METAL GEAR SOLID 3: Snake Eater - Master Collection Version

For this you need to capture one of every consumable flora and fauna in the game. Human-made foods like rations are not required. You also do not need to eat them, just collect them. They can be either dead or alive. Thermal goggles and the motion sensor will be helpful for finding critters hiding in tall grass. You can do this on any difficulty, but the following locations are known to work for the Easy difficulty.

Maybe make a spreadsheet with the different foods and check them off as you get them. Or alternatively, eat the organism and it will be listed in the statuses in the cure menu.

Food does transfer between the Virtuous Mission and Operation: Snake Eater.

I did not get the achievement while also getting the Tsuchinoko endgame ranking. So if you go for this, capture the Tsuchinoko and then eat it. You also should make sure you get an alert once and kill a soldier once, since those rankings will also override the Markhor rank. If you are achievement hunting, make a save right before the final fight so you can complete the last requirements for a peaceful/total stealth/Tsuchinoko run.

With that out of the way, here is every animal, vegetable and mineral in the game that you need. I'll list the first locations that I found them, however most things spawn in multiple locations.

Birds
[Bird A] - Parrot. Potentially a pain to get. Will spawn during the fight with The End. I recommend playing on Very Easy/Easy just for this little critter. See my guide on collecting all birds for more details.
[Bird B] - White-Rumped Vulture. Krasnogorrje Mountain Base.
[Bird C] - Red Avadavat. Graniny Gorki Exterior. Stun grenades work if you suspect that one is in some brush.
[Bird D] - Magpie. Dremuchij North. Also on the roof of the building in Rassvet.
[Bird E] - Sunda Whistling Thrush. Dremuchij North.

Fish
[Fish A] - Bigeye Trevally. Ponizovje South.
[Fish B] - Maroon Shark. Ponizovje South.
[Fish C] - Arowana. Chyornyj Prud.

Frogs
[Frog A] - Otton Frog. Chyornyj Prud.
[Frog B] - Tree Frog. Chyornyj Prud.
[Frog C] - Poison Dart Frog. Chyornyj Prud.

Snakes:
[Snake A] - King cobra. Dremuchij North. Left of the exit in the tall grass.
[Snake B] - Taiwanese cobra. Chyornya Peschera Cave Branch. Caves right after the fight with Ocelot.
[Snake C] - Thai Cobra. Chyornya Peschera Cave Branch. Later they spawn in Krasnogorrje Mountain Base.
[Snake D] - Coral Snake. Chyornyj Prud, Bolshaya Past Crevice, or Sokrovenno South.
[Snake E] - Milk Snake. Chyornyj Prud. To tell the difference between milk and coral snakes, a little rhyme my step-dad once told me was "If red touches black, you're okay Jack. If red touches yellow, you're a dead fellow."
[Snake F] - Green Tree Python. Dremuchij North.
[Snake G] - Giant Anaconda. Dremuchij South.
[Snake H] - Reticulated Python. Dremuchij South.
[Snake I] - Snake Liquid. Rokovoj Bereg. The last location in the game where you fight The Boss. Look near a log.
[Snake J] - Snake Solid. Rokovoj Bereg. Look near another log.
[Snake K] - Snake Solidus. Rokovoj Bereg. Look near yet another log.

Other animals
[Bat] - Vampire Bat. In the caves after the fight with Ocelot.
[Crab] - Kenyan Mangrove Crab. In the caves after the fight with Ocelot.
[Gavial] - Indian Gavial. Chyornyj Prud.
[Markhor] - Markhor. Where you fight The End.
[Nest] - Baltic Hornet's Nest. Dolinovodno.
[Rabbit] - European Rabbit. Bolshaya Past Crevice.
[Rat] - Rat. Rassvet. Underneath the building where you find Sokolov.
[Scorpion] - Emperor Scorpion. Krasnogorrje Mountain Base.
[Spider] - Cobalt Blue Tarantula. Krasnogorrje Mountain Base.
[Squirrel] - Japanese Flying Squirrel. Graniny Gorki South.
[Tchnko] - Tsuchinoko. See my guide on how to catch the little critter.

Fruits
[Fruit A] - Yabloko Moloko. Dremuchij North.
[Fruit B] - Russian False Mango. Dremuchij South.
[Fruit C] - Golova. Dremuchij North.

[Vegetable] - Vine Melon. Svytagornyj South. Looks kind of like a cucumber hanging from the trees.

Mushrooms
[Mushroom A] - Russian Oyster. First area of the game.
[Mushroom B] - Ural Luminescent. Svytagornyj West. Look at the base of trees.
[Mushroom C] - Siberian Ink Cap. First area of the game.
[Mushroom D] - Fly Agaric. Graniny Gorki South.
[Mushroom E] - Russian Glow Cap. Bioluminescent mushrooms in most caves.
[Mushroom F] - Spatsa. Svytagornyj South.
[Mushroom G] - Baikal Scaly Tooth. Svytagornyj South.

Medicinal plants (NOT THOSE KIND OF PLANTS!)
Styptic Plant. Svytagornyj South.
Cold Medicine Plant. Dremuchij East.
Disinfectant Plant. Svytagornyj South.
Splint Plant. Svytagornyj South.

The medicinal plants are annoying. You must actually pick them up for them to count. And they must come from the plants, not as pre-existing items. If your health supplies are full, use an explosive at close range and hurt yourself. Then go to the Cure menu and use one the items your full on. This will free up space for more. Medicinal plant do indeed count for the rank, even though they're not named and you do not eat them. Pre-made foods like rations do not count, although it's unlikely that you won't have found a bunch of them by the game's end regardless.