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Estrone (E1) is one of the natural estrogens, which can be degraded but is not always completely removed in wastewater treatment plants. E1 is suspected of causing the endocrine disruption of aquatic organisms in the receiving water body. We identified dominant E1-incorporating bacteria, which should include E1-degrading bacteria, in activated sludge treating domestic wastewater. Sphaerotilus-Leptothrix-related bacteria, which had never been reported in the previous attempts based on culture-dependent approach, occupied 60-80% of the E1-incorporating bacteria. This study demonstrates the identification of functionally active bacteria to degrade micro-pollutants at sub-milligram per litre level.