Fortunately we have a tool to help on both fronts: metegenomic sequencing. It's only just starting to be used in clinical settings in a non-retrospective way, but many groups are interested in how the gut microbiome (or changes of) can impact the etiology of GI disease. Several pharma startups are looking at therapies for GI disease that rely on changing the gut microbiome, either directly via introduction of new flora (fecal transplant or introduction of tailored microbial cocktails), or via small molecules that can shape the taxonomic distribution. Microbial cultures introduced to the GI tract tend to either die off entirely, or become dominant. It's a bit of an unsolved puzzle why the trend isn't toward plurality. The microbial therapies for
C. diff. are one example.
Beyond GI disease there's also indication that the gut microbiome has psychological impact, and metabolic impact. There's a lot we don't know.
Metagenomic sequencing can disentangle the various organisms present in a sample and report all of the taxa present, but the results are only as good/complete as the database used, and unknowns can be a significant slice of the pie.
When our group does deep-enough sequencing and de novo viral genome assembly, we often have enough contigs beyond our organism of interest to assemble genomes for other viruses, and sometimes they are novel. Yes, there are more infectious diseases out there.
A Chinese team exploring the viruses of invertebrates found nearly 1,500 new viruses [1]. That one study expanded the list of known viruses by a significant number, we're talking double-digit percentage change. Many more viruses will be found, and some of them will be pathogenic.
In the (hopefully) near future it will be reasonable (if not yet cost effective) to use tools like high-throughput sequencing to look at everything in a sample, rather than ordering specific assays for individual pathogens. It's a long road until sequencing will be part of the standard of care, but we're in a golden age of biomedical exploration, enabled by sequencing and new molecular methods.
1. http://www.nature.com/nature/journal/v540/n7634/full/nature2...