It's only confusing because you are used to being in a place with air

Mot of the universe is "empty". The stuff tends to all congregate in certain areas due to gravity.

Air is attracted to dense objects. The further away from dense objects you get, the less of everything there is.

Nothing. A vaccume is just the absence of air.

I guess in a way you can say gravity encapsulates it by holding air onto large objects.

The tube only encapsulates the vacuum on earth because earths gravity holds an atmosphere - the tube is keeping that atmosphere at bay. In space there is no atmosphere to keep at bay - the amount of matter is incredibly tiny compared to the vast distances between clumps of it.

The more bizarre thought is that in space “nothing” is holding the small amount of “somethings”.

It's the reverse -gravity is encapsulating the atmosphere, and therefore atmospheric pressure.

Empty space is the result

Vacuum is the normal state of space. You live in an atmosphere pressurised by gravity. To create a vacuum within that pressurised atmosphere we have to counteract the effect of gravity, but we only have enough power to do in for small spaces, hence a container.

It isn't the vacuum that causes the capsule to collapse but the atmospheric pressure outside of the capsule that causes it to collapse. It is exactly the same with a submarine. It is impossible for humans to survive pressurizing the inside of a submarine to equal the thousands of pounds per square inch water pressure on the outside of the submarine. The submarine implodes if a breach in the vessel occurs. A breach in a spacecraft or an aircraft at 30,000 feet causes the spacecraft or aircraft to explode into the lower pressure outside. Space is a vacuum because it has a volume without molecular pressure that is so vast it approaches infinite. There are vast interstellar clouds of molecules in space but they are so widely dispersed that the pressure is still so miniscule as to be a vacuum by comparison to the atmospheric pressure at 150,000 feet above the Earth's surface.

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Gravity. The atmosphere stays close to the surface of the earth because of earth’s gravity. When you get up high enough, gravity doesn’t pull hard enough to keep the air molecules bound to the planet. But lower down, the weight of the molecules above the ones at that level help keep them bound to the earth.

This is also why Mars doesn’t have a thick atmosphere.

You only have to "encapsulate" it if there's something to separate it from.

In space, there's not.

First, the vacuum of space isn't inside something else. Remember that a vacuum is a volume with nothing inside it; no gas, liquid, or solid, nada (technically the vacuum of space isn't perfectly empty, but it's close enough). The reason space is a vacuum is that matter, like those gases, liquids, and solids, has mass; things with mass attract other things with mass (that's what gravity is). Simply put, matter clumps together, which is why stars, planets, and other things form.

Since that matter ends up clumped together, the space left between those clumps is more or less empty -- in other words, a vacuum.

Second, the negative pressure of the vacuum by itself is not what causes a collapse. Remember how matter clumps together because of its mass? The more mass something has, the stronger its gravity, and the more firmly things are clumped up. Earth's mass is great enough, and its gravity strong enough, that the gases in the atmosphere squeeze things inside it very strongly; at sea level, the weight of the air that is above a square inch of paper, going in a column all the way up to the top of the atmosphere, is almost 15 pounds. The higher up you go, the less air there is above you pressing down, which is why air pressure gets less the higher you go. In addition to that, those gases want to fill any empty space (because gases expand), so if there's an area that they can expand into, they will.

Combine those two things, and the air around you is actually pressing quite strongly on everything around it. So if you take a water bottle, and suck all the air out of it, there's nothing inside it -- in other words, a vacuum. But because a vacuum is literally nothing, then there's nothing inside that bottle pushing back against the air outside it -- which, as we just saw, is pushing really hard against that bottle. If the bottle had water inside, it would be strong enough to resist the air pressure at sea level -- even if it had air from the room it would be strong enough, because that air would be at the same pressure -- but the plastic along isn't strong enough. So it goes squish.

What causes the bottle to collapse isn't the negative pressure by itself; it's the difference between the positive air pressure outside crushing the bottle, and the lack of pressure -- negative pressure -- inside.

Imagine two people leaning against each other with their hands. Suddenly one of them lets go and steps out of the way real fast. With nothing stopping them, the other person falls forward, squashing anything that's under them. Removing the air from the bottle is like that person stepping away.

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Vacuum doesn't create negative pressure, the atmosphere creates positive pressure. For us on earth this difference isn't significant, but it does explain stuff like why the vacuum of space doesn't pull the atmosphere off the earth.

So when your teacher opens the vacuum flask and lets the air rush in it isn't because the vacuum inside the flask pulls the air in, it's because the air pressure outside pushes it in.

Look at this image

The vertical axis is the escape velocity in kilometers per second.

The horizontal axis is surface temperature in Kelvin.

Surface temperature causes gas atoms to speed up. The higher the temperature the faster the speed.

Simply speaking, if the speed of gas atoms caused by the surface temperature exceeds the escape velocity caused by gravity, gas atoms float off into space.

The so-called vacuum of space happens because gravity attracts more gas atoms to stars, planets, moons, asteroids, comets, etc. than are floating in the space between these objects.

Here is an article on the atmosphere of the Moon.

I feel like we’re all ignoring the fact that a physics teacher doesn’t understand gravity.