Amplicon sequencing data of the V3-V4 16S rRNA region of several laboratory marine sediment incubations, sampled from the suboxic zone. The goal of this study was to create a targeted enrichment of a single strain of a target organism: Ca. Electrothrix scaldis. The microbial community composition of three incubation-types were analysed. Incubation A: natural sediment enrichment, where sediment acquired from Rattekaai (Eastern Scheldt river) was incubated for several weeks with overlaying aerated seawater. Incubation B: autoclaved sediment, where sediment from Incubation A was autoclaved. Incubation C: clonal enrichment , where sediment from Incubation B was incubated with a single cable bacteria filament from strain Ca. Electrothrix scaldis GW3-3.