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Microbial Species Abundance Distributions Guide Human Population Size Estimation from Sewage Metagenomes

By Fangqiong Ling, Likai Chen, Lin Zhang, Xiaoqian Yu, Claire Duvallet, Siavash Isazadeh, Chengzhen Dai, Shinkyu Park, Katya Frois-Moniz, Fabio Duarte, Carlo Ratti, Eric J. Alm

Posted 15 Dec 2020
bioRxiv DOI: 10.1101/2020.12.15.390716

The metagenome embedded in urban sewage is an attractive new data source to understand urban ecology and assess human health status at scales beyond a single host. However, using census-based population size instead of real-time population estimates can mislead the interpretation of data acquired from sewage, hindering assessment of representativeness, inference of prevalence, or comparisons of taxa across sites. Here, we develop a new method to estimate human population size in light of recent developments in species-abundance distributions of microbial ecosystems. Using a population-scale human gut microbiome sample of over 1,100 people, we found that taxon-abundance distributions of gut-associated multi-person microbiomes exhibited generalizable relationships in response to human population size. We present a new non-parametric model, MicrobiomeCensus, for estimating human population size from sewage samples. MicrobiomeCensus harnesses the inter-individual variability in human gut microbiomes and performs maximum likelihood estimation based on simultaneous deviation of multiple taxon relative abundances from their population means. MicrobiomeCensus outperformed generic algorithms in data-driven simulation benchmarks and detected population size differences in field data. This research provides a mathematical framework for inferring population sizes in real time from sewage samples, paving the way for more accurate ecological and public health studies utilizing the sewage metagenome.

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