$ cat file
0   k__Bacteria  p__Firmicutes   c__Bacilli     foo     bar
1   k__Bacteria  p__Firmicutes   c__Clostridia  the   quick     brown
2   k__Bacteria  p__Bacteroidetes    c__Bacteroidia     fox jumped      over
3   k__Bacteria  p__Bacteroidetes    c__Bacteroidia     the lazy dogs back

$ awk -v skip=1 '{match($0,"([^[:space:]]+[[:space:]]+){"skip"}"); head=substr($0,1,RSTART+RLENGTH); tail=substr($0,RSTART+RLENGTH+1); gsub(/[[:space:]]+/,";",tail); print head tail}' file
0   k__Bacteria;p__Firmicutes;c__Bacilli;foo;bar
1   k__Bacteria;p__Firmicutes;c__Clostridia;the;quick;brown
2   k__Bacteria;p__Bacteroidetes;c__Bacteroidia;fox;jumped;over
3   k__Bacteria;p__Bacteroidetes;c__Bacteroidia;the;lazy;dogs;back

$ awk -v skip=2 '{match($0,"([^[:space:]]+[[:space:]]+){"skip"}"); head=substr($0,1,RSTART+RLENGTH); tail=substr($0,RSTART+RLENGTH+1); gsub(/[[:space:]]+/,";",tail); print head tail}' file
0   k__Bacteria  p__Firmicutes;c__Bacilli;foo;bar
1   k__Bacteria  p__Firmicutes;c__Clostridia;the;quick;brown
2   k__Bacteria  p__Bacteroidetes;c__Bacteroidia;fox;jumped;over
3   k__Bacteria  p__Bacteroidetes;c__Bacteroidia;the;lazy;dogs;back

$ awk -v skip=3 '{match($0,"([^[:space:]]+[[:space:]]+){"skip"}"); head=substr($0,1,RSTART+RLENGTH); tail=substr($0,RSTART+RLENGTH+1); gsub(/[[:space:]]+/,";",tail); print head tail}' file
0   k__Bacteria  p__Firmicutes   c__Bacilli;foo;bar
1   k__Bacteria  p__Firmicutes   c__Clostridia;the;quick;brown
2   k__Bacteria  p__Bacteroidetes    c__Bacteroidia;fox;jumped;over
3   k__Bacteria  p__Bacteroidetes    c__Bacteroidia;the;lazy;dogs;back