TY  - JOUR
A1  - Costea, Paul I.
A1  - Coelho, Louis Pedro
A1  - Sunagawa, Shinichi
A1  - Munch, Robin
A1  - Huerta-Cepas, Jaime
A1  - Forslund, Kristoffer
A1  - Hildebrand, Falk
A1  - Kushugulova, Almagul
A1  - Zeller, Georg
A1  - Bork, Peer
T1  - Subspecies in the global human gut microbiome
JF  - Molecular Systems Biology
N2  - Population genomics of prokaryotes has been studied in depth in only a small number of primarily pathogenic bacteria, as genome sequences of isolates of diverse origin are lacking for most species. Here, we conducted a large‐scale survey of population structure in prevalent human gut microbial species, sampled from their natural environment, with a culture‐independent metagenomic approach. We examined the variation landscape of 71 species in 2,144 human fecal metagenomes and found that in 44 of these, accounting for 72% of the total assigned microbial abundance, single‐nucleotide variation clearly indicates the existence of sub‐populations (here termed subspecies). A single subspecies (per species) usually dominates within each host, as expected from ecological theory. At the global scale, geographic distributions of subspecies differ between phyla, with Firmicutes subspecies being significantly more geographically restricted. To investigate the functional significance of the delineated subspecies, we identified genes that consistently distinguish them in a manner that is independent of reference genomes. We further associated these subspecies‐specific genes with properties of the microbial community and the host. For example, two of the three Eubacterium rectale subspecies consistently harbor an accessory pro‐inflammatory flagellum operon that is associated with lower gut community diversity, higher host BMI, and higher blood fasting insulin levels. Using an additional 676 human oral samples, we further demonstrate the existence of niche specialized subspecies in the different parts of the oral cavity. Taken together, we provide evidence for subspecies in the majority of abundant gut prokaryotes, leading to a better functional and ecological understanding of the human gut microbiome in conjunction with its host.
KW  - biology
KW  - genetic variation
KW  - metagenomics
KW  - microbiome
KW  - population structure
KW  - prokaryotic subspecies
Y1  - 2017
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-172674
VL  - 13
IS  - 12
ER  -