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Human microbiome

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**1. Microbiome Composition and Analysis:**
– Estimated 38 trillion bacterial cells in the human body, outnumbering human cells.
Human microbiome contains around 2 million bacterial genes, 100 times more than human genes.
– Techniques like marker gene analysis using 16S rRNA for bacteria and ITS for fungi provide low-resolution classification of microbial samples.
– Computational challenges arise in metagenome assembly due to the poorer quality of metagenomes.
Human Microbiome Project focuses on sequencing human microbiota genomes using DNA-based methods like targeted amplicon and shotgun metagenomic studies.

**2. Core Microbiome and Human Health:**
– Early life microbiota play a crucial role in long-term health outcomes.
Gut microbiota composition is influenced by factors like delivery mode and breastfeeding.
– Presence of beneficial bacteria and potential probiotics in breast milk supports immune system development and metabolism regulation.
– Healthy microbiota in early life promotes immune system development and metabolism regulation.
– Understanding the microbiota’s role in early life health is essential for interventions to improve health outcomes.

**3. Microbial Diversity in Different Body Sites:**
– Various bacterial species inhabit different body sites, with unique mechanisms underlying inflammation in conditions like COPD.
– The skin hosts numerous fungal genera, with specific genera dominating during pathological conditions.
– Archaea, particularly Methanogens like Methanobrevibacter smithii, are dominant in the human gut.
– Different body sites host distinctive bacterial communities, with commensal bacteria preventing inflammation and pathogens activating proinflammatory signaling pathways.

**4. Anatomical Areas and Microbiome Composition:**
– The gastrointestinal microbiome is established at birth, with gut microbial composition differing between C-section and vaginal delivery.
– Healthy human skin harbors diverse bacterial genera, with certain fungal genera dominating in pathological conditions.
– Vaginal flora varies with menstrual cycle stages and ethnicity, impacted by factors like sexual intercourse and antibiotics.
– The oral microbiome influences health and disease, with proper oral hygiene crucial for prevention.
– The lung microbiota differs in the upper and lower respiratory tracts, particularly notable in individuals with cystic fibrosis.

**5. Impact on Disease and Health:**
– The human microbiome provides essential nutrients and influences various diseases from diabetes to mental health conditions.
– Symbiotic relationships with gut microbiota affect immune responses, with gut microbe metabolites playing a role in type 2 diabetes.
– Microbiome-based treatments show promise for drug-resistant infections, highlighting the potential for microbiome interventions in disease management.

Human microbiome (Wikipedia)

The human microbiome is the aggregate of all microbiota that reside on or within human tissues and biofluids along with the corresponding anatomical sites in which they reside, including the gastrointestinal tract, skin, mammary glands, seminal fluid, uterus, ovarian follicles, lung, saliva, oral mucosa, conjunctiva, and the biliary tract. Types of human microbiota include bacteria, archaea, fungi, protists, and viruses. Though micro-animals can also live on the human body, they are typically excluded from this definition. In the context of genomics, the term human microbiome is sometimes used to refer to the collective genomes of resident microorganisms; however, the term human metagenome has the same meaning.

Graphic depicting the human skin microbiota, with relative prevalences of various classes of bacteria

The human body hosts many microorganisms, with approximately the same order of magnitude of non-human cells as human cells. Some microorganisms that humans host are commensal, meaning they co-exist without harming humans; others have a mutualistic relationship with their human hosts. Conversely, some non-pathogenic microorganisms can harm human hosts via the metabolites they produce, like trimethylamine, which the human body converts to trimethylamine N-oxide via FMO3-mediated oxidation. Certain microorganisms perform tasks that are known to be useful to the human host, but the role of most of them is not well understood. Those that are expected to be present, and that under normal circumstances do not cause disease, are sometimes deemed normal flora or normal microbiota.

During early life, the establishment of a diverse and balanced human microbiota plays a critical role in shaping an individual's long-term health. Studies have shown that the composition of the gut microbiota during infancy is influenced by various factors, including mode of delivery, breastfeeding, and exposure to environmental factors. There are several beneficial species of bacteria and potential probiotics present in breast milk. Research has highlighted the beneficial effects of a healthy microbiota in early life, such as the promotion of immune system development, regulation of metabolism, and protection against pathogenic microorganisms. Understanding the complex interplay between the human microbiota and early life health is crucial for developing interventions and strategies to support optimal microbiota development and improve overall health outcomes in individuals.

The Human Microbiome Project (HMP) took on the project of sequencing the genome of the human microbiota, focusing particularly on the microbiota that normally inhabit the skin, mouth, nose, digestive tract, and vagina. It reached a milestone in 2012 when it published its initial results.

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