Hi Nick,
That worked! What took some digging was how to use the "--p-where." I detail this below with information to be inserted in capital letters:
qiime feature-table filter-samples
--i-table INPUT_TABLE
--m-metadata-file METADATA_FILE
--p-where "[METADATA_HEADER]='SUBGROUP_WITHIN_MD_HEADER'"
--p-no-exclude-ids
--o-filtered-table OUTPUT_TABLE