Conventional wisdom would have us think the uterus is a fairly pristine environment, at least as far as germs go. Recent studies on fresh placentas, amniotic fluid, and even baby's first poop, have consistently said otherwise.

But what if the microbes isolated in those cases were simply contaminants? Now, that's looking less likely than ever, with researchers taking unprecedented care in a recent study to ensure the microflora they uncovered could have come from only one place.

A group of Australian researchers from Edith Cowan University and the University of Western Australia applied rigorous control measures in their efforts to isolate bacteria from amniotic fluid and meconium - a faecal-like material produced by newborns.

"Over the last decade, numerous studies have detected bacterial DNA in amniotic fluid and first-pass meconium [baby's first poop], challenging the long-held assumption that the womb is sterile," says reproductive biologist Lisa Stinson from the University of Western Australia.

"However, some argue that the results are false positives – contaminants in the reagents used in DNA analysis."

This isn't to cast aspersions on the manufacturers of laboratory products. But bacteria have had billions of years to perfect their ability to survive conditions we'd imagine too hostile for life.

When it comes to establishing something as controversial as our microbiome developing before we're even born, nobody wants a cheeky stray bacterium posing as a red herring.

To really make sure their materials were as clean as clean could get them, Stinson and her team pulled out all the stops, leaving little room for doubt that any bacteria in their samples were there prior to extraction.

Some of those samples came from 43 pregnant women who gave birth via a caesarean section. During the delivery procedure, 10 millilitres of amniotic fluid were carefully collected immediately on incision and transferred into sterilised tubes.

Over the following day, 50 samples of meconium were collected from the volunteer's newborns, also taken with care to preserve their sterile nature.

The team went on the hunt for signs of bacterial DNA. To ensure there were no stray genomes hiding in the reagents, they dosed them with an enzyme that would rip double-stranded DNA fragments to shreds.

"Despite these measures, we still found bacterial DNA in almost all samples," says Stinson.

"Interestingly, the meconium microbiome varied hugely between individual newborns. The amniotic fluid microbiome for the most part contained typical skin bacteria, such as Propionibacterium acnes and Staphylococcus species."

With zero indications that these were the result of infection, it's fairly safe to presume this represents a healthy process, with bacteria colonising a new human body long before it's ventured into the world.

It was long believed that infants get their starting dose of microbes as they squeeze through the birth canal. That would mean a caesarean delivery wouldn't provide access to the vagina's microbiome, leading some to even swab newborns with a 'seed' of vaginal fluids.

But recent research has shown that this belief, and subsequently vaginal seeding itself, isn't based on sound evidence.

While our early environment can shape the selection of bacteria that set up shop inside our bodies, it's seeming more clear than ever that there are already some founding members on our skin and in our guts before we're born.

They're probably not just sitting around twiddling their bacterial thumbs, either.

"We found that levels of important immune modulators in meconium and inflammatory mediators in amniotic fluid varied according to the amount and species of bacterial DNA present. This suggests that the foetal microbiome has the potential to influence the developing foetal immune system," says Stinson.

It's important to emphasise that in spite of the team's efforts, it's impossible to categorically rule out contamination of any sort.

One species called Pelomonas puraquae was found in virtually all the samples in amounts high enough to make them question if it was an outside intruder. But it was also possible that it was a contaminant from the meconium itself, jumping between samples, while ultimately still representing uterine bacteria.

Given results describe bacteria DNA and not functional cells, we should also leave room for the possibility that these are the remains of destroyed invaders.

"Here we've proven that bacterial DNA is present in the womb, but the next step will be to show whether these are alive and constitute a true microbiome," says Stinson.

If so, microbes really could be shaping our development from some of the earliest moments in life.

This research was published in Frontiers in Microbiology.