Making microbes public workshop - 3rd and 4th May

Stories about the human microbiome are increasingly being reported in the media and many people –  myself included – are fascinated by the relationship between humans and the microscopic ‘bugs’ that live on, in, and around us. I was part of a workshop last week, where a group of interdisciplinary scholars explored this relationship under the theme of ‘Making Microbes Public’.

The workshop began with an afternoon keynote presentation from microbiologist Anne Madden, who was fresh from delivering a TED talk in Vancouver on ‘bugs and bodies’. Anne gave us a frontline view of the work of scientists working with microbes and especially those who closely collaborate with industry partners. Anne describes herself as a ‘microbe wrangler’ and she focusses on how to harness the positive attributes of microbes and apply these in practical ways that will benefit humans.

The next day, we started with a session on ‘Microbes in Society’, and presentations from three anthropologists. Alex Nading began by introducing us to the bureaucratic routines that are part of the day-to-day biopolitics of food sanitation in Nicaragua. He provided a detailed and nuanced account of the interactions between bureaucrats and citizens that occurs during the food handling certification process. Food workers must undergo a blood test and provide a stool sample for analysis and this process is caught up in different layers of informal cultural practices and formal legal requirements. Alex’s narrative of the Nicaraguan public hygiene system reveals how social relations, understandings about microbes, and bureaucracy become intertwined.

Another anthropologist, Amber Benezra, took us on a fascinating journey which linked the work of scientists in North America to the daily life of poorer people living in Dhaka. This presentation revealed there is a problem when microbial science focusses on a ‘technological fix’ such as probiotics for malnutrition, when infrastructure problems such as open drains and other health sanitation issues also need to be addressed. It seems that by working closely with scientists, anthropologists can help resolve some of the disconnections between the laboratory and the realities of everyday life problems. But Amber also raised the question of who holds scientists to account especially when biological science aims to solve problems which are beyond the scope of ‘the biological’.

The third presentation, was from Eben Kirksey who introduced us to bacteria called wolbachia.  This is an extremely common parasitic species that lives in insects. This species can reorganise the bodies of their hosts at the microbial level, including changing the sex of their hosts. Interestingly, the ubiquitous and sheer numbers of wolbachia in the world, challenges the notion of heteronormative sex.  Eben left us to consider a potential future where polyamorous and promiscuous bacteria like wombachia could survive well beyond human life.

The second session of the day was called ‘Doing Microbiology with Citizens’. This began with Jamie Lorimer and Tim Hodgetts outlining their research on the Good Germs/Bad Germs project. They have been exploring the domestic microbiome through the development of a participatory approach to microbiology. This project involves households in Oxford, going on a ‘kitchen safari’, where participants and the researchers have worked together to design experiments on kitchen microbiomes. Findings from the research suggest it is challenging to move beyond thinking about microbes as pathogens. There has also been positive feedback from some participants who have felt empowered by their involvement in the research design and data collection.

Claire Waterton then provided an overview of her research on the impact of algae (cyanobacteria) blooms on a Lake District community. This interdisciplinary project is tracing the relationship between the microbial organisms who live in the lake and the human residents living alongside it. We heard about how it was difficult to assign blame for the cause of the algae blooms, due to the complex natural and human systems that are in the area. The project set up a collective which enabled different stakeholders’ viewpoints to be incorporated into a complex, and sometimes uncomfortable, debate about community life on the lake.

The next presentation, from social and cultural geographer Emma Roe, described her work engaging health professionals in hand hygiene practices. This research used experimental methods to map the movement of microbes in a hospital setting, including asking two nurses to put UV powder on their gloves and then carry out some routine activities in a ‘mock ward’.  Under UV light, all the places that were touched could be mapped. And it turned out that in a 4 minute bed chance, there are over 200 moments of touch! Emma’s research team have produced a video which encourages health professionals to ‘keep washing, keep caring’.

The final presentation before lunch included a gastronomical experience, where we were able to taste a number of fermented yeast products. Josh Evans, who will be coming to Oxford in the fall to commence his doctoral studies, talked about the relationship we have with microbes through food. He explained how fermentation can be understood as a collaboration between humans and microbes. Josh has been working at the Nordic Food Lab in Copenhagen where some ‘convivial experiments’ relating to fermentation techniques are taking place between chefs and scientists (and microbes!) We were given two liquids to taste as well as a teaspoon of dark paste. Although some of us were a bit unsure about tasting these concoctions, they turned out to be rather interesting. (I especially liked the elder vinegar made from fermented elder berries).

After feeding ourselves (and our microbes) at lunch, we had an afternoon of presentations relating to aesthetic interactions between humans and microbes, and science and art, called ‘Microbial Sense-making’. Microbiologist Simon Park explained his interest in ‘microgeography’ which involves using a portable microscope to examine traces left behind of microbial and human interactions within urban environments. Simon has also worked with several artists, such as JoWOnder and Sarah Roberts, to produce microbial art. These artworks incorporate the activities of live bacteria into their creation.

Simon and artist Sarah Craske were then interviewed by Charlotte Sleigh to give us a window of understanding into the process behind producing a series of pieces called Metamorphoses. This intriguing project involved taking an antique (18thC) book and applying a range of scientific and artistic techniques to it. The interview revealed how exciting and truly interdisciplinary this type of project can be. It also revealed some anxieties during the creative process, such as deciding whether to move from non-destructive to destructive analysis of the book. The project also raised questions about the agency of bacteria, and also thinking about whether we can have an ‘ethical relationship’ with microbes.

The final presentation of the workshop was from Adam Bencard, who is a curator at the Copenhagen Medical Museum. Adam provided us with an overview of the preparations that went into a new exhibition called ‘Mind the Gut’ which considers the link between the gut microbiome and the mind. This exhibition has developed through an ‘experiment in co-curation’, involving a mix of artists and scientists, which involved a lengthy planning process over many months. The exhibition itself follows an untraditional format where different rooms are based around ‘action symbols’ or themes that reflect gut/brain relationships at different times. One of the aims of the exhibition is to display the body as ‘messy’ and complex, and to also demonstrate how science itself is an unfinished project. The exhibition will run for at least 3-4 years and is a must see for anyone travelling to Copenhagen!

This blog post was written by Carmen McLeod. Carmen is a social anthropologist currently based in the Nottingham Synthetic Biology Research Centre. She is moving to University of Oxford in June 2017 to work on the Good Germs/Bad Germs project and the Oxford Interdisciplinary Microbiome Project (IMP).





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.