Microbiology Biome Project 1. I need a research paper on gut biome? 2. Be sure to address the following: WHAT IS A BIOME a. What constitutes a healthy biome b. Signs of a healthy biome c. Signs of an unhealthy biome d. How does life-style impact the biome e. Which microbes are important and why f. How does the biome communicate with the immune system g. How does the biome protect against infectious h. How does the biome protect against inflammation i. How does the biome protect against autoimmune disease j. How does the biome communicate with the neurological system (brain) k. What can we do to obtain a healthy biome l. 

A biome is a community of living organisms that possess similar life forms and are exposed to similar environmental conditions (Boucher et al., 2013). This is the largest known physical unit and it is often named after a specific dominant life form. A single biome can be scattered across a large region on the planet, making it one of the dominant biomes. For example, in our physical environment, we have biomes like coral reefs and the tropical rainforest (Boucher et al., 2013). Biomes also exist in the form of different communities of microorganisms inside the gastrointestinal tract. These microbes exist in different anatomic locations and they all influence health outcomes differently (Engevik et al., 2020).

A healthy gut biome consists of comparatively greater biodiversity and relatively greater numbers of particular genera and phyla of microbes (Engevik et al., 2020). These specific genera and phyla of microorganisms have been studied and identified as beneficial to the functions and the overall health of the human gut (Engevik et al., 2020). Individuals with alterations or imbalances in the population of the beneficial gastrointestinal microbes often develop conditions such as diabetes, bowel disease, and colorectal cancer (Engevik et al., 2020). These alterations and variations in the human gut biome are often a result of lifestyle or behaviors and are used as biomarkers for certain diseases (Dai et al., 2020). Therefore, having a healthy gut biome is crucial to human health.

A healthy biome is indicated by gut microbiome alpha-diversity. This means that a healthy gut should consist of a wide variety of beneficial microbes (Dai et al., 2020). For instance, studies conducted among African and European populations found that a higher diversity of microbiomes in the human gut was directly linked to the abundance of genera Bacteroidetes (Dai et al., 2020). However, this indicator may vary depending on the lifestyle and diet of other individuals. In other studies, the presence of the two Firmicutes families, Lachnospiraceae and Ruminococcaceae, also indicates a healthy gut biome since they are crucial in the breaking down of fiber and the production of butyrate (Dai et al., 2020). These findings indicate that there may not be a single specific state of a healthy gut biome but a variety of varied states that are contributed to by different beneficial microbes.

The most common sign of an unhealthy gut biome is reduced gut biome diversity. In many cases, an inactive lifestyle and the consumption of a diet that is mainly composed of processed carbohydrates, salty foods, and foods with low dietary fiber, directly influences the depletion of the microbiome (Davis et al., 2019). This kind of lifestyle and diet is also linked to the onset of chronic diseases.  The general composition of an individual’s diet directly influences the abundance of the gut microbiota (Davis et al., 2019). Additionally, stool consistency and stool frequency are also indicators of an unhealthy gut biome. Shorter colonic transit intervals are associated with a lack of gut microbiota diversity (Davis et al., 2019).

It is safe to say that non-dietary lifestyle factors affect the gut biome. Tendencies such as smoking and physical inactivity are risk factors for colorectal cancer. These tendencies impact the large bowel, which eventually affects the abundance and balance of the gut microbiota (Bird & Conlon, 2015). Smoking increases the abundance of Bacteroides-Prevotella, which increases the risk of developing Crohn’s Disease. Another lifestyle factor, stress, directly influences the motor activity in the colon by altering the gut-brain axis that may in turn change the population of the digestive tract’s microbes. In many cases, stress results in lower numbers of beneficial Lactobacillus (Bird & Conlon, 2015). Physical inactivity and obesity are linked to shifts in microbial populations, increasing the Firmicutes and decreasing the Bacteroidetes. All these unusual shifts result in poor health outcomes which eventually contribute to the development of lifestyle diseases.

In the human gut, bacteria such as Bifidobacterium secrete vitamins K, B12, Folate, Thiamine, and Biotin. Lactobacillus, Bifidobacterium, and Bacteroides synthesize bile acids which are crucial in the turnover and transportation of lipids.  Bifidobacterium also prevents pathogenic infections by producing acetate (Bird & Conlon, 2015). Numerous microbes, such as Bacteroides thetaiotamicron, produce enzymes that are crucial in the digestion process and general health outcomes (Bird & Conlon, 2015). Bacterial phytases break down phytic acid that is present in grains to release minerals such as magnesium, phosphates, and calcium to make them available for absorption. There is a strong relationship between the human digestive system and the microbes that exist in the gut (Bird & Conlon, 2015).

The intestinal microbiota also has a strong relationship with the immune system of the human body since both secrete compounds that affect the other (Bird & Conlon, 2015). The immune system has a great effect on the types of microorganisms that are present in the gut. The most common type of bacteria in the digestive system is commensal bacteria, which are beneficial to the human body. On the other hand, pathogenic bacteria are the type of bacteria that can cause infection through inflammation and invasiveness (Da Guia et al., 2015). Symbiosis takes place when the balance between the beneficial and harmful bacteria is desirable over some time. Therefore, the interaction between the microbiota, mucosal immune system, and intestinal walls remains in local and systemic homeostasis (Da Guia et al., 2015). However, if there is an imbalance between the commensal and pathogenic bacteria, then the homeostasis is disrupted. The disruption of homeostasis is often a result of local inflammation and infection or other complications that may affect the normal functioning of the human systems (Da Guia et al., 2015).

Intestinal microbes prevent infections by actively influencing the development and maintenance of the immune system. Any deficits in the microbes in the digestive system result in the incomplete maturation of the immune system. Additionally, the gut biome plays an active role in regulating the immune system (Hui-Yong et al., 2019). Apart from regulating and promoting the maturation of the immune system, gut microbes also help fight against infections that are caused by foreign microbes. For instance, intestinal microbes produce antibacterial substances that help impair the function of these foreign microbes. Well over 170 gut microbes produce bacteriocins that have been identified (Hui-Yong et al., 2019). Gut microbes can also help fight off infection through the competition for nutrients with foreign microbes. This process is known as colonization resistance. The gut microbes can also prevent foreign microbes from attaching to the walls of the intestines by forming an anatomical barrier (Hui-Yong et al., 2019). Therefore, any imbalance in the microbiota in the digestive tract may result in the onset of an infection.

The gut biome performs different functions that range from immune regulation and natural defenses against infections. However, the presence of some types of bacteria in the digestive system increases the chances of developing inflammation (Al Bander et al., 2020). This is these bacteria are associated with molecules that trigger inflammation of various body tissues. Inflammation can be a result of the structural components of the bacteria or the metabolic processes that take place in the bacteria (Al Bander et al., 2020). In turn, inflammation in the tissues results in the onset of conditions such as obesity, type 2 diabetes mellitus, atherosclerosis, and inflammatory bowel disease (Al-Bander et al., 2020). However, these processes differ in different individuals depending on a variety of factors, including diet and lifestyle.

The gut biome plays an active role in the onset and progression of autoimmune diseases through processes such as molecular mimicry, antigenic mimicry, impacts of the permeability of the intestinal mucosa, and the immune response that results from the microbiota (Cao et al., 2019). These alterations, which are caused by the gastrointestinal microbiota, are directly linked to autoimmune diseases. The gut biome interferes with immune sensing, which may also trigger the onset of autoimmune diseases (Cao et al., 2019). Signs of impaired gut barriers are often detected in patients with autoimmune diseases, which usually result from immune exposure to beneficial gut biome. Additionally, the interference of the mucosal immune tolerance results in pathological immune responses in the gut biome, resulting in increased disease severity (Cao et al., 2019).  

The gut biome also communicates with the human neurological system. The development of the neurological system is determined by intrinsic and extrinsic factors (Geschwind, 2016). Recent research supports the communication between the brain and the gut through the manifestation of conditions such as depression, anxiety, and autism spectrum disorder, and cognition (Geschwind, 2016). The development of a properly functioning brain depends on both prenatal and postnatal events that are highly influenced by signals emanating from the gut microbiome. The gut biome has also been found to contribute significantly to basic neurogenerative processes in the body such as myelination, neurogenesis, the maturation of micro ganglia, and the development of the blood-brain-barrier (Geschwind, 2016).  Therefore, the gut microbiome is crucial in the development of the neurological system.

To obtain a healthy biome, we should focus on developing habits that facilitate the development of a diverse gut biome. This can be done by taking a diet that consists of probiotics, prebiotics, fermented foods, and a variety of healthy food options (BBC Future, n.d.). Probiotics are bacteria that are known to contribute towards the development and maintenance of a healthy gut biome (BBC Future, n.d.). They come in form of supplements and healthy food options such as yogurt. Probiotics help increase the diversity of beneficial bacteria in the gut. Prebiotics provide a rich source of food to probiotics that exist in the human gut (BBC Future, n.d.). Therefore, prebiotics help increase the number of beneficial bacteria in the gut. Eating fermented foods and including a variety of healthy food options in one’s diet are also believed to help increase the diversity of the gut biome (BBC Future, n.d.).

Outline

1. Title page
2. Microbiology Biome Project
   1. What is a biome?
   2. What constitutes a healthy biome?
   3. Signs of a healthy biome.
   4. Signs of an unhealthy biome.
   5. How does life-style impact the biome?
   6. Which microbes are important and why?
   7. How does the biome communicate with the immune system?
   8. How does the biome protect against infections?
   1. How does the biome protect against inflammation?
   10. How does the biome protect against autoimmune diseases?
   11. How does the biome communicate with the neurological system (brain)?
   50. What can we do to obtain a healthy biome?