Add some neutral vegetable oil to a large pot and bring to medium-low heat. Add in the sliced onions and shallots and cook down for about 30 minutes, covered. Stir occasionally until onions are soft and caramelized. Be careful not to burn your onions!

Then, add in the minced garlic and sauté until fragrant, about 1 minute.

Add lentils, water, salt, and thyme. Simmer for about 30-45 minutes, uncovered, until lentils are soft. Add miso paste and mix well.

Taste, and adjust seasonings if necessary, keep warm.

Meanwhile, toast bread with cheese. Serve hot soup with cheesy toast croutons.