In alternative embodiments, the invention provides computational algorithms, computer programs, software and other methods, systems and products of manufacture (e.g., computers, devices or apparatus) for identifying members of microbial communities, their abundance and distribution from amplicon sequence data, and comparing microbial communities and consortia. In alternative embodiments, the invention provides computer-implemented methods comprising a subset of, substantially all, or all of the steps as set forth in the flow chart of FIG. 1, FIG. 3 or FIG. 4. In alternative embodiments, the invention provides methods for identification of consortia, optionally followed by construction of artificial microbial consortia from pure strains or enrichment cultures. In alternative embodiments, the invention provides compositions, fluids, bioreactors, muds, reservoirs or products of manufacture comprising a synthetic microbial consortium made by the method of the invention.