Could the Gut Microbiome be the Answer to Chronic Kidney Disease?

Background

The microbiome of the gut specifically plays a role in chronic metabolic disease, one of which is Chronic Kidney Disease (CKD) (Ren et al. 2020) which this blog post specifically covers. CKD is a chronic condition because the damage to kidneys occurs over a long time period, inhibiting their ability to filter blood and toxins. As the damage occurs over time there is increasing risk that patients will end up on dialysis or need transplantation. The sooner CKD can be diagnosed the higher chance a patient has to protect their kidneys (“What is chronic Kidney disease?” 2017). CKD is an important disease to discuss since approximately 13.4% of the global population suffers from it and around 30 million people in the U.S. (Ren et al. 2020). Sufferers have a greatly increased risk of morbidity and mortality, as well as suffering from the significant healthcare costs that arise with this disease. For most patients CKD is not diagnosed until it is in a very progressed stage because the clinical symptoms are normally nonexistent in the early stages, meaning that most end up in end-stage renal failure (ESRF) which requires dialysis, transplantation, or other costly and long-term medical procedures. In 2012, Viziri et al. demonstrated the relationship between the gut microbiome and CKD. Gut derived uremic toxins, created by enzymes that the microbiota of the gut harbor are a factor in the progression of CKD and in previous studies it has been observed that as renal function decreases there is an increase in these toxins. Even though we know the connections with advanced stages of the disease, there is little research that has been done to potentially use the microbiome to diagnose early stage CKD, which leads to the researchers main question. Continue reading “Could the Gut Microbiome be the Answer to Chronic Kidney Disease?”

Could Your Body’s Bacteria be the Reason You’re Proven Guilty of Murder?

Background

 Many studies on human microbiomes have demonstrated the great interpersonal variability of microbial communities, as well as the potential for specific aspects of the microbiome to uniquely tie to an individual. The significance of this study lies both in criminal forensic applications, as well as in privacy concerns for individuals that participate in microbiome research studies. Despite criminal forensic’s history of personal identification through fingerprints, DNA, and blood type, there have been no real efforts to establish microbial data as a method of personal identification.

Image retrieved from “The Scientist” news post: “Who Are We Really?” by Kieran Doherty

The scientific community has already begun brainstorming how microbial data could be leveraged for forensic use. Using knowledge on how an individual’s microbiota changes depending on diet, lifestyle, medication, and pathology, forensic analysts may be able to trace suspects from their bacterial sheddings at a crime scene. Even without direct identification, the aforementioned lifestyle information could assist in apprehension of an assailant (Hampton-Marcell et al. 2017). This study’s purpose is to investigate the capabilities of “fingerprinting” individuals using their microbiome. Microbial fingerprinting (MF) will be defined as using a set of microbial data to trace and identify a unique individual from a larger population. The benefits of microbial fingerprinting in forensics would be numerous, allowing for suspect identification when human DNA is not usable. This pro to microbial fingerprinting comes from the resilience of bacterial DNA; it is not as easily destroyed as human DNA (Nema 2018).  While researchers in the past have used metagenomic shotgun sequencing to identify microbial populations, they found that increases in data set size decreased efficacy for this profiling method. (Segata et al. 2012). For this reason, this study uses a method described in a publication from Segata et al. (2012), where clade-specific marker genes are used to identify microbial clades in larger data sets. Continue reading “Could Your Body’s Bacteria be the Reason You’re Proven Guilty of Murder?”

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”