Probiotic urbanisation and the genealogies of filth

Abstract

The relationships between ‘filth’, microbial ecologies, and the urban environment are complex and dynamic. In Global North contexts, nineteenth century epidemics caused by pathogenic microorganisms forced major political and infrastructural urban reorganisation. More recent scientific and sociocultural imaginaries of microbial exposure and curated forms of ‘filth’ as positive for human health, i.e., probiotic (govern)mentalities, are finding their way into the conceptualisation and governance of urban environments. This groundwork paves the way for expanded accounts of urban human-microbial relationality and co-evolution, including the consideration of extracorporeal and distributed urban microbiomes and their interactions with both ‘bacteriological’ and ‘probiotic’ renderings of urbanity. Firstly, the technological success of the bacteriological city was underpinned by the generation of a set of highly productive microbial ecologies that protected public health, namely those involved in the treatment of drinking water and wastewater. These early efforts at putting bacteria to work suggest the co-existence of various imaginaries of microbes - as ‘good’ and ‘bad’ - at the turn of the twentieth century. Secondly, these foundations open the door for the excavation of alternative genealogies of human-microbial-urban dynamics, including those from the Global South, the Global East, and the role of interactions in deep time. Finally, the lessons of antimicrobial resistance further complicate contemporary celebrations of ‘good bacteria.’ The analytical framework of probiotic blowback may be useful for charting the material trajectories and possible futures of socio-microbial relationality across space and time.

Introduction: Microbes, filth and the city

Lorimer et al.'s (2025) perspective article filth and the city raises some timely questions about the social meanings, material production, and governance of “filth” in urban contexts. Their article focuses on changing understandings of human-microbial relationships, the metabolic city, and urban nature to argue the need for “a major rethinking of the social and biological issue of filth”. One theme that runs strong throughout their perspective is that of microbiology, the human (gut) microbiome, probiosis, and their implications for urban life. Changing understandings of microbes, and particularly their roles in human health, have impacted the functioning of cities in significant and formative ways over the past century and a half. Emerging views of human-microbial interactions as primarily ecological and relational, as opposed to pathogenic and conflictual, is a relatively recent perspective that reconfigures how we understand the pasts and presents of urban development as well as its possible futures.

This commentary provides two observations that build on Lorimer et al.'s article and aims to provide an expanded perspective on urban human-microbial entanglements and their relation to filth. The first is that an emphasis on contemporary understandings of the human gut microbiome and positive microbial exposure opens the door to the analysis of a wider field of human-microbial interaction that is equally important for the form and function of the urban. The second is that chronological accounts of probiosis and the bacteriological city provide the backdrop for illuminating more entangled and nuanced chronologies of human-microbial relations, their biosocial antecedents, and potential downstream consequences.

Extracorporeal microbiomes and the urban fabric

Over the past 50-years or so, an emphasis on the benefits of microbial exposure for human immunological and physiological development has worked its way into sociocultural and technoscientific imaginaries. This ‘new’ microbiology is variously informed by the work of renegade scientists like Lynn Margulis who theorised the central role of symbiosis in (human) evolution (Bradshaw, 2020; Clark, 2000) and large scale ‘big data’ projects aimed at analysing human microbiome diversity, composition, and function. Prior to this, the emergence of germ theory had major impacts on the design and governance of urban environments. Whilst analyses of the bacteriological city (Gandy, 2006; Lorimer et al., 2025) provide the historical and microbiological context for recent ‘probiotic’ shifts, they also provide opportunities for exploring the distributed set of non-pathogenic, extracorporeal microbiomes that underpinned the technological success of the bacteriological city in the first instance. A deeper analysis of the microbial communities involved in water and wastewater treatment, for instance, provide a wider context to current urban infrastructural developments, their associated imaginaries, and their material entanglement with human microbiota.

Since the 1850s drinking water in London has been treated via slow sand filtration (SSF), an approach whose efficacy is fundamentally dependent on a microbial community biofilm that colonises the upper layer of sand. This ‘Schmutzdecke’ ¹ predates upon and out competes pathogenic microbes, such as Vibrio cholerae and Corynebacterium diphtheriae, in the raw water influent. These mechanisms recall the function of healthy human gut microbiota and suggest sociomaterial connections between embodied and infrastructural microbiomes. Although the role of microbes in SSF wasn’t fully recognised until at least the turn of the twentieth century, the discovery of activated sludge - the primary method of wastewater treatment - was always tied to an acknowledgement of microbial activity (Platt, 2004; see also Bradshaw, 2024a). Early experimentation in sewage treatment suggests alternate imaginaries of “good” and “bad” microbes that were implemented into practice by 1920 (in Davyhulme Sewage Works, Manchester). From a Global North context, these infrastructures were both critical components for the technopolitical realisation of the bacteriological city and continue to be essential for the integrity of urban organisation. Chugging away quietly in the background of cutting edge architectural theory and probiotic design are the activated sludge tanks and slow sand filters that, for better or worse, have been functioning for well over 100 years.

Within the UK context, and particularly in London, wastewater infrastructures are increasingly failing with sewage being dumped into rivers, connecting anxieties over filth, infectious disease, and sanitation with broader issues of chemical pollution, toxicity, and ecological destabilisation. This situation recalls miasmatic theories in which the complexities of urban exposure and toxicity connect more with imaginaries of chemically diverse ‘clouds’ than with networks of contagion and proliferation (Liboiron, 2013). The political ecological dimensions to this crisis deserve further exploration, as does the historicity and biological agency of water treatment systems as urban ecologies in their own right (Adolphi and Rainer, 2025). The historical and ongoing production of these distributed microbiomes further suggest the need to connect theories of filth and practices sanitation with the materialities of emerging contaminants and the biophysical trajectories of bacterial life. Here there are also opportunities to integrate urban political ecological perspectives on filth with those on chemical exposure, toxicity, and the uneven chemical landscapes of modern urban centres. The links between microbiome evolution, and particularly the emergence of human microbiota dysbiosis, and industrial-urban chemical pollution, repositions impoverished human-microbial relations within wider landscapes of uneven exposure (see Bradshaw, 2024b). This can bring embodied approaches to living-with pollution, including feminist approaches, as well as concerns with multispecies and urban ecological dimensions of polluted environments, into conversation with structural analyses of capitalist dynamics. An additional consideration is the temporalities of filth and the possibility of leveraging analytical frameworks like ‘slow violence’ for exploring its undersides.

An imaginary of filth which may aid in the conceptualisation of these more extended microbiomes and patterns of exposure is that of slime. As a material, semiotic, and discursive category, slime has a lot to teach us about nonhuman generativity, human disgust, and more-than-human relationality. Correspondingly, attention to slime is slowly creeping into critical environmental scholarship. Simon Estok (2024) foregrounds the elemental aspects of slime, noting that slime is not an object but a substrate out of which other things emerge, just as the bacteriological city emerges from the slimy microbial communities of the SSF and the wastewater treatment plant. These productive urban microbiomes are also elemental insofar as they represent “the indeterminate but influential conditions in which perception and sensing takes place for different bodies” (Engelmann and McCormack, 2021). ² Whilst a focus on the human gut microbiota risks discretising our understanding of human-microbial relations, a turn to elementality and the imaginaries of slime has the potential to unravel the interlocking scales and registers of human-microbial interactions.

Urban microbial genealogies: Deep times, speculative futures

Standard chronologies of the relationships between urban theory and microbiology tend to follow a linear trajectory of pre-germ theory, the ascendance of bacteriology, and onto recent concepts of probiosis and beneficial microbial exposure. Emerging zoonoses such as covid-19 have led to the positing of a fourth phase of (urban) human-microbial relationality summarised by rubrics like “zoonotic urbanism” and the “fourth epidemiological transition” (Gandy, 2023). This broad-brush model provides a framework for investigating some of the more nuanced and entangled relations between microbial ecologies and urbanisation. The first slow sand filter in the UK (London; see above), for instance, was operational by 1829, when Pasteur was only seven years old. Its antecedents date to experiments in Scotland in 1804. Historians note that it was the applied success of this filter, as opposed to the dominance of any one theory about disease transmission, that led to the Metropolitan Water Act of 1852, a legislative cornerstone of the bacteriological city (Hardy, 1984; Luckin, 1977). Given that some architects were discussing microbes as our “indispensable friends” as early as 1911 (Putnam; 50), can early scientific knowledge of water-associated socio-microbiomes be traced into imaginaries of ‘good’ microbes in the city? How does the ongoing reliance of millions of Londoners on the SSF ecology for safe drinking water inflect our understanding of contemporary probiotic urbanisms?

Further, scholars have pointed out that this microbiological narrativisation is as much spatial as it is temporal. As a form of governmentality and material relationality, probiosis does not replace antibiosis (and specifically its blowback) as much as it displaces it, often to areas like the Global South, but also within cities (Hinchliffe, 2022). As Lorimer et al. (2025) point out, scholars are working to map the “patchy” geographies of probiosis and to trace “the persistence of racialized imaginaries of filth into probiotic microbiology.” There is a clear need to continue constructing these alternative genealogies of the probiotic, including those from the Global South and Indigenous worlds (e.g., Giraldo Herrera, 2018), and specifically how they interact with urbanisation. These are genealogies in which the ‘antibiotic’ plays a distinct social, material, and biological role than in the dominant Global North context (see, for example, Nading, 2016).

Work on the “historical coproduction of microbiology and urban theory” (Lorimer et al., 2025) might also pay more attention to the historical role of microbial ecology in the Global East and its emphasis on diversity over purity (Grote, 2018). How did different scientific and political perspectives on the agency and relational ecologies of microbes affect the governance of cities across the Soviet Union, for instance? In the twentieth century USSR, the theorisation of ‘plagues’ as emerging in complex ecologies was tied in with both the ideological assumptions of prevailing political objectives and their material realisation (Jones and Amramina, 2018). Such analyses may contribute new perspectives on the fetishisation of diversity and multispecies ecologies currently playing out in privileged Global North contexts (Paxson and Helmreich, 2014). Scholars should also investigate the dynamic presents and possible futures of probiosis. Hannah Landecker's “biology of history” (2016) and recent analysis of “life as aftermath” (2025) suggest that the economically exploitative dimensions to capitalist probiosis are likely to be matched by undesirable material consequences, spatially but also temporally (see also Bradshaw, 2024b for the evolution of urban microbiomes in the Anthropocene). Developing the concept of ‘probiotic blowback’, offered here as the unintended impacts of ‘beneficial’ microbial exposure, might respond to these complex and entangled temporalities.

Another perspective is that of the deep time relations between humans and microbial ecologies. ³ One example which forms productive connections and tensions with recent probiotic shifts, is prehistoric fermentation. Archeologists have identified evidence of humans using fermentation for the nutritional transformation and preservation of food for at least 10,000 years. Sibesson's article (2022), “reclaiming the rotten”, demonstrates that fermentation transforms edible substrates into a form ‘filth’ that was both desirable and productive of social cohesion and complexification in the Neolithic. The role of fermentation in the evolution of the human brain (Bryant et al., 2023) and its demonstrated ability to set up delayed return economies may have been important for the shift to sedentary lifestyles (Craig, 2021) that ultimately evolved into various forms of urbanisation. Further, the earliest urban centres were sites of experimentation for co-productive human-microbial relations, for instance in the brewing of beer (Damerow, 2012). These considerations sketch an additional and different kind of relationship between filth and the city, one in which filth is productive of the biosocial relations out of which urbanity emerges, its bio-energetic and nutritional grounding. These considerations suggest the need to construct multispecies archeologies of filth that go beyond the intentional acts of human agents to frontstage geomicrobial agencies.

Conclusion

The city not only produces, regulates, governs - and moralises - filth, but it is also built on it. Expanded conceptions of human-microbial relations and an acknowledgement of microbes beyond the human body, including those which do not necessarily exert their agency via the gut microbiota, are integral for understanding the pasts, presents, and futures of the urban environment. “Slimic” imaginaries can help us to conceptualise the ways in which urban bodies and infrastructures are held together–but also retain mobility–via the agency of distributed microbial ecologies. Urban political ecology might consider how these socioecologies follow geographical and historically specific trajectories that can be archeologically traced to a multitude of starting points beyond the human. The dynamics of antimicrobial resistance also suggest the need to pay close attention to the material futures of human-microbial relations, the potential for probiotic blowback, and its spatial unevenness. The analysis of urbanisation and microbes reveals spatial and temporal heterogeneity and complexity. Future research should respond to this diversity and help map out pathways towards more equitable human-microbial relations.