What Lives in the Sewers? From Rats to Microbes

Sewers host an entire ecosystem, from the Norway rats most people picture all the way down to viruses and free-floating strands of antibiotic-resistance genes. Far from being barren pipes carrying waste from point A to point B, sewer networks function as sprawling underground habitats with layered microbial communities, invertebrate populations, and mammals that have adapted to thrive in darkness, warmth, and a constant supply of organic matter. What lives down there tells us a surprising amount about the health of the cities above.

Rats and the Mammals That Thrive Below

The Norway rat is the signature sewer animal for good reason. Sewer infrastructure provides rats with shelter from predators, stable temperatures year-round, and an endless buffet of food waste. A study of rat populations in urban slums in Brazil found that the presence of sewer access was a strong predictor of where adult rats would be captured, with the odds roughly tripling compared to sites without sewer infrastructure.¹ Males, which range more widely to establish territory, were especially likely to be found near sewer entry points.

Rats are not just a nuisance. They are vectors for diseases that can jump to humans. In Tokyo, a review of leptospirosis cases found that every patient had a documented history of exposure to rats before falling ill, reinforcing the link between sewer-dwelling rodent populations and urban disease risk.² Leptospirosis spreads through contact with water contaminated by rat urine, and sewer workers, flood-zone residents, and people living near open drainage are the most exposed groups.

Insects at the Sewer’s Edge

Blow flies are among the most medically relevant invertebrates associated with sewer infrastructure. These flies breed in organic waste, and when combined sewer systems overflow during heavy rain, the insects move between sewage-contaminated environments and the neighborhoods above. Research on blow flies caught near combined sewer overflow sites found that over half tested positive for at least one gene associated with an enteric pathogen. Flies caught farther from overflow points were far less likely to carry traces of human waste, with the risk of detecting human mitochondrial DNA dropping by about 68 percent beyond a one-kilometer radius.³

Beyond blow flies, cockroaches are common sewer inhabitants in warmer climates, and drain flies breed in the slimy biofilms that coat pipe walls. These invertebrates act as shuttles, physically carrying bacteria and other microorganisms from the sewer environment into homes, restaurants, and public spaces. Their role as disease vectors is less dramatic than a rat bite but potentially more widespread, because the insects are harder to keep out and easier to overlook.

The Bacterial Communities Running the Show

If rats are the most visible sewer residents, bacteria are the most numerous by an almost incomprehensible margin. Every surface inside a sewer pipe is coated with biofilms, and every liter of wastewater carries billions of bacterial cells. The dominant groups found in raw sewage inflow are Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria, which together can account for well over 90 percent of the community.⁴ These are broad bacterial phyla, each containing hundreds to thousands of species with wildly different metabolic strategies.

What makes sewer microbiology genuinely interesting is that the community living in the pipes is not simply the community flushed from human guts. Research tracking microbes from human stool through the sewer system to wastewater treatment plants found that gut-associated genera like Faecalibacterium and Parabacteroides decline sharply once they enter the pipes. Their dominance gets replaced by organisms like Arcobacter, Trichococcus, and Acinetobacter, genera that are rare in human stool but abundant in sewer environments.⁵ The sewer, in other words, selects for its own residents. Organisms that can tolerate fluctuating oxygen levels, constant flow, and a complex stew of organic chemicals outcompete the ones that evolved to live inside a warm, stable human intestine.

These sewer-adapted communities even follow seasonal rhythms. Wastewater microbial communities across Europe shift with geography and season, with more pronounced seasonal swings at higher latitudes where temperature differences between summer and winter are more extreme.⁶ The sewer microbiome is not static. It responds to rainfall, temperature, and the mix of chemicals entering the system from households and industry.

Anaerobic Layers and the Gases They Produce

Deeper inside sewer biofilms, where oxygen cannot penetrate, a completely different set of organisms takes over. Methane-producing archaea and sulfate-reducing bacteria coexist in these oxygen-free zones, and their layered arrangement explains one of the most hazardous aspects of sewer work: the simultaneous production of methane and hydrogen sulfide gas.⁷

These two groups of microorganisms compete for the same food sources, so in theory one should outcompete the other. In practice, they partition the biofilm by depth. Sulfate-reducing bacteria dominate the outer surface layer where some sulfate still diffuses in, while methane-producing archaea concentrate in the deeper interior. Research on anaerobic sewer biofilms found that methanogens increased from roughly 10 percent of the microbial population near the surface to about 75 percent at a depth of 700 micrometers.⁸ This vertical stratification means a single millimeter-thick biofilm can contain radically different ecosystems stacked on top of each other.

The practical consequences are serious. Hydrogen sulfide is toxic at relatively low concentrations and is responsible for the “rotten egg” smell people associate with sewers. Methane, meanwhile, is flammable and a potent greenhouse gas. Sewer workers entering confined spaces face a double threat from these biologically generated gases, which is why atmospheric monitoring before entry is standard practice.

Microbes That Eat the Pipes

Some of the most destructive sewer residents are acid-loving bacteria that literally dissolve concrete. Hydrogen sulfide gas produced in the anaerobic layers rises to the crown of the pipe, where a different community of bacteria, particularly species of Acidithiobacillus, converts it first into elemental sulfur and ultimately into sulfuric acid.⁹ The acid eats into the concrete, a process called microbially induced corrosion that costs water utilities billions of dollars worldwide in pipe repairs and replacements.

These acidophilic microbes thrive at pH levels that would kill most other organisms. They oxidize hydrogen sulfide and elemental sulfur through a chain of enzymatic steps, passing electrons along their cell membranes to generate energy.¹⁰ The end product, sulfuric acid, can drop the pH at the pipe surface to below 1, which is more acidic than stomach acid. Over years and decades, this biological process can reduce a thick concrete pipe wall to a crumbly paste. It is one of the clearest examples of how invisible microbial activity creates massive infrastructure costs.

Fatbergs as Microbial Habitats

Fatbergs, the infamous solid masses of congealed grease, wet wipes, and other debris that can grow to fill entire sewer tunnels, are ecosystems in their own right. Researchers who sampled fatberg material from blockage sites in the UK found diverse communities of environmental bacteria colonizing the grease, including highly lipolytic strains (bacteria that specialize in breaking down fats). Isolated species included Serratia, Klebsiella, and Acinetobacter strains whose genomes contained the genetic machinery for harvesting fatty acids and using them as a carbon source.¹¹

Fatbergs form when fats, oils, and grease poured down drains solidify and bond with non-flushable materials. Once established, they create a stable surface that microbes colonize and metabolize. The bacteria found in fatbergs are not the same community as the free-floating wastewater microbes or the pipe-wall biofilm communities. They represent yet another distinct niche within the sewer, shaped by the unusual carbon sources (cooking oil, animal fats) available in the grease matrix.

Viruses, Bacteriophages, and What Sewage Surveillance Reveals

Sewers carry enormous viral loads, including human pathogens shed in feces and urine. Wastewater-based epidemiology has become a mainstream public health tool, particularly since the COVID-19 pandemic demonstrated that monitoring sewage for viral genetic material could detect outbreaks days before clinical testing picked them up.¹² Today, sewage surveillance tracks pathogens including influenza, norovirus, respiratory syncytial virus, and poliovirus in cities around the world.

But human viruses are a minority of the viral population in sewage. Bacteriophages, viruses that infect bacteria, are far more abundant and play a crucial ecological role. In sewer environments teeming with bacterial biofilms, phages act as population regulators, killing some bacterial strains and allowing others to flourish. Phage cocktails have even been studied as tools for managing antibiotic-resistant bacteria in wastewater. Research has shown that phage cocktails can delay the development of resistance, penetrate biofilms more effectively than single phage strains, and achieve prolonged suppression of multidrug-resistant bacteria when the phages are co-evolved with their targets.¹³

Antibiotic Resistance Brewing Underground

Sewers are increasingly recognized as hotspots for the spread of antibiotic resistance. Hospital wastewater, household antibiotics flushed down drains, and agricultural runoff all feed resistance genes into the system. A study of hospital-impacted urban sewage found that some antibiotics, such as amoxicillin, reached concentrations high enough to promote the transfer of resistance genes between bacteria. The most common resistance genes belonged to beta-lactam and aminoglycoside antibiotic classes, and aminoglycoside resistance genes were about 50 percent more prevalent in sewage than in clinical samples, likely reflecting inputs from agricultural and aquaculture sources.¹⁴

What makes this especially concerning is that resistance genes do not stay put. The same study identified over 80 resistance genes linked to mobile genetic elements, the biological tools bacteria use to share DNA with unrelated species. Of the genomes analyzed, the majority carried resistance genes associated with these mobile elements. Sewer biofilms, where diverse bacterial species are packed tightly together in a shared matrix, create ideal conditions for this kind of gene swapping. Resistance traits that evolve in a hospital pathogen can end up in an environmental bacterium, and vice versa, all facilitated by the warm, nutrient-rich sewer environment.

Microplastics as Floating Colonies

A relatively recent discovery is that microplastics in wastewater serve as miniature habitats for microbial communities. Tiny fragments of synthetic material shed from clothing, packaging, and personal care products flow into sewers and quickly become coated in biofilms. These “plastisphere” communities are distinct from the microbes floating in the surrounding water or growing on pipe walls.¹⁵ Research has found that microplastic-associated communities host a marked proportion of unique bacterial genera and show enhanced metabolic activity, with elevated potential for harboring human pathogens.

These biofilm-coated particles can carry pathogens and antimicrobial resistance genes through the wastewater treatment process and out into receiving waters.¹⁶ Microplastics are, in effect, tiny rafts that protect hitchhiking bacteria from the disinfection and settling steps designed to remove them. The surfaces of different plastic types attract different microbial communities, adding another layer of variability to what is already a complex system.¹⁷

When the Sewer Spills Into the River

Everything living in the sewer becomes a problem for surface water when combined sewer overflows occur. In older cities where stormwater and sewage share the same pipes, heavy rainfall overwhelms capacity and forces untreated or partially treated sewage directly into rivers, lakes, and coastal waters.¹⁸ The overflow carries the full suite of sewer residents: bacteria, viruses, resistance genes, microplastic-bound biofilms, and chemical pollutants.

The ecological damage is driven by several overlapping processes. Research modeling overflow impacts on a large urban river found that the dissolved oxygen crash following a spill event is primarily caused by heterotrophic bacteria degrading the organic matter in the sewage, though the initial dilution with oxygen-poor overflow water and reduced sunlight penetration from increased turbidity also contribute.¹⁹ Fish kills, algal blooms, and long-term shifts in aquatic species composition are common downstream consequences, and the severity depends on both the volume of the overflow and how quickly it is diluted.

Sewage as a Mirror of the City

The diversity of life in sewers has given scientists an unexpected surveillance tool that goes well beyond tracking infectious disease. Because everything a population consumes, metabolizes, and excretes eventually enters the sewer, wastewater analysis can reveal patterns of drug use, pharmaceutical consumption, dietary habits, and chemical exposure at the community level. Early work in Milan, Lugano, and London demonstrated that cocaine metabolites in sewage produced reproducible city-specific consumption profiles, with use in Milan rising significantly on weekends.²⁰

Wastewater-based epidemiology has since expanded dramatically. It now tracks opioid trends, emerging synthetic drugs, fentanyl analogues, stimulants, and even prescription pharmaceuticals like antidepressants and antipsychotics as proxies for community mental health.²¹ A large-scale English study covering roughly seven million people analyzed wastewater for dozens of chemical and biological markers simultaneously, building what the researchers called a model of “city metabolism” that captured lifestyle choices, disease prevalence, pharmaceutical use, and environmental chemical exposure in a single analytical framework.²² The sewer microbiome and its chemical context have become, somewhat unexpectedly, one of the most honest portraits of urban life available to public health researchers.