The researchers found nearly 150 genes in the human genome that did not come from our ancestors but via horizontal transfer from donor species like bacteria.
The traditional view of evolution is that the struggle to survive influences how genes of individual organisms are passed on to new generations through Darwin's natural selection.
And an assumption in that view is that it is the organism's package of genes - the individual's genome - alone that changes subject to this pressure, and passes on the "competitive advantage" to future generations in the form of mutations.
But recent discoveries - especially to do with cohabiting species - are beginning to challenge this view, and suggest that the boundaries of what genes are being passed on in evolution are not as clear as we might think.
For instance, in the journal Science in July 2013, scientists from Vanderbilt University in Nashville, TN, show - after studying wasps and their gut microbes - that it is not just the host organism but the host accompanied by its microbiome that evolves.
'Foreign' genes can enter animal genomes 'sideways' via horizontal transfer
And now a new study from the University of Cambridge in the UK suggests that "foreign" genes can enter the genome of humans and other animals "sideways" - through horizontal transfer from micro-organisms cohabiting the same environment.
The researchers show not only that this happened in the past, but that in some lineages, the process is still ongoing.
Horizontal gene transfer as a source of competitive advantage is not a new idea - there is a lot of evidence that it happens in bacteria and other micro-organisms. For instance, it is well-known that this type of gene-swapping is a driver of antibiotic resistance.
Gene-swapping is also thought to play a role in the evolution of some animals. Nematode worms, for example, have acquired genes from micro-organisms and plants. There are beetles that can digest coffee berries thanks to enzymes coded by genes their ancestors acquired from bacteria.
But the idea that horizontal gene transfer occurs in more complex animals like humans and primates is more controversial.
Lead author of the new study, Alastair Crisp, of Cambridge's Department of Chemical Engineering and Biotechnology, says theirs is the first study to show that horizontal gene transfer occurs widely in animals and humans - giving rise to tens or hundreds of active "foreign" genes.
He notes that far from being a rare occurrence, it appears that horizontal gene transfer "has contributed to the evolution of many, perhaps all, animals and that the process is ongoing."
"We may need to re-evaluate how we think about evolution," he adds.
Nearly 150 human genes were acquired via horizontal transfer from other species
For their study, the team studied the genomes of four species of nematode worm, 12 species of fruit fly, and 10 species of primate, including humans.
They compared how well the genes in each of the genomes of one species aligned to similar genes in the genomes of the other species. From this they could estimate how likely they were to be foreign in origin and how long ago they were acquired.
They found 17 previously known genes in humans that were acquired through horizontal transfer and identified a further 128 that were not known.
One of the genes - the ABO gene that determines blood group - was also confirmed as being acquired by vertebrates from horizontal gene transfer. Most of the genes were related to enzymes involved in metabolism.
Some of the genes thought to have arrived in the human genome through horizontal transfer are involved in the metabolism of fat molecules and amino acids, in various immune processes, protein modification, and antioxidant activity.
Bacteria one of the most common donors of horizontally transferred genes
The team also identified where the horizontally transferred genes came from. The most common donors were bacteria and another type of micro-organism called protists. Other genes came from fungi and they also found viruses had donated more than 50 genes to primates.
Their analyses suggest that while fruit flies and nematodes have continued to acquire foreign genes via horizontal transfer throughout their evolution, humans and other primates have gained relatively few since their common ancestor.
However, the authors also say they may have underestimated the true extent of horizontal gene transfer in animals and note that transfer between complex organisms is also plausible, and already known in some host-parasite relationships.
They note that their study also has wider implications for genome sequencing research. For instance, many studies exclude evidence of bacterial genes from results because the researchers assume they got there through contamination.
Co-author Dr. Chiara Boschetti, also from the Department of Chemical Engineering and Biotechnology at Cambridge, explains:
"It's important to screen for contamination when we're doing genome sequencing, but our study shows that we shouldn't ignore the potential for bacterial sequences being a genuine part of an animal's genome originating from horizontal gene transfer."
The European Research Council funded the study.