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

Area of Science:

• Microbiome research
• Spatial metagenomics
• Human gut microbial ecology

Background:

• Microbial community structure and function are influenced by spatial arrangement.
• The spatial organization of the human gut microbiome remains largely uncharacterized.

Purpose of the Study:

• To develop and apply a high-throughput method for analyzing the spatial organization of the human gut microbiome.
• To identify co-occurring microbial taxa and their spatial distribution.
• To investigate the impact of dietary changes on microbial spatial arrangement.

Main Methods:

• Development of SAMPL-seq (split-and-pool barcoding) for sampling micron-scale sub-communities.
• Application of SAMPL-seq to analyze the gut microbiome of healthy human subjects.
• Dietary perturbation study using inulin to observe microbiome spatial rearrangement.

Main Results:

• Identification of bacterial taxa pairs that consistently co-occur over time and across individuals.
• Discovery of spatially distinct microbial groups or "spatial hubs" dominated by Bacteroideceae, Ruminococceae, and Lachnospiraceae.
• Observation of reversible spatial rearrangement of the gut microbiome in response to inulin dietary perturbation.

Conclusions:

• SAMPL-seq is an effective method for capturing spatial colocalization in complex microbial communities.
• The human gut microbiome exhibits structured spatial organization into "spatial hubs".
• Dietary interventions can induce dynamic and reversible changes in microbial spatial arrangements, impacting community structure and function.