"Within your guts is an entire ecosystem of bacteria, that you rely on for many of the day to day activities of your life. They produce vitamins, aid in digestion and serve a number of other useful purposes – like bolstering your immune system. But here’s the thing – Neanderthals almost certain had their own ecosystem of gut bacteria. It’s not known right now, though, exactly what those flora were. Indeed, it’s not known exactly what human gut flora is. The NIH has an entire initiative – the Human Microbiome Project – dedicated to finding that out. What’s definitely not known, though, is whether a Neanderthal could survive with the gut flora that modern humans take for granted."
Is It Possible To Clone A Neanderthal? - Forbes