title: Metagenomic Analysis of Milk of Healthy and Mastitis-Suffering Women.
abstract: BACKGROUND
  Some studies have been conducted to assess the composition of the bacterial communities inhabiting human milk, but they did not evaluate the presence of other microorganisms, such as fungi, archaea, protozoa, or viruses.
  
  
  OBJECTIVE
  This study aimed to compare the metagenome of human milk samples provided by healthy and mastitis-suffering women.
  
  
  METHODS
  DNA was isolated from human milk samples collected from 10 healthy women and 10 women with symptoms of lactational mastitis. Shotgun libraries from total extracted DNA were constructed and the libraries were sequenced by 454 pyrosequencing.
  
  
  RESULTS
  The amount of human DNA sequences was ≥ 90% in all the samples. Among the bacterial sequences, the predominant phyla were Proteobacteria, Firmicutes, and Bacteroidetes. The healthy core microbiome included the genera Staphylococcus, Streptococcus, Bacteroides, Faecalibacterium, Ruminococcus, Lactobacillus, and Propionibacterium. At the species level, a high degree of inter-individual variability was observed among healthy women. In contrast, Staphylococcus aureus clearly dominated the microbiome in the samples from the women with acute mastitis whereas high increases in Staphylococcus epidermidis-related reads were observed in the milk of those suffering from subacute mastitis. Fungal and protozoa-related reads were identified in most of the samples, whereas Archaea reads were absent in samples from women with mastitis. Some viral-related sequence reads were also detected.
  
  
  CONCLUSIONS
  Human milk contains a complex microbial metagenome constituted by the genomes of bacteria, archaea, viruses, fungi, and protozoa. In mastitis cases, the milk microbiome reflects a loss of bacterial diversity and a high increase of the sequences related to the presumptive etiological agents.
authors.affiliation: Department of Nutrition, Food Science and Technology, Complutense University of Madrid, Madrid, Spain Probisearch, Tres Cantos, Madrid, Spain.
authors.forename: Esther
authors.initials: E
authors.lastname: Jiménez
authors.affiliation: Department of Nutrition, Food Science and Technology, Complutense University of Madrid, Madrid, Spain Probisearch, Tres Cantos, Madrid, Spain.
authors.forename: Javier
authors.initials: J
authors.lastname: de Andrés
authors.affiliation: Era7 Bioinformatics, Granada, Spain.
authors.forename: Marina
authors.initials: M
authors.lastname: Manrique
authors.affiliation: Era7 Bioinformatics, Granada, Spain.
authors.forename: Pablo
authors.initials: P
authors.lastname: Pareja-Tobes
authors.affiliation: Era7 Bioinformatics, Granada, Spain.
authors.forename: Raquel
authors.initials: R
authors.lastname: Tobes
authors.affiliation: Lifesequencing S.L., Parc Científic Universitat de València, Paterna, Spain.
authors.forename: Juan F
authors.initials: JF
authors.lastname: Martínez-Blanch
authors.affiliation: Lifesequencing S.L., Parc Científic Universitat de València, Paterna, Spain.
authors.forename: Francisco M
authors.initials: FM
authors.lastname: Codoñer
authors.affiliation: Lifesequencing S.L., Parc Científic Universitat de València, Paterna, Spain.
authors.forename: Daniel
authors.initials: D
authors.lastname: Ramón
authors.affiliation: Department of Nutrition, Food Science and Technology, Complutense University of Madrid, Madrid, Spain Probisearch, Tres Cantos, Madrid, Spain.
authors.forename: Leónides
authors.initials: L
authors.lastname: Fernández
authors.affiliation: Department of Nutrition, Food Science and Technology, Complutense University of Madrid, Madrid, Spain Probisearch, Tres Cantos, Madrid, Spain jmrodrig@ucm.es.
authors.forename: Juan M
authors.initials: JM
authors.lastname: Rodríguez
mesh_terms: D016022:Case-Control Studies; D005260:Female; D006801:Humans; D008413:Mastitis / Q000382:microbiology*; D054892:Metagenome; D064307:Microbiota / Q000235:genetics*; D008895:Milk, Human / Q000382:microbiology*
keywords: breastfeeding; human milk; mastitis; metagenome; microbiome