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High Throughput Co-culture Assays for the Investigation of Microbial Interactions
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Gut microbial interactions based on network construction and bacterial pairwise cultivation.

Min-Zhi Jiang1, Chang Liu1, Chang Xu1

  • 1State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China.

Science China. Life Sciences
|April 10, 2024
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Summary

This study integrates in vitro time series network (TSN) associations and co-cultivation to validate bacterial interactions in the human gut microbiome. Results show most interactions are neutral, with positive relationships often overestimated, and highlight the role of nutrients in microbial communities.

Keywords:
association networkco-culturegut microbial pairwise interactionhuman gut microbiomemicrobial community

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Area of Science:

  • Microbiology
  • Systems Biology
  • Metagenomics

Background:

  • Association networks are crucial for predicting bacterial interactions in human gut microbiomes.
  • Experimental validation of these interactions is hindered by microbiome complexity and limited bacterial cultivation.

Purpose of the Study:

  • To integrate in vitro time series network (TSN) associations with co-cultivation for validating predicted bacterial interactions.
  • To investigate the types of interactions and underlying mechanisms in the human gut microbiome.

Main Methods:

  • Cultivation and enrichment of human gut microbiomes on YCFA agar for 13 days.
  • Metagenomic sequencing to recover 198 metagenome-assembled genomes (MAGs).
  • Pairwise co-cultivation of selected bacterial strains to validate network-inferred interactions.

Main Results:

  • Co-culture experiments revealed neutralism (51.67%) as the predominant interaction, followed by commensalism (21.67%) and amensalism (18.33%).
  • Genome-centric analysis indicated that commensal bacteria interact via exchanges of amino acids, short-chain fatty acids, and vitamins.
  • Supplementation experiments confirmed that 66.7% of beneficiary strains' growth was promoted by specific additives.

Conclusions:

  • The study provides a robust approach for validating microbial interactions in complex gut communities.
  • Positive relationships in gut microbial communities may be overestimated; nutrients like amino acids, SCFAs, and vitamins are key contributors to positive interactions.