"From the perspective of an ecologist, and more specifically a microbial ecologists, diversity is something you want in an ecosystem. Greater diversity is associated with resilience, or the microbiomes ability to deal with such things as opportunistic pathogens or perturbations from diet. A less biodiverse gut microbiome may handle your five-donut binge at the office, or your bottle and half of red wine one night, instead of your usual two glasses, very differently. Dietary pulses or longer term shifts in diet, like antibiotics, are perturbations that can shift the composition of your gut microbiome and reduce diversity, as some species become more dominant under the perturbation."
Slumdog Microbiome More Diverse - Human Food Project