When to suspect contamination rather than colonization - lessons from a putative fetal sheep microbiome

Area of Science:

• Microbiology
• Genomics
• Animal Science

Background:

• The existence of a prenatal fetal microbiome is controversial, challenging the sterile womb paradigm.
• Studies rely on DNA-based evidence, facing criticism regarding contamination and germ-free animal derivation.
• Critical assessment of new studies is crucial to prevent scientific misinformation.

Purpose of the Study:

• To critically evaluate a recent publication claiming a fetal microbiome in sheep.
• To reanalyze metagenomic and metatranscriptomic data to assess the validity of prenatal microbial colonization findings.
• To identify potential contamination sources and propose methods to improve microbiome research confidence.

Main Methods:

• Reanalysis of published metagenomic and metatranscriptomic sequence data from a sheep study.
• Identification and characterization of microbial contamination in all analyzed samples.
• Comparative analysis of microbial profiles to distinguish true biological signals from contamination.

Main Results:

• Evidence of contamination affecting all samples, explaining the reported findings without necessitating a fetal microbiome.
• The original study's conclusions regarding a prenatal fetal lamb microbiome are challenged.
• Common issues in low-biomass microbiome projects were highlighted.

Conclusions:

• The findings do not support the existence of a prenatal fetal lamb microbiome as previously reported.
• Contamination is a significant confounder in low-biomass microbiome studies.
• Genomic independence at the microbial strain level is proposed as a novel marker for validating metagenomics in controversial low-biomass research.