New Pilot Study: Dogs and Microbes in the Thames

Oxford Interdisciplinary Microbiome Project (IMP) members, Jamie Lorimer and Carmen McLeod, are collaborating with Andrew Singer from the NERC Centre of Hydrology and Ecology to carry out a new pilot study in Oxfordshire involving dog walkers and their dogs. The aim of the study is to gather data that begins to map out the microbes that dogs are exposed to when interacting with the River Thames, as well as gathering associated qualitative data from dog walkers. This research will involve a mixed methods approach, including the analysis of genetic material from dog faeces and a qualitative survey, with follow up interviews and a focus group with dog owners.

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What will the study involve?

Dog walkers who take part in the study will be asked to complete a short survey about their dog and any interactions with the River Thames, like swimming or drinking. We will also be asking for a sample of their dog’s poo, which will be sequenced in the lab by Andrew and a PhD student, Holly Tipper, in order to find out what microbes are present and the prevalence of genes that indicate exposure to river water. Dog owners who participate will be invited to provide their contact details if they wish to find out the results of the data collection, and to discuss the results of the sequencing at interview and in a focus group.

We are commencing our study on Saturday 18th November at the Bullcroft Park in Wallingford from 9 am (Waitrose-side entry), so if you are walking your dog in the area and are interested in finding out more, please come along and say hello to the team.

Making microbes public workshop - 3rd-4th May 2017

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).

Emotions and the Immune System

Our thanks to Thursday's speaker Fulvio D'Acquisto, Professor of Immunopharmacology at the William Harvey Research Institute, Queen Mary University of London. 

Fulvio's talk posed a series of questions. Should we consider the emotional response as an integral part of autoimmune manifestation of the disease? Do autoimmunity and mental wellbeing share the same pathways? And is there a therapeutic vantage in treating the emotional side of immune diseases?

In addressing these questions, Fulvio made explicit the assumptions from which his answers were derived. First, that the immune system is the 'mirror' of the emotional state. And second, that emotional wellbeing is the 'mirror' of the immunological state. He talked about his research with mouse models, where the genetic modification of genes specific to the immune system (a gene that is specific to T-cells) led to OCD and anxiety in mice. He also showed research showing how the presence or absence of T-cells in the blood (of mice) affects behaviour (and 'mood') and the brain. Then he showed that the brain can regulate immune response in mice as well. So there is, he suggests, an emotion-immunesystem circuit. Fulvio also talked about his attempts to model the effect of massage therapy on the immune system through an experiment that involved stroking mice - and this did induce observable changes in the immune system. And he showed how mice have preferences for "emotionally comforting" - and also "immunostimulatory" - textiles.

Fulvio's talk also covered some of his outreach projects, particularly 'life-is-shit' and the 'affective immunology' project, as well as his work on 'dreaming autoimmunity'. Thanks again to Fulvio for a memorable seminar. 

The OxIMP project will be running a further series of seminars in Trinity term. Announcements will be made online and through our mailing list (sign up below).

The microbiome, human health, babies and therapies

Lindsay Hall, a research leader and lecturer at the Institute of Food Research of the University of East Anglia, gave the third talk of this term's Oxford IMP seminar series. Lindsay's work looks at the role of early life gut microbiota in resistance to enteric (gut) infections, and particularly the role of bifidobacteria.

Lindsay gave a wide-ranging talk that traced the development of recent microbiome science and its links to human health. For example, she told us about her work using new, fast and cheap technologies for DNA sequencing to facilitate new forms of testing in clinical settings that could make significant differences in health outcomes for premature babies with bacterial infections. She also talked about her work on a project called BAMBI - or 'baby associated microbiota of the intestine', which is a longitudinal study looking at the use of probiotics in premature babies.

But Lindsay's talk was not limited to her own work. It covered a broad introduction to the recent science of the microbiome, especially the evolution of bacterial ecologies in human guts, and the role of the microbiota in producing vitamins, influencing brain functions, developing the immune system, modulating GI tracts, metabolising nutrients, and provide colonisation resistance. She also explained how the microbiota can be be disturbed by genetic factors, antibiotics, infections, diet, environment, childbirth method, and even stress. 

Drawing on work by Blaser and Falkow on 'microbiota de-evolution', Lindsay explained how human societies are experiencing generational losses in microbiota diversity (due tothe reasons listed above), and how we are likely to require both microbiota therapies and nutritional therapies (probiotics) in the future. The group spent much of the Q&A discussing various of these putative futures.

Our thanks once again to Lindsay for an inspiring and intriguing talk. 


The next seminar in the OxIMP calendar is on 9th March, when Fulvio D'Acquisto will present 'The immunological side of emotions and feeling: What's s..t got to do with it?'

The Food of our Food

What lessons about the microbiome can we learn from considering the history of using growth promoters in food for livestock? This was the theme of Hannah Landecker's talk and workshop with the OxIMP network, the second in this term's seminar series.

In Wednesday's session the focus was on the 'food of our food'. Through linking together stories around human metabolic processes and animal feed, Hannah raised a number of key themes pertinent to the social implications of the microbiome. These included shifting from linear to systemic modes of thinking, shifting from considering things to considering processes, 'thinking chemically', and developing the concept of the anthropocene at a cellular scale.

The first part of the talk considered the metabolic processes through which humans cope with toxic compounds in the environment. Hannah explained in some detail the links between the metabolism of both foods and toxins, and how the latter links to chromosomal instability - and thus also to various diseases. She gave the example of arsenical compounds in the environment being linked to diabetes through the effect they have on genome instability. 

The second part turned to the history of using growth promoters in animal feed - largely antimicrobial or antibiotic compounds, and with a history that pre-dates the antibiotic era. In the 1930s farm animals were, in the US, increasingly conceptualised as machines made of food. The agricultural logics centred around input/output ratios - how much food was required to produce how much meat. Growth promoters were seen as a way to improve efficiency, with little regard to their possible wider impacts. Various derivatives of arsenic were among the 'magic bullet' precursors to antibiotics, and became important in agriculture. They were found to be very good at controlling intestinal parasites in chicken - but also had growth promoting qualities.

The two parts of the talk started to draw together as Hannah discussed the emerging links between the historical use of these arsenical compounds, and contemporary human health. She cited a 2012 US Consumer Reports study that showed babyfood sweetened with brown rice syrup had high levels of arsenic. One pathway: historical chicken feed had incorporated arsenical compounds as a growth promoter; waste from these chickens had been used as a fertiliser in rice production (arsenical compounds in pesticides are also implicated).

The last section of Hannah's talk drew these two stories together, by making links between arsenic and the microbiome. The microbiome metabolises arsenic too. Arsenical exposures in the microbiome change population structures of bacteria and thus also the production ratios of metabolites. They also lead to antimicrobial resistance. So there are microbiome mediated effects on human health - the final irony in this tale is that a western diet has been shown in mouse models to accentuate the injurious effects of arsenic - i.e. the substance has a stronger deleterious impact in the context of the dietary systems that it makes possible. As Hannah put it, 'nurture metabolises nature'.

The OxIMP network would like to thank Hannah for her time, company and insight.

Hannah Landecker is a sociologist at UCLA and the Director of the Institute for Society and Genetics. She has written previously on the history of antibiotic use and the development of antibiotic resistance, and is currently working on a book provisionally titled 'American Metabolism'. The book aims to explore recent developments in the metabolic sciences and their various social implications.

AMR Seminar with Andrew Singer

The OxIMP network met on Thursday for the first of this term's seminars. Andrew Singer, Senior Scientist at the Centre for Ecology and Hydrology started things off with a talk about antimicrobial resistance (AMR) in the wider environment, and what it means for environmental policy.

AMR is now widely recognised as a pressing concern for public health agencies worldwide. In the U.K. the government has prioritised policy responses that focus on surveillance, reducing infection, the prudent use of antibiotics, and education. However, current policy responses have largely been limited to "upstream" issues around the use of antibiotics, and have paid little attention to the "downstream" issues of AMR in the wider environment.

Andrew told us that 30-90% of the antibiotics we take are excreted into the sewage system. They tend to pass through the sewage system unaltered and enter the UK's rivers. Andrew's work (based on analyses of sediment in rivers) reveals that proximity to a sewage works explains up to 50% of the prevalence of AMR genes in a river - and this is despite the variable and weather-dependent effects of agricultural run-off. 

EU regulation is based on the notion that the threshold for intervention is when the concentration of antibiotic is high enough to kill more than 5% of the bacteria present. The 5% threshold is an arbitrary risk assessment measure, is based on the assumption that bacteria in the environment will respond exactly as those in a laboratory (with no supporting evidence that this is true), and tells us nothing about what that concentration of antibiotics does in terms of selection pressure for resistance genes in bacteria. Recent research suggests that the "minimum selective concentration" (the amount of antibiotic required to provide a selective advantage to a resistant microbe relative to a nonresistant microbe) could be ten times lower than the 5% mortality threshold. On that measure, our rivers are in trouble. For example, looking at the Thames catchment,  three quarters of the rivers are "at risk" of quinolone (a type of antibiotic) resistance. If you wanted to reduce that level to say 10% of rivers having resistance pressures, current calculations using Andrew and his colleagues' model suggests that antibiotic use in humans would need to be reduced by as much as 80-88% - an unrealistic number in contemporary public health.

The scale of AMR selection pressures raises significant questions about how policy can address these environmental concerns - particularly when you also consider the selection pressures introduced to the environment by biocides in many different forms. Biocides act in a similar way to select for AMR in microbes, because resistance genes often confer 'co-resistance' and 'cross-resistance' (i.e. the group of genes, or single gene, that is selected for by resistance pressures confers resistance to both biocides and antibiotics). And in fact, the use of metals as biocides might by far more important in co-selecting for resistance in the environment than antibiotic use in humans and animals.

The missing link in this story is transmission of AMR bacteria from the environment to humans. This is much harder to show, and is a serious data gap at present- we just don't know how much AMR in the environment links to resistant bacterial infections in humans. There are some very credible reasons to suggest this link exists, and some clues towards transmission pathways, but Andrew suggested that at present the uncertainty itself is perhaps reason enough to invoke the precautionary principle.

After the talk, Andrew and members of the OxIMP network reconvened to discuss some of the issues raised by his fascinating talk, including reducing antibiotic and biocide usage, quantifying environmental transmission, rethinking sewage systems and pollution policy, and the prospects for long term sustainable health systems.

The next seminar in the series is on Wednesday 15th February with Hannah Landecker - more details are available here.


The Hilary Term Seminar Series: speakers and dates announced

The speakers have now been confirmed for our Hilary Term seminar series.

The programme includes both natural and social scientists, each of whom will consider the social implications of the microbiome with respect to their field of research.

The speakers are:

  • Andrew Singer from the Centre for Ecology and Hydrology
  • Hannah Landecker from UCLA (Institute for Society and Genetics; Sociology)
  • Lindsay Hall from the University of East Anglia (Institute for Food Research)

More details about the speakers, dates, times and locations are available here.


The IMP has officially begun!

Last week the Oxford Interdisciplinary Microbiome Project held its first event: a workshop for collaborators from across the University to meet, talk, and discuss shared interests around the social implications of microbiome research. 


 Bio-artist Anna Dumitru and historian Dr Claas Kirchhelle making a Winogradsky Column at the IMP launch event.

Bio-artist Anna Dumitru and historian Dr Claas Kirchhelle making a Winogradsky Column at the IMP launch event.

The event began with a curator-led tour of the "Back from the Dead: Demystifying Antibiotics" exhibition at Oxford's Museum of the History of Science. Artist Anna Dumitriu then led the group in a microbial bio-art workshop, which involved making Winogradsky columns with local soils, designing 'votive microbes' for the exhibition, and experimenting with antimicrobial compounds in petri dishes. 


Project Leader Dr Jamie Lorimer explained that the workshop aimed "to introduce the project and its participants and to start some conversations about the microbiome and its potential for future research collaborations". To learn more about participating in the project and future events, watch this site for further announcements or contact Dr Lorimer.