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Microbiota of Attine Ants' Gardens: Visualizing a Microbial Landscape by Scanning Electron Microscopy

Microbiota of Attine Ants' Gardens: Visualizing a Microbial Landscape by Scanning Electron Microscopy

Published on: October 4, 2024

Stochastic block models reveal a robust nested pattern in healthy human gut microbiomes.

Sergio Cobo-López¹, Vinod K Gupta^2,3, Jaeyun Sung^2,3

¹Departament d'Enginyeria Química, Universitat Rovira i Virgili, 40007 Tarragona, Catalonia, Spain.

|February 6, 2023

Summary

Human gut microbiomes exhibit a robust nested structure, revealing distinct ecological roles for microbes and hosts as generalists and specialists. This pattern offers new insights into the taxonomic composition of the human gut ecosystem.

Keywords:

ecological networks human microbiome nestedness statistical inference stochastic block models

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Area of Science:

Microbiology
Ecology
Bioinformatics

Background:

Understanding the structural patterns in human gut microbiome composition is a key research question.
Previous studies have explored concepts like enterotypes, but robust, universally applicable patterns remain elusive.

Purpose of the Study:

To identify and characterize robust structural patterns in the taxonomic composition of healthy human gut microbiomes.
To introduce and apply the concept of mixed-membership enterotypes using network inference.

Main Methods:

Utilized whole metagenomic datasets from healthy human gut samples.
Employed a network inference approach based on stochastic block models to identify mixed-membership enterotypes.
Analyzed the nested structure of microbial taxonomies and associated host-microbe ecological roles.

Main Results:

Discovered a robust nested structure in human gut microbiomes, analogous to patterns seen in other ecological systems.
Defined distinct ecological roles for microbes and hosts: generalists and specialists.
Demonstrated that generalist hosts harbor diverse microbiomes, while specialist hosts host only generalist microbes, and specialist microbes are found only in generalist hosts.
Showed that these microbial ecological roles are conserved across datasets.

Conclusions:

The taxonomic composition of healthy human gut microbiomes is structured by robust combinations of generalist and specialist species.
The identified nested structure and ecological roles provide a new framework for understanding gut microbiome organization beyond conventional enterotypes.