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dc.contributor.authorBihl, Simone
dc.contributor.authorde Goffau, Marcus
dc.contributor.authorPodlesny, Daniel
dc.contributor.authorSegata, Nicola
dc.contributor.authorShanahan, Fergus
dc.contributor.authorWalter, Jens
dc.contributor.authorFricke, W Florian
dc.date.accessioned2022-01-19T16:03:11Z
dc.date.available2022-01-19T16:03:11Z
dc.date.issued2022
dc.identifier.urihttp://hdl.handle.net/10713/17586
dc.description.abstractThere is an ongoing controversy around the existence of a prenatal, fetal microbiome in humans, livestock, and other animals. The 'in utero microbial colonization' hypothesis challenges the clinical paradigm of the 'sterile womb' but has been criticized for its reliance on DNA-based evidence to detect microbiomes and the failure to conciliate the routine experimental derivation of germ-free animals from surgically resected embryos with a thriving fetal microbiome. In order to avoid the propagation of misinformation in the scientific literature, a critical assessment and careful review of newly published studies, particularly those that challenge the convincing current clinical dogma of the sterile womb, is of critical importance.We read with interest a recent publication that postulated the presence of a fetal microbiome in sheep, but questioned the plausibility of the reported findings and their meaningfulness to prove "microbial colonisation of the fetal gut […] in utero". We reanalyzed the published metagenomic and metatranscriptomic sequence data from the original publication and identified evidence for different types of contamination that affected all samples alike and could explain the reported findings without requiring the existence of a fetal microbiome.Our reanalysis challenges the reported findings as supportive of a prenatal fetal lamb microbiome. The shortcomings of the original analysis and data interpretation highlight common problems of low-biomass microbiome projects. We propose genomic independence of separate biological samples, i.e. distinctive profiles at the microbial strain level, as a potential new microbiome marker to increase confidence in metagenomics analyses of controversial low-biomass microbiomes.en_US
dc.description.urihttps://doi.org/10.1080/19490976.2021.2005751en_US
dc.language.isoenen_US
dc.publisherTaylor and Francis Inc.en_US
dc.relation.ispartofGut Microbesen_US
dc.subjectFetal microbiomeen_US
dc.subjectcontaminationen_US
dc.subjectmetagenomicsen_US
dc.subjectmetatranscriptomicsen_US
dc.subjectmicrobial strainsen_US
dc.subjectphiXen_US
dc.subjectsheepen_US
dc.titleWhen to suspect contamination rather than colonization - lessons from a putative fetal sheep microbiome.en_US
dc.typeArticleen_US
dc.identifier.doi10.1080/19490976.2021.2005751
dc.identifier.pmid34923897
dc.source.journaltitleGut microbes
dc.source.volume14
dc.source.issue1
dc.source.beginpage2005751
dc.source.endpage
dc.source.countryUnited States


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