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  - Hickl, Oskar
A1  - Heintz-Buschart, Anna
A1  - Trautwein-Schult, Anke
A1  - Hercog, Rajna
A1  - Bork, Peer
A1  - Wilmes, Paul
A1  - Becher, Dörte
T1  - Sample preservation and storage significantly impact taxonomic and functional profiles in metaproteomics studies of the human gut microbiome
JF  - Microorganisms
N2  - With the technological advances of the last decade, it is now feasible to analyze microbiome samples, such as human stool specimens, using multi-omic techniques. Given the inherent sample complexity, there exists a need for sample methods which preserve as much information as possible about the biological system at the time of sampling. Here, we analyzed human stool samples preserved and stored using different methods, applying metagenomics as well as metaproteomics. Our results demonstrate that sample preservation and storage have a significant effect on the taxonomic composition of identified proteins. The overall identification rates, as well as the proportion of proteins from Actinobacteria were much higher when samples were flash frozen. Preservation in RNAlater overall led to fewer protein identifications and a considerable increase in the share of Bacteroidetes, as well as Proteobacteria. Additionally, a decrease in the share of metabolism-related proteins and an increase of the relative amount of proteins involved in the processing of genetic information was observed for RNAlater-stored samples. This suggests that great care should be taken in choosing methods for the preservation and storage of microbiome samples, as well as in comparing the results of analyses using different sampling and storage methods. Flash freezing and subsequent storage at −80 °C should be chosen wherever possible.
KW  - proteomics
KW  - metaproteomics
KW  - metagenomics
KW  - microbiome
KW  - microbiota
KW  - flash freezing
KW  - RNAlater
KW  - sample storage
Y1  - 2019
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-195976
SN  - 2076-2607
VL  - 7
IS  - 9
ER  -