Integrated network-diversity analyses suggest suppressive effect of Hodgkin’s lymphoma and slightly relieving effect of chemotherapy on human milk microbiome

Abstract

We aim to investigate the effects of Hodgkin’s lymphoma and the chemotherapy for treating the disease on the human milk microbiome through integrated network and community diversity analyses. Our analyses suggest that Hodgkin’s lymphoma seems to have a suppressing effect on the milk microbiome by lowering the milk microbial community diversity, as measured by the Hill numbers profiles. Although the diversity analysis did not reveal an effect of chemotherapy on community diversity, bacterial species interaction network analysis shows that chemotherapy may help to slightly restore the milk microbiome impacted by Hodgkin’s lymphoma through its influence on the interactions among species (or OTUs). We further constructed diversity-metabolites network, which suggests that the milk microbial diversity is positively correlated with some beneficial milk metabolites such as DHA (DocosaHexaenoic Acid), and that the diversity is negatively correlated with some potentially harmful metabolites such as Butanal. We hence postulate that higher milk microbial diversity should be a signature of healthy mothers and beneficial to infants. Finally, we constructed metabolites OTU correlation networks, from which we identified some special OTUs. These OTUs deserve further investigations given their apparent involvements in regulating the levels of critical milk metabolites such as DHA, Inositol and Butanal.

The Microbiota of the Human Mammary Ecosystem

“…Changes in the metabolic profile of milk, characterized by a decrease of inositol and docosahexaenoic, were also observed (Urbaniak et al, 2014b). The second study provided contradictory results since no negative effect of chemotherapy on community diversity was found (Ma et al, 2016).…”

Commentary: Relationship between Milk Microbiota, Bacterial Load, Macronutrients, and Human Cells during Lactation

“…The robust microbiotas, able to regain their original function upon disturbances, should be identified. The proposed networking approach on the breast milk dataset was recently employed for the geographically distinct healthy cohort (Ma et al, 2015 ) and was also applied (Ma et al, 2016 ) in the preliminary comparative analysis of Hodgkin's lymphoma milk microbiome after drug administration. Moreover, the authors suggested the metabolites-microbial species networks to be very useful in identifying the active bacterial taxa really involved in the milk microbial communities conferred to infants.…”

FBA Ecological Guild: Trio of Firmicutes-Bacteroidetes Alliance against Actinobacteria in Human Oral Microbiome

“…The network analysis approach. We adopted standard approach for correlation network analysis to construct and analyze the human oral microbiome network with the 16s-rRNA datasets originally reported by Zaura et al 24,[36][37][38][39] . To reduce the noise effect of the OTUs with extremely low abundance and potentially spurious OTU reads, we filtered out the OTUs whose total reads in all 29 samples were less than 30, i.e., approximately one read per sample, equivalent to removing the so-called singleton, which is a common practice in ecological analysis.…”