Defining the Core: the Human Gut Pan-Microbiome

Background:

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 https://pixnio.com
Background:

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?”

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!”

For the microbiomes of our future

Picture of a baby with bacteria visualized on it.
University of Utah (Learn Genetics)

The vaginal microbiome: We live in a world of microbes, and yet we are still learning new things about these millions of ‘germs’ every day and how they influence us, but what about our children? New research suggests a mother’s stress during pregnancy could be another puzzle piece in the development of baby’s microbiome and brain. According to the CDC nearly 4 million children were born in the United States in 2016, which resulted in mothers giving their offspring microbes, whether the baby was born through c-section or vaginally. Recent research (Rutayisire et al., 2016) is starting to show that there may be an advantage to birthing vaginally, as young are exposed to their mother’s microbiome. Continue reading “For the microbiomes of our future”

How Does Your Microbe Community Change During Pregnancy?

Background

The vaginal microbiota undergoes major compositional changes throughout a women’s lifespan from birth, to puberty, to menopause. However, very little is known about the composition of the vaginal microbiota throughout these transitional stages (Romero 2014). So if the microbial community of the vagina changes throughout a women’s life, how does pregnancy change it, if it does at all? Continue reading “How Does Your Microbe Community Change During Pregnancy?”

Which came first, antibiotics, or antibiotic-resistance? A study of Uncontacted Amerindians.

The geographical location of the Yanomami tribe as a whole. The specific village exists in the highlighted region.  (Image courtesy of Viralfast)

Background

The Yanomami people are patches of isolated South American tribes who occupy mountainous regions of southern Venezuela. Recently, a Yanomami tribe of 34 subjects discovered by helicopter, was investigated by a team of researchers who accompanied medical care professionals who were providing care to the villagers. These researchers, Clemente et. al. (2015), then wrote the paper, “The microbiome of uncontacted Amerindians” to analyze this population which was uniquely untouched by Western Society. An interesting topic that this research paper addresses is antibiotic-resistant bacteria. Antibiotic-resistance are the adaptations of a bacterial species in response to antibiotics. Antibiotics are medications that have been developed in more recent times to destroy bacteria cells but not human cells. They do this by targeting specific differences between the two types of cells, for instance, penicillin inhibits the synthesis of the peptidoglycan layer of bacterial cell walls a feature not present in animal cells. Other bacteria have distinct DNA replication processes and some antibiotics are able to interrupt that function as well. This Yanomami population is intriguing because their microbiomes are likely the most accurate representation of an ancient human microbiome due to their isolation from the Western world. The presence of antibiotic-resistant bacteria in the Yanomami gut provides evidence for the claim that antibiotic-resistant bacteria have been around since before the invention of antibiotics, so stay tuned for a persuasive evidentiary argument further down. Clemente et. al. also state that the Yanomami population that is sampled is the most diverse microbiome ever recorded. It is important to understand what kind of diversity the researchers are talking about. The Yanomami show extremely high beta diversity when compared to Guahibo, Malawi, and U.S. populations but exhibit low alpha diversity amongst individuals in the village population. Beta diversity represents the differences in species composition among samples while alpha diversity is just the diversity of each sample. This means that the Yanomami microbiome sample is extremely unique but microbiomes within that sample are very similar, this is most likely due to the Yanomami leading vastly different lifestyles than Western societies and individuals in the village being in extremely close quarters with each other (eating the same food, drinking from the same water source, no waste removal, etc.). Continue reading “Which came first, antibiotics, or antibiotic-resistance? A study of Uncontacted Amerindians.”

Bacteria Protect Cancer from Chemotherapy

In the picture there are bacteria fluorescing in green inside of a pancreatic cancer cell.
Figure 1: Bacteria, in green, inside a pancreatic cancer cell (picture from Yong, 2017 , picture by Leore Geller)

Background:

Between the years of 2010 and 2014 2,910,588 people died of cancer in the United States despite our best efforts to fight cancer with methods like chemotherapy and surgery (Howlader et al., 2017). While there are many reasons why cancers might prevail over our best efforts, a relatively common reason is the devolvement of chemotherapy resistance (Housman et al., 2014). This resistance can come in many forms; ranging from drug inactivation to changing the target site of the drug. In an attempt to combat resistance, chemotherapy drugs have been given out in cocktails containing multiple drugs that all work in a different way in the hope of killing all the resistant cells at once. This method was based off of the theory that while the mechanisms of resistance are known to be complex, the resistance always stems from cancer cells themselves. However this theory has been challenged in the last few years with the discovery that cancer cells could be protected from chemotherapy drugs by the normal cells (stroma) around the cancer cells (Feig et al., 2012; Klemm and Joyce, 2015). Continue reading “Bacteria Protect Cancer from Chemotherapy”

Association Between The Human Microbiota and Type II Diabetes Mellitus

Microbes in a gut under magnifying glass (from www.diabetesdaily.com 2016)

Type II diabetes mellitus is increasing at an alarming rate, especially in children. According to the World Health Organization (WHO) statistics, the number of individuals with type II diabetes is projected to rise to more than 590 million by the year 2035 (Diabetes, 2017 and Upadhyaya, 2015). Type II diabetes is the result of the body’s resistance to insulin, a hormone that regulates blood sugar. The WHO states that type II is largely the effect of being overweight and very little exercise. Type I diabetes is distinguished by the bodies inability to produce insulin and there is no way to prevent it. Symptoms of type II diabetes include thirst, constant hunger, weight loss, vision loss, numbness in feet, and tiredness (Diabetes, 2017).  Scientists are trying to discover new ways to mediate the effects of type II diabetes and many think that the gut microbiota of the human body might correlate with diabetes in an interesting way. Continue reading “Association Between The Human Microbiota and Type II Diabetes Mellitus”

Depression and Microbial Dysfunction: A Link Between Gut Microbiota and the Brain.

Background

Depression is a mood disorder that is heterogeneous in nature.  Depression  causes severe symptoms that affect how a person feels, thinks, and handles daily activities (NIMH, 2017).  According to the World Health Organization, depression affects over 300 million people and is a major worldwide contributor to the burden of diseases. This is especially pertinent considering that depression is one of the mood disorders associated with suicide, some others being anxiety, schizophrenia and PTSD.  On an annual basis suicide leads to the death of nearly 800,000 people and is the second leading cause of death within the age group of 15 to 29 year olds (WHO, 2017). The underlying causes of depression are a complex interaction of social, psychological, and biological factors. It is essential to analyze these factors to understand the contribution of each in the development and maintenance of major depressive disorders.   Continue reading “Depression and Microbial Dysfunction: A Link Between Gut Microbiota and the Brain.”

The Gut Microbiome; a Battleground Between Pathogens and the Host/Gut-Residents

Picture courtesy of https://cathe.com/can-exercise-change-your-gut-microbiome

Background

A unique and diverse array of inter-specific relationships can be found within the microbiome of the human gut. Due to the constant flow of microbe-carrying nutrients through it, the gut is subject to a high risk of foreign invaders. Fortunately the immune system, as well as the digestive tract (with the help of its residential microbes), have processes to rid themselves of the pathogenic strains (Ichinohe et al, 2011).  These bodily systems provide a unique example of positive interactions between co-existent, and co-dependent, systems. Although the body can protect itself from damage induced by invading species, certain medical diseases such as inflammatory bowel disease (IBD) and Crohn’s disease (CD), when combined with inflammation and intestinal distress are prone to exhibit symptoms such as “severe muscle wasting and fat loss” (Schieber et al 2015).  Although the gut biome and the immune system may not always be capable of preventing these resultant health issues on their own, in conjunction they are capable of properly defending the body from muscular wasting caused by pathogenic effects.

The intestinal tract, while utilizing physical and chemical forces to break down and absorb vital nutrients, also houses a diverse community of microorganisms, a microbiota. This microbiota, which aids in  increasing efficiency in digestion and absorption, is the product  of coevolution and tolerance within both the host (providing this environment) and the residential microorganisms (Schieber et al 2015). Continue reading “The Gut Microbiome; a Battleground Between Pathogens and the Host/Gut-Residents”