Wombat pouch microbes: protecting the young?

Marsupials are born without a functioning immune system, yet they manage to survive, how?

Being born young has its challenges. In humans, preterm babies (born before 37 weeks in the womb) have poorer survival outcomes compared to babies born at full term. The same is not true for marsupials, who, unlike us, are born at a much earlier stage (within 1-6 weeks).

While marsupials share many features with placental mammals like us (e.g. providing milk to their young), we are actually quite distantly related. Current evidence suggests that we share a common ancestor with marsupials ~160 million years ago – back when dinosaurs dominated Earth! A big difference between us is that marsupials have pouches; this is highlighted in the name, as marsupial derives from the Latin marsupium, meaning bag, pouch, or purse. Upon birth, the tiny joey (baby of the marsupial world) embarks on an epic journey, crawling from the birth canal to the pouch while exposed to the harsh outside world (watch this video to witness how this happens in kangaroos). Once in the protective pouch, the joey attaches itself to one of the mother’s teats and grows. When the joey is too big for the pouch, it witnesses a ‘second birth’, leaving its mother’s cosy pouch for the outside world.

How does the underdeveloped joey survive being born into a microbially rich world without a functioning immune system to protect itself? The mother has a few strategies up her sleeve to help. She packs immune cells and antibodies into her milk which she feeds to her joey. Her pouch itself changes and starts secreting antimicrobial compounds that bathes her joey and protects it from infection. Researchers in the 1970’s and 1980’s tested whether pouch secretions inhibited microbes, by taking samples from the pouches of quokkas. They could not grow microbes (or grew very few) from the pouches of quokkas with joeys (or pregnant mothers soon expecting), whereas microbes could be grown from samples from non-reproductively active females. Microbiology has come a long way since the 1970’s, and it’s now possible to survey microbes without growing them by isolating and reading their DNA. This method allows for a better assessment of microbial diversity, as many microbes still can’t be grown in labs. With this in mind, for our study we wanted to use modern DNA technology to investigate what microbes are found in the pouch, and how they change in response to the reproductive cycle of the mother.

The marsupial we chose to study was the Southern Hairy-nosed Wombat (Lasiorhinus latifrons), the faunal emblem of South Australia. How did we collect pouch samples from these wombats, who spend most of their time underground? This is where Dr David ‘Tags’ Taggart, a co-author of the study comes in. Tags has over 30 years of experience studying the ecology and behaviour of this species and has developed an effective method for capturing them in the field. We went out under the cover of darkness, armed with custom-made wombat nets (10-foot steel poles braced with ultra-tough netting). A spotter would shine a high-powered spotlight onto a wombat (usually sitting on its burrow doing its business), which would temporarily stun it, allowing the people with nets enough time to swoop in and make a catch. Easier said than done, considering the finesse involved in running over uneven terrain with minimal visibility all while carrying a 10-foot steel net. Wombats are also exceptionally strong, with some reaching weights of up to 30 kg!

Over three field trips, we managed to capture and sample 26 wild female wombats, from which we collected microbial samples from their pouches using swabs. We took these swabs back to the lab, where we isolated and read the microbial DNA. From this data, we found that the diversity of microbes was very high in the pouches of non-reproductively active females (similar level to control skin swabs), with this diversity dropping drastically if the female had a joey in the pouch or was expecting. The types of microbes that we found in the pouches of reproductively active females did not appear random, with 4-5 microbial species dominating the community. We next searched a large DNA reference database to see if these dominant microbial species had any matches to microbes previously isolated. While we did not find any exact matches, the closest match for three of these species were to pouch microbes previously isolated from tammar wallabies. The number of genetic changes between these microbes is consistent with the time we think wombats and tammar wallabies shared a common ancestor (~50 million years ago), which could suggest that these pouch microbes have been cospeciating with marsupials.

To summarise, our study was the first to investigate wombat pouch microbes, and using newer DNA-based methods, we replicated previous pouch microbe research that found drastic drops in pouch microbial diversity associated with the mother protecting its newly born joey. Our results highlight that the microbes that manage to survive in the wombat pouch are not random and may be found in the pouches of other marsupials. Could these microbes be another form of protection for the joey? Microbes are adept at fighting other microbes, and from an evolutionary point of view, microbes that benefit their host (e.g. through protection) would improve their own survival by having a host to live in. There is much still to learn here, and we hope that future research in the pouch will expand our understanding of how animals and microbes can work together to each other’s benefit. Such research may also discover novel and medically-relevant antimicrobials, which are desperately needed given the rise of antibiotic resistance plaguing our hospitals.

Dr Raphael Eisenhofer, Post-doctoral Researcher, School of Biological Sciences, University of Adelaide.

Professor Kristofer Helgen, Chief Scientist and Director, Australian Museum Research Institute.