Sökning: onr:"swepub:oai:DiVA.org:uu-427345" >
Assessment of In Vi...
Assessment of In Vitro and In Silico Protocols for Sequence-Based Characterization of the Human Vaginal Microbiome
-
- Hugerth, Luisa W (författare)
- Karolinska Institutet
-
- Pereira, Marcela (författare)
- Karolinska Institutet
-
- Zha, Yinghua (författare)
- Centre for Translational Microbiome Research, Department of Microbiology, Tumour and Cell Biology, Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
-
visa fler...
-
- Seifert, Maike (författare)
- Karolinska Institutet
-
- Kaldhusdal, Vilde (författare)
- Karolinska Institutet
-
- Boulund, Fredrik (författare)
- Karolinska Institutet
-
- Krog, Maria C (författare)
- The Recurrent Pregnancy Loss Unit, Capital Region of Denmark, Rigshospitalet and Hvidovre Hospital, Copenhagen, Denmark
-
- Bashir, Zahra (författare)
- The Recurrent Pregnancy Loss Unit, Capital Region of Denmark, Rigshospitalet and Hvidovre Hospital, Copenhagen, Denmark
-
- Hamsten, Marica (författare)
- Karolinska Institutet
-
- Fransson, Emma, PhD, 1973- (författare)
- Karolinska Institutet,Uppsala universitet,Obstetrisk och reproduktiv hälsoforskning,Centre for Translational Microbiome Research, Department of Microbiology, Tumour and Cell Biology, Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
-
- Svarre-Nielsen, Henriette (författare)
- The Recurrent Pregnancy Loss Unit, Capital Region of Denmark, Rigshospitalet and Hvidovre Hospital, Copenhagen, Denmark
-
- Schuppe-Koistinen, Ina (författare)
- Karolinska Institutet
-
- Engstrand, Lars (författare)
- Karolinska Institutet
-
visa färre...
-
(creator_code:org_t)
- American Society for Microbiology, 2020
- 2020
- Engelska.
-
Ingår i: mSphere. - : American Society for Microbiology. - 2379-5042. ; 5:6
- Relaterad länk:
-
https://doi.org/10.1...
-
visa fler...
-
https://uu.diva-port... (primary) (Raw object)
-
https://urn.kb.se/re...
-
https://doi.org/10.1...
-
http://kipublication...
-
visa färre...
Abstract
Ämnesord
Stäng
- The vaginal microbiome has been connected to a wide range of health outcomes. This has led to a thriving research environment but also to the use of conflicting methodologies to study its microbial composition. Here, we systematically assessed best practices for the sequencing-based characterization of the human vaginal microbiome. As far as 16S rRNA gene sequencing is concerned, the V1-V3 region performed best in silico, but limitations of current sequencing technologies meant that the V3-V4 region performed equally well. Both approaches presented very good agreement with qPCR quantification of key taxa, provided that an appropriate bioinformatic pipeline was used. Shotgun metagenomic sequencing presents an interesting alternative to 16S rRNA gene amplification and sequencing but requires deeper sequencing and more bioinformatic expertise and infrastructure. We assessed different tools for the removal of host reads and the taxonomic annotation of metagenomic reads, including a new, easy-to-build and -use reference database of vaginal taxa. This curated database performed as well as the best-performing previously published strategies. Despite the many advantages of shotgun sequencing, none of the shotgun approaches assessed here agreed with the qPCR data as well as the 16S rRNA gene sequencing.IMPORTANCE The vaginal microbiome has been connected to various aspects of host health, including susceptibility to sexually transmitted infections as well as gynecological cancers and pregnancy outcomes. This has led to a thriving research environment but also to conflicting available methodologies, including many studies that do not report their molecular biological and bioinformatic methods in sufficient detail to be considered reproducible. This can lead to conflicting messages and delay progress from descriptive to intervention studies. By systematically assessing best practices for the characterization of the human vaginal microbiome, this study will enable past studies to be assessed more critically and assist future studies in the selection of appropriate methods for their specific research questions.
Ämnesord
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Mikrobiologi inom det medicinska området (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Microbiology in the medical area (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinsk bioteknologi -- Medicinsk bioteknologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Medical Biotechnology -- Medical Biotechnology (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin -- Reproduktionsmedicin och gynekologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine -- Obstetrics, Gynaecology and Reproductive Medicine (hsv//eng)
Nyckelord
- 16S rRNA
- PCR
- amplicon
- human microbiome
- metagenomics
- molecular methods
- quantitative methods
- vaginal microbiome
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
Hitta via bibliotek
-
mSphere
(Sök värdpublikationen i LIBRIS)
Till lärosätets databas
- Av författaren/redakt...
-
Hugerth, Luisa W
-
Pereira, Marcela
-
Zha, Yinghua
-
Seifert, Maike
-
Kaldhusdal, Vild ...
-
Boulund, Fredrik
-
visa fler...
-
Krog, Maria C
-
Bashir, Zahra
-
Hamsten, Marica
-
Fransson, Emma, ...
-
Svarre-Nielsen, ...
-
Schuppe-Koistine ...
-
Engstrand, Lars
-
visa färre...
- Om ämnet
-
- MEDICIN OCH HÄLSOVETENSKAP
-
MEDICIN OCH HÄLS ...
-
och Medicinska och f ...
-
och Mikrobiologi ino ...
-
- MEDICIN OCH HÄLSOVETENSKAP
-
MEDICIN OCH HÄLS ...
-
och Medicinsk biotek ...
-
och Medicinsk biotek ...
-
- MEDICIN OCH HÄLSOVETENSKAP
-
MEDICIN OCH HÄLS ...
-
och Klinisk medicin
-
och Reproduktionsmed ...
- Artiklar i publikationen
-
mSphere
- Av lärosätet
-
Uppsala universitet
-
Karolinska Institutet