TY  - JOUR
A1  - Schmidt, Thomas S. B.
A1  - Hayward, Matthew R.
A1  - Coelho, Luiis P.
A1  - Li, Simone S.
A1  - Costea, Paul I.
A1  - Voigt, Anita Y.
A1  - Wirbel, Jakob
A1  - Maistrenko, Oleksandr M.
A1  - Alves, Renato J. C.
A1  - Bergsten, Emma
A1  - de Beaufort, Carine
A1  - Sobhani, Iradj
A1  - Heintz-Buschart, Anna
A1  - Sunagawa, Shinichi
A1  - Zeller, Georg
A1  - Wilmes, Paul
A1  - Bork, Peer
T1  - Extensive transmission of microbes along the gastrointestinal tract
JF  - eLife
N2  - The gastrointestinal tract is abundantly colonized by microbes, yet the translocation of oral species to the intestine is considered a rare aberrant event, and a hallmark of disease. By studying salivary and fecal microbial strain populations of 310 species in 470 individuals from five countries, we found that transmission to, and subsequent colonization of, the large intestine by oral microbes is common and extensive among healthy individuals. We found evidence for a vast majority of oral species to be transferable, with increased levels of transmission in colorectal cancer and rheumatoid arthritis patients and, more generally, for species described as opportunistic pathogens. This establishes the oral cavity as an endogenous reservoir for gut microbial strains, and oral-fecal transmission as an important process that shapes the gastrointestinal microbiome in health and disease.
KW  - Colonization
KW  - Annotation
KW  - Dynamics
KW  - Accurate
KW  - Strains
KW  - Barrier
KW  - Health
KW  - Acids
KW  - Research Article
KW  - Computational and Systems Biology
KW  - Microbiology and Infectious Disease
KW  - microbiome
KW  - gastrointestinal tract
KW  - colorectal cancer
KW  - rheumatoid arthritis
KW  - metagenomics
Y1  - 2019
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-228954
VL  - 8
ER  - 
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  -