Well, I'm not sure if having a table of counts aggregated at genus level is recommended to estimate the Chao metric. I don't think so, because this index relies on species abundance. Though it is common in microbial ecology the use of taxonomic units (OTUs/ASVs) as an approximation for species, and that's why people use it. Although estimating the true richness or alpha-diversity in a sample is very hard, and there are many researchers suggesting that this is not possible or adequate to do it from next-generation sequencing data.

By singletons or doubletons I mean a taxonomic unit that appears only once or twice in your data set. S̶o̶, i̶n̶ y̶o̶u̶r̶ c̶a̶s̶e̶, c̶o̶n̶s̶i̶d̶e̶r̶i̶n̶g̶ "t̶a̶x̶o̶n̶o̶m̶i̶c̶ u̶n̶i̶t̶s̶" a̶s̶ g̶e̶n̶e̶r̶a̶, i̶t̶ w̶o̶u̶l̶d̶ b̶e̶ a̶n̶y̶ g̶e̶n̶e̶r̶a̶ t̶h̶a̶t̶ a̶p̶p̶e̶a̶r̶s̶ o̶n̶l̶y̶ a̶c̶r̶o̶s̶s̶ o̶n̶e̶ s̶a̶m̶p̶l̶e̶ (̶=̶ s̶i̶n̶g̶l̶e̶t̶o̶n̶)̶ o̶r̶ t̶w̶o̶ s̶a̶m̶p̶l̶e̶s̶ (̶=̶ d̶o̶u̶b̶l̶e̶t̶o̶n̶)̶. S̶o̶, l̶e̶t̶'s̶ s̶a̶y̶ t̶h̶a̶t̶ E̶s̶c̶h̶e̶r̶i̶c̶h̶i̶a̶ i̶s̶ a̶ s̶i̶n̶g̶l̶e̶t̶o̶n̶ i̶n̶ y̶o̶u̶r̶ d̶a̶t̶a̶ s̶e̶t̶. I̶t̶ m̶e̶a̶n̶s̶ t̶h̶a̶t̶ o̶n̶l̶y̶ a̶p̶p̶e̶a̶r̶s̶/w̶a̶s̶ d̶e̶t̶e̶c̶t̶e̶d̶ i̶n̶ o̶n̶e̶ s̶a̶m̶p̶l̶e̶ a̶c̶r̶o̶s̶s̶ 6̶ s̶a̶m̶p̶l̶e̶s̶ t̶h̶a̶t̶ y̶o̶u̶ m̶i̶g̶h̶t̶ h̶a̶v̶e̶ (̶l̶e̶t̶'s̶ s̶a̶y̶ t̶h̶a̶t̶ y̶o̶u̶'v̶e̶ 6̶ s̶a̶m̶p̶l̶e̶s̶)̶. S̶o̶, i̶n̶ t̶h̶e̶ s̶a̶m̶p̶l̶e̶ t̶h̶a̶t̶ i̶t̶ a̶p̶p̶e̶a̶r̶s̶ h̶a̶s̶ a̶ v̶a̶l̶u̶e̶ o̶f̶ a̶b̶u̶n̶d̶a̶n̶c̶e̶ d̶i̶f̶f̶e̶r̶e̶n̶t̶ t̶h̶a̶n̶ z̶e̶r̶o̶ a̶n̶d̶ i̶n̶ t̶h̶e̶ r̶e̶m̶a̶i̶n̶i̶n̶g̶ o̶n̶e̶s̶ h̶a̶s̶ z̶e̶r̶o̶.

This is very important because Chao metric relies on singletons and doubletons to estimate the true richness in a sample.

Check the following mothur wiki page that explains the index: https://mothur.org/wiki/chao/

I hope this helps,

António