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Surveying What's Flushed Away

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Surveying What's Flushed Away NEWS & ANALYSIS GENOME WATCH Surveying what’s flushed away Gregorio Iraola and Nitin Kumar This month’s Genome Watch highlights MetaSUB consortium3 have performed exten- metagenomics data from different body sites the use of metagenomics to survey urban sive metagenomic surveys of public transport to predict metabolomes. Using this approach, waste waters as a proxy for studying the systems to analyse the spread of pathogens the authors recapitulated the observed dif- gut microbiota in the local population and and antibiotic resistance. ferences between the oral, skin, faecal and discusses how predictive models based on Tons of human waste that pass through vaginal microbiota from the relative counts this data could inform public health. municipal sewage systems each day could of predicted metabolites. Additionally, con- be used to gain a broad overview of the gut sistent correlations were observed after com- The development of global- scale initiatives microbiota of large populations living in paring predicted and measured metabolomes, to characterize the human gut microbiome, urban areas. In a recent study, Newton et al.4 supporting the application of metagenome- like the Human Microbiome Project1 or the analyzed the waste waters of 71 cities in the guided modeling to infer phenotypic traits Metagenomics of the Human Intestinal Tract United States using 16S ribosomal RNA from diverse environments. (MetaHIT) consortium2, is enabling us to (rRNA) amplicon sequencing and concluded In summary, the development of meth- better understand associations between its that sewage can be used as a proxy for stud- ods to investigate gut bacteria in waste water compositional variability and the develop- ying microbiomes in human populations. using multiomics data could be useful for ment of diseases such as cancer, obesity and After filtering out reads belonging to non- public health initiatives. The routine applica- inflammatory bowel diseases. Most efforts faecal bacteria, the authors recaptured most tion of these approaches brings us closer to to characterize the gut microbiota use faecal (97%) of the oligotypes (taxonomic units of the concept of smart cities, which could detect samples as the starting material, however, the organisms that are classified according to environmental changes in real time, like the increasing awareness of the microbiota in primary DNA sequence) that are present in production of enterotoxins or antibiotic the built environment is expanding our poten- individual stool samples and found that the metabolites. Also, these tools could inform us tial to understand human health from a holis- relative abundances of species correlated of dietary habits, the use of drugs or any meas- tic perspective by acquiring samples from our between sewage- derived and individual stool urable parameter just from the composition environment. samples. Also, sewage bacteria were found to and functional patterns of the environmental, Today, more than a half of the human be a good predictor of the incidence of obe- human- associated microbiota. population live in cities, so studying micro- sity. Specifically, higher Bacteroides spp. and Gregorio Iraola1,2,3* and Nitin Kumar3* bial dynamics in urban environments is being lower Faecalibacterium spp. abundances were 1Wellcome Sanger Institute, Wellcome Genome considered for public health. Indeed, the observed in cities with a higher percentage of Campus, Hinxton, UK. individuals with obesity. These results sug- 2Institut Pasteur de Montevideo, Montevideo, Uruguay. gest that gut bacteria present in sewage can 3Universidad Mayor Santiago de Chile, Santiago, Chile. be used as population- level biomarkers for *e- mail: [email protected] demographics and public health. https://doi.org/10.1038/s41579-018-0047-7 Amplicon sequencing is useful for study- 1. Turnbaugh, P. J. et al. The human Microbiome Project. ing the diversity of microbial communities, Nature 449, 804–810 (2007). but shotgun metagenomics enables their 2. Li, J. et al. An integrated catalog of reference genes in the human gut microbiome. Nat. Biotechnol. 32, functions to be investigated. Hence, the strat- 834–841 (2014). 4 egy used by Newton et al. may be enhanced 3. Consortium, T. M. I. The Metagenomics and by integrating functional profiles inferred Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural from shotgun metagenomics or whole- meeting report. Microbiome 4, 24 (2016). genome sequencing data, providing more 4. Newton, R. J. et al. Sewage Reflects the Microbiomes of Human Populations. mBio 6, e02574–14 information about virulence, antibiotic resist- (2015). ance or metabolic traits in the gut microbiota 5. Garza, D. R., Verk, M. C., Huynen, M. A. & Dutilh, B. E. Towards predicting the environmental metabolome of human populations. Indeed, a recent study from metagenomics with a mechanistic model. ed s Limit 5 blisher Nat. Microbiol. 3, 456–460 (2018). llan Pu by Garza et al. reconstructed genome- scale Macmi tenall/ hilip Pa metabolic models from over 1,500 human- Competing interests redit: P C associated bacteria and then integrated The authors declare no competing interests. 456 | AUGUST 2018 | VOLUME 16 www.nature.com/nrmicro © 2018 Macmillan Publishers Limited, part of Springer Nature. All rights reserved..
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