file contains comprehensive, anonymized data on patient dietary intake. Columns include:

• pid: Patient ID.
• Meal: Meal category (e.g., breakfast, lunch, dinner).
• Food_NSC: Food name.
• fdrt: Diet entry day, relative to transplant.
• Unit: Unit of measurement for food quantity (e.g., grams, ounces).
• Por_eaten: Portion of food consumed.
• Food_code, description: Food code and corresponding description from the Food and Nutrient Database for Dietary Studies (FNDDS).
• Total calories, weight: Caloric content and weight of the consumed portion.
• Individual macronutrients (grams): Gram weight of each macronutrient (e.g., protein, fat, sugar, fiber as well as carbohydrate that excludes sugar and fiber) in the consumed portion.
• Dehydrated weight: Total weight of the consumed portion minus the water weight.

Data S3. Summarized Dietary Intake, Clinical Variables, and Macronutrients for Bayesian Modeling (filename: 153_combined_META.csv)

This file provides summarized dietary intake data, macronutrient profiles, and relevant clinical variables used in the Bayesian model. Columns include:

• pid: Unique patient identifier.

• sampleid: Unique stool sample identifier.

• sdrt: Stool sample collection day, relative to transplant.

• fg_egg ... fg_veggie: Average intake (in grams) of foods belonging to nine broad food groups (e.g., eggs, vegetables) during the two days preceding stool sample collection.

• ave_Calories_kcal, ave_Protein_g, ave_Fat_g, ave_Carbohydrates_g, ave_Fibers_g, ave_Sugars_g: Average daily caloric intake (kcal) and macronutrient intake (grams of protein, fat, carbohydrates, fiber, and sugar) during the two days prior to stool sample collection.

• intensity: Intensity of the conditioning regimen.

• empirical: Binary indicator (TRUE/FALSE) of patient exposure to specific antibiotics (piperacillin/tazobactam, carbapenems, cefepime, linezolid, oral vancomycin, and metronidazole) in the two days prior to stool sample collection.

• simpson_reciprocal: α-diversity of the stool sample, calculated using the Simpson reciprocal index.

• TPN, EN: Binary indicators (TRUE/FALSE) of a patient receiving total parenteral nutrition (TPN) or enteral nutrition (EN) in the two days prior to stool sample collection.

• timebin: Time interval of stool sample collection, categorized by week relative to transplant.

Data S4. Medication Exposure Overlapping With Stool Samples

This file contains a record of all medication exposures that occurred during the 48-hour period before each stool sample was collected. This window was chosen to investigate the potential impact of recent medication use on the stool microbiome. The table includes the following columns:

• sampleid: A unique identifier assigned to each stool sample.

• pid: Patient ID.

• sdrt: Stool sample collection day, relative to transplant.

• class: The pharmacological class of the administered medication (e.g., "quinolones", "beta-lactamase inhibitors", etc.).

• drug_name_clean: The name of the medication (e.g., "ciprofloxacin", "vancomycin").

• route_clean: The route of administration (e.g., "IV", "oral").

• drug_category_for_this_study: A study-specific categorization of the medication, based on its potential impact on the gut microbiome. The categories are:

  • > * broad_spectrum: Broad-spectrum antibiotics, as classified in this study: piperacillin/tazobactam, carbapenems, cefepime, linezolid, oral vancomycin, and metronidazole 

  • > * fluoroquinolones: Fluoroquinolone antibiotics (ciprofloxacin or levofloxacin).

  • > * other_antibacterial: Antibacterial medications not classified as broad-spectrum or fluoroquinolones.

  • > * not_antibacterial: Medications not expected to have a direct antibacterial effect.

Data S5.  Nutrient Profiles of Foods Consumed (FNDDS 2015-2016)

This supplemental file contains the complete nutrient values for food codes listed in the USDA Food and Nutrient Database for Dietary Studies (FNDDS) 2015-2016. All nutrient values in this file are reported per 100 grams of edible portion, meaning it includes the water content of the food. See the column labeled "Water (g)" explicitly lists the grams of water contained within each 100g portion.

This table is downloaded from: https://www.ars.usda.gov/northeast-area/beltsville-md-bhnrc/beltsville-human-nutrition-research-center/food-surveys-research-group/docs/fndds-download-databases/

Data S6.  Individual patient data. Line plots illustrate the observed patterns in daily caloric intake, daily diet α-diversity (Faith's phylogenetic distance), and fecal microbiota α-diversity (inverse Simpson index) across patient hospitalizations.

Each panel displays the longitudinal data for a single patient. The number of days with recorded dietary data and the number of evaluable stool samples are annotated in red and blue, respectively, within each panel. The red, black, and blue lines plot daily caloric intake, diet α-diversity, and fecal microbiota α-diversity, respectively. Patients with only one or no stool sample collected will not have a line representing their fecal α-diversity over time. The first two have values on the same numeric scale and share the same left y-axis. Microbiome α-diversity value is quantified on the y-axis on the right. The vertical grey line is the day of cell infusion (day 0). The vertical dotted green line is the day of neutrophil engraftment. All panels share the same y-axis ranges; x-axis ranges are specific to the per-patient data availability. Alphanumeric codes are anonymized patient identifiers.

Additional File: Filled-out STORMS checklist

This file is a filled-out STORMS checklist for the manuscript. It is version 1.03, downloaded from 10.5281/zenodo.5703116. The STORMS checklist is a standardized checklist for microbiome studies, published in the journal Nature Medicine (https://www.nature.com/articles/s41591-021-01552-x).