Personally I think Root is too powerful... My two cents on the subject: To me it sounds like you aren't putting enough into damage and accuracy mutations... Ammo is not at all helpful unless you feel like you're strong enough already or you use the translator (you can get plenty of ammo refills from Trish, the fish, and the reload upgrade)... And you do need a lot of health upgrades (mutation or not)... But it's mainly important as a thing to spend on damage/accuracy... You don't need to have a high max health (more than 6) if you're beating every enemy by the second turn at most (first boss should take three turns)... Golden bullets are great when you're dealing 7+ base damage (and then add gunpowder into the mix for good measure)...
Getting a lot of combats is important... But you can't exactly force that... So instead you can be mindful of which enemies you can beat on the first turn and focus on them... And also enemies you can beat on the second turn because those are a good backup... Though early on you want to visit Trish a couple of times for ammo...
Meadow's gimmick is technically meant to counter Root's damage output... But she (like every boss) gets countered easily by her if you have an obscene damage output and just win on the first turn with a few golden bullets (she really should start the combat with mosquitos)... Alternatively you want to get things that allow you to attack more than once per turn... Like floss/fossil/second hand smoke... Cult's robe effectively allows you to skip Deer headed man (or the previous boss but there are other ways to skip that one like cigarettes or snake scales)... And Crucifix is a great way to recover between the many bosses...
Obviously not everything I said is strictly required for victory... I'm just throwing all the ideas I could think of...
TL;DR: Ammo mutation bad... Pump a ton into the other mutations... Stash some ammo early... Try to keep track of enemy max health... And get things that allow you to attack more than once per turn... (And get strong items/upgrades in between as you normally would...)
Side note: Root's gun does work with snake eyes... You can reduce her health to 0... It doesn't matter that she heals after you've already done that...