Capturing the diversity of the human milk microbiota through culture-enriched molecular profiling: a feasibility study.


Moossavi S(1)(2)(3)(4), Fontes ME(5), Rossi L(5), Fusch G(6), Surette MG(5)(7), Azad MB(2)(8).
Author information:
(1)Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
(2)Manitoba Interdisciplinary Lactation Centre
(MILC), Children's Hospital Research Institute of Manitoba, Winnipeg, MB R3E 3P4, Canada.
(3)Digestive Oncology Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran 14117-13135, Iran.
(4)Microbiome and Microbial Ecology Interest Group
(MMEIG), Universal Scientific Education and Research Network
(USERN), Calgary, AB T2N 4Z1, Canada.
(5)Department of Medicine and Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada.
(6)Department of Pediatrics, McMaster University, Hamilton, ON L8S 4L8, Canada.
(7)Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON L8S 4L8, Canada.
(8)Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB R3A 1S1, Canada.


Previous human milk studies have confirmed the existence of a highly diverse bacterial community using culture-independent and targeted culture-dependent techniques. However, culture-enriched molecular profiling of milk microbiota has not been done. Additionally, the impact of storage conditions and milk fractionation on microbiota composition is not understood. In this feasibility study, we optimized and applied culture-enriched molecular profiling to study culturable milk microbiota in eight milk samples collected from mothers of infants admitted to a neonatal intensive care unit. Fresh samples were immediately plated or stored at -80°C for 2 weeks (short-term frozen). Long-term samples were stored at -20°C for >6 months. Samples were cultured using 10 different culture media and incubated both aerobically and anaerobically. We successfully isolated major milk bacteria, including Streptococcus, Staphylococcus and Bifidobacterium, from fresh milk samples, but were unable to culture any bacteria from the long-term frozen samples. Short-term freezing shifted the composition of viable milk bacteria from the original composition in fresh samples. Nevertheless, the inter-individual variability of milk microbiota composition was observed even after short-term storage. There was no major difference in the overall milk microbiota composition between milk fractions in this feasibility study. This is among the first studies on culture-enriched molecular profiling of the milk microbiota demonstrating the effect of storage and fractionation on milk microbiota composition.