The panda’s woes are well-documented. Their habitat is shrinking, they are incredibly fussy eaters and they have an unusually lacklustre approach to sex.

Now scientists have discovered that the bears are also poorly adapted for digesting bamboo, despite the plant being almost the only thing they eat. The research shows that two million years after shifting to a herbivore lifestyle, the giant panda still has carnivore-like gut bacteria, which is better at breaking down protein.

The discovery could explain some of the animal’s more baffling traits, including spending almost every waking hour eating and its apparent indifference towards attempts at reproduction.

Zhihe Zhang, director of the Chengdu Research Base of Giant Panda Breeding, China, and lead author, said: “Unlike other plant-eating animals that have successfully evolved anatomically-specialised digestive systems to efficiently deconstruct fibrous plant matter, the giant panda still retains a gastrointestinal tract typical of carnivores. The animals also do not have the genes for plant-digesting enzymes in their own genome. This combined scenario may have increased their risk for extinction.”

Iain Valentine, Director of Giant Pandas at Edinburgh Zoo, described the findings as “hugely interesting and an important piece of the panda’s evolutionary jigsaw.”

Giant pandas evolved from bears that ate both plants and meat, and started eating bamboo exclusively about two million years ago. It is unclear what triggered the shift away from meat – possibly the lack of available prey or the relative abundance of bamboo. Scientists believe that the transition to a herbivore lifestyle may have become permanent, however, because pandas are known to have lost the gene for the savoury “umami” taste receptor. “We think they lost the gene that is the driver behind them wanting to eat meat,” said Valentine.

But while they lost their taste for meat, they do not appear to have developed any of the usual digestive apparatus of herbivores. They retain a carnivore’s digestive system, with a simple stomach and a short intestine rather than the four-chambered stomachs that cows rely on to digest plants efficiently.

The latest study shows they also lack the gut flora that would allow them to extract most energy from fibrous plant material.

As a result, pandas spend up to 14 hours each day consuming up to 12.5 kg (27.5 pounds) of leaves and stems, but digest only about 17% of it. To conserve energy, the bears also spend up to 12 hours each day sleeping, giving the impression of an animal that eats purely to have enough energy to carry on eating.

In the study, published in the American Society for Microbiology journal mBio, the scientists sequenced the bacteria from 121 faecal samples from 45 giant pandas living in Zhang’s Research Base. Samples were obtained during the spring, summer and late autumn of one year. The pandas typically ate at least 10 kg of bamboo leaves and shoots each day, and 500 to 800g (1.1 to 1.7 pounds) of steamed bread.

The gut bacteria was found to be similar to that of carnivorous and omnivorous bears, but very different from other plant eaters. The panda lacked plant-digesting bacteria such as Ruminococcaceae and Bacteroides and instead had guts dominated by Escherichia/Shigella and Streptococcus, which are efficient at processing proteins.

“This result is unexpected and quite interesting, because it implies the giant panda’s gut microbiota may not have well adapted to its unique diet, and places pandas at an evolutionary dilemma,” said Xiaoyan Pang, of Shanghai Jiao Tong University and a co-author.

Valentine said the findings add to the picture that the panda has adopted an almost unique digestive strategy. “The upside is they’ve got a digestive system that deals with very large volumes of material very quickly,” he said. “You have to remember there aren’t many predators around so they’ve got the time on their hands to sit around eating all day.”

He added that the findings may help to inform an ongoing study in Edinburgh, involving the zoo’s pair of pandas Tian Tian and Yang Guang, into colic, which often afflicts pandas and is also thought to be linked to changes in gut microbes.

“It’s similar to irritable bowel syndrome (IBS) in humans,” said Valentine. “They get stomach cramps, go off their food and lie in a heap for a few days.”

The inefficiency of the panda’s digestive system could explain the animal’s apparent reluctance to reproduce. Female pandas ovulate only once a year, in the spring, and have a window of only two to three days around ovulation when they are able to conceive.

The embryo then has a couple of months of “delayed implantation” when it remains in a state of arrested development until it attaches to the uterus and starts to grow.

Scientists now think that the precise timing of conception, implantation and birth may all be driven by the seasonal availability of different nutrients in bamboo plants.

“The accusation that they’re rubbish at reproducing isn’t really fair,” said Simon Watt, author of The Ugly Animals: We Can’t All be Pandas. “They bred OK in the wild. Part of the problem now is that the small population means that the pandas that are bumping into each other are all related.”