Liam Shaw, University of Oxford and Nicola C. Sugden, University of Manchester*

A portable DNA sequencer in action. UGA CAES/Extension/Flickr

The Democratic Republic of Congo is battling an Ebola outbreak. As is the case with any disease caused by pathogenic viruses – like Zika or influenza – Ebola spreads dangerously and unpredictably. This makes tracking the movement of viruses around the world a major challenge.

Researchers have increasingly turned to DNA sequencing to help identify and track these sorts of diseases. They use portable DNA sequencers, which are the size of a USB and can be easily carried for use in the field. One such sequencer, the MinION from Oxford Nanopore Technologies was used during the 2016 Zika virus epidemic in Brazil. It’s also being used to track the DRC’s Ebola outbreak.

Some researchers hope it will soon be possible to combine sequencing data collected in this way with other information to tell us even more about disease outbreaks. Integrating different kinds of data into a global infectious disease surveillance system that continuously scans for new epidemics might make it possible to detect outbreaks and sequence viruses as they emerge, allowing public health responses to be suggested in real time.

There’s no doubt these efforts are driven by good intentions. But, as we argue in our new research, this technology – which supporters hope will become increasingly available to members of the public – could have serious privacy implications.

Metagenomic data – the kind that could be collected on a sequencer such as MinION or others such as the Chan Zuckerberg Initiative’s new platform IDSeq – contains an enormous amount of information about who we are and how we live. In combination with other widely available information someone could potentially use that data to work out where you live, or with whom you have a close relationship.

The reality is that, as improvements in data analysis methods allow us to extract new insights from old data (or de-anonymise anonymised data), it’s impossible to be absolutely sure what the potential uses of data will be.

Signing away your data

Imagine having an app on your smart phone that allows you to analyse samples from the world around you. You could use it to sequence your pet cat’s DNA, or to figure out whether the mould growing in your shower is dangerous.

Sound far-fetched? It’s not. The technology required is already here. For example, the Chan Zuckerberg Initiative recently announced IDSeq, a new platform and database for infectious disease surveillance where registered users can upload their metagenomic sequencing data to have it analysed for free.

There’s just one catch, as there would be with any sequencing app: you have to sign over permissions to the data. Most people will do this unthinkingly. Author Jamie Susskind has called this pervasive and common arrangement “the data deal”: people accept whatever a company asks so they can use an app or product, and worry about the implications later.

This is the case with IDSeq. Initially enthusiastic researchers became concerned when they realised the platform’s terms and conditions contained a clause granting the Chan Zuckerberg Initiative “perpetual” permission to “use”, reproduce, distribute, display and create derivative works” from the data.

The current justification given for this clause is that it’s intended to permit users’ research data to be used for improving IDSeq. However, in principle the data could later be shared with “any third party that purchases” part of the assets or organisation.

A world of information

So why does it matter if you share metagenomic data from your everyday life? Quite simply, because the data from that cat hair or mould sample might contain more information than you realise – and far more than you intended to sign away.

It could contain not only the DNA you wanted to sequence, but also DNA from your fingers when you loaded the sample, from the bacteria on your skin from the last person you hugged, or from the gardens your cat visited last night. In short, that data contains vital information about your microbiome – the vast collection of microorganisms that live on and in our bodies. And your microbiome can tell someone an awful lot about you.

As we learn more about our microbiomes, we are beginning to understand how much they are personalised. Even if we could filter out the human DNA sequences from datasets, our microbiomes could theoretically still be used to identify us.

The microbiome contains information not only about our lifestyles, like our diet and drug intake, but also our social relationships, such as who we live with. That’s a lot of information to work with, in a world where we already share a great deal of data about ourselves via platforms like Facebook and Instagram, or personal fitness trackers. This data could feasibly be merged with metagenomic data, making it even more powerful.

There are ever more surprising examples of incidental data being used in dramatic and unexpected ways that are far removed from the original reasons for collecting it. Data from a murder victim’s Fitbit was used to convict her killer. And data from users of the fitness app Strava inadvertently revealed the location of secret US army bases.

There is every reason to believe that data from portable sequencers collected primarily for disease surveillance would contain information that could be used in similarly surprising, and concerning, ways. Metagenomic sequencing data is highly personalised. It contains implicit information about who we interact with and where we go, which makes it commercially valuable.

These concerns shouldn’t (and won’t) stop portable sequencers being used for infectious disease surveillance. Corporations and governments will promise great benefits from the use of this technology. For example, the IDSeq privacy notice justifies data collection by appealing to “legitimate interest in investigating and stopping the spread of infectious diseases and promoting global health”.

We need to continue scrutinising these organisations to make sure we understand exactly what’s being done with our data. The consequences of widespread portable sequencing, like emerging infectious diseases themselves, will be highly unpredictable.

*Liam Shaw, Computational biologist, University of Oxford and Nicola C. Sugden, PhD Researcher, University of Manchester. This article is republished from The Conversation under a Creative Commons license. Read the original blog post.

Liam and Nicola’s Geo: Geography and Environment article, ‘Portable sequencing, genomic data, and scale in global emerging infectious disease surveillance’, is available via https://rgs-ibg.onlinelibrary.wiley.com/doi/full/10.1002/geo2.66. All Geo articles are open access.

By Carmen McLeod, Erika Szymanski, Joshua Evans, Anna Krzywoszynska, and Alexandra Sexton 

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Microbes are everywhere. Headlines announce that microbes have been found in all sorts of spaces, from NASA’s cleanrooms to the vitreous fluid inside the human eye, in addition to such now-familiar residences as soil, skin, and all around our homes. And beyond simply being found, microbes are increasingly seen as significant and often valuable in virtually every space humans study—leading to more and more calls for research that flows between and beyond the natural and social sciences, as with this Geo: Geography and Environment open collection.

Repeating the truism that ‘microbes are everywhere’, however, can risk flattening microbial life into a sameness that is so much less interesting and useful than the diversity this ‘everywhere’ implies. Moreover, reifying ‘the microbe’ would suggest that the single-celled microbial body—one of many possible units of analysis—is always at the root of microbial life and human workings with it.

For these reasons and more, we propose deeper critical discussion of current approaches to thinking about and with microbes in the social sciences. This concern motivates our Geo: Geography and Environment-sponsored session at the upcoming RGS-IBG conference in Cardiff, where we will present and discuss work exploring some of these potentials and limitations. Our experiences working with human–microbial communities in a range of settings have spurred us to consider how social sciences might get better at dealing with microbes as crucial societal and environmental agents. We invite you to join us in this exciting debate.

To give a taste of the session, we thought each of us would share an image and anecdote about how we’ve found and followed our microbial fascinations, and the promise and trouble they bring.

Click on the contributor’s name, or scroll down, to read more about their work:

• Carmen McLeod 
• Erika Szymanski
• Joshua Evans
• Anna Krzywoszynska
• Alexandra Sexton

Carmen McLeod

Synthetic biologists’ crocheted imaginings of microbes for public engagement activities

In 2015, I began working in a UK synthetic biology research centre. As the only full-time social scientist amongst microbiologists and other natural science-related disciplines, I was tasked with embedding a Responsible Research and Innovation (RRI) framework within the work of the centre. I assumed that much of my work would centre on the ‘big picture’ relationship between science and society. As it turns out, I have become fascinated by the smaller and intimate relations between humans and microbes. This began as I became aware of the complex ways that my scientific colleagues interact with microbes. Interviews and ethnographic fieldwork revealed that laboratory work encompasses what could be termed ‘cultures of care’ for microbial life and relationships that go far beyond scientific goals. My interest has extended to other specific relations that emerge when considering the context of the human microbiome. In particular, my work is looking at the key role that the gut microbiome plays in health and wellbeing, and the new (and old) human–microbial relations this reveals. Faecal microbiota transplantation (FMT), for example, is an ancient treatment for a disrupted gut microbiome, and FMT applications are growing in both the clinic and ‘DIY’ settings, revealing new sociocultural and ethical considerations. I am excited by the cross-disciplinary opportunities that emerge from studying and illuminating the places where humans and microbes meet. This area of scholarship has the potential to disrupt binary categories, such as human/non-human; science/society; and nature/culture, and my hope is that there will be increasing interest in the work of scholars exploring these messy human–microbial spaces.

Erika Szymanski

My companionable sourdough starter and the current contents of my nightstand which, to be fair, don’t usually live on top of each other.

Yeast has been following me around since my childhood, when I baked bread with my mother and helped destem grapes for my parents’ tiny backyard winery. Notwithstanding a brief affair with gram-negative bacteria as a microbiology student, it wouldn’t be inaccurate to say that I’ve followed yeast through childhood hobbies and adolescent reading to higher education in microbiology, through humanities and now into the social sciences. There might seem little mystery in why someone initially trained in microbiology has, in her later career as a social scientist, chosen to work on microbes. But why have microbes stuck when so much else has not? Yeast, I find, is able to follow me anywhere—or, rather, I am able to follow it—as a common inhabitant of so many spaces where science, technology, culture, and domestic life happen. It is mundane to say that microbes are everywhere. But a corollary that seems to be articulated less often is that everywhere there are ways of coming to know microbes, and that these myriad ways of knowing may often be complementary to each other. In some of my recent work with the synthetic yeast project (Saccharomyces cerevisiae 2.0), I’ve suggested that conceptualizing microbes as collaborators to be listened to, learned from, and worked with—not just as tools or machines to be completely controlled—may offer new routes for achieving human design goals with living systems.

Joshua Evans

While the Kimbucha is a more recent encounter of mine with microbes involved in food fermentation, it illustrates much of what both enthralls me about microbes, and what suggests to me that current approaches to making sense of them may be insufficient. Kim Wejendorp is a friend and collaborator who works as a chef and crazy brain at a restaurant called Amass in Copenhagen. This screenshot, from his instagram account, details how he arrived at making a kombucha from scratch. Kim’s primary motivation is to produce new flavours for the restaurant’s menu, but it strikes me that with this project he has also inadvertently levelled a challenge at both received fermentation orthodoxy and the scientific literature, both of which generally agree that kombucha can only be made from existing culture. The question of whether this is a kombucha, sensu stricto, cannot simply be answered by looking at which cellular bodies are living in it or which ‘species’ emerge from its metagenome—it must also and mainly involve considerations of flavour, culinary use, and social function. We might indeed typically expect social scientists to highlight these factors; yet strangely, most social researchers studying human–microbe relationships have so far worked rather uncritically from the stories scientists tell, without questioning what other stories are missing and possible. By revealing such gaps, these novel fermentation projects are rich sites for investigating alternative and as-yet-unaccounted-for ways in which microbes come to matter.

Anna Krzywoszynska

“If you build it, they will come.” Jokingly quoting from a Kevin Costner movie, the farmer I am interviewing brings the invisible microbes in this clod of soil into the conversation; he explains how his changed land management practices are creating a hospitable environment for this microbial life to inhabit. In the UK and across the world a ‘microbial turn’ is taking place in conventional agriculture as farmers and scientists turn to soil biota for solutions to climate change adaptation, productivity increases, and even planetary salvation (through the much discussed capacity of soils to act as carbon sinks). There are similarities between the current interest in microbial life in the farming community, and my previous experiences of following microbes through the worlds of organic winemaking. The invisibility of microbes invites scientific forms of ‘making sense’ of human–microbe encounters and relationships. At the same time, everyday practices of living and working with microbes in fields and wineries have more to do with changing personal identities and ethics then with deploying ‘certified’ knowledges. Scientific tools and narratives are both embraced, refuted, and imaginatively redeployed; working with microbes thus goes to the heart of classic social scientific questions about the relationships between knowledge and power. But there is more here than interpretation. What I see are experiments in living on the planet differently through microbes, with microbes. The  most exciting moments come when the microbes thwart the stories I, my research participants, or my natural science colleagues are able to tell about them: when a wild yeast fermentation creates an unforgettable and unplanned rosé wine; when the unexpected alliance between cover crops, soil biota, and slugs wipes out a harvest. These moments challenge me to think about the relationship between the agential cuts I make as a social scientist in deciding what is and what is not an object of my inquiry when I say I am researching ‘human–microbe relations’. They gesture towards the need for new social scientific understandings of human and nonhuman agency which go beyond the struggle between control and co-existence—which are about finding ways to be human well in a busy world. I am excited to think through the kinds of social and inter-disciplinary science which are needed to be better at living (and making a living) in a world where humans do not call all the shots (something I have been thinking through in the context of soil for a while).

Alexandra Sexton

There have been many stories told over human history about the ‘future of food’. These stories are important not only for tracing evolutions in technological promise but also for taking a pulse of the food-related anxieties that have been felt across different times and spaces. Taken from a Demo Day of tech start-ups in San Francisco, the image above is one of the current stories being told by an emerging technological movement in Silicon Valley, California. In short, this story describes a broken global food system, particularly livestock-based food, and that salvation lies in the innovation streams and business models of Big (bio)Tech. When I took this photo I didn’t know that I was soon to encounter microbes through more stories presented by the start-ups during their pitches. Speaking to an audience of venture capitalists and media personnel, I heard microbes framed as a ‘logical’, ‘sustainable’, ‘ethical’ and, perhaps most emphatically, lucrative solution to future food production. I also heard that there are “literally no down sides” to these new microbe-based food factories. I was shown graphs of predicted company growth and projected environmental savings. Microbes were conjured as biology-turned-technology, their ‘natural’ behaviours reimagined through notions of the ‘synthetic’ that rendered them more useful for feeding (some of) us and making (some of) us rich in the process. Reflecting on the microbe in these stories has quietly forced me to ask new questions in my research, particularly concerning how the invisible is made visible through the mechanisms of the Valley, venture capital and media hype; and conversely, it has invited consideration of the agents and stories made purposefully silent. These are all inherently political acts disguised through the seemingly apolitical, controllable and distinct ‘bodies’ of microbes. The task set for myself as a social scientist, then, is to critically unpack the hype and find ways of staying open to the ability of microbes to resist and exceed the stories that are told about them.

Taken together, we believe these and other stories suggest why more and more diverse microbe-focussed studies might be useful. We invite you to join us at our session at RGS (Wednesday, August 29, 9-10:40am) to discuss the shape critical microbe studies might take, and to learn more about Microbe Work—our new network for facilitating cross-disciplinary inquiry into microbe–human relations.

Carmen McLeod is a senior research fellow in Responsible Research and Innovation at the University of Nottingham. Erika Szymanski is a research fellow in Science, Technology, and Innovation Studies at the University of Edinburgh. Joshua Evans is a DPhil candidate in the School of Geography and the Environment at the University of Oxford. Anna Krzywoszynska is a Leverhulme Early Career Fellow in Geography at the University of Sheffield. Alexandra Sexton is a research fellow in the School of Geography and the Environment at the University of Oxford.