This 2021 review investigated gut microbiota self-organizing units:

“We discuss how to use guilds as the aggregation unit to reduce dimensionality and sparsity in microbiome-wide association studies for identifying candidate gut bacteria that may causatively contribute to human health and diseases. Due to strain-level genetic complexity of gut microbiota, microbiome datasets are challenging to identify putative causative agents of a particular disease phenotype.

Members of an ecosystem seldomly live independently from each other. Instead, they develop local interactions and form inter-member organizations to influence higher-level patterns and functions of the ecosystem. In this context, members of a guild tend to exhibit co-abundance patterns by thriving or declining together without regard to their taxonomic positions whenever resources become available or depleted.

Genus-level results showed positive correlations between Bacteroides genus and disease phenotypes, giving the impression that all OTUs in this genus may play a detrimental role in host health. Guild-based analysis clustered these 13 Bacteroides OTUs into seven different guilds.

a shows that correlations between clinical parameters and prevalent genera are significantly different among PCOS patients and non-obese controls. b and c show different abundance distributions of Bacteroides genus and 3 Bacteroides OTUs or Alistipes genus and 2 Alistipes OTUs in different patient groups (CN, non-obese control; CO, obese control; PN, non-obese PCOS; PO, obese PCOS):

• Bacteroides OTU4 belonged to a guild that was positively correlated with disease phenotype, while Bacteroides OTU7 and Bacteroides OTU63 belonged to a negatively correlated guild.
• Alistipes OTU200 belonged to a guild that was positively correlated with disease phenotype, and Alistipes OTU130 belonged to a guild that was negatively correlated with disease phenotype.

Aggregating microbial populations into guilds facilitates pattern recognition between microbiome and host phenotypes. Recognized patterns and isolates can help identify key functional gut bacteria contributing to human health and diseases causatively.”

https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-021-00840-y “Guild-based analysis for understanding gut microbiome in human health and diseases”