Human milk microbiota and mycobiota in the CHILD cohort study
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Date
2020
Authors
Moossavi, Shirin
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Abstract
Introduction: Previous studies have confirmed the existence of a highly diverse bacterial community in human milk and suggested that its composition might be affected by mode of delivery and maternal health. However, these findings have not yet been reproduced in large-scale studies. Additionally, the compositions of milk microbiota such as milk fungi are less frequently studied.
Methods: Milk microbiota (bacteria) and mycobiota (fungi) were profiled in 393 and 271 mother-infant dyads from the CHILD Cohort Study using amplicon sequencing. Additionally, the milk microbiota was examined in a pilot study using culture-enriched molecular profiling. Finally, the impact of the bioinformatics processing on the results of downstream statistical analysis was compared.
Results: Using multiple analytic techniques including causal modelling, evidence is provided that mode of breastfeeding (directly at the breast vs. pumped and bottle-fed) has a significant association with the composition of milk bacteria potentially highlighting the importance of exogenously-derived bacteria as sources of milk bacteria. The composition of other major milk components were associated with the overall composition of the milk microbiota while controlling for relevant confounding factors.
Defining fungal presence at minimum threshold of 1000 reads per sample, the majority of milk samples did not contain detectable fungi and that presence of fungi was associated with residential characteristics and milk microbiota composition. Fungi diversity was associated with mode of delivery, maternal atopy, and home environment.
We were able to isolate major milk bacteria using culture-enriched methods. Short-term freezing considerably impacted the composition of milk bacteria while we were not able to grow any bacterial isolates from the long-term frozen samples.
Finally, milk microbiota richness was strongly impacted by the choice of the bioinformatics approach. However, there was an acceptable agreement and consistency in the relative abundances of the dominant milk bacteria and milk diversity. Importantly, the main conclusions remained robust to the choice of data processing.
Conclusion: This is among the largest studies of human milk microbiota and mycobiota performed to date. Moreover, this is among the first studies of milk microbiota culture-enriched molecular profiling. Together, these results considerably expand upon existing knowledge about milk microbiota and mycobiota.
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Keywords
Microbiome, Mycobiome, Breastfeeding