16s rRNA amplicon sequence files generated from the C-CoMP B2P BIOS Research Week 2024 exometabolite incubation experiment conducted at the Bermuda Institute of Ocean Sciences in March 2024. Sequence data files were generated from both natural, unamended seawater microbial communities (Bulk1_..., Bulk2_..., Bulk3_...) and experimental end-member communities, including: triplicate biotic (unamended) community DNA collected after 56 hours of incubation (B1_..., B2_..., B3_...), triplicate DNA samples from microbial communities amended with Micromonas commoda-derived metabolite mix after 56 hours (Mic1_..., Mic2_..., Mic3_...), and triplicate DNA samples from microbial communities amended with Prochlorococcus marinus-derived metabolite mix after 56 hours (Pro1_..., Pro2_..., Pro3_...). An average of 1800 mL of seawater was filtered to obtain DNA in the unamended seawater microbial communities, while an average of 800 mL seawater was filtered to obtain the end-member community DNA samples. The Dyhrman Lab extracted DNA, and library prep and sequencing were performed at Argonne National Laboratory on an Illumina MiSeq platform in May 2024. Code for bioinformatics analysis is stored at https://github.com/C-CoMP-STC/B2P23-BIOS-Week.