Introduction to the Microbiome

This section will provide more specific information on bacteria, yeast, fungi, and protozoa. Dr. Cirino will include cases reports, photos, and articles.

Did you know that your microbiome consists of trillions of bacteria, viruses, and fungi in and on your body? The number is estimated to be in the range of 30 to 50 million! There are even more bacterial cells than human cells (1.3: 1)

The invisible world of microbes interfaces with the human at the various surfaces of the body, including the skin, the mouth and nasopharynx (nose/throat), the gut, and the vagina. Even though we hear about all the infections that are caused by bacteria, they provide significant benefits. They likely played an essential role in how humans evolved.

Microbes: From Colonization to Infection

Just like we decorate our homes for our immediate environment, so too do we prepare an environment for our microbiome. Bacteria have diverse needs, and the temperature, nutrient sources, ph, and moisture all play a role in where a bacteria grows the most optimally on our bodies.

The innate immune system plays a significant role in creating selective environments for bacteria and preventing infection. Whether from a barrier (skin and membranes), secretions (saliva, tears, and mucus), small proteins and enzymes (antimicrobial peptides on the skin, gastric acid), or systems (respiratory mucosal elevator, cough reflex), the body has a way to regulate and prevent bacterial invasion and infection.

Even if the bacteria can cause an infection, there are often enough bacteria of our normal flora to outcompete it for space. In the normal body, the system is working smoothly, fueled by wholesome, natural foods. The vascular system is working optimally, and the body is regulating itself from any infection risk.

Examples of bacteria considered normal flora to some people:

• Staphylococcus aureus, found in about 30% of the US population, prefers the nose, skin, groin, and gut. Various risk factors may make it more common, including diabetes, chronic skin conditions, steroid medications, antibiotics, crowded settings, and illicit drug use.
• Yeast like Candida albicans is found in the mouth, vagina, and skin folds. Diabetes, steroid medications, and antibiotics increase yeast growth and can lead to infections.
• Escherichia coli is found in the colon and is the common cause of urinary tract infections. In the book Meike and the Microbiome Bunch, Edgar the Escherichia coli occupied the “Big Colon,” helped digest fiber, and protected the rental space from some of the villains, like Claus the Clostridium difficile.
• Clostridium difficile resides in the colon in some people. The body’s gut immunity (secretory IgA) keeps it in check. Other bacteria usually outcompete against Claus for space. However, if a person is given antibiotics, Claus might have a chance to overpopulate, produce toxins, and causing C. diff diarrhea and colitis.

Here are a few reasons that people develop infections from their normal flora.

• Bacteria are introduced and sequestered into a nutritious space. An example of this is after a surgical procedure where bleeding provides the protein. Surgical site skin infections mostly are caused by the “usual suspects,” normal flora of the skin, including Staph and Streptococci (e.g., Streptococcus pyogenes). Abdominal site infections are usually polymicrobial (many bacteria), caused by E. coli, Klebsiella, Bacteroides, and some Strep and Enterococcus species. Another example of this is the development of pneumonia after aspiration.
• Trauma may lead to damage. dysfunction, and entry of enough bacteria to cause an infection. Examples include cellulitis, a skin infection caused by Strep species, and a urinary tract infection after sex.
• Some medications can select for overgrowth of certain bacteria and yeast, which then gain a foothold and cause mucosal surface infections, e.g. urinary tract infection, C. diff diarrhea.

About Dr. Cirino’s Career Journey

Dr. Cirino, the founder of Your Health Forum, develop a passion for microbiology at a young age. He had his first microscope when he was about 10 years old. His mother was studying to become a nurse when he was 12 years old, and she would refer to her books that showed infectious diseases. Dr. Cirino would page through them in awe of how the body developed diseases.

In college, microbiology was a natural fit. He developed a knowledge base in the field of bacteria. He worked in the research lab during his junior and senior years in college to gain greater experience in the field. He became a teaching assistant his senior year for the juniors in the pathogenic microbiology lab, his favorite course.

This experience set Dr. Cirino on a course to studying medicine at an osteopathic medical school, then later concentrating on infectious diseases for his fellowship. During his training, he would spend at least one month yearly volunteering in other countries in public health and clinical settings. This shaped his diverse background and improved his skillset in physical findings and diagnosis.