SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome.

Area of Science:

• Microbiome research
• Spatial metagenomics
• Microbial ecology

Background:

• Microbial community structure and function are influenced by spatial arrangement.
• Understanding the micron-scale spatial organization of the human gut microbiome is limited.

Purpose of the Study:

• To develop a high-throughput method for analyzing spatial co-localization in microbial communities.
• To investigate the spatial organization of the healthy human gut microbiome at the micron scale.
• To observe the impact of dietary changes on gut microbiome spatial structure.

Main Methods:

• Split-And-pool Metagenomic Plot-sampling sequencing (SAMPL-seq) was developed for high-throughput spatial analysis.
• The method uses split-and-pool barcoding to determine microbial composition of micron-scale subcommunities.
• SAMPL-seq was applied to the healthy human gut microbiome and analyzed under dietary perturbation (inulin).

Main Results:

• SAMPL-seq identified consistently co-occurring bacterial taxa pairs in the human gut microbiome.
• These co-localized microbes form distinct spatial groups or 'spatial hubs', notably involving Bacteroidaceae, Ruminococcaceae, and Lachnospiraceae.
• Dietary inulin induced reversible spatial rearrangement, with specific taxa forming new local partnerships.

Conclusions:

• SAMPL-seq is an effective method for capturing micron-scale spatial organization in complex microbial consortia.
• The human gut microbiome exhibits structured spatial organization with distinct bacterial hubs.
• Dietary interventions can dynamically alter gut microbiome spatial structure, highlighting the plasticity of microbial communities.