Early Colonization of Microbes by Mode of Delivery


Microscopic organisms, microorganisms, and microbes for short, are all terms that encompass all organisms too small to see with the naked eye. Microbes, being as small as they are, pretty much keep the planet running. Some important functions of microbes on a planetary scale include breaking down pollutants, ensuring that the soil is fertile, and powering the Earth’s biogeochemical cycles (Falkowski et al 2008). We need all these external microbes to live, but we also need microbes in and on our bodies to live. You can view the human body as a planet and the microbes being the inhabitants. Just like the planet earth, the human body also has varying climates where certain species thrive. Microbial communities in the human body have their own community structure and function (Human Microbiome Project Consortium 2012). Continue reading “Early Colonization of Microbes by Mode of Delivery”

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


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?”

How does IBS impact the gut microbiome?


What is IBS?  Irritable Bowel Syndrome is a functional bowel disorder.  Functional GI (gastrointestinal) Disorders are defined as being related to how your gut and brain work together: this can make your intestines more sensitive, which can change how the muscles associated with your gut contract.  IBS is most often associated with abdominal pain and cramping, changes in bowel movement and excess gas.  Though IBS is non-fatal there are significant impacts on the quality of life of those affected, leading to mobility issues, chronic pain, and increases in anxiety and depression.  While IBS is often a diagnosis of exclusion and the exact cause is not known, some risk factors of IBS are family history; if you are young (under the age of 50), are female, or have mental health issues, like anxiety or depression (1).   IBS has also been known as a spastic colon, spastic colitis, and mucous colitis. Continue reading “How does IBS impact the gut microbiome?”

Make More Friends: It’s Good For Your Gut

It is currently estimated that the number of bacterial cells in our body roughly matches or exceeds the number of human cells, with the majority of these bacteria residing in the gut (Sender, et. al 2016). You may be familiar with literature identifying a “gut-brain” axis, i.e. a relationship between mental health and the composition of our microbiota. Studies have shown correlations between bacterial community makeup and disorders such as autism, depression and schizophrenia (Foster & Neufield 2013), (Dickerson, et. al 2017). Bacterial disbalance has also been correlated with diseases such as diabetes and obesity (Hartstra, et. al. 2014). A common factor between these disorders is that they are generally associated with lower microbial diversity.  While there is a growing body of literature supporting the relationships between disease and dysbiosis, a perturbation of the microbial community, little research has explored the relationships between personality and patterns in variation of the healthy microbiome.

Artwork by Anna & Ellen Balbusso

Enter Dr. Katrina Johnson of Oxford, who is especially interested in understanding how microbiota help to create the spectrum of human personality in the general population. To measure variation in personality, Johnson uses the “The Big Five” inventory which measures variation in personality using the following measures:  Continue reading “Make More Friends: It’s Good For Your Gut”

From Microplastics to Microorganisms


Over the last decade, plastic has become a more and more concerning source of pollution. In 2013 alone, almost 300 million pounds of plastic were produced worldwide (Lu et al 2017)Microplastics are defined as any plastic particle smaller than 5mm in diameter. Microplastics have been well documented as health concerns for marine life as more plastic accumulates in the ocean than any other place on earth. Additionally, microplastics have been found in a variety of household products including toothpaste and cosmetic products. We are just beginning to understand the extent microplastics have infiltrated our environment as well as our bodies, let alone the health risks they pose. One area of study deserving attention is the effect these plastics have on the microbiome of an organism. A microbiome is all of the bacteria, fungi, and viruses that live within or on a specific organism. Some of these microorganisms provide essential services to their host and maintaining a healthy microbiome has been tied to overall organismal health. Past studies have linked altered microbiomes to everything from obesity (Ridura et al 2013) to asthma (Stein et al 2016) Continue reading “From Microplastics to Microorganisms”

How Microbes are Affecting Dairy Farmers


There are many common bovine diseases yet there is one in particular that is undetected, difficult to treat and detrimental for farmers. Endometritis is a common bovine disease that is an inflammation of the innermost layer of the uterus. It is typically seen 21 days postpartum and there are no symptoms of illness. Endometritis  occurs due to the dilating of the cervix and relaxation of the vagina; this natural occurrence post-birth allows the essential barriers to become impaired and the uterus becomes compromised (“Endometritis in Cattle”). Another reason this occurs is that the cow’s immune system is suppressed in the last few weeks of pregnancy and post-birth.

Endometritis can be split into two groups: subclinical and clinical. Subclinical is the non-severe form that is typically undiagnosed because there is no external clinical finding. Clinical is the diagnosed and treated disease; typically showing vaginal discharge. Whereas subclinical is only diagnosed through cytology. Continue reading “How Microbes are Affecting Dairy Farmers”

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


 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?”

What’s that smell? Uncovering the mechanisms and bacteria behind body odor in pre-pubescent children and teenager


Body odor is a biological process that affects all humans. Many animals have scent glands and body odors that serve different purposes, and humans are no different. It is believed that human body odors might signal familial recognition and communication regarding sexual attraction and reproduction (Hoover, K. 2010). While some human-produced scents may be inoffensive or appealing at best, others are found to be entirely unpleasant (body malodor). These unpleasant aromas are created through interactions between the microbes that live on our skin and substances created by our bodies. Metabolic pathways facilitated by our skin bacteria result in the breakdown of lactic, acetic, and other acids that leave our bodies through sweat, which, by itself, is odorless (Barzantny, H. et al 2011).

Continue reading “What’s that smell? Uncovering the mechanisms and bacteria behind body odor in pre-pubescent children and teenager”

The changing microbiome in cystic fibrosis: a key to diagnosis and treatment?


Monogenic disorders are estimated to affect 1/100 people at birth (WHO). They are caused by individual mutations in individual genes that result in non-functional products such as RNA molecules or proteins. In the case of cystic fibrosis (CF), a mutation in an ion-transport protein causes CF patients to have thick, sticky mucus that easily traps bacteria, viruses and other contaminants that can cause disease. Thick mucus is particularly an issue in the lungs where trapped microbes can lead to lung inflammation and infection (Cystic Fibrosis Foundation). In healthy individuals, microbes are not uncommon in the upper and lower respiratory tracts. Usually, microbes are eliminated by little hairs that sweep microbes trapped in free-flowing mucus up and out of the respiratory tract to be coughed up or swallowed (Huffnagle et al., 2016). However, in CF patients thick mucus limits this elimination of microbes, trapping them in the lungs and respiratory tract (Fig. 1). 

Figure 1. Comparison of the healthy vs. diseased airway. Buildup of mucus in cystic fibrosis patients changes the respiratory tract environment, allowing pathogens to proliferate. (Huffnagle et al., 2016)

Continue reading “The changing microbiome in cystic fibrosis: a key to diagnosis and treatment?”