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Introduction to the Human Microbiota

Introduction to the Human Microbiota

Microorganisms colonize various regions of the human body, including the mouth, nasal passages, throat, stomach, intestines, urogenital tract, and skin. The total number of microbial cells is estimated to range from 10¹³ to 10¹⁴—comparable to, or exceeding, the number of human somatic cells. This host–microbiome relationship has led to the conceptualization of humans as supraorganisms, wherein microbial communities perform vital roles in development, immunity, and disease...

Development of Human Microbiota

Development of Human Microbiota

The human microbiota begins developing at birth and undergoes continual change as we age. Infancy marks a critical period of microbial sensitivity, offering a “window of opportunity” during which beneficial microbes help mature the immune system. By age three, children typically develop a more stable and diverse microbial community. Newborns acquire microbes from their immediate environment; vaginal delivery favors maternal vaginal microbes, while cesarean births favor microbes from the skin...

The Oral Microbiota

The Oral Microbiota

The oral microbiome includes a complex ecosystem comprising over 700 microbial species, identified through genomic sequencing and culture-based analyses to date. This community includes a core microbiome, found universally among individuals, and a variable component influenced by environmental factors such as diet, lifestyle, and host genetics. Site-specific conditions, including oxygen gradients, pH levels, and nutrient availability, determine the spatial distribution of these microorganisms...

Microbial Interactions: Cooperation

Microbial Interactions: Cooperation

Microbial cooperation involves beneficial interactions in which different species work together for individual or mutual advantage. These interactions can profoundly influence ecological dynamics and evolutionary processes, and they are essential to many pathogenic and symbiotic relationships.Nematode–Bacteria CooperationA striking example is the relationship between the Gram-negative bacterium Xenorhabdus nematophila and the parasitic nematode Steinernema carpocapsae. Juvenile nematodes...

Microbial Interactions: Mutualism

Microbial Interactions: Mutualism

Mutualism is a symbiotic interaction in which all participating organisms benefit. These relationships can be obligate or facultative and are fundamental to ecosystem functions across diverse biological systems.Plant–Fungi MutualismOne well-known example is the association between plant roots and mycorrhizal fungi, such as Rhizophagus species. The fungal hyphae penetrate the root hairs and the epidermis, forming an extensive hyphal network that establishes a symbiotic association. Through this...

Microbiota of the Urogenital Tract

Microbiota of the Urogenital Tract

The human urogenital system, once thought to be sterile in healthy individuals, is now recognized as a complex microbial habitat. Advancements in molecular sequencing techniques have revealed that even in healthy adults, the kidneys and bladder harbor microbial populations similar to those found in the distal urethra, albeit in much lower abundance. These resident microorganisms, while generally innocuous, can become opportunistic pathogens under conditions that alter the urogenital...

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Related Experiment Video

Updated: May 20, 2026

Investigation of Microbial Cooperation via Imaging Mass Spectrometry Analysis of Bacterial Colonies Grown on Agar and in Tissue During Infection

Investigation of Microbial Cooperation via Imaging Mass Spectrometry Analysis of Bacterial Colonies Grown on Agar and in Tissue During Infection

Published on: November 18, 2022

Microbial co-occurrence relationships in the human microbiome.

Karoline Faust¹, J Fah Sathirapongsasuti, Jacques Izard

¹Department of Structural Biology, VIB, Brussels, Belgium.

Plos Computational Biology

|July 19, 2012

Summary

This summary is machine-generated.

The human microbiome exhibits significant variation due to microbial interactions. Analyzing the Human Microbiome Project data revealed 3,005 co-occurrence and co-exclusion relationships, highlighting niche specialization and diverse ecological mechanisms.

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Area of Science:

Microbial ecology
Human microbiome research
Systems biology

Background:

The human microbiome displays substantial variability influenced by ecological interactions between microbes.
Understanding these microbial relationships is crucial for deciphering microbiome function and health.

Purpose of the Study:

To analyze microbial co-occurrence and co-exclusion patterns within the human microbiome.
To identify ecological relationships and their underlying mechanisms across different body sites.

Main Methods:

Utilized an ensemble method with multiple similarity measures and generalized boosted linear models (GBLMs).
Analyzed 16S rRNA gene profiles from the initial Human Microbiome Project (HMP) cohort (239 individuals, 18 habitats).

Main Results:

Constructed a global network of 3,005 significant relationships between 197 microbial clades.
Revealed strong niche specialization, with most interactions occurring within body sites.
Identified distinct microbial communities in the oropharynx and varied interaction patterns across body sites like the vagina.

Conclusions:

Microbial interactions are key drivers of microbiome structure and function.
The study provides a framework for understanding microbial ecology and opens avenues for targeted mechanistic research.