Researchers took 4700 samples from mass transit systems in 60 cities across the world, swabbing common touch points like turnstiles and railings in bustling subways and bus stations across the world. Using metagenomic sequencing, they created a global atlas of the urban microbial ecosystem, the first systematic catalog of its kind. The results suggest that no 2 cities are alike, with each major metropolis studied so far revealing a unique molecular echo of the microbial species that inhabit it, distinct from populations found in other urban environments.

2023-10-12: Dark matter

Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 27k metagenomes and identify 1.17b protein sequences longer than 35 amino acids with no similarity to any sequences from reference genomes. Using massively parallel graph-based clustering, we group these proteins into 106k novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.

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