Vitamin B12.
Vitamin D (actually even carnivores can be deficient as they need sunlight to make it)
Long Chain Omega 3 fatty acids.
Iodine
Iron
Calcium
Zinc
Well-planned vegan diets can fulfil nutrition needs for all stages of life.
That said, certain nutrient requirements may be difficult to achieve through diet and fortified foods alone.
This is especially true for vitamin B12, vitamin D and long-chain omega-3s.
True, but a typical meat-eater's diet can also be deficient in such things.
You can generally get sufficient Omega-3 by ensuring you eat stuff like chia seed, hemp seed, or walnuts, and of course you can get sufficient Vitamin D by simply making sure you are outdoors for a good few hours every day.
B12 is a definite problem, though for a strict vegan. As you say, a lot of the supplements are animal derived.
A good way of supporting the gut biome is to consume fermented foods like kimchi or kombucha.
