Here's a perl alternate
perl -alne 'print unless $F =~ /\((\d+)\)$/ && $1 < 60'
- match and capture a parenthesized sequence of decimal digits at the end of the 3rd (zero-indexed) field
- if a match is found, test the captured group's numerical value and print accordingly
$ perl -alne 'print unless $F =~ /\((\d+)\)$/ && $1 < 60' file
12713 Bacteria(100) Bacteroidetes(100) Bacteroidia(100)
Note that this implements the logic "remove all lines in a file which have a number less than 60 in column 3" as stated in your question - which is slightly different from printing lines that have a number greater than or equal to 60.
If your files really are comma separated (rather than whitespace delimited as shown in your question), then you will need to change the delimiter i.e.
perl -F, -lne 'print unless $F =~ /\((\d+)\)$/ && $1 < 60'