Defining the Core: the Human Gut Pan-Microbiome


In 1996, Kenneth Wilson and Rhonda Blitchington pioneered the use of DNA sequencing to analyze the composition of microbes in human fecal samples (Wilson and Blitchington 1996). Since then, studies around the world have investigated the specific make-up of the human gut microbiome via sequencing technologies. The most common way to analyze the composition of the microbiome is Next Generation Sequencing (NGS). The use of NGS has   identified of a large number of microorganisms found in the human gut.

Analysis of sequence data can identify types, abundances, and shifts in the composition of the gut microbiome of people with medical conditions and health concerns. Finding potential links between diseased states and the makeup of the human gut microbiome begins with DNA analysis of the “condition” gut, and continues with comparison to the types and abundances of microbiota in the “healthy” human gut. Continue reading “Defining the Core: the Human Gut Pan-Microbiome”

Leafy Greens and Friends: who’s hangin’ out on your lettuce?

Image of a healthy vibrant-green head of lettuce with water droplets on it.
Image of a lettuce head from

To the general public, the idea that there are tiny organisms living all around (and inside) of us might be a scary concept. Naturally, if all the news you get on a regular basis is concerning the totally-terrifying E. Coli that can give you food poisoning, or that fiendish-foe influenza–it’s not surprising that people often have negative reactions to the term “microbe.’ The reality is that we’re mostly made up of microbes, we encounter them every day, and most of the time they’re harmless or even beneficial! In fact, we often use microbes to ferment sugars so we can make things like yogurt and bread, and just as we use these microbes for our own benefit–plants can do the same! Continue reading “Leafy Greens and Friends: who’s hangin’ out on your lettuce?”

The skin microbiome and psoriasis: An emerging relationship

Background Information:

Psoriasis is an autoimmune disease that affects 1-3% of the world’s population and is influenced by both genetic and environmental factors, such as diet, stress-level, skin-care routine, etc. (Alekseyenko et al., 2013). People with psoriasis suffer from lesions (often called plaques) of dry, red, itchy, inflamed, and often “scaly’ skin (Langley et al., 2005). Lesions are created, in part, by an overactive inflammatory response in the skin, as well as the increased division of specific cells of the epidermis. In the recent past, researchers have specifically identified immune cells that play a role in this process by producing chemicals that increase inflammation (Chang et al., 2018; Lowes et al., 2008). Continue reading “The skin microbiome and psoriasis: An emerging relationship”

Does Gut Microbiota Influence Lipid Metabolism in the Sexes?


Differences between human males and females can be large or small; one of our largest problems in the more recent years may be influenced by a very small thing, or things rather. It turns out that the microbes living in our gut can affect our metabolism of fats (Eldin et al, 2016), impacting fat storage and digestion in the body.

In the paper by Baars et al (2018), the authors investigated the differences in male and female lipid (fat) metabolism, responsible for the breakdown and storage of fats (Goldberg, 2018),  by looking at their gut microbes. These authors are researching this difference in lipid metabolism based on the previous study done by Sugiyama, M. G. and L. B. Agellon (2012) that suggested that microbes and host sex can influence the metabolism. In this study, the authors are testing whether or not the bacteria in our gut has an effect on the lipid metabolism in our bodies, specifically between males and females. Continue reading “Does Gut Microbiota Influence Lipid Metabolism in the Sexes?”

Microbiome from Maternal Body Sites Helps to Develop Infants Gut Microbiome


Microbial colonization in infants gut influences human physiology, including the maturation of the immune system, nutrient absorption and metabolism, and the protection against pathogen colonization (Buffie and Pamer, 2013). Several factors including the mode of delivery (Dominguez-Bello et al., 2010, 2016), gestational age at birth (La Rosa et al., 2014),  maternal and infant antibiotic usage (Lemas et al., 2016) and feeding method (formula or breastfeeding) (Backhed et al., 2015) are very important to the early development of the infant microbiome. Wider environmental exposure (H.  Shin et al., 2015) and early intimate relations, particularly with the mother, also play a key role in the early microbial development of an infant. Microbiomes are responsible for different diseases of infants like asthma, diabetes, obesity etc (Nagpal et al. 2018). While the importance of the host-microbiome interplay is not in question, the mechanisms by which an infant acquires these microbes, and from what source, remain largely unexplored. Just a few months ago, a study demonstrated that the maternal microbiome is an important source in the early development of microbial species and strains in the infant gut (Korpela et al., 2018). Yet there has been no comprehensive assessment of the multiple potential maternal sources (like skin, breast milk, fecal, vaginal, oral ect.) of microbial transmission, and how ultimately they contribute to the development of the infant microbiome within hours of birth and over the first few months of life. Continue reading “Microbiome from Maternal Body Sites Helps to Develop Infants Gut Microbiome”

Microbial interactions with eczema: is your fungal community irritating you?


The skin is our largest organ and plays an important role in our health and well being. One key role of our skin is preventing infections by acting as a physical barrier to pathogens and secreting antimicrobial enzymes in our sweat (Parham, 2015). However, whether from genetic or environmental factors, sometimes this defense system goes wrong.

Skin lesions caused by eczema (WebMD)

Eczema is an umbrella term for a group of diseases that result in the inflammation of the skin (atopic dermatitis or AD). According to the American Academy of Dermatology, AD is a common skin disease in children, affecting up to 20% (American Academy of Dermatology, 2018). Most kids grow out of the disease, but somewhere between 10 and 30% do not (Eichenfield et al., 2014). Continue reading “Microbial interactions with eczema: is your fungal community irritating you?”

Little life-forms inside your head!

A little bit of background

What in the world is ADHD you might ask? ADHD stands for Attention Deficit/Hyperactivity Disorder and it is a common mental disorder that is found in school-aged children, but can also affect many adults (Parekh et al. 2017)! Symptoms of ADHD include inattention, impulsivity, and/or hyperactivity. If you have ever driven a vehicle without power-steering, you might have experienced the vehicle steering less sharply than what was intended by the driver. Some people describe their experience of having ADHD as if their brain is doing this! With ADHD, you might find yourself having to put in a lot more effort in a specific task just to avoid going off of the road. Continue reading “Little life-forms inside your head!”

Another One Bites the Dust: Kicking Asthma to the Curb


In 2016, the CDC reported that 8.3% of children have asthma. Asthma is a chronic lung disease in which airways become inflamed and narrowed. The cause of asthma is unknown, but scientists suspect that genetics, infections as a child, and exposure to certain allergens or viruses may have an impact on one’s development of asthma. There is no cure for this disease, although there are medicines that can help reduce an asthmatic person’s symptoms. (NIH National Heart, Lung, and Blood Institute)

Previous research has shown that children who grow up on traditional dairy farms have an apparent protection from asthma due to high levels of microbial exposure (Ege et al 2011). The problem is that researchers have been unable to define the exact effect that these microbes have on the immune systems of dairy farm children. Stein et al (2016) developed a protocol that would hopefully bridge the gap of the causes and effects of the dairy farm lifestyle and immunity against asthma. Continue reading “Another One Bites the Dust: Kicking Asthma to the Curb”

Moms and Microbiomes: Making the Breast(feeding) Decision


Parents want to know the best ways to protect and maintain their child’s health. Most parents have strong opinions about the best way to ensure their child stays healthy. The decision to breastfeed or use formula is just one example of a highly controversial parenting choice in recent years. Another very contested issue is the maternal diet during pregnancy, which has been found to have lasting impacts on the child’s health. Continue reading “Moms and Microbiomes: Making the Breast(feeding) Decision”

Antibiotic Resistant Bacteria in the Human Water Cycle

Image provided by International Water Association

About 70% of the planet is covered in water with about 60% of your body being made up of water. Lakes, rivers, and reservoirs contain some of the most diverse and abundant communities of bacteria according to a 16S rRNA gene study by Tamames et al. (2010). Our own microbiota interact daily with these different communities as we drink, bathe, and excrete bacteria. One of the more pressing issues in today’s modern medicine is antibiotic resistant bacteria that are becoming increasingly hard to treat. Antibiotic resistance is caused by evolution of bacteria, which is the bacteria gaining antibiotic genes that increase its fitness. In the presences of antibiotics, bacteria that are lacking a resistance mutation die, whereas bacteria with immunity to antibiotics have a higher survival rate. These antibiotic resistant bacteria then pass on that resistance to antibiotics to the next generation, as well as potentially other bacteria through lateral gene transfer, which is the transfer of genetic material between a parent and daughter bacteria. Continue reading “Antibiotic Resistant Bacteria in the Human Water Cycle”