title: Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota.
abstract: 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.
authors.affiliation: Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA.
authors.forename: Abigail P
authors.initials: AP
authors.lastname: Lauder
authors.affiliation: Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA.
authors.forename: Aoife M
authors.initials: AM
authors.lastname: Roche
authors.affiliation: Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA.
authors.forename: Scott
authors.initials: S
authors.lastname: Sherrill-Mix
authors.affiliation: Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA.
authors.forename: Aubrey
authors.initials: A
authors.lastname: Bailey
authors.affiliation: Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA.
authors.forename: Alice L
authors.initials: AL
authors.lastname: Laughlin
authors.affiliation: Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA.
authors.forename: Kyle
authors.initials: K
authors.lastname: Bittinger
authors.affiliation: Department of Obstetrics and Gynecology, Maternal and Child Health Research Program, Perelman School of Medicine at the University of Pennsylvania, 3400 Spruce Street, Philadelphia, PA, 19104, USA.
authors.forename: Rita
authors.initials: R
authors.lastname: Leite
authors.affiliation: Department of Obstetrics and Gynecology, Maternal and Child Health Research Program, Perelman School of Medicine at the University of Pennsylvania, 3400 Spruce Street, Philadelphia, PA, 19104, USA.
authors.forename: Michal A
authors.initials: MA
authors.lastname: Elovitz
authors.affiliation: Department of Obstetrics and Gynecology, Maternal and Child Health Research Program, Perelman School of Medicine at the University of Pennsylvania, 3400 Spruce Street, Philadelphia, PA, 19104, USA. parry@mail.med.upenn.edu.
authors.forename: Samuel
authors.initials: S
authors.lastname: Parry
authors.affiliation: Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA. bushman@mail.med.upenn.edu.
authors.forename: Frederic D
authors.initials: FD
authors.lastname: Bushman
mesh_terms: D005260:Female; D018628:Gene Dosage; D006801:Humans; D064307:Microbiota; D009055:Mouth / Q000382:microbiology; D010920:Placenta / Q000382:microbiology*; D011247:Pregnancy; D012336:RNA, Ribosomal, 16S / Q000032:analysis* / Q000592:standards; D017422:Sequence Analysis, DNA; D013048:Specimen Handling / Q000592:standards*
chemical_list: D012336:RNA, Ribosomal, 16S
keywords: 16S rRNA gene; Low biomass samples; Microbiome; Placenta; Reagent contamination