Whether microbiota are beneficial or not depends on our relationship with them. 

On the one hand, our bodies may in fact contain more "microbes" than we realize.

There is strong evidence that mitochondria
evolved from ancient bacteria that coevolved with early
eukaryotic organisms. The relationship
between mitochondria and their hosts eventually
became so intimate that we no longer even think of these
bacteria as species. 

J. N. Thompson 
Department of Ecology and Evolutionary Biology,
University of California, Santa Cruz



However, because of our favored lives in the modern world, we forget that microbes are the chief cause of death in other parts of the world.

In high-income countries more than two-thirds of all people live beyond the age of 70 and die of chronic diseases: cardiovascular disease, chronic obstructive lung disease, cancers, diabetes or dementia. 
Lung infection remains the only leading infectious cause of death.

In low-income countries less than a quarter of all people reach the age of 70, and nearly a third of all deaths are among children under 14. Although cardiovascular diseases together represent the leading cause of death in these countries, infectious diseases (above all HIV/AIDS, lung infections, tuberculosis, diarrhoeal diseases and malaria) together claim more lives. 

http://www.who.int/mediacentre/factsheets/fs310.pdf

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