The Gut And The Microbiome

The logistics of poo! Researching the microbiome: A Q&A with Dr Nigel Field

Parenting Science Gang has a new group looking at the microbiome.

For two weeks, our citizen scientist parents are working with Dr. Nigel Field (UCL) Prof. Peter Brocklehurst (Birmingham) and Rachel Plachinski (NCT) from the upcoming Baby Biome Cohort Study – a large scale study that plans to follow 40,000 babies from birth to find out more about the fascinating science of the microbiome.

The success of this project depends largely on… lots of baby poo!

Here, we chat with Dr Nigel Field to explore how the study could get even better at collecting poo!

Dr Nigel FieldNigel: Hi everyone joining this evening. Thanks in advance for your help!

Currently, we are collecting the following samples around the time of birth: mum’s poo sample and vaginal swab, and cord blood from the baby

Then we collect a poo sample from the baby at 7 days and 6 and 12 months after birth.

We did well in the pilot study, but the success in sample return has a big impact on the success of the study, basically driving many of the costs, so anything we can do to improve the success of sample collection – i.e the proportion of participants providing a sample, would really help

We didn’t pay our participants, but they were kind enough to provide samples in the following proportions to give you an idea of where we are at:

  • mum’s poo about 10%
  • vaginal swab 65%
  • cord blood 40%
  • baby poo at 7 days 50%
  • baby poo at 6 months also about 50%

The study also includes collection of baby poo at 12 months

PSG E: With the numbers above, does this mean that you could only use those who provided everything, which would mean max 10% of people who signed up but more likely less?

Nigel: It depends on the question – but the key driver of our sample size is the return rate of the baby poo.

PSG E: I’m intrigued as to why that was the critical issue… babies make so much poo! I’d be happy to give it away 😀

PSG F: So if baby doesn’t poo on day 7, they won’t be included in that percentage? My son pooed about 100 times a day in the first week but my daughter only pooed 2 or 3 times in the first 2 weeks!

Nigel: We were a bit more flexible than that – but aimed for around 7 days

PSG G: How much of the variation was down to the mums and whether they agreed, and how much down to the HCPs and what they did?

PSG F: Did you get any feedback as to why the return rate was so low on maternal stools? We are all theorising a lot on how each of us would or wouldn’t have been able to give a sample, I’d be interested to know how many actually couldn’t give a sample vs how many simply forgot or didn’t have anyone (mw?) to help

Nigel: Not a lot of feedback – and hard to give you the break down you’ve asked for – I would love to know this too. Overall, I think it is a difficult and socially awkward sample to give and therefore perhaps quite easy to give it a miss at a time when there is a lot of other things going on

How to improve the response rate?

Nigel: What I would be interested to know is to focus on the return of samples and understand what might help us to improve the response rates. Particularly the return of baby poo samples, but also return of mum’s poo.

PSG G: For the baby poo samples, do you give people a receptacle and a stamped addressed envelope? Or what? And so you remind them in some way?

Nigel: Yes, exactly, the mums leave hospital with a kit including a tube with a spoon in the lid, a short form to complete, and an infographic to explain what to do.

PSG H: If there was something like a Facebook or other social media group (or maybe some kind of closed app, if you don’t want discussing all on FB), I wonder if that may help keep the participating mums in the loop. And remind them to do their samples. Two times, I didn’t know what day it was when I had a newborn. But I was still able to get on FB every once in a while.

Nigel: Nice idea – we don’t have a Facebook group actually – and perhaps needs to embrace social media more in the first weeks of recruitment of participants to the study. Thanks!

PSG A: Yes a FB group is good, then people could discuss it and other parenting stuff plus get reminders – get them more engaged.


PSG F: Nigel, you mentioned that questionnaires were required, we’re these paper based ones? I would be far more likely to answer an online one, I always have my phone on me but rarely know where a pen is! You could send links / reminders to these via Facebook messenger / WhatsApp / email etc and tie this in with the sample reminder.

Nigel: Yes, pilot study used paper-based questionnaires because we didn’t have resources to develop online systems for the pilot. We would almost certainly do both for the main study though.

PSG G: You spend a lot of time online in your phone in the middle of the night when you have a new baby. Or I did any way.

PSG F: I definitely did!

PSG H: me too!

The logistics of poo

PSG D: Babies poo a lot to begin with. I’d have no issue with that. It’s the logistics of getting mine…

PSG C: So you need to get baby poo three times – at 7 days, 6 months and 12 months. How do the mothers need to actually get it to you?
e.g. do they need to post it / give it to someone / does it get collected?

Nigel: They post it back – we found that poo was stable in the post for up to a week. Although had some sympathy for the postman!

PSG H: I’ve had to do something like this when I had food poisoning – send a sample away in the post to confirm what I was dealing with. Wasn’t the most pleasant thing I’ve ever done, but the postie had no idea.

Nigel: Yes, postman should never know – and sample is in proper bag and envelope required for a ‘biological sample’…still

PSG C: So did the mothers simply get a stamped addressed envelope?

Nigel: Yes – the pack or kit we gave also contained a stamped addressed envelope

PSG R: My son is part of a trial at the moment for babies with Down syndrome and we didn’t do a birth poo as we joined the trial late but we’ve done it at 6 months and 12 month. The 6 month one I had to provide my own sample also. the kit was very easy to do and pop in a pre done envelope and post. Was no problem at all.

PSG C: If you had to return an envelope containing baby poo, would you find going to the post box or a courier coming to your house easier?

PSG K: If you can just pop it in a normal post box I’d find that easier than staying in waiting for a courier.

PSG J: Post box, because courier knocking and coming in would potentially wake a sleeping baby.

PSG B: Post box as agree wouldn’t want to wait in

PSG E: Definitely post box

PSG L: 100% courier, particularly for the 7 day old poo. I wonder how many of the pilot study participants collected the poo but then didn’t get around to posting in time and so just didn’t bother?

PSG F: Post box – but would the time taken to return be an issue? All our post boxes are emptied pre 9am round here!

PSG A: Probably post box but could you give people the option – like with online shopping returns where you’ve got several options of how to return?!

PSG H: I would have preferred post box rather than deal with even more people, but there’s one very close to me. Not sure how I’d feel if I had to walk a mile to find one.

PSG G: On balance, post box. Cos then you can drop it off on your way somewhere and don’t need to wait it.

PSG M: Post box, who wants to hang round waiting in for a courier who will ring the door bell at the wrong time be it you’ve just got baby down for a nap or you’re juggling baby and boob!

PSG N: I think I may have preferred courier at 7 days but post box for others

Reminders & incentives

Nigel: We could design simple experiments into the main study of 40,000 to test the ideas here in a randomised way to see whether, for instance, small financial incentives might increase the response rates for poo.

PSG B: Obviously I don’t know how you did it before but I think as long as there was a ‘kit’ (swab and bottle) and a pre paid envelope in the way you want it packaged then most people would probably return. Maybe a leaflet about how important their contribution is to the research, particularly for the 12 month sample as by then I bet they will have forgotten!

Nigel: We did text mums to remind them at 7 days, and we hope this helped.

PSG D: That would have worked for me. Think we had our first outing on day 7

PSG C: I would need lots of texts I think! Could you do an experiment with different amounts of alerts? Or even asking people how many alerts they want? I know I like reminders, so I’d pick lots.
But some people find it intrusive so lots of reminders could be counter productive.

Nigel: Yes, thanks – we could try different numbers of texts, and I like the idea of giving participants the option. The text reminders were automated, so this is something that might be reasonably easy to set up and test.

PSG E: Regarding baby poo at 6 months and 12 months, what communication or reminders did mums receive on this? Were there email reminders or phone calls? I would have likely needed this, though the action of capturing and posting the poo would have been straight forward.

Nigel: We sent a one-page letter, briefly explaining and thanking participants, and we also sent a text reminder. Difficult to balance being annoying to participants with trying to remind them and get the best return rates

PSG C: Could you ask them what level of reminders they want? I know I’d like lots, others know they don’t want many.

PSG E: I’m not saying it’s the best idea, but if you were to go down the email route too, you can get analytics that shows you open/click through/etc, and also schedule customised follow up emails based on the actions taken. I don’t think it’s too intrusive if you communicate at sign up what they can expect to receive from you at various times. I think it’s fair that if you are signing up to what may lead to a 70 year long study to expect that the researchers are heavily invested in your engagement! But I think that the combination of text + follow up phone call would be the most effective as a busy mum.

Nigel: This is helpful – as a researcher, it is often difficult to know what level of interaction is okay – and we spend quite a lot of time thinking about this and then taking it through ethics – we haven’t tried email. Phone calls are possible but then become time consuming compared to text or email which can be at least partially automated

PSG G: I would think a couple of countdown reminders, and then several more reminders that you should have done it by now!

PSG E: Yes, if you keep an unsubscribe option readily available I really don’t think you need to worry too much about hassling them with reminders!

Rachel: Regarding good reminders about returning poo, I’m wondering about giving parents something they will find useful, which has the study name and logo on it. So for the birth sample you could give them a copy of the NCT leaflet on ‘What’s in a Nappy?’  and get it co-branded. This only covers the first week or so, so we could talk to NCT about producing another one, covering poo changes around introducing solid foods, and send that out as part of the pack for the six month sample. What does everyone think?

PSG E: Good idea. All new mums are obsessed with what their baby’s poo looks like, so would probably love a good leaflet with pictures

Nigel: Nice idea – thanks, Rachel. We had a bag with the study logo on, but that was mainly for the midwives. We didn’t give the participants anything like this

PSG O: Rachel brilliant idea.

Rachel: I’ve been trying to think of things that people will see and think “oh, that’s useful” so they keep it to hand. Can’t think of a good 12 month ‘bribe’.

PSG A: Could have something weaning related for 6 months?

PSG H: This would be very handy. I managed to forget almost all of my weaning advice between one baby and the next.

PSG K: In terms of reminders for the later samples I think it’d help if you posted the sample kit to the parents at ~5 months and ~11 months with perhaps a text reminder at 12 and 6 months. I’d have mislaid them by the time it got to then if I’d been given them when I signed up

PSG I: Two email or text message reminders per sample ? I’ve such a bad memory; thanks to sleep deprivation. An option to join a Facebook group would be great

PSG D: Oh yeah a Facebook group would be good

PSG Q: I like the idea of a Facebook group to help encourage and remind mums. Might also remind them that they’re involved in something positive and interesting which may be an incentive in itself.

PSG C: The dynamic of the cohort group being in contact and how they support each other could be an interesting study in itself!

Rebecca: Thinking back to those early days, what would make you battle through the challenges of the early days of motherhood if you were finding it tough, to get out to post some poo?
What incentive (if any) would work for you?

PSG K: Getting children centre groups and NCT groups involved could be a good way of improving responses as there tends to be groups where everyone gives birth within a few months of each other so can act to remind each other

PSG F: With my first, I was bed bound for a couple of weeks so my husband was amazing. Incentives wouldn’t have made any difference, he made it out to register the birth, get food etc so could have easily posted something for me. Reminders would have been more important than incentives

PSG H: Information about my own kid’s biome. 🙂
But realistically speaking, the promise of an Amazon voucher will also get me to answer surveys, so that would work for me too. 😉

PSG J: A lot of new mums look at joining groups to build a new baby based network – Baby Sensory / music groups / massage etc. You could try to partner to offer free sessions?

Nigel: Interesting – would probably have to be something national level to make it feasible – or via FB or other social media

PSG E: I believe that blood donation research shows that it’s mostly done for altruistic reasons, and research from business shows that sometimes paying people more reduces their motivation… I wonder if it’s similar for people signing up for this study?

If you wanted to trial it for a smaller group, the timing of incentives would be important though, if you want to encourage them to get the 7 day sample sent back. So maybe giving them something at the hospital once all the hospital samples are collected would be most effective (I’m not sure how you would hand it over though). My thoughts would be something that combines humour, intellectual interest and a small financial recognition (but small) would cover the most bases for motivation. Maybe the financial amount could increase as they send the subsequent samples.

PSG E: I wouldn’t have been doing it for a reward, but as you say, it’s a tough time to ask for anything extra from a new Mum. Feedback on your own personal results would be the only thing I’d want, I think. Or maybe acknowledge and thanks after the team have received each sample.

PSG M: Personally wouldn’t need an incentive as I’d take part out of interest.
Maybe some kind of momento of the project that was a keepsake for your child would be a nice way to explain how they were part of science right from birth!

PSG D: Honestly just a reason to leave the house. Post box does that for me! ?

PSG C: Do participants currently get feedback on their results?

PSG O: Or perhaps something like planting a tree in one’s baby’s name, or something like that, could make a really good incentive.

Nigel: I like the idea – perhaps something like this could be done for every 100th (probably wouldn’t be able to afford for all!)

PSG A: It’s tough, we’re all here because we’re interested in the science and therefore probably wouldn’t need much extra motivation but I’m guessing a lot of people will sign up without necessarily being as interested as us so a small extra push might help at 7 days post partum when it all seems too hard! I would say probably vouchers and/or special feedback on your child’s results/the study. A memento is a nice idea, particularly if it’s going to be a longer term thing that has significance to the child in an ongoing way.

Nigel: Agree – we have to think about the widest possible group of people who might take part and their reasons for taking part – so that we get a diverse selection of people in the study

PSG E: I’ve been given vouchers for research and they became increasingly valuable the further I went into maternity leave.

PSG B: I have a baby who is 7 weeks now and I think actually the hardest bit would be getting to the post box ? but I wouldn’t want a reward. I think to receive personal data back about your child’s biome would definitely be interesting though although not everyone is science minded.

Nigel: True – we did talk about that a bit – although it is currently hard to know how to interpret an individual’s microbiome. Would still be interesting though

PSG M: I’d love a copy of my child’s microbiome even if it didn’t mean much to me, that along with the results of the entire study would be an amazing incentive/keepsake.

PSG N: I think something for my child would be an incentive, a cool key ring about the microbiome for them to keep!
I think cash would get people just wanting to get the money and might compromise the samples, or giving false answers on questionnaires in case they are worried a certain answer would mean they don’t get paid

PSG O: Nigel have you considered a certificate of participation?

PSG L: I think it would help to tie the poo collection to something else where someone else could help remind / collect the sample. I know I’d probably lose the collection kit, forget to collect poo at most nappy changes, and then struggle to get out the house and post it once collected.
If the 7 day poo could be collected a bit earlier / later perhaps midwife could support this at the day 5 / 10 visit?

I also wonder if a Facebook group of participants might help – mums can share tips about best way to collect poo (invariably someone will have questions) and it also acts as a reminder and a bit of an incentive to keep participating?

PSG C: I love this idea! People would get instant gratification when they’ve posted the poo by being congratulated people who totally get it! If I posted my poo at 7 days I’d be totally chuffed – but not sure any of my other friends would be that amazed!

But if I could say to the other participants “hey, I posted the 7 day poo today!” I’m sure people would congratulate me and that would incentivise other people to do it too wouldn’t it!

Nigel: Facebook group suggestion is a good one, and coming up a few times, although we’d have to be mindful of the people who didn’t engage with social media and the potential biases therein

PSG P: Incentives… I don’t think I’d want an incentive. I’ve taken part in a few studies and one did give love to shop vouchers (it was a Gestational Diabetes study) and I just felt really guilty every time one arrived, I’d rather just do it and hope I was helping in some way. I do think though, if any incentive is offered a voucher isn’t a bad idea-people aren’t getting something they don’t want so money isn’t wasted.

PSG C: What made you feel bad about it? Was it taking money from the project?

PSG P: Yes, studies like that tend to struggle to get funding anyway so I just thought the money could be better used somewhere else. I do understand its a good tool to get people involved generally but I (like) to think people are happy to engage in studies around maternity/newborn/infant matters for more altruistic reasons.

Collecting samples at labour

Rachel: Does the type of birth make it easier (or harder) to collect samples? Some of the points made on the group today were about how difficult it can be to poo after birth.

Nigel: Yes – we found this did have an impact. For example, cord blood was higher in C-section babies, and I think poo samples from mums were lower in that group

Rachel: How close to birth does the sample have to be produced? Could a midwife collect any poo produced during labour, for example?

PSG E: Regarding the issue of the 10% returning birth-day poo from mums, what was the window of time you permitted on either side of the birth? For instance would you allow 24hrs on either side of the time of birth? I am conscious that not everyone poos every day, and although those with vaginal births are quite likely to poo during labour (and it could be caught if pre-agreed), those with c-sections may be more likely to be missed, or those with very long labours (mine was 1.5 days) may poo too early in labour. My personal view (episiotomy and stitches) is that getting poo pre-birth is somewhat easier than getting it post-birth if you are working to a fairly tight window of time.

Nigel: We did allow flexibility either side of birth for the mum’s sample to help with differences in regularity!

PSG A: And if mums were going in for induction or planned Cesarean could they collect their last poo pre heading to the hospital?

Nigel: The mum’s poo can be within a few days either side of birth. The baby poo is more fixed – and needs to be at 7 days after birth, and then at 6 months and 12 months after birth

PSG B: How do you take the cord blood sample and how much do you need? As I know people might be concerned as to whether it would impact their choice to have delayed cord clamping.

Nigel: We wait until the clinical needs are completed, and that includes delayed clamping – and cord cell banking takes precedence. So we hope to allay that concern

PSG D: I’d give it go on 2nd birth, but not first. I was pretty preoccupied with pushing out a human and stitches.

PSG C: I was high as a kite after a whole day of gas an air! I couldn’t even tell you if I’d pooed or not!
I’d need help from someone to collect it – like the midwife / doula, definitely!

PSG D: Snap! I’d find it much easier to have a midwife collect it while I was birthing I think

Nigel: Ha! Yes, we hoped midwives might be able to help with collecting poo from mums.
However, when we asked about acceptability, we found the midwives found it a bit less acceptable than mums … suggesting we had some work to do convincing them too!

PSG D: But presumably they are removing any stools for the sake of cleanliness as a matter of course? Suppose it might slow things down a bit and mean that attention is diverted at a pretty crucial time though

Nigel: True – on both cleanliness and having a huge number of other things to do and worry about.

PSG E: Did they have to return it to the hospital or did someone collect?

PSG D: Or can you post it like with bowel cancer screening?

Nigel: The baby poo samples (and some of the mum’s poo) was returned to our lab by post

PSG D: I donated cord blood and had delayed clamping. Would it be possible to do all 3?

Nigel: It depends on the amount of blood in the placenta – I would say possible, but unlikely.

PSG I: For c section would it be possible for midwife to do a swab ? I had c section with my second and frankly given how invasive it is; would not have minded a swab.

Nigel: Yes, we gave participants the option of taking the swab themselves, or getting a midwife to do it.

PSG I: The affect of non vaginal delivery on baby’s microbiome was a major concern for me

That would help with collection rates for c section. Also simple balanced literature explaining the value of the study related to non vaginal birth.

PSG J: For mothers – unless there was collection by midwife at the point of birth the idea of self collection in a pot etc may not be that appealing. Perhaps you could design/employ some kind of toilet seat type apparatus to filter and collect the poo?

Nigel: It was certainly not that appealing to mums – we tried various options of a pot that slung below the seat, and a kind of cling-film sling … didn’t seem to make a big difference to our success though!

PSG D: Because it is painful for a lot of mums post birth I think. And honestly there’s a lot to think about ‘down there’

PSG D: Could you combine the request with a booklet of tips to make post birth poo more comfortable?

PSG J: It’s just not going to be high on the agenda. It’s painful and I recall feeling anxious! It might be that you have to engage the staff if mums are flagged as within the study the nurses assist with the implementation of the capture contraption within the toilet? So perhaps financial incentives for them rather than the mums?!

Nigel: Yes – also interesting idea to give a booklet and advice about this. I think it can often be an issue, so might be welcome advice even if someone didn’t want to give us the sample

Rachel: NCT also used to produce a leaflet on Blood Loss After Birth, which was very popular with mums. We could cost co-branding that, or perhaps expanding it a bit to talk about bowels and tips for coping with stitches and constipation, perhaps! …

PSG E: Maybe it would be worth targeting fathers/birth partners and giving them the task of reminding about the sample. Brand new mums have a lot going on.

PSG D: I might have killed my partner to be fair.

Nigel: I agree that partners could be important – I hope that many of the posted poos were taken to the post box by the partner…

PSG C: I hope so too, but I wouldn’t be too certain to be honest. The reality in our culture is that for a lot of couples, all-thing-baby fall to the mother in the early days. That may also include sending off poo samples.
I may be wrong – just a hunch!

PSG F: That’s the closest my husband would have got to my sample, it would have to be fully sealed before he’d have anything to do with it ?

PSG P: I’d be happy to donate anything I (or baby) didn’t need but I’d need the midwife/ hca to collect, couldn’t cope with husband doing it!

PSG L: When it comes to the maternal poo sample, I can see this being difficult if it’s not collected during labour. Is an actual poo sample needed or could a swab do the trick (eg swab before you wipe)? This would be a fair bit easier and less challenging to achieve

PSG H: I like the idea of a maternal swab. I was constipated pretty badly towards the final weeks and had two water births. And was frayed on no sleep and keen on getting out of postnatal ward asap. So, unless the midwives were able to add setting aside the big sieve to their to-do lists, I’d probably find a swab more achievable.

Nigel: Rectal swab would be great. Unfortunately, we are pretty sure that a swab is not going to give us what we need – we think it would mostly have bacteria from the skin, rather than from the bowel, and it might not have the bugs present in the appropriate proportions, so would be difficult to compare with other studies, including our own pilot

PSG A: Just thinking about my personal experience – my son was 5wks premature so still in hospital at 7 days. Yet you don’t want to lose those babies from the sample as they will be getting interventions that affect their microbiome. Could you have a stash of spare sample kits in the hospitals where you are targeting participants? Otherwise they may not have thought to put the baby sample stuff in the hospital bag so may not have it to hand and low down the list to send someone home to find it.

Nigel: Yes – this was a big issue for us – and we got a lot of help from neonate wards, where is did try to stash kits. Space always an issue on the labour ward and neonatal wards though!

PSG S: Is it possible to collaborate with NHS trusts, and thus getting midwives and health visitors to help remind participants to keep sending samples.

Nigel: Yes, we’ve tried to collaborate with the NHS trusts as much as possible – and in the future would want to link with the community midwives and their home visits

Related Links

The Baby Biome Study

Does vaginal seeding boost health?

The Second Genome: Dirt & Development (Radio 4)



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