The Microbiome: Seeding Some Questions

The current next big thing in health news seems to be the Microbiome. According to a growing number of reports it could be involved in everything from Schizophrenia to Obesity. So there has been speculation about where it comes from and if how a baby is born, either vaginally or by C section, could determine the make up of their Microbiome and even their future health. In this post I’m going to take a look at those claims and at some newly published research which attempted to “seed” the Microbiome of babies born by caesarean.

I’ve been re watching some classic episodes of the X files recently. One (Ice) starts with a panicked man repeating the phrase ” We are not who we are”. It turns out he’s being controlled by a tiny alien parasite, which is all pretty fantastical (also mid 90’s CGI – lol). But there is growing evidence that our physical, and even mental, health could be influenced by the huge number of microbes living in and on us. It is a fascinating, huge and complex new field of research so I’ve been wondering just how excited should we be getting about it right now and do we know enough to start making changes to our lives, or our children’s lives, based on it?
A study published this week starts to bring together three threads of the Microbiome story; 
1- Many previous studies have reported links between the Microbiome and a huge range of medical conditions. 
2-Others report that babies born by C section are more likely to develop certain diseases. 
3- A final set have found differences between the Microbiomes of babies born vaginally and those born by C section. 
So it’s tempting to suggest (as many media reports have) that:  C section = bad Microbiome = poor health. 
Or even that the worldwide increase in obesity and other diseases should be blamed on the increasing C section rate. But that seems like a bit of a leap at the moment, and there are quite a few blanks that need to filled in in that equation before we can be sure. 
The idea behind the new study is that babies born vaginally rub against and swallow their first dose of Microbiome organisms as they make their way through their Mother’s vagina. Babies born surgically clearly don’t do this, so the researchers attempted to “seed” the microbiomes of the caesarean born babies by placing a swab in their Mother’s vagina for an hour prior to birth. Then wiping it over the new born’s mouth and skin. 
Some people reading this may think it’s about as weird as something Mulder and Scully would investigate, but a few Mums are already requesting the procedure and others are advocating it strongly as a way to restore some of the natural processes of birth. So this first published data will no doubt be of interest.
But I have a few questions,

Actually I have loads of um, first up….

Is the Microbiome Cause or Coincidence?
Just because a study shows a link between certain Microbiome characteristics and a disease, that doesn’t prove the former is causing the latter. The same can be said for links between C sections and medical conditions. 
I wrote in 2014  about a study which found an increase in obesity in people born by C section. Both factors are becoming more common in many countries but does that mean c sections are causing obesity? Could the two increases just be a coincidence or could there be a third factor that’s driving up both? It’s really not clear yet and that’s before we start thinking about how/if the Microbiome is involved. Unfortunately throwing in speculation about healthy and unhealthy Microbiomes seems to be a good way to grab a bit of media attention though (see this post from November for an example of this). 


What is a healthy Microbiome anyway?
While quite a few studies have shown that the Microbiome of C section born babies is different to that of their vaginally born peers, it’s worth remembering that different doesn’t necessarily mean worse. It’s easy to assume that the Microbiome of vaginally born babies is better because it was acquired through a natural process. Maybe it is, but nature doesn’t go about producing perfect finished products and as I said above, we don’t yet have much evidence for Microbiome changes actually causing or preventing specific diseases.

One big thing that isn’t made clear in a lot of Microbiome news stories – we don’t really know what’s there. Current tests can miss some species all together and only notice others at the genus level. Lactobacillus were looked at in the seeding study, but there are at least 180 different species included in the Lactobacillus genus, they may all do subtly different things.

Another problem is that most Microbiome research looks at what’s in the gut using, well, poo samples. Not all the bacteria will come out in poop. So we have even less chance of identifying those hanging on in there in the gut.

So instead of charting the entire Microbiome, most studies look at the presence or proportions of particular bacteria. But our Microbiome is likely to be a complex ecosystem and the way different species work together may be even more important than the percentage of a particular individual.

Where Does Seeding Some in?

The seeding study found that babies who were born by C section and then had the seeding procedure carried out, developed Microbiomes that were more like those of vaginally born babies than of C section babies without the seeding. So if more evidence comes in that my c section = bad stuff equation is actually true, it could be a way of preventing that bad stuff.

Some more buts though…

This is (as the authors make clear) a very preliminary study and the numbers involved are tiny I mean seriously tiny. The test group was made up of just four babies and there is also no information on how they were chosen. So it is possible that the reason for the C section or even the mother’s reason for agreeing to take part, could also influence her Microbiome and that of the baby. For example, Mums agreeing to seeding might have been strongly motivated to make their births as natural as possible, these values could also alter their diet, how they care for their baby or their home environment.

 Another important issue is that the study only checked on the babies until they were one month old. So we can’t know if the differences continued once they hit crucial milestones like weaning, and crawling around sucking on shoes (that’s not just my kids right?). It certainly doesn’t tell us anything about the health of these babies in the long term.

Again the authors are quite clear on this – more work is needed, way more, for longer periods and with more babies. If seeding does turn out to be useful this might not even be the best way to do it. In the future we may be able to identify the key beneficial organisms, and produce a simple treatment containing them. The Microbiome of the gut seems to be very important but wiping a gauze over a baby might not be enough to get that going.

But if there are possible benefits should we just give it a go?

The study authors also state that they aren’t provided a guide for DIY seeding.

Everyone’s Microbiome is unique. It’s not just a couple of species, it’s a whole, complex ecosystem and ecosystems are rarely made up entirely of the cute and harmless. Some bugs, which live unnoticed on a full grown adult, can be very dangerous for new borns. We probably all have some nasties lurking around, perhaps kept in check by the other species surrounding them. The process of seeding won’t transfer as many bacteria to a baby as they would get in a vaginal birth but worse, it’s possible that it could transfer the wrong mix, with more of the harmful bacteria making it across. There needs to be a huge amount of work done to optimise the procedure before we can be sure it works or even that it’s safe.

A couple of things struck me as potentially problematic with the protocol in the study. Firstly not everyone has an hours notice of their C section so many Mums won’t have time to do the gauze technique and planned C sections can get delayed (mine was by hours) leaving the gauze in place too long may encourage nasty bacteria. The researchers also wiped the baby with the swab within two minutes of birth, before handing the baby to doctors for “standard detailed checks”. This means the baby wasn’t spending it’s first few minutes next to it’s mother’s skin. Something which is often now considered the ideal and which may itself aid Microbiome seeding.

The Ranty Bit

Along with epigentics, the Microbiome seems to be the current fashionable scientific field for health news and, as ever, some of that news is a bit misleading. In researching this I’ve come across stories based on tiny or poorly designed studies and on unpublished data, press releases and interviews. If this post seems overly negative it is only because so much of what I’ve read veers wildly in the other direction, So a great deal of caution is needed when trying to draw out useful facts from the noisy excitement. But with all that said, I still think the Microbiome is fascinating and may live up to all the hype around it. In the future we may well be thinking about food and supplements not just for their taste or nutritional value but for how they will benefit our internal ecosystems. I just don’t think we are quite there yet.

In terms of seeding, lots of babies have been born by C section and most of them live normal healthy lives. Surgical birth clearly doesn’t determine a child’s entire destiny, and I am wary that the idea of seeding may be pursued by some because of a belief that C sections are unnatural and therefore, somehow, always inherently wrong. I was disappointed to see that both the seeding paper and a comment article about it claimed that only 10 – 15 % of c sections were medically necessary and referenced the long since outdated and abandoned WHO claims on this.We certainly need to understand the risks of surgical birth, but we need facts for that, not just belief in the wonders of nature.

 If I was going to opt for any kind of medical intervention with a precious new born, be that seeding or vitamin K injection* or anything else, I’d want to weigh up the risks and benefits. With the microbiome we don’t even know what the risks and benefits are yet, never mind how they stack up against each other. The new natural worlds we’re discovering in our own bodies are fascinating and wonderful but to try to recreate them based on our current understanding would be like trying grow a new Amazon when we’ve only identified parrots, ants and few Brazil nuts and our gardening experience amounts to growing cress in an egg shell. This study is just a first attempt at preparing the ground.

I’m sure we’ll be hearing a lot more about this in the coming years as more work is done on the subject, and as all X Files fan’s know:


* The benefits of vitamin K injections are well understood, as are the risks, the benefits definatly win by the way.

PS. Thanks to Clare and Selina on the Caesarean In Focus group for sharing links and to Lisa my lovely microbiologist friend who knows way more about bacteria than I do!

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