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Related Concept Videos

Introduction to the Human Microbiota01:22

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 Microbiota01:30

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...
Methods to Assess Microbial Communities01:19

Methods to Assess Microbial Communities

Microbial communities, comprising bacteria, archaea, and eukaryotic microorganisms, inhabit diverse ecosystems and play crucial roles in environmental and biological processes. Their diversity is defined by three main parameters: species richness (the number of distinct species), species abundance (the relative quantity of each species), and species evenness (how uniformly individual species are distributed in various locations). These factors together shape the structure and ecological balance...
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
Development of the Oral Microbiota01:28

Development of the Oral Microbiota

The establishment of the oral microbiome begins before birth, challenging the long-held belief that the fetal oral cavity is sterile. The presence of oral microbes such as Streptococcus and Fusobacterium in amniotic fluid suggests that microbial exposure may occur in utero, potentially through translocation from the maternal oral or gastrointestinal tract. This early colonization primes the neonatal immune system and sets the stage for subsequent microbial succession. Maternal health,...
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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...

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Updated: Jun 25, 2026

Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing
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Published on: March 19, 2018

Towards Key Principles of Host-Associated Microbiome Assembly.

Gui Araujo1, Torsten Thomas2, José M Montoya3

  • 1Department of Biosciences, Swansea University, Swansea, UK.

Ecology Letters
|June 24, 2026
PubMed
Summary
This summary is machine-generated.

Microbiome assembly in symbiotic relationships is shaped by individual-level processes. A new model links these mechanisms to community structure, applicable to marine sponges and human microbiomes.

Keywords:
assembly mechanismscommunity ecologyconsumer–resource modeldynamical systemssponge microbiomesymbiosis

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Last Updated: Jun 25, 2026

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08:05

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11:22

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09:55

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Published on: May 2, 2018

Area of Science:

  • Microbial ecology
  • Systems biology
  • Ecological modeling

Background:

  • Symbiotic relationships involve complex microbial communities crucial for host health and ecological dynamics.
  • Community structure is influenced by individual-level mechanisms like dispersal, host selection, and microbe-resource interactions.
  • Understanding the interplay of these mechanisms in microbiome assembly remains a challenge.

Purpose of the Study:

  • To present a mechanistic model explaining how distinct microbial community structures arise.
  • To bridge mechanistic modeling with empirical microbiome data.
  • To explore the generalizability of microbiome assembly mechanisms across different host systems.

Main Methods:

  • Developed a model to describe microbiome assembly from individual-level processes.
  • Simulated microbiome data from marine sponges to validate the model.
  • Applied the model to human microbiome data for cross-system relevance.

Main Results:

  • The model successfully links individual microbial processes to community-level patterns.
  • Simulations with marine sponge data demonstrated the model's ability to replicate empirical patterns.
  • Application to human data suggests a core set of mechanisms govern diverse microbiome structures.

Conclusions:

  • Individual-level microbial processes are key drivers of community-scale microbiome assembly.
  • A unified set of ecological mechanisms may explain microbiome patterns across diverse hosts.
  • This work advances ecological theory by connecting micro- and macro-level processes in symbiosis.