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  - Wheeler, Nicole E.
A1  - Barquist, Lars
A1  - Kingsley, Robert A.
A1  - Gardner, Paul P.
T1  - A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes
JF  - Bioinformatics
N2  - Motivation: 
Next generation sequencing technologies have provided us with a wealth of information on genetic variation, but predi cting the functional significance of this variation is a difficult task. While many comparative genomics studies have focused on gene flux and large scale changes, relatively little attention has been paid to quantifying the effects of single nucleotide polymorphisms and indels on protein function, particularly in bacterial genomics.

Results: 
We present a hidden Markov model based approach we call delta-bitscore (DBS) for identifying orthologous proteins that have diverged at the amino acid sequence level in a way that is likely to impact biological function. We benchmark this approach with several widely used datasets and apply it to a proof-of-concept study of orthologous proteomes in an investigation of host adaptation in Salmonella enterica. We highlight the value of the method in identifying functional divergence of genes, and suggest that this tool may be a better approach than the commonly used dN/dS metric for identifying functionally significant genetic changes occurring in recently diverged organisms.
KW  - Host adaptation
KW  - Salmonella-enteritidis
KW  - Sequence identity
KW  - Rapid evolution
KW  - Variants
KW  - Cystic-fibriosis
KW  - Strains
KW  - Pathogenicity
KW  - Typhimurium
KW  - Yersinia
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-186502
VL  - 32
IS  - 23
ER  -