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Bacillus is one of the most common genus of bacteria in the human gut.

 

It is known for their rod-shaped (bacillus) morphology. They are commonly found in various environments, including soil, water, and the gastrointestinal tract of animals. Some species of Bacillus are beneficial, used in industrial processes like fermentation and in agriculture as probiotics, while others can be pathogenic, causing diseases in plants and animals.

 

“Gut Bacillus” typically refers to the species of Bacillus bacteria that play important roles in digestion, nutrient absorption, and immune system regulation. Some strains of gut Bacillus are considered probiotics and can confer health benefits when consumed in adequate amounts, such as promoting gut health and preventing gastrointestinal disorders.

Healthy Bacillus species can be found in various fermented foods. Some common sources include Yogurt, Kimchi, Sauerkraut, Miso, and Tempeh.

 

Consuming these fermented foods can help introduce beneficial Bacillus bacteria into the gut, promoting digestive health and overall well-being.

 

 

 

A March 12, 2024 issue of Phys.org, reported a conclusive study that our gut microbiome not only vary widely from one person to another, but are indeed unique to each individual much like our fingerprint.

 

The study is led by Michael Snyder, Ph.D., the Stanford W. Ascherman, MD, FACS Professor in Genetics and director of the Stanford Center for Genomics and Personalized Medicine and co-authored by Xin Zhou, Ph.D., a postdoctoral scholar in genetics. Snyder, Zhou and their team studied the gut, mouth, nose and skin microbiomes of 86 individuals.

 

Each person’s sheer massive size of their microbiome—around 39 trillion microbe—and the fact that it can constantly change make it difficult to study. 

 

While there are common microbial species found across individuals, the specific strains, proportions, and functions can be very different. Additionally, each individual’s microbial composition are fluid and constantly changing over time.

Dr. Snyder says this is the first time researchers have looked at the entire microbiome of different body sites as a single, fluid system.

 

Enterococcus is a type of bacteria commonly found in the gastrointestinal tracts of humans and animals. Better known for its negative effects on our health, Enterococcus is beneficial as well. Some strains are used in probiotics and can help maintain a healthy balance of gut bacteria. They help us digest food, produce certain vitamins, and help prevent the growth of harmful bacteria in the intestines.

 

Flavor development: Additionally, certain Enterococcus strains are used in food fermentation processes, contributing to the development of flavor and texture in foods like cheeses and sausages.

 

Beneficial Strains of Enterococcus:

Some beneficial strains of Enterococcus commonly used in probiotics and food fermentation include:

 

Enterococcus faecium: Often used in probiotic supplements to support digestive health and boost immune function.

Enterococcus faecalis: Some strains aid in digestion and compete against harmful bacteria.

Enterococcus durans: Found in fermented foods and sometimes used in probiotic formulations for its potential health benefits.

It’s important to take everything in balance; consuming too much, can become harmful. While these strains can be beneficial, they should be consumed in appropriate amounts and under proper guidance, especially in probiotic supplements, to ensure safety and efficacy.

 

Good sources of Enterococcus in foods and herbs:

Enterococcus bacteria are commonly found in various foods, especially those that undergo fermentation processes. Here are some foods and herbs where Enterococcus can be found in:

 

Fermented Foods:

1. Cheeses: Especially soft cheeses like Camembert, Brie, and certain blue cheeses.

2. Yogurt: Some yogurt products contain strains of Enterococcus along with other probiotic bacteria.

3. Fermented Vegetables: Sauerkraut, pickles, and kimchi can sometimes contain Enterococcus due to natural fermentation.

 

Herbs: 

1. Basil: Fresh basil leaves can sometimes harbor bacteria, including Enterococcus, especially if not handled and stored properly.

2. Rosemary: Like other herbs, fresh rosemary can occasionally harbor bacteria, including Enterococcus.

 

Harmful Effects: While some strains are harmless, others can cause infections, especially in people with weakened immune systems or underlying health conditions. Enterococcus can cause urinary tract infections, bloodstream infections, wound infections, and more. Proper hygiene and antibiotic stewardship are important to prevent the spread of resistant strains.

 

Harmful Strains of Enterococcus:

It becomes obvious that Enterococcus can be both beneficial and harmful, depending on strain type and quantity.

 

Some strains of Enterococcus can be harmful, especially when they cause infections. The most commonly identified pathogenic strains are:

Enterococcus faecalis: This is one of the most common Enterococcus species associated with infections in humans. It can cause urinary tract infections, bloodstream infections, and wound infections.

Enterococcus faecium: Another species that can be pathogenic, especially in healthcare settings. It has become a concern due to its resistance to multiple antibiotics.
These pathogenic strains can cause infections in people with weakened immune systems, those with underlying health conditions, or patients in healthcare settings like hospitals. Proper hygiene, infection control measures, and antibiotic stewardship are essential to prevent and manage infections caused by these harmful Enterococcus strains.

 

Summary: It’s important to note that the presence of Enterococcus in foods and herbs is generally not a cause for concern, especially if the foods are prepared and stored properly. In fact, in fermented foods, Enterococcus plays a role in the fermentation process and can contribute to flavor development. Proper food handling, storage, and cooking practices can help reduce the risk of foodborne illnesses.

– authored by Chris Kenji Beer, Herbsprout writer (some sourcing from ChatGPT)

 

 

Akkermansia muciniphila is a species of bacteria naturally present in the human gut microbiota known for its ability to degrade mucin, a glycoprotein that lines the digestive tract. In addition to maintaining a healthy mucus layer in the gut, it thrives in the mucous layer that lines the intestines, where it feeds on mucin, a glycoprotein produced by the cells that line the digestive tract.

Its potential health benefits include promoting gut barrier function, reducing inflammation, and improving metabolic health.

Akkermansia muciniphila has specialized enzymes that allow it to break down and consume mucin as its primary energy source. By doing so, it helps maintain the integrity of the gut barrier and overall gut health.

While specific foods containing Akkermansia muciniphila are not widely studied, certain dietary factors can potentially promote its growth. These include:

1) Polyphenol-rich foods like berries, nuts, seeds, and tea. Certain vegetables also contain polyphenols, which can support the growth of Akkermansia muciniphila.

2) Prebiotic fiber: Foods rich in prebiotic fibers, such as onions, garlic, leeks, asparagus, bananas, and whole grains, can also encourage the growth of Akkermansia muciniphila.

3) Fermented foods: Fermented foods like yogurt, kefir, sauerkraut, and kimchi may indirectly support the growth of beneficial bacteria like Akkermansia muciniphila by fostering a healthy gut microbiome environment.

While these foods may help promote a healthy gut microbiome, it’s important to note that individual responses to dietary changes can vary, and further research is needed to fully understand the impact of specific foods on Akkermansia muciniphila levels.

 

 

Socioeconomic status and population density influence our gut microbiome, according to recent studies.

In one report published by Ars Technicaon March 14 2024, urban humans have lost their ability to digest plants, specifically cellulose which line the walls of plants (1). While humans are host to a mix of cellulose-eating bacteria, urban living has caused the number of these bacteria to shrink dramatically, possibly down to one species. Present-day hunter/gatherers and those living in a rural environment, both of whom eat very high fiber diets, still had about 20 percent prevalence of these cellulose-digesting species. By contrast, those in industrialized countries had a prevalence under 5 percent.

For example, according to a March 15 2024 Science report, researchers found numerous rumicococcus strains, Candidatus Ruminococcus primaciens, Ruminococcus hominiciens, and Ruminococcus ruminiciens, all of which help digest cellulose. These species are found prevalent in great apes and primates, and today’s rural populations, but not in industrialized urban populations (2).

On the flip side, researchers found a number of factors of socioeconomic status (SES). A March 11 2024 the Food and Microbiome Longitudinal Investigation (FAMiLI) study, published in Nature of 825 participants determined the relationship of a range of individual- and neighborhood-level SES indicators with the gut microbiome. Lower socioeconomic status (SES) is related to increased incidence and mortality due to chronic diseases, but this study suggests biological factors that influence SES (3).

Certain gut bacteria were found prevalent among low SES, others among high SES participants. For example , low SES individuals showed a higher abundance of Prevotella and a lower abundance of Bacteroides. 

These are broad generalizations, but the study found that Hispanic and Black participants were more likely in poor neighborhoods to have lower SES, including lower education, occupation, neighborhood income, and deprivation. United States-born participants had higher SES as compared to foreign-born participants, according to New Medical (4).

 

1) https://arstechnica.com/science/2024/03/human-gut-bacteria-that-can-digest-plant-matter-probably-came-from-cows/

2) https://www.science.org/doi/10.1126/science.adj9223

3) https://www.nature.com/articles/s41522-024-00491-y

4) https://www.news-medical.net/news/20240314/Socioeconomic-status-shapes-the-gut-microbiome-in-diverse-US-population.aspx

Escherichia coli (E. coli) is a species of bacteria commonly found in the intestines of humans and other animals. While some strains of E. coli can cause illness, such as food poisoning, many strains are harmless and even beneficial.

 

In the gut, E. coli plays a role in maintaining a healthy microbial community and provides benefits such as producing vitamin K2 and preventing the colonization of harmful bacteria.

 

Escherichia coli (E. coli) can be beneficial in several ways:

Normal Gut Flora: E. coli is a natural inhabitant of the human gut microbiota, where it contributes to the balance of microbial communities and helps prevent colonization by harmful bacteria. It competes for resources and space, thus aiding in gut health.

Vitamin Synthesis: Some strains of E. coli are capable of synthesizing vitamin K2, which is essential for blood clotting and bone health. By producing this vitamin in the gut, E. coli contributes to the host’s overall well-being.

Immune System Stimulation: E. coli can stimulate the immune system, promoting the development and maintenance of a healthy immune response. This interaction between gut bacteria, including E. coli, and the immune system helps protect against pathogens and maintain gut homeostasis.

Overall, E. coli is beneficial when it resides in the gut in appropriate quantities and under normal conditions.

 

However, certain strains can cause illness if they proliferate excessively or if they contain virulence factors that enable them to cause infections. Certain strains of E. coli can cause infections if they enter the bloodstream or other parts of the body.

 

(written by Chris Kenji Beer with help from ChatGPT)

Polyphenols are a diverse group of naturally occurring compounds found in plants. They are known for their antioxidant properties, which help protect cells from damage caused by free radicals. Additionally, polyphenols have been linked to various health benefits, including reducing inflammation, improving heart health, and potentially lowering the risk of certain chronic diseases such as cancer and neurodegenerative disorders.

Specifically, they neutralize free radicals which are naturally created unpaired electrons (but also created by air pollution, UV radiation or cigarette smoke). These unpaired electrons in our bodies can damage our cells, proteins, and DNA, leading to oxidative stress and life threatening diseases.

 

A March 18 2024 Medical News Today report referred to the health benefits of polyphenols to our gut. Research by National University of Natural Medicine in Portland, Oregon, based on data from the International Cohort on Lifestyle Determinants of Health (INCLD HealthTrusted Source), showed an increase of polyphenols in our diet leads to an increase in healthy gut bacteria such as Lactobacillus and a decrease in harmful bacteria among participants in the study.

 

Polyphenols are commonly found in foods like fruits, vegetables, tea, coffee, red wine, and dark chocolate.

 

Examples of polyphenols found in plants are:

 

Flavonoids: Found in fruits (such as apples, berries, and citrus fruits), vegetables (like onions and kale), tea, red wine, and cocoa. Subtypes include quercetin, catechins, and anthocyanins.

Phenolic acids: Present in fruits (especially berries), vegetables (like spinach and potatoes), whole grains, and some beverages such as coffee and wine. Examples include caffeic acid, ferulic acid, and ellagic acid.
Stilbenes: Found in grapes (especially in the skin), berries, peanuts, and red wine. Resveratrol is a well-known stilbene.

Lignans: Abundant in flaxseeds, sesame seeds, whole grains, and some fruits and vegetables.

Tannins: Present in tea, wine, nuts, berries, and some legumes. They contribute to the astringent taste in foods and beverages.

These are just a few examples, as polyphenols are widespread in the plant kingdom and can be found in various plant-based foods.

What do these polyphenols do?

Polyphenols such as flavonoids, have several beneficial effects on health:

Antioxidant activity: Flavonoids help neutralize harmful free radicals in the body, protecting cells from oxidative damage.

Anti-inflammatory properties: They can help reduce inflammation, which is linked to various chronic diseases such as heart disease, cancer, and arthritis.

Cardiovascular benefits: Flavonoids may improve heart health by promoting healthy blood flow, reducing blood pressure, and improving blood vessel function.
Immune system support: Some flavonoids have been shown to enhance the immune system’s response to infections and other challenges.

Potential cancer protection: Certain flavonoids have been studied for their potential anti-cancer properties, including inhibiting the growth of cancer cells and reducing the risk of tumor formation.

Neuroprotective effects: Flavonoids may help protect brain cells from damage, potentially reducing the risk of neurodegenerative diseases like Alzheimer’s and Parkinson’s.
Overall, including flavonoid-rich foods in your diet, such as fruits, vegetables, tea, and dark chocolate, can contribute to better health and well-being.

 

 

More on MCTs and polyphenols:

The first two of the “gut microbe series are well known relative to the other top 10. Though “Number 3, Faecalibacterium prausnitzii,” is a lesser known bacteria in our gut, it plays an important role in maintaining a healthy gut.

 

Faecalibacterium prausnitzii produces butyrate, a short-chain fatty acid (SCFA) that nourishes the cells lining the colon and has anti-inflammatory properties.

 

Overall, SCFAs play a critical role in protecting the colon by maintaining barrier function, reducing inflammation, providing energy, and regulating immune function. Faecalibacterium prausnitzii primarily produce butyrate, although it can also produce small amounts of acetate and formate. Butyrate is the main short-chain fatty acid it produces.

 

Short-chain fatty acids (SCFAs), such as butyrate, acetate, and propionate, play a crucial role in protecting the colon in several ways:

 

Maintaining Gut Barrier Integrity: SCFAs help to strengthen the intestinal barrier, which prevents harmful substances from entering the bloodstream and reduces the risk of inflammation and infection.

 

Anti-inflammatory Effects: Butyrate, in particular, has potent anti-inflammatory properties. It helps to reduce inflammation in the colon, which is important for conditions like inflammatory bowel disease (IBD).

 

Providing Energy: SCFAs serve as an energy source for the cells lining the colon. This helps to maintain the health and function of these cells, contributing to overall gut health.
Regulating Immune Function: SCFAs can modulate the activity of immune cells in the gut, helping to maintain immune homeostasis and prevent excessive immune responses that can lead to inflammation and tissue damage.

 

Because faecalibacterium prausnitzii naturally inhabits the human gut it cannot be found in specific foods or herbs. While Faecalibacterium prausnitzii may not be directly present in foods, consuming probiotic-rich foods can contribute to overall gut health. You can promote the growth of this beneficial bacterium by consuming the following:

 

Dietary Fiber: Foods rich in dietary fiber, such as fruits, vegetables, whole grains, legumes, and nuts.

 

Prebiotics: Certain types of fiber, known as prebiotics, include inulin, found in chicory root, garlic, onions, and leeks, and oligosaccharides found in foods like legumes.

 

Polyphenol-rich Foods: Polyphenols, found in foods like berries, cocoa, green tea, and red wine.

Fermented Foods: Foods like yogurt, kefir, sauerkraut, kimchi, and kombucha contain probiotics.
While specific foods can support the growth of Faecalibacterium prausnitzii indirectly, maintaining a diverse and balanced diet that includes plenty of fiber-rich foods, prebiotics, and polyphenols is key to promoting the growth of beneficial gut bacteria, such as Faecalibacterium prausnitzii.

Generally, Blastocystis, the world’s most common protist–a form of unicellular microscopic organism, can lead to a healthy gut for some individuals, and be problematic for others.

 

Researchers at the National University of Singapore (NUS) studied the biology of Blastocystis (ST7), Professors Yong Loo Lin and Kevin Tan from the school’s Department of Microbiology and Immunology, and found that this rare subtype weakens the gut and immune system. Blastocystis ST7, an intestinal bacteria more common among Asian people, produces indole-3-acetyldehyde (I3AA) which which blocks healthy bacteria in our gut when it metabolizes, according to a September 29, 2023 article in Medical Express (1).

 

In a mouse study on the topic, scientists saw a reduction of anti‐inflammatory Treg cells and simultaneous expansion of pro‐inflammatory Th17 responders, according to Embopress.org (2). Blastocystis ST7 effectively degrades tryptophan, an essential amino acid needed for normal human growth, especially in babies (3).

 

Researchers also discovered that lactobacillus—commonly found in foods like yogurt, cottage cheese, sourdough bread, could aid in curing patients from Blastocystis ST7-associated diarrhea.

 

1. https://medicalxpress.com/news/2023-09-gut-inflammation-substance-secreted-microbe.amp

 

2. https://www.embopress.org/doi/full/10.15252/embj.2022112963

 

3. https://medlineplus.gov/ency/article/002332.htm#:~:text=Tryptophan%20is%20an%20amino%20acid,get%20it%20from%20your%20diet