BEACON Researchers at Work: Of Milk and Microbes

This week’s BEACON Researchers at Work blog post is by University of Idaho graduate student Janet Williams. 

JanetMilk and microbes, what do these two things have to do with each other? For many years, milk was thought to be sterile and any bacteria present were considered to be pathogenic or due to “contamination” of milk. It is true that certain bacteria, like Salmonella, E. coli and Listeria, in unpasteurized milk can be cause for concern. However, recent evidence has clearly demonstrated that “healthy” milk contains diverse bacterial communities (Figures 1 and 2 below)1,2. And what’s even more intriguing is the thought that certain bacteria in milk are actually good for the newborn. These bacterial communities in milk likely serve important roles in maturation of the nursing newborn’s gastrointestinal (GI) tract and immune system.3 Hmmm… bacteria in a food being consumed and conferring a health benefit to the host. Sound familiar? Sounds like a probiotic to me. This concept may or may not surprise you. In fact, you can now most likely find infant formulas supplemented with probiotics on the shelves of your local grocery store. If you are curious and want to read more about this, check out the recent review by McGuire and McGuire (2014)4 that explores the idea that milk is actually Mother Nature’s prototypical probiotic food.

Figure 1: Example of immune and bacterial cells found in “healthy” human milk

Figure 1: Example of immune and bacterial cells found in “healthy” human milk

Here is another interesting thought… milk has not only evolved to contain nutrients to “meet the diverse reproductive and environmental demands of different species” but to also contain bacteria that increase the chance of survival and development of the nursing young in diverse environments.

So are milk bacterial communities similar across different mammals? Are milk bacterial communities similar across different human populations? Does maternal diet influence milk bacterial communities? Do host genetics play a role in structuring the milk bacterial communities? What components in milk influence the structure of milk bacterial communities? How has the evolution of those components impacted the microbial diversity found in milk? What types of bacteria-bacteria interactions may be at play in structuring the bacterial communities? I could go on for a long time adding to this list. I’m fascinated with how all these factors are intertwined and how together they influence maternal and newborn health. 

Figure 2: Community composition of 15 abundant bacterial genera in milk samples, from Hunt et al 2011

Figure 2: Community composition of 15 abundant bacterial genera in milk samples, from Hunt et al 2011

Right now, we don’t have the answers to many of these questions. This is one of the reasons I am pursuing a PhD in Bioinformatics and Computational Biology at the University of Idaho. I work in the laboratory of Dr. Mark McGuire (Animal & Veterinary Sciences Dept, UI) and in close collaboration with Dr. Shelley McGuire (School of Biological Sciences, WSU). The McGuire labs have been engaged in the study and hands-on collection, extraction, and analysis of various components of interest from human and cow milk (e.g., lipid, protein, sugars, host RNA) for many years. We are now venturing into the computational arena of processing and interpreting massive amounts of sequencing data from bacterial DNA.

I work on both the “wet lab bench” side and the computational side of things in the laboratory. Although most of my experience prior to starting the PhD program was at the lab bench, my current focus is analyzing 16S rRNA sequence data from a variety of samples (human and cow milk, human fecal, dairy cow rumen and fecal, and newt skin swabs). I am trying to understand some of the complexities in the dynamics in the microbial communities and how other factors (e.g. diet and/or spatial/geographical location) may influence the structure of these communities.

For the human milk samples, we are currently working to address the question of how diet influences the milk microbiome in much the same way that others have looked at how diet influences the gastrointestinal (GI) microbiota. Initially it’s just about characterization of what bacteria populations are present over the course of lactation at the different taxonomic levels. The next step is to see if there is any structure to the variation of the bacterial communities. Can a large part of the variation in the milk bacterial communities be explained by maternal diet? By time postpartum? By some other nutrient or component in human milk? It’s important to understand the composition of the bacterial communities that are present as it has been suggested that the milk microbiota may be directly involved in colonization of the newborn GI tract and the GI microbial composition has potential short- and long-term effects on the health of that individual.

One of the reasons that I’m a part of BEACON is because I’d also like to try and investigate the evolutionary forces that potentially influence milk composition and the microbial communities in milk. And that’s where you, the reader, might be able to provide insight or suggestions. Now that you know some of what we do, what thoughts or ideas have come to mind as you have read this in how we might approach some of the questions above? Let me know what you think. I’d be interested in having a conversation with you. 

1Hunt K, Foster J, Forney L, Schütte U, Beck D, Abdo Z, et al. (2011). Characterization of the diversity and temporal stability of bacterial communities in human milk. PloS ONE 6:e21313.

2Quigley L, O’Sullivan O, Stanton C, Beresford TP, Ross RP, Fitzgerald GF, Cotter PD (2013) The complex microbiota of raw milk. FEMS Microbiol Rev 37:664-698.

3Fernández L, Langa S, Martín V, Maldonado A, Jiménez E, Martín R, Rodríguez JM (2013) The human milk microbiota: Origin and potential roles in health and disease. Pharm Res 69:1-10.

4McGuire MK, McGuire MA (2015) Human milk: Mother nature’s prototypical probiotic food? Adv Nutr (in press).

For more information about Janet’s work, you can contact her at janetw at uidaho dot edu.

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