Microbiome

Created February 2021

items in Microbiome category  - see also Gut   Antibiotics, probiotics

Note: Many pages still need to be moved from Antibiotics, probiotics

* There are about 3X as more nonhuman than human cells in the body * The gut is just one of the scores of microbiome locations in the body * There is a huge intraction between Vitamin D and human gut Microbiome * The term ‘microbiome’ was coined in 2001 by Joshua Lederberg * and refers to the variety of microorganisms that are present in a particular environment * 'human gut microbiome’, for instance, refers to the population of bacteria, archaea, fungi, viruses and protists that live in the human gut. Microbiones: Gut + 8 of many others Synergy Health and Wellness 2014 image (More Microbiome info below this box) {include}

19 of the 117,000 studies which have Microbiome in the title

Google Scholar - July 2025

Vedanta Biosciences is starting to make bacteria pills to fight specific diseases - Dec 2024

Substack

Please describe the goals of Vedanta Biosciences - Perplexity Dec 16, 2024

What are the key diseases Vedanta Biosciences is targeting with their microbiome-based therapies? - Perplexity AI Dec 16, 2024

  • Costridioides difficile Infection (CDI), Inflammatory Bowel Disease (IBD), ulcerative colitis, Multidrug-Resistant Organism Infections, Food allergies, Liver disease. Immune-mediated diseases
What companies are in competition with Vedanta Biosciences? - Perplexity AI Dec 15, 2024

Major Competitors

  • Seres Therapeutics: A commercial-stage company developing microbiome therapeutics for serious diseases, including C. difficile infection and ulcerative colitis

  • Finch Therapeutics: Focused on developing microbiome-based therapies, including treatments for C. difficile infection and autism spectrum disorder

  • Evelo Biosciences: Develops oral biologics that modulate systemic immunology through interactions with human cells in the gut

  • 4D Pharma: Creates live biotherapeutic products for various conditions, including gastrointestinal diseases and cancer7.

  • Rebiotix (acquired by Ferring Pharmaceuticals): Developed Rebyota, an FDA-approved fecal microbiota transplantation therapy for recurrent C. difficile infection

    Other Notable Competitors

  • Enterome: Develops therapies for cancer and immune diseases using gut bacteria-derived peptides and proteins

  • Second Genome: Focuses on microbiome-based therapeutics

  • MaaT Pharma: Develops microbiome therapies for cancer patients and neurological conditions

  • Microbiotica: Works on microbiome-based therapeutics

  • Locus Biosciences: Develops CRISPR-engineered bacteriophage therapeutics

The person-to-person transmission landscape of the gut and oral microbiomes - Jan 2023

Table of Contents of PDF

image

The human microbiome is an integral component of the human body and a co-determinant of several health conditions1,2. However, the extent to which interpersonal relations shape the individual genetic makeup of the microbiome and its transmission within and across populations remains largely unknown3,4.

Here, capitalizing on more than 9,700 human metagenomes and computational strain-level profiling, we detected extensive bacterial strain sharing across individuals (more than 10 million instances) with distinct mother-to-infant, intra-household and intra-population transmission patterns.

Mother-to-infant gut microbiome transmission was considerable and stable during infancy (around 50% of the same strains among shared species (strain-sharing rate)) and remained detectable at older ages.

By contrast, the transmission of the oral microbiome occurred largely horizontally and was enhanced by the duration of cohabitation.

There was substantial strain sharing among cohabiting individuals, with 12% and 32% median strain-sharing rates for the gut and oral microbiomes, and time since cohabitation affected strain sharing more than age or genetics did.

Bacterial strain sharing additionally recapitulated host population structures better than species-level profiles did. Finally, distinct taxa appeared as efficient spreaders across transmission modes and were associated with different predicted bacterial phenotypes linked with out-of-host survival capabilities. The extent of microorganism transmission that we describe underscores its relevance in human microbiome studies5, especially those on non-infectious, microbiome-associated diseases.

📄 Download the PDF from VitaminDWiki

Study was extensively reviewed in QuantaMagazine - March 2023

Unlocking the ‘gut microbiome’ – and its massive significance to our health - July 2021

The Guardian

Scientists are only just discovering the enormous impact of our gut health – and how it could hold the key to everything from tackling obesity to overcoming anxiety and boosting immunity

A few snips from their excellent overview

  • "Your gut microbiome weighs about 2kg and is bigger than the average human brain. It’s a bustling community of trillions of bacteria, archaea, fungi and viruses, containing at least 150 times more genes than the human genome. We are filled to the brim with microbes, which form microbiomes on our skin, in our mouths, lungs, eyes, and reproductive systems. These have co-evolved alongside us since the beginning of human history. But the gut’s is the largest and most significant for our short- and long-term health. It is massively complex and its residents vary enormously from person to person. According to a study in 2020 by the European Bioinformatics Institute, which pooled more than 200,000 gut genomes to create a genetic database of human gut microbes, 70% of the microbial populations it listed – 2,000 species – hadn’t yet been cultured in a lab and were previously unknown."

  • “Over the past 80 years and since the dawn of antibiotics, there has been multi-generational loss of microbes that appear to be important for human health, ” he says. “They’re passed from mother to child [during birth, via breastmilk and skin contact] throughout the generations, but at some point in the last three or four generations, we lost some. We’re not entirely sure if the cause was our lifestyle, our diet, cleanliness in our homes or the use of antibiotics. We’re also missing certain immune stimulants that people in the developing world have plenty of.”

  • To do this, microbes need about 30g of fibre a day, but the average intake in the UK is just 10-15g. Is this why modern, low fibre, ultra-processed, high-sugar diets seem so problematic for human gut health?

  • The great opportunity – but also the great difficulty – of gut microbiome science is that poor gut health is associated with such a vast range of conditions, from obesity and degenerative brain diseases to depression, inflammatory bowel disease and chronic inflammation. “The microbiome is associated with everything,”

  • "Spector’s 30-year-long study of 15,000 twins, TwinsUK, and his PREDICT studies have shown that even genetically identical people respond to the same foods very differently (our microbiomes are so variable that twins share only 30% of the same gut microbes)."

  • "A very small Italian study using a similar commercial probiotic, Sivomixx, piqued his interest after it suggested acute Covid patients treated with it might be less likely to end up in ICU or to die, and eight times less likely to suffer respiratory failure . Bjarnason is hoping to start a larger study in the next few months."

How Your Microbiome Affects Your Emotions and Wellbeing - GrassrootsHealth Sept 2021

Short article and 7 min. video

Selected Microbiome items

Some of the Microbiome articles

articles in both of the categories Microbiome and Gut

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Per mL: Mouth:100,000, Esophagus:10 Million, Stomach: 1,000, Small Intestine: 1,000 to 100 Million, Large Intestine: up to 1 Trillion

colony-forming units (CFU) per milliliter (mL)

What Lives in Your Gut? Mercola Feb 2024

📄 Download the PDF from VitaminDWiki

Where are the different microbiomes in the human body?- Perplexity AI May 2024

The human body hosts a variety of microbiomes, each located in distinct anatomical sites. These microbiomes consist of diverse communities of microorganisms, including bacteria, archaea, fungi, viruses, and other microbes. Here are the primary locations of microbiomes in the human body:

1. Gastrointestinal Tract

Gut Microbiome: The largest and most diverse microbiome, primarily composed of bacteria, but also includes fungi, viruses, and archaea. It plays a crucial role in digestion, immune function, and overall health.

2. Skin

Skin Microbiome: Composed of bacteria, fungi, and viruses, the skin microbiome varies significantly across different areas of the body, such as the face, hands, armpits, and feet. It helps protect against pathogens and maintains skin health.

3. Oral Cavity

Oral Microbiome: Includes bacteria, fungi, and viruses found on the tongue, teeth, gums, and saliva. It is essential for oral health and can influence systemic health.

4. Respiratory Tract

Respiratory Microbiome: Found in the nasal cavity, throat, and lungs, this microbiome includes bacteria and viruses that can impact respiratory health and disease susceptibility.

5. Urogenital Tract

Vaginal Microbiome: Dominated by Lactobacillus species, it plays a key role in protecting against infections and maintaining reproductive health.

Male Reproductive Tract Microbiome: Includes bacteria found in seminal fluid, which can affect sperm quality and reproductive health.

**6. Mammary Glands

Breast Microbiome: Includes bacteria that can influence breast health and potentially impact breastfeeding.* 7. Other Sites * Oral Mucosa and Saliva *: These areas host diverse microbial communities that contribute to oral and systemic health. Conjunctiva *: The eye's surface has its own microbiome that helps protect against infections.

Each of these microbiomes is adapted to its specific environment and plays a unique role in maintaining the health and function of its respective body site. The composition and function of these microbiomes can be influenced by factors such as diet, lifestyle, genetics, and environmental exposures.* Click here *to see 13 references online

All Microbiome articles

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All Antibiotic - Probiotic articles

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Tags: Details Microbiome