The microbial components of soil heath are poorly understood, despite the increasing popularity of this concept. Widely used soil health tests, such as Haney and Solvita, rely on a measure of short term microbial activity, but relationships between these tests and specific bacterial populations have not been explored. We sampled 118 locations at two depths (0-10 and 10-20 cm) in two fields; one long-term no-till and the other conventionally-tilled. Depth had a larger effect on soil communities than tillage. Samples from the shallow depths were enriched in Proteobacteria and Bacteroides, while samples from deeper depths were enriched in Actinobacteria and Acidobacteria. Significant correlations between the abundances of bacterial families and soil variables were found in the shallow soil layer. We found significant positive correlations between grain yield and Caulobacteraceae and negative correlations with Micromonosporaceae. Oxalobacteraceae, Cytophagaceae, Comamonadaceae, Verrucomicrobiaceae and Pseudomonadaceae were positively correlated with the Haney and Solvita tests. Further, random forest regression identified key taxa related to soil health measures, soil characteristics, and grain yield. In conclusion, there are strong associations between specific bacterial families and components of soil health measurements. Although it remains unclear whether relationships are causal, the bacteria tended to represent root-associated taxa and reside in the upper soil depths where root density is highest.