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. 

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.

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).