Introduction Gut microbial community plays a key role in maintaining host immune homeostasis. However, current analytical approaches treat microbiomes at taxon-level and miss community-level functions in the so-called ecological guilds. Therefore, to understand community-level impact on the host, it is essential to reconstruct co-occurring ecological partners and understand their joint metabolic function. Methods In this study, we first decomposed the fecal microbiota of tuberculosis patients an