Abstract Summary We previously developed the LDM for testing hypotheses about the microbiome that performs the test at both the community level and the individual taxon level. The LDM can be applied to relative abundance data and presence–absence data separately, which work well when associated taxa are abundant and rare, respectively. Here, we propose LDM-omni3 that combines LDM analyses at the relative abundance and presence–absence data scales, thereby offering optimal power across scenarios with different association mechanisms. The new LDM-omni3 test is available for the wide range of data types and analyses that are supported by the LDM. Availability and implementation The LDM-omni3 test has been added to the R package LDM, which is available on GitHub at https://github.com/yijuanhu/LDM. Supplementary information Supplementary data are available at Bioinformatics online.