How would the Great Atmospheric Catastrophe come about?

Around ~2.3 Billion Years ago, the Atmosphere changed radically: Cyanobacteria started pumping out Oxygen and the atmosphere gradually became Oxygen rich.

~2.3 Billion Years is a long time, even in a geological timescale, I want to see a great De-Oxygenation event take place on a more human timescale, say a thousand years. The change doesn't have to be permanent (though that would be nice) and should occur naturally (eg: reverse-cyanobacteria, all oxygen producing plants dying due to a cross-species virus, etc) but may not be geological (so no volcanoes). The change only has to reduce or remove Oxygen, other gasses don't matter.

To be clear: the change should be caused by something in the biosphere, that includes humans, but it should not be deliberate. The new atmosphere should be unbreathable, or at lease harmful over long periods.

The less time that it takes for the atmosphere to become unbreathable, the better.

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How would the Great Atmospheric Catastrophe come about?

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