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  - 
TY  - JOUR
A1  - Claus, Heike
A1  - Hubert, Kerstin
A1  - Becher, Dörte
A1  - Otto, Andreas
A1  - Pawlik, Marie-Christin
A1  - Lappann, Ines
A1  - Strobel, Lea
A1  - Vogel, Ulrich
A1  - Johswich, Kay
T1  - A homopolymeric adenosine tract in the promoter region of nspA influences factor H-mediated serum resistance in Neisseria meningitidis
JF  - Scientific Reports
N2  - Although usually asymptomatically colonizing the human nasopharynx, the Gram-negative bacterium Neisseria meningitidis (meningococcus) can spread to the blood stream and cause invasive disease. For survival in blood, N. meningitidis evades the complement system by expression of a polysaccharide capsule and surface proteins sequestering the complement regulator factor H (fH). Meningococcal strains belonging to the sequence type (ST-) 41/44 clonal complex (cc41/44) cause a major proportion of serogroup B meningococcal disease worldwide, but they are also common in asymptomatic carriers. Proteome analysis comparing cc41/44 isolates from invasive disease versus carriage revealed differential expression levels of the outer membrane protein NspA, which binds fH. Deletion of nspA reduced serum resistance and NspA expression correlated with fH sequestration. Expression levels of NspA depended on the length of a homopolymeric tract in the nspA promoter: A 5-adenosine tract dictated low NspA expression, whereas a 6-adenosine motif guided high NspA expression. Screening German cc41/44 strain collections revealed the 6-adenosine motif in 39% of disease isolates, but only in 3.4% of carriage isolates. Thus, high NspA expression is associated with disease, but not strictly required. The 6-adenosine nspA promoter is most common to the cc41/44, but is also found in other hypervirulent clonal complexes.
KW  - Meningitis
KW  - Pathogens
Y1  - 2019
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-200956
VL  - 9
ER  -