Mining the urban sewage for safe water indicators

Hello readers,

I am Fangqiong. I recently received the Microbiology of the Built Environment Postdoc Fellowship from the Alfred P. Sloan Foundation. I will be studying a kind of built environment microbiome, the microbiome in the urban water cycle, in Professor Eric Alm’s lab at MIT. I am very grateful to the Sloan Foundation for this opportunity. This blog post is to introduce the work I’m going to carry out with support from the Sloan Foundation. On a side note, as a long-time follower of, I’m very excited to contribute a post to the website!

Rethinking the urban water cycle

I see my work fitting into a larger process of redefining the urban water cycle. In any modern city, the man-made water cycle supplies water for drinking and carries the waste away. Just like the water flow which seldom stops, the infrastructure supporting the water cycle has never been static. As an environmental engineer, I find it inspiring to learn about how the water infrastructure evolved from simple physical transport in the Roman era to including various chemical and physical-chemical treatment and disinfection technologies[1]. These technologies have virtually eradicated the epidemics of waterborne diseases such as cholera and typhoid.

Currently, another revolution on the urban water cycle has begun. On the supply side, cities challenged by water shortages are looking into water sources that traditionally have not been viewed as suitable for consumption. In extremely water-stressed areas such as California and Texas, some cities are experimenting with the idea of “direct potable reuse”, which means connecting treated wastewater streams directly to a drinking water treatment facility[2]. On the sewage side, the underground urban wastewater is emerging as a source of energy, nutrients, and information. While technologies are available for turning the energy and nutrients into useful forms (e.g., biogas production and nitrogen/phosphorous recovery), how to make use of the vast information embedded in the urban sewage is like a revolution within the revolution.

Layers of stories within the water cycle microbiome

Along with the fluids traveling in the water cycle, there are streams of microbes. Water supplies bring in microbes from the source water. The time scale of urban water cycling could allow demographic dynamics in the microbial community, and the various chemical conditions involved in water treatments and distribution presents changes in the habitats of the microbes. For the sewage, human water use introduces a flux of human-associated bacteria and virus into the sewer. Together with that, the sewage streams also carry metabolites, food waste, residuals of personal care products and medicine from our daily life.

Cohabiting with microbes in the water cycle, we have a complicated relationship with them. What fascinates me the most is that we can look at them from different perspectives. Through drinking, hand washing, and inhaling shower aerosols, we receive fluxes of microbes through the water supply[3]. At the same time, their presence and distribution can be viewed as a source of information. We may be able to probe human activities and disease outbreaks from the sewage microbiome, or to develop new water treatment targets for recycled wastewater.

Mining the “Underworlds”

In the proposed research, we aim to explore the capability of sewage microbiome in reflecting the microbiome of urban human populations. We aim to identify human-associated microbial species and functional genes on a city scale by systematically cataloguing the microbiome of untreated sewage in Cambridge, MA.  This would involve amplicon and metagenomics sequencing of the bacterial and viral fractions of the sewage samples. These experiments will be followed by computational analysis on the whole bacterial community and certain targeted viral populations. Such data can be utilized to develop candidate targets for monitoring sewage impact of the water supply and better manage the water cycle.


[1] For a reference on stages of water supply technology revolutions: Sedlak, D. (2014). Water 4.0: the past, present, and future of the world’s most vital resource. Yale University Press.

[2] An example of established direct potable reuse plant:

Commission on Environmental Quality. Extended Drought Fosters New Approaches. Natural Outlook (2013). at <>

National Public Radio. Drought-Stricken Texas Town Turns To Toilets For Water. (2014). at <>

An example of water reuse demonstration project:

City of San Diego Diego. Water Purification Demonstration Project. at <>

[3] Click to read a story on microbial communities in household water meters from my doctoral research:

One thought on “Mining the urban sewage for safe water indicators

Leave a Reply