Since these bacteria can't live on their own I don't understand what differentiates them from true multicellular organisms.

Hi there, first author of the paper here. We would argue that they are a true multicellular organism, which is rather unconventional for Bacteria. They do indeed have some level of genomic heterogeneity between individual cells within a single consortium but it appears this is actually purposefully maintained by the organism, likely to facilitate their evolution. They have a large genome (8 Mb) compared to E. coli (4 Mb) and have duplicate genes that are under higher rate of evolution (dN/dS) compared to the rest of the genome.

The article says "individual cells within MMB consortia are not genetically identical, they differ slightly in their genetic blueprint."