Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota
Open accessAbstract
BACKGROUND: Recent studies have suggested that bacteria associated with the placenta-a "placental microbiome"-may be important in reproductive health and disease. However, a challenge in working with specimens with low bacterial biomass, such as placental samples, is that some or all of the bacterial DNA may derive from contamination in dust or commercial reagents. To investigate this, we compared placental samples from healthy deliveries to a matched set of contamination controls, as well as to oral and vaginal samples from the same women. RESULTS: We quantified total 16S rRNA gene copies using quantitative PCR and found that placental samples and negative controls contained low and indistinguishable copy numbers. Oral and vaginal swab samples, in contrast, showed higher copy numbers. We carried out 16S rRNA gene sequencing and community analysis and found no separation between communities from placental samples and contamination controls, though oral and vaginal samples showed characteristic, distinctive composition. Two different DNA purification methods were compared with similar conclusions, though the composition of the contamination background differed. Authentically present microbiota should yield mostly similar results regardless of the purification method used-this was seen for oral samples, but no placental bacterial lineages were (1) shared between extraction methods, (2) present at >1 % of the total, and (3) present at greater abundance in placental samples than contamination controls. CONCLUSIONS: We conclude that for this sample set, using the methods described, we could not distinguish between placental samples and contamination introduced during DNA purification.
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Prior research has indicated that the differences between 16S qPCR copy numbers produced from the same samples but extracted with both PSP and MoBio kit were statistically negligible.
“Prior research has indicated that the differences between 16S qPCR copy numbers produced from the same samples but extracted with both PSP and MoBio kit were statistically negligible [84]”
From Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana (2019) · cites this paper as [84]
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- Authors
- Lauder, A. P., Roche, A. M., Sherrill-Mix, S., Bailey, A., Laughlin, A. L., Bittinger, K., Leite, R., Elovitz, M. A., Parry, S., & Bushman, F. D.
- Affiliations
- University of Pennsylvania (US)
- Corresponding author
- Parry, Samuel
- Bushman, Frederic D.
- ORCID
- Venue
- Microbiome
- Published
- 2016-06-23
- Volume
- 4
- Issue
- 1
- Pages
- 29-29
- ISSN
- 2049-2618 (ISSN-L)
- PMC
- PMC4917942
- OpenAlex
- W2462800864
- Cited by
- 539
- References
- 47
- Citations by year
- 2026: 23 · 2025: 24 · 2024: 34 · 2023: 47 · 2022: 45 · 2021: 84 · 2020: 84 · 2019: 84 · 2018: 64 · 2017: 44 · 2016: 4
- FWCI
- 33.95
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Microbiome (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- National Institute of Allergy and Infectious Diseases (T32 AI007632, P30 AI045008)
- March of Dimes Foundation (March of Dimes Prematurity Research Center at the University of Pennsylvania)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Immunology and Microbiology › Microbiology › Reproductive tract infections research
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- placental microbiome, placenta, contamination control, 16S rRNA gene sequencing, DNA extraction methods, bacterial DNA contamination, oral microbiota, vaginal microbiota, 16S rRNA gene copy number, low-biomass samples
- MeSH terms
- Female, Humans, Mouth, Placenta, Pregnancy, RNA, Ribosomal, 16S, Specimen Handling, Sequence Analysis, DNA, Gene Dosage, Microbiota
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