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Related Concept Videos

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...
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...
Gut-Brain Axis01:22

Gut-Brain Axis

The gut–brain axis is a bidirectional communication system that connects the gastrointestinal tract and the brain. This interaction is mediated through multiple pathways, including the vagus nerve, hormonal signals, immune responses, and chemical messengers produced by gut microbes.Microbial Contributions to Brain FunctionGut microbiota contributes significantly to brain function by producing neuroactive compounds. These include neuroactive compounds that influence neurotransmitters such as...
Functions of the Gut Microbiota01:18

Functions of the Gut Microbiota

The gut microbiota includes trillions of microorganisms that colonize the human gastrointestinal tract, including bacteria, archaea, viruses, and fungi. This complex ecosystem plays a critical role in maintaining intestinal and systemic health. Most of these microbes inhabit the large intestine, establishing a relatively stable and diverse community that contributes to gut homeostasis through various metabolic, immunological, and protective mechanisms.Dominant bacterial phyla, such as...
Microbiota of the Large Intestine01:27

Microbiota of the Large Intestine

The large intestine hosts the most densely populated microbial ecosystem in the human body. This complex community primarily consists of anaerobic bacteria, with Bacillota (formerly Firmicutes) and Bacteroidota (formerly Bacteroidetes) as the predominant groups. The distribution of these microbes varies along different sections of the large intestine, influenced by local environmental factors such as oxygen availability and nutrient composition.The cecum, located at the beginning of the large...
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...

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Updated: May 26, 2026

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
11:22

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Published on: October 15, 2019

Microbiome mediation analysis: methods, assumptions, and practical considerations.

Ziman Jiang1, Gen Li1

  • 1Department of Biostatistics, University of Michigan, Ann Arbor, MI, United States.

Frontiers in Cellular and Infection Microbiology
|May 25, 2026
PubMed
Summary
This summary is machine-generated.

Microbiome mediation analysis helps understand how exposures affect health via gut microbes. This review covers methods addressing complex microbiome data challenges for valid analysis.

Keywords:
Dirichlet regressioncompositional data analysiscounterfactual causal inferencemicrobiome analysisstructural equation modeling

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Area of Science:

  • Microbiome research
  • Causal inference
  • Statistical genetics

Background:

  • Microbiome mediation analysis links exposures to health outcomes through microbial pathways.
  • Microbiome data's compositional, sparse, and high-dimensional nature presents analytical challenges.

Purpose of the Study:

  • To review methodological advancements in microbiome mediation analysis.
  • To discuss assumptions, limitations, and applications of current methods.
  • To identify research gaps and future directions.

Main Methods:

  • Review of statistical approaches including structural equation modeling, counterfactual inference, distance-based testing, Bayesian methods, and nonparametric techniques.
  • Emphasis on addressing challenges posed by microbiome data characteristics.

Main Results:

  • Various methods exist to handle complex microbiome data for mediation analysis.
  • Understanding the assumptions and limitations of each method is crucial for valid interpretation.

Conclusions:

  • Methodological developments enable robust microbiome mediation analysis.
  • Further research is needed to refine existing methods and develop new approaches for complex biological systems.