Bacterial communities on chopping boards

Last week we met up with our group of citizen scientists to discuss the results of their chopping board experiment.

The experiment saw the group splitting into two teams. One team selected wooden chopping boards, the other plastic ones. Each household unpacked their new board and washed it according to their own habits. Each household also kept a record of the different foodstuffs they chopped on their board each day.

Each chopping board was swabbed six times over a period of 14 days. The swabs were prepared and analysed using 16S sequencing to identify the types of bacteria found on them at each time interval. 

The graph below is a similarity plot. The red points are from plastic boards, and the blue points from wooden ones. Each point on the graph is a community of bacteria on a chopping board. How close two points are to each other reflects how similar their bacterial communities are. You don't need to try and understand the axes - just think of them like the grid squares on a road atlas.

Similarity Plot for bacterial communities on chopping boards. Red dots = plastic boards; Blue dots = wooden boards.

Similarity Plot for bacterial communities on chopping boards. Red dots = plastic boards; Blue dots = wooden boards.

As you can see, the bacterial communities we found don't seem to be that different based on the type of board. We were a bit surprised by this, as we thought we might see different types of bacterial community preferring different surfaces. Perhaps we would need to keep swabbing the boards over a longer period for this to occur? Or perhaps the frequent washing and seeding of the boards with different foodstuffs stopped identifiable patterns emerging? There was no clear signal emerging from the type of foodstuff being chopped on each board, but this may have been due to the general diversity in foodstuffs being prepared across all the boards.

Similarity plots for all chopping boards, sampled 6 times over 14 days. Red dots = swabs from day 14. Grey dots = swabs from previous days.

Similarity plots for all chopping boards, sampled 6 times over 14 days. Red dots = swabs from day 14. Grey dots = swabs from previous days.

This second plot is from the end of the two-week period. The red dots are from the swabs on day 14, and all the grey dots are from swabs on previous days. As project microbiologist Rich explains,

"It looks as though perhaps that the points are becoming a little bit closer together - a hint that there is such a thing as a set of bacterial species that are happy on chopping boards. In the past, at day zero, you had all sorts of things living on them, and then the ones that aren't so happy on plastic or wood are dying off." 

So whilst we didn't see much difference between wooden and plastic boards, we did perhaps see the beginnings of an emerging, generic "chopping board" community of bacteria.

Gut Flora Exhibition

Many thanks to one of our participants for sharing this: they recently visited the Radcliffe Science Library's "Gut Flora" exhibition. This art-photography series showcases University research about gut bacteria, how these bacteria interact with antibiotics, and what the interactions mean for our health. 

The collection was created by University medical researcher Dr Nicola Fawcett and photographer Chris Wood, and is on display in the Hooke Staircase of the library until May 2017. Access is restricted to those with a University card, but you can view all of the images online here (scroll down for the individual images and their explanations).

As the exhibition material explains:

"Microbes live on us, and with us. They don't just make us ill - they also protect us from infection, and keep us healthy. Our gut is like a forest, or garden, where microbes flourish in a balanced, mini ecosystem."
"Competition keeps bacteria under control. One way we can prevent the spread of 'antibiotic-resistant bacteria' is by preserving the 'good' bacteria in our guts, to heep the resistant ones in check. We can do this by not overusing antibiotics, and saving them only for when we really need them"

You can read more about Nicola Fawcett's work on her blog.

 

Fridge ecologies

At the recent meeting of the Good Germs project, the participants drew up a shortlist of possible microbial mapping experiments for the coming months. The list included mapping: the microbial signatures of their pets, the microbes in their food, those radiating from compost caddies or on kitchen utensils and food containers, as well as mapping the microbes in their fridges. This week we've had an online vote, and the fridge mapping experiment has won. 

So, the next round of microbial mapping is going to explore "fridge ecologies". Each of our participant households is going to swab the inside of their fridges. Then they are going to swab four different food items, straight from the shopping bag or allotment basket, before they put them in the fridge. Some of these will be wrapped (and the packaging swabbed), others not wrapped (and the skins and surfaces swabbed). One week later, they will swab the inside of the fridges again. Watch this space to find out what happens!

Cleaning products and bacterial ecologies

A few months ago, our participants conducted their second attempt at bacterial mapping. 

Their experiment explored how different cleaning methods affected the bacterial communities found on their kitchen surfaces. They tested eight different methods for cleaning kitchen surfaces: washing up liquid, warm water, anti-bacterial surface cleaner, bleach, environmentally-friendly detergent, vinegar, special cloths, and even a probiotic cleaner. They swabbed the surfaces before cleaning them; they swabbed the cloths they used in cleaning; and they swabbed the surfaces afterwards. The swabs were then taken to the lab, and prepared for sequencing. 

This graphic shows combined data from 26 separate cleaning product experiments. Each experiment swabbed a surface before cleaning, swabbed the cloth used for cleaning (using one of eight possible products), and swabbed the surface again after cleaning.

This graphic shows combined data from 26 separate cleaning product experiments. Each experiment swabbed a surface before cleaning, swabbed the cloth used for cleaning (using one of eight possible products), and swabbed the surface again after cleaning.

The results from the 16S sequencing are tricky to interpret. First, the method doesn't distinguish between "live" and "dead" DNA - so the swabs done after cleaning don't tell you if the bacterial DNA represents live bacteria or not. And second, there is some controversy amongst microbiologists about whether sequencing "reads" can be interpreted as proxies for bacterial abundance. 

This graphic shows the data from an individual household. Each household tested two products.

This graphic shows the data from an individual household. Each household tested two products.

Nevertheless, the patterns found are pretty interesting. The bacterial communities found on kitchen surfaces after cleaning tend to look an awful lot like either: (i) the community found before cleaning, (ii) the community found on the cloth used to do the cleaning; or (iii) a mix of the two. And they don't look anything like some other surfaces we swabbed as controls, which is reassuring. Also, if the abundance measures are to be believed, most of the cleaning techniques lead to very little reduction in bacterial abundance (although for those products that work by killing bacteria rather than removing them, the DNA found may well represent dead bacteria).

This graphic aggregates the 26 experiments according to which cleaning product was used. The number at the top of each column represents how many households tested this method - which was their own choice.

We met to discuss these findings last week - and a big thanks are due to Adam Hardgrave from the Food Standards Agency who came along to help us interpret the data!

Project film and experiment update

We have just released a short film that introduces the Good Germs project. You can watch it on the website here

Thanks to everyone who was involved in making the film!

We are currently gearing up to the next meeting with our participants in Oxford, and analysing the data generated in their second experiment. In it, they each tested two approaches to cleaning the work surfaces in their kitchens. The various methods included hot water and washing up liquid, vinegar, antibacterial cleaners, eco-cloths, eco-detergents, and bleach. The surfaces were swabbed for bacteria before and after cleaning, as were the cloths that everyone used. We have the data from the sequencing lab, and are currently working through the analysis - watch this space for the results!

Mapping the bacteria that colonise chopping boards

On the hottest day of the year our project participants met up to talk about the bacteria they've found in their kitchens. 

Project scientist Rich talked about the results so far, including maps of the most and least diverse areas (floors seem more diverse than sinks; door handles more diverse than chopping boards) and bubble charts showing the different groups of bacteria most prevalent in particular places. The group then discussed the difficulties involved when trying to make sense of 'good' and 'bad' bacteria when there are so many different types of bug; and when the broader taxonomic groupings (and even individual species) include both good and bad germs. The challenge of visualising the data produced through bacterial sequencing to address such concerns remains tricky and, at times, frustrating for all!

chopping boards.jpg

In the second part of the meeting, the group came up with an idea for a new experiment: one that looks at how bacterial communities colonise food preparation equipment, and how those communities change (or stabilise) over time. They decided to focus on chopping boards, and are going to swab new boards six times over the course of two weeks to see what bacteria are found on these boards and how that changes (or not) over the fortnight. Seven households are going to use plastic boards, and seven wooden boards, to see if this makes a difference to the colonies that form. Each household is going to keep a 'chopping diary' of the types of food they prepare on the board. And given that we already have data on the bacteria found in each household, we might be able to see if the boards take on the 'microbial signature' of the kitchen to which they are issued. We're all excited about what we might find!

A huge thanks again to all our microbial explorers,

The Good Germs Bad Germs team.

Chopping boards and bacteria

Our visualisation team (Rich and Andrew) are continuing to work with the data from the first kitchen safari conducted by our participants earlier this year. Below are some more of their early results.

The bubble charts below show the types of bacteria on chopping boards, and were produced using the open-source platform Phinch. The data comes from several of our participating households in Oxford, and is organised according to phyla (the highest taxonomic level used to categorise types of bacteria). The size of each bubble shows how many of the different sorts of bacteria we found belong to each phyla. This data is still pretty raw - for example, we haven't yet removed the data from plant material DNA that might be boosting the relative abundance of cyanobacteria (both chloroplasts in plants, and cyanobacteria produce energy through photosynthesis, and they share a genetic heritage which affects the sequencing results). Finding remnants of lettuce on kitchen chopping boards would hardly be surprising! But nevertheless you can see some interesting bacterial similarities and differences between the various households. 

Each picture shows the types of bacteria (at the phyla level) found on a single chopping board:

Kitchen Microbe Maps

Below is a map of bacterial diversity in the kitchens of East Oxford, collated from the 14 households taking part in our project. It comes with a whole bunch of scientific caveats, some of which I discuss below, but is interesting nevertheless. Kitchen floors seem to be the bacterial equivalent of rainforests, teeming with all manner of different microbial creatures. Sinks and chopping boards, by contrast, seem to be more specialised habitats, attracting a discerning set of bacterial denizens. 

Map 1: Microbial diversity in all the kitchens sampled

microbial diversity in kitchens map

The data comes from a ‘kitchen safari’ conducted by our participants earlier this year. Each household swabbed five common locations in their kitchens: chopping boards, work surfaces, sinks, door handles, and floors. The swabs were analysed using 16S sequencing, and the map is an early output of our analysis. But since it will take a while to analyse the data in full, the maps are based solely on the bacteria that we can recognise immediately (by comparing them to a "library" of known DNA sequences). Further analysis might change the overall patterns. And we have also had to make a series of assumptions in order to use this early data as a proxy for diversity – we will write more about this in another blogpost soon.

Despite the caveats, the broad patterns shown in the map above seem interesting – and especially when compared to what our group was expecting to find. Before we plugged the map into the dataset, we asked all of our participants to colour it in themselves, based on their own hunches about microbial life. Three things stand out. First, when combined, peoples’ hunches were pretty accurate. Second, the outlier seems to be sinks, in which the diversity appears to be relatively lower than people were expecting. This might say something about cleaning practices, constant immersion with water, or about the particularities of sinks as microbial habitats – plenty for us to explore going forward. And third, we should have asked people to swab their waste bins and their pet’s living quarters! Maybe next time that is what they will choose to swab themselves.

Map 2: Expected microbial diversity according to group meeting drawings

map of expected microbial diversity in kitchens

Getting the data

The last few weeks have been a busy time here at the Good Germs Bad Germs project.

First, the metagenomic sequencing data we have been waiting for has finally arrived from the laboratory. The data relates to our participants' first "kitchen safari", in which they sampled five common areas: sinks, worktops, chopping boards, cupboard handles, and the kitchen floor. Each household also chose one further location to sample, which ranged from fridge shelves to their pets' water bowls. Rich is currently analysing the data using the power of cloud computing, to try and make sense of all the DNA fragments that have been identified - so we should be getting the bacterial diversity results within the next few days.

Second, our households' next experiment is well underway. This time, our participants have chosen to explore the micro-ecological effects of different cleaning products on their kitchen surfaces. The group has tested the effects of anti-bacterial cleaners, eco-detergents, standard washing-up liquids, vinegar, bleach, warm water, and even 'pro-biotic' cleaners (that 'seed' surfaces with 'good' bacteria in order to make them inhospitable to 'bad' ones). All the pre-sequencing steps have now been completed, and these samples are in line for the sequencing machine - watch this space!

And finally, we have also been hosting a camera crew who are making a short film about the project. Thanks again to everyone who made time for the camera people, especially those who hosted us in their homes. 

 

Group meeting and colouring pencils

A massive thanks to our Oxford participants for giving up their Tuesday evening to talk about bacteria! In the first of a series of meetings scheduled for the next eight months, we met to talk about good germs and bad germs, where they might live in kitchens, and how ‘metagenomic sequencing’ might help us visualise their abundance and diversity.

What is ‘metagenomic sequencing’? It’s a technique for finding out what bacteria are present in a sample by ‘reading’ their DNA. Traditional methods of microbiology relied on growing bacteria in petri dishes – of the sort you might remember from school biology classes. But it turns out that many bacteria don’t grow too well in a dish. Metagenomic techniques don’t have that problem, because they don’t require live bacteria to work: just DNA. And they let you find out about the whole bacterial community in a sample, not just about single species.

Our plan with this project is to use metagenomic techniques to help people explore the bacterial communities that live around their kitchens. We are still waiting for the results from our first ‘kitchen safari’, in which our participants sampled their chopping boards, worktops, sinks, cupboard handles and kitchen floors. But the results should be with us in the next few weeks.

When the results arrive, we should be able to see which areas of our participants’ kitchens have the most bacterial diversity, and which areas the least – like showing where the microbial equivalent of the Amazon rainforest is (chopping boards, perhaps?), and where the bacterial Saharan desert might be found (freshly cleaned worktops?). We will then be able to compare these ‘actual’ results to what our participants thought we ‘might’ find – as shown in the pictures attached. These are ‘heat maps’, coloured in by our participants to show where they expect to find the most diversity, and where the least.

 

Whilst we wait for that data, we are also waiting for the result of our participant vote on the next kitchen experiment. Will our group choose to explore the bacterial communities that emerge on freshly washed cutlery and plates, those on their various kitchen bins, or even the communities to be found in fermenting food? Watch this space!