GENERAL INFORMATION Title of Dataset: Supplemental Data from: Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide Author Name: Peter J. Diebold ORCID: https://orcid.org/0000-0002-9189-9941 Institution: Cornell University Email: pd378@cornell.edu Co-Author/Alternate Contact Information Name: Ilana Lauren Brito ORCID: https://orcid.org/0000-0002-2250-3480 Institution: Cornell University Information about funding sources that supported the collection of the data: This work was supported by funding from the U.S. National Institutes of Health (1R01AI151059, 1DP2HL141007), the National Sciences Foundation (1650122, 1661338), the Gates Foundation (OPP1161064), the NOMIS Foundation (GR108454-CON-80002144) and SCENERI project funded by AXA (to N.T.H.). SHARING/ACCESS INFORMATION Licenses/restrictions placed on the data: This dataset is shared under a Creative Commons 1.0 Universal Public Domain Dedication (https://creativecommons.org/publicdomain/zero/1.0/). The material can be copied, modified and used without permission, but attribution to the original authors is always appreciated. Links to publications that cite or use the data: Pasolli E, Schiffer L, Manghi P, Renson A, Obenchain V, Truong D, Beghini F, Malik F, Ramos M, Dowd J, Huttenhower C, Morgan M, Segata N, Waldron L (2017). Accessible, curated metagenomic data through ExperimentHub. Nat. Methods, 14 (11), 1023-1024. ISSN 1548-7091, 1548-7105, doi: 10.1038/nmeth.4468. Peter Diebold, Rhee, Matthew, Shi, Qiaojuan, Nguyen, Vinh Trung, Umrani, Fayaz, Ahmed, Sheraz, Kulkarni, Vandana, Deshpande, Prasad, Alexander, Mallika, Ngo, Thi Hoa, Christakis, Nicholas, Iqbal, Najeeha, Ali, Asad, Mathad, Jyoti, Ilana Brito. (2023) Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide. Nature Communications (submitted) Recommended citation for this dataset: Peter Diebold, Rhee, Matthew, Shi, Qiaojuan, Nguyen, Vinh Trung, Umrani, Fayaz, Ahmed, Sheraz, Kulkarni, Vandana, Deshpande, Prasad, Alexander, Mallika, Ngo, Thi Hoa, Christakis, Nicholas, Iqbal, Najeeha, Ali, Asad, Mathad, Jyoti, Ilana Brito. (2023) Supplemental Data from: Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide. [dataset] Cornell University eCommons Repository. https://doi.org/10.7298/aq1k-vf97 DATA & FILE OVERVIEW File List: supp_data_1_curatedMetagenomicData_metadata_v3.2.3.csv supp_data_2_main_analysis_kma_results.res.zip supp_data_3_main_analysis_AR_profiles_v2.txt supp_data_4_all_genome_metadata.txt.zip supp_data_5_genome_rgi_results.txt.zip supp_data_6_gene_families_emergence.xlsx supp_data_7_additional_metagenome_metadata.xlsx supp_data_8_additional_metagenome_kma_results.res.zip supp_data_9_additional_metagenomes_AR_profiles.txt supp_data_10_primers_and_sequences.xlsx supp_data_11_OIL_16S_libraries.xlsx METHODOLOGICAL INFORMATION Refer to the publication in Nature Communications for additional information regarding this dataset FILE DESCRIPTIONS: Supplemental Data Table 1: Metadata for human metagenomic samples considered in this study. A comprehensive table of metadata for the human metagenomes used in Figure 1 and Supplemental Figure 1. The table was adapted from the Waldron lab’s curatedMetagenomicData Bioconductor package25 and contains columns pertaining to sample and participant identifiers, study association with year published, sample type, number of reads, health status, gender, age, and SRA numbers Supplemental Data Table 2. KMA output of human metagenomes Unfiltered KMA output of metagenomes from Supplementary Table 1 aligning trimmed metagenomic reads to the CARD database. Files are tab delimited Supplemental Data Table 3. AR gene profiles of human metagenomes AR gene profiles generated from KMA results in Supplementary Table 2 indicating presence or absence of all AR gene families by sample. Supplemental Data Table 4. Genomes used in this study. Metadata for all the genomes used in this study, including the taxonomy, ftp path, and file name Supplemental Data Table 5. RGI results for genomes used in this study. Unprocessed RGI output from the isolate genomes combined into a single file Supplemental Data Table 6. List of AR genes included in this study. A list of AR gene examined as part of this study, along with the class of antibiotics to which they provide resistance and the year of their first report in the scientific literature. Supplemental Data Table 7. Metadata for non-human and inpatient metagenomes Curated set of metagenomes from inpatients, hospital air and wastewater, wastewater treatment plants, and farm animals Supplemental Data Table 8. KMA output from non-human and inpatient metagenomes Unfiltered KMA output of metagenomes from Supplementary Table 7 aligning trimmed metagenomic reads to the CARD database. Files are tab delimited. Supplemental Data Table 9. AR gene profiles from non-human and inpatient metagenomes AR gene profiles generated from KMA results in Supplementary Table 8 indicating presence or absence of all AR gene families by sample. Supplemental Data Table 10. List of primers used for OIL-PCR, qPCR, and cloning. Supplemental Data Table 11. List of OIL-PCR and 16S sequencing libraries List of sequencing libraries used to generate Figure 3.