ArticleMicrobiome2021
Batch effects account for the main findings of an in utero human intestinal bacterial colonization study.
Article in Microbiome, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
28 citing papers in PubMed, 51 citations in OpenAlex.
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- Randomized Trial Demonstrating No Translocation of Intact Intestinal Bacteria During Hemodialysis or Hemodiafiltration.Kidney international reports · 2025Article
- Influence of angiotensin II on the gut microbiome: modest effects in comparison to experimental factors.Cardiovascular research · 2024Article
- Impacts of Maternal Nutrition on Sow Performance and Potential Positive Effects on Piglet Performance.Animals : an open access journal from MDPI · 2024Review
- Environmental stressor assessment of hydrocarbonoclastic bacteria biofilms from a marine oil spill.Biotechnology reports (Amsterdam, Netherlands) · 2024Article
- Comparative evaluation of soil DNA extraction kits for long read metagenomic sequencing.Access microbiology · 2024Article
- Caution regarding the specificities of pan-cancer microbial structure.Microbial genomics · 2023Article
- Review
- PLSDA-batch: a multivariate framework to correct for batch effects in microbiome data.Briefings in bioinformatics · 2023Article
- The Colonization of Rumen Microbiota and Intervention in Pre-Weaned Ruminants.Animals : an open access journal from MDPI · 2023Review
- Microbial communities of the upper respiratory tract in mild and severe COVID-19 patients: a possible link with the disease course.Frontiers in microbiomes · 2023Article
- Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies.Nature · 2023Review
- Assessment of the human placental microbiome in early pregnancy.Frontiers in medicine · 2023Article
- Microbiome-Induced Autoimmunity and Novel Therapeutic Intervention.Advances in experimental medicine and biology · 2023Review
- The importance of the timing of microbial signals for perinatal immune system development.Microbiome research reports · 2023Article
- Intestinal microbiota and its interaction to intestinal health in nursery pigs.Animal nutrition (Zhongguo xu mu shou yi xue hui) · 2022Review
- Does the Amniotic Fluid of Mice Contain a Viable Microbiota?Frontiers in immunology · 2022Article
- Bovine Animal Model for Studying the Maternal Microbiome,Frontiers in microbiology · 2022Review
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Authors and funding
4 authors at 2 institutions in 1 country.
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Abstract
A recent study by Rackaityte et al. reported evidence for a low level of bacterial colonization, specifically of Micrococcus luteus, in the intestine of second trimester human fetuses. We have re-analyzed their sequence data and identified a batch effect which violates the underlying assumptions of the bioinformatic method used for contamination removal. This batch effect resulted in Micrococcus not being identified as a contaminant in the original work and being falsely assigned to the fetal samples. We further provide evidence that the micrographs presented by Rackaityte et al. are unlikely to show Micrococci or other bacteria as the size of the particles shown exceeds that of related bacterial cells. Finally, phylogenetic analysis showed that the microbes cultured from the fetal samples differed significantly from those detected by sequencing. Overall, our findings show that the presence of Micrococcus in the fetal gut is not supported by the primary sequence data. Our findings underline important aspects of the nature of contamination for both sequencing and culture approaches in microbiome studies and the appropriate use of automated contamination identification tools.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.