His hypotheses about the "red rain" phenomenon in Kerala have attracted controversy.
In April 2008, he published a paper in which he hypothesised that samples of particles from the "blood-coloured" rain that fell in his state of Kerala, India in the summer of 2001 were the result of a comet disintegrating in the upper atmosphere which comprised mainly microbes from outer space.
Other scientists disagreed early on with Louis' hypothesis regarding the red rain's origin.
[3] Since October 2006 Louis has been at Department of Physics, Cochin University of Science and Technology (CUSAT) in Kochi, Kerala.
In August 2010 Louis and his collaborators presented a paper at the SPIE astrobiology conference held in San Diego, USA, claiming that the red rain cells develop internal daughter cells and multiply when exposed to extreme temperature of 121 °C in an autoclave for two hours, and that the fluorescent behavior of the red cells is similar to the extended red emission observed in the Red Rectangle nebula.