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Related Concept Videos

Introduction to the Human Microbiota01:22

Introduction to the Human Microbiota

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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,...
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Genome Annotation and Assembly03:36

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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.
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Methods to Assess Microbial Communities01:19

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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...
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Development of Human Microbiota01:30

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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...
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Methods to Assess Microbial Populations01:30

Methods to Assess Microbial Populations

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Assessing microbial populations is crucial for understanding microbial roles in health, ecology, and industry. Various complementary techniques—both culture-based and molecular—enable detailed analysis of microbial abundance, diversity, and function.Viable Plate CountThe viable plate count is a traditional culture-based method used to estimate the number of living microbes in a sample. After serial dilution, the sample is spread onto nutrient agar plates. Each viable cell forms a...
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Evolution of Microbial Genome01:08

Evolution of Microbial Genome

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Microbial genome evolution is a highly dynamic process shaped by continual gene gain and loss across species and strains. This genomic flexibility allows microorganisms to adapt rapidly to environmental pressures and interactions with other organisms. Central to understanding this diversity is the distinction between the core and pan genomes.The core genome comprises the genes shared by all sampled strains of a species, representing essential functions needed for fundamental cellular processes.
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Related Experiment Video

Updated: Apr 14, 2026

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
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Microbiome assembly statistics toward ecosystem-scale insights, forecasting, and management.

Hirokazu Toju1,2, Kenta Suzuki3,4, Martina Sánchez-Pinillos5

  • 1Laboratory of Ecosystems and Coevolution, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan.

The ISME Journal
|April 12, 2026
PubMed
Summary

Microbiome research uses ecological stability theory to predict and maintain beneficial microbial communities. Understanding community dynamics helps prevent abrupt shifts to dysfunctional states, crucial for health and sustainability.

Keywords:
alternative stable statesattractorscommunity dynamicscompetitionecosystem functionsmultistabilitypriority effectsregime shiftsstability

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Area of Science:

  • Microbiology
  • Ecology
  • Systems Biology

Background:

  • Microbiomes offer unique biological functions vital for health and sustainability.
  • Maintaining stable, functional microbiome states is challenging due to abrupt community shifts.

Purpose of the Study:

  • To present statistical frameworks integrating ecological stability theory with microbiome analysis.
  • To enable inference of microbiome structure-function relationships along environmental gradients.
  • To provide methods for maintaining or restoring functional microbiome states and forecasting dysbiosis.

Main Methods:

  • Integrating ecological stability theory with empirical microbiome structure and function analyses.
  • Utilizing "stability landscapes" to infer community structure-assembly potential relationships.
  • Identifying attractors of microbiome dynamics to forecast transitions.

Main Results:

  • "Stability landscapes" offer insights into how community structure changes with environmental gradients.
  • Empirical analyses provide perspectives for managing microbiome functions.
  • Identifying dynamic attractors aids in predicting shifts to dysfunctional states (dysbiosis).

Conclusions:

  • Bridging ecological theory and microbiome analysis deepens understanding of community assembly.
  • This approach expands the application of microbiome-based solutions in medicine, industry, agriculture, and environmental science.