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

Data S1. Amplicon Sequencing Data and Metadata for Microbiome Samples

This file contains two sheets:

• Sheet 1: Sample IDs and Amplicon Sequencing Accession Numbers for human microbiome samples. A table listing sample IDs paired with their corresponding accession numbers for the amplicon sequencing files of human microbiome samples.
• Sheet 2: Sample Metadata and  Amplicon Sequencing Accession Numbers for mouse microbiome samples. Detailed metadata for each sample, including sample ID, experiment number, sample collection day, mouse number, antibiotic and diet treatments administered to the mice, and the NCBI Sequence Read Archive (SRA) accession number for the corresponding sequencing data.

Data S2. Detailed Nutritional Intake Data for Anonymized Patients

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 Food Group Intake and Clinical Variables for Bayesian Modeling

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

• 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.

• intensity: Intensity of the conditioning regimen.

• empirical: Binary indicator (yes/no) 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: Alpha diversity of the stool sample, calculated using the Simpson reciprocal index.

• TPN, EN: Binary indicators (yes/no) of 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.