Comparison of Bacterial DNA Profiles in Mid-Trimester Amniotic Fluid Samples From Preterm and Term Deliveries

Stinson, Lisa F.; Hallingström, Maria; Barman, Malin; Viklund, Felicia; Keelan, Jeffrey A.; Kacerovský, Marian; Payne, Matthew S.; Jacobsson, Bo

doi:10.3389/fmicb.2020.00415

Cited by 35 publications

(56 citation statements)

References 50 publications

(97 reference statements)

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“…Kit NM is designed for the extraction of genomic DNA from milk and has been used to extract DNA from human (Drago et al 2017) and bovine milk (Rahman et al 2015;Perin et al 2017), so it was not surprising that this kit extracted DNA from all samples. Kit QM is predominantly marketed for the automated isolation of DNA from pure microbial cultures, food cultures and swabs; however, it has also been used to extract DNA from low-biomass samples such as amniotic fluid (Stinson et al 2020). Considering that HM is a low-biomass sample (Perez et al 2007), it is important to validate and optimize DNA extraction methods so that DNA can be efficiently extracted from these samples.…”

Section: Discussionmentioning

confidence: 99%

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DNA extraction method influences human milk bacterial profiles

Cheema

Stinson

Lai

et al. 2020

J. Appl. Microbiol.

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Aims: To evaluate four DNA extraction methods to elucidate the most effective method for bacterial DNA recovery from human milk (HM). Methods and Results: Human milk DNA was extracted using the following methods: (i) Qiagen MagAttract Microbial DNA Isolation Kit (kit QM), (ii) Norgen Milk Bacterial DNA Isolation Kit (kit NM), (iii) Qiagen MagAttract Microbiome DNA/RNA Isolation Kit (kit MM) and (iv) TRIzol LS Reagent (method LS). The full-length 16S rRNA gene was sequenced. Kits MM and method LS were unable to extract detectable levels of DNA in 9/11 samples. Detectable levels of DNA were recovered from all samples using kits NM (mean = 0Á68 ng ll À1) and QM (mean = 0Á55 ng ll À1). For kits NM and QM, the greatest number of reads were associated with Staphylococcus epidermidis, Streptococcus vestibularis, Propionibacterium acnes, Veillonella dispar and Rothia mucilaginosa. Contamination profiles varied substantially between kits, with one bacterial species detected in negative extraction controls generated with kit QM and six with kit NM. Conclusions: Kit QM is the most suitable of the kits tested for the extraction of bacterial DNA from human milk. Significance and Impact of the Study: Choice of extraction method impacts the efficiency of bacterial DNA extraction from human milk and the resultant bacterial community profiles generated from these samples.

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Section: Discussionmentioning

confidence: 99%

“…Kit QM is predominantly marketed for the automated isolation of DNA from pure microbial cultures, food cultures and swabs; however, it has also been used to extract DNA from low‐biomass samples such as amniotic fluid (Stinson et al . 2020). Considering that HM is a low‐biomass sample (Perez et al .…”

Section: Discussionmentioning

confidence: 99%

DNA extraction method influences human milk bacterial profiles

Cheema

Stinson

Lai

et al. 2020

J. Appl. Microbiol.

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“…According to the authors themselves, only 30% of fetal intestinal specimens produced a bacterial profile different from the controls [ 27 ]. Another research group of outspoken advocates of the colonized womb paradigm [ 5 , 9 ] concluded that findings in their 2020 publication “at the very least support the notion that exposure to bacterial DNA may occur prior to birth in some healthy pregnancies” [ 8 ], although less than 20% of the samples contained detectable bacterial DNA. Why would the main conclusion of both publications be based on findings in less than 30% of the samples even though the signals were sparse and despite the limitation that clinical samples cannot be taken aseptically?…”

Section: The Prenatal Microbiome Debate In the Light Of Karl Popper’smentioning

confidence: 99%

“…Ignited by a 2014 research study by Aagaard and coworkers that applied next-generation sequencing to describe a unique microbiome in the placenta of humans [1], an entire research field emerged on microbial communities in the fetal environment (placenta, cord blood, amniotic fluid, fetus, meconium) of humans [2][3][4][5][6][7][8][9][10]. Speculations about the role of these microbial communities, which were often referred to as microbiomes, in initiating the establishment of the human microbiome via in utero transmission and shaping human health were the topic of many commentaries and review articles [2,3,[5][6][7].…”

Section: Introductionmentioning

confidence: 99%

A philosophical perspective on the prenatal in utero microbiome debate

Walter

Hornef

2021

Microbiome

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Within the last 6 years, a research field has emerged that focuses on the characterization of microbial communities in the prenatal intrauterine environment of humans and their putative role in human health. However, there is considerable controversy around the existence of such microbial populations. The often contentious debate is primarily focused on technical aspects of the research, such as difficulties to assure aseptic sampling and to differentiate legitimate signals in the data from contamination. Although such discussions are clearly important, we feel that the problems with the prenatal microbiome field go deeper. In this commentary, we apply a philosophical framework to evaluate the foundations, experimental approaches, and interpretations used by scientists on both sides of the debate. We argue that the evidence for a “sterile womb” is based on a scientific approach that aligns well with important principles of the philosophy of science as genuine tests of the hypothesis and multiple angles of explanatory considerations were applied. In contrast, research in support of the “in utero colonization hypothesis” is solely based on descriptive verifications that do not provide explanatory insight, which weakens the evidence for a prenatal intrauterine microbiome. We propose that a reflection on philosophical principles can inform not only the debate on the prenatal intrauterine microbiome but also other disciplines that attempt to study low-biomass microbial communities.

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“…The incidence of preterm birth (PTB) is about 5%‐18%, but it causes 85% of neonatal death 1,2 . Intrauterine infection is a major cause of preterm delivery, accounting for 40% of all PTB cases worldwide 3,4 .…”

Section: Introductionmentioning

confidence: 99%

Effect of RvD1/FPR2 on inflammatory response in chorioamnionitis

Zhang

et al. 2020

J Cellular Molecular Medi

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Chorioamnionitis (CAM), as a common intrauterine infectious disease, is the leading cause of premature birth, stillbirth, neonatal infection and sepsis. The formyl peptide receptor 2 (FPR2) is a member of GPCRs widely distributed in a variety of tissues and is associated with many inflammatory diseases. With the discovery of FPR2 in human placenta, the possibility of exploring the function of FPR2 in obstetrics is evolving. The Resolvin D1 (RvD1) plays an important role in the resolution of inflammation by combining with FPR2. In this study, we evaluated the role of FPR2 and RvD1 in CAM, not only in the human placenta but also in mouse models. The expression of FPR2 increased in the placenta of CAM patients and the downstream PPARγ/NF‐κB signalling changed accordingly. Moreover, Fpr2−/− mice were highly susceptible to LPS, displaying a worse CAM symptom, compared with WT mice. By establishing a model of trophoblast inflammation in vitro, it was confirmed that RvD1 rescued the effect of LPS on inflammation by combining with FPR2 and its downstream PPARγ/NF‐κB pathway. Otherwise, RvD1 improved the preterm labour in a mouse model of CAM induced by LPS. Altogether, these findings show that RvD1 alleviated the inflammation of trophoblast in vivo and in vitro through FPR2/PPARγ/NF‐κB pathway, suggesting RvD1/FPR2 might be a novel therapeutic strategy to alleviate CAM.

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Comparison of Bacterial DNA Profiles in Mid-Trimester Amniotic Fluid Samples From Preterm and Term Deliveries

Cited by 35 publications

References 50 publications

DNA extraction method influences human milk bacterial profiles

DNA extraction method influences human milk bacterial profiles

A philosophical perspective on the prenatal in utero microbiome debate

Effect of RvD1/FPR2 on inflammatory response in chorioamnionitis

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