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Updated: Jul 9, 2025

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

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

Published on: October 15, 2019

A computational framework for resolving the microbiome diversity conundrum.

Itay Daybog¹, Oren Kolodny²

¹Department of Ecology, Evolution and Behavior, The A. Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel. itay.daybog@mail.huji.ac.il.

Nature Communications

|December 2, 2023

Summary

This summary is machine-generated.

Host microbiome composition is vital for health, yet varies greatly among individuals. This study resolves the microbial beta-diversity conundrum by modeling host-microbiome dynamics, showing how fitness can be microbiome-dependent without impacting population selection.

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Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

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Last Updated: Jul 9, 2025

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

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Compost Microcosms as Microbially Diverse, Natural-like Environments for Microbiome Research in Caenorhabditis elegans

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Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Published on: August 25, 2018

Area of Science:

Microbiome Research
Ecology
Evolutionary Biology

Background:

Host microbiome composition is critical for host wellbeing and survival.
Significant variation exists in microbiome composition among healthy individuals, posing a challenge to understanding its role in fitness.
Gnotobiotic models demonstrate the microbiome's importance, yet arbitrary microbial introductions can rescue deleterious phenotypes, creating a paradox.

Purpose of the Study:

To resolve the 'microbial beta-diversity conundrum' concerning host fitness and microbiome composition.
To explain the paradox of microbiome importance versus variability and rescue effects.
To investigate the influence of host population dynamics on microbiome-host interactions.

Main Methods:

Computational framework simulating host and microbiome population dynamics over multiple generations.
Modeling of microbial beta-diversity and its impact on host fitness.
Analysis of factors including host population size, mode of microbial contribution to fitness, and microbiome richness.

Main Results:

Host fitness can be entirely dependent on microbiome composition.
Microbiome composition may have minimal impact on population-level natural selection dynamics.
Solutions to the conundrum involve host population size, microbial contribution mechanisms, and microbiome richness.

Conclusions:

The microbial beta-diversity conundrum can be resolved by considering population dynamics and specific ecological factors.
Host fitness is intricately linked to microbiome composition, but this relationship does not necessarily drive population-level evolutionary trajectories.
Understanding host-microbiome interactions requires a multi-generational, population-level perspective.