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. 2025 Jan 11;19(1):jjae125.
doi: 10.1093/ecco-jcc/jjae125.

Specific Bacterial Co-abundance Groups Are Associated With Inflammatory Status in Patients With Ulcerative Colitis

Sushrut Jangi  1 , Naisi Zhao  2 , Katie Hsia  1 , Young Soo Park  3 , Dominique S Michaud  2 , Hyuk Yoon  3   4
Affiliations

Specific Bacterial Co-abundance Groups Are Associated With Inflammatory Status in Patients With Ulcerative Colitis

Sushrut Jangi et al. J Crohns Colitis. .

Abstract

Background and aims: While there is increasing interest in microbiome-directed therapies for patients with ulcerative colitis (UC), the identification of microbial targets remains elusive, underlining the need for novel approaches.

Methods: Utilizing metagenomic data from the Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease (SPARC IBD), available via the IBD Plexus Program of the Crohn's & Colitis Foundation, we used a tree-based dichotomous approach to assemble distinct clusters of species-level bacterial co-abundance groups (CAGs). We evaluated the abundance of bacterial CAGs and fungal taxa during remission (n = 166) and activity (n = 46). We examined if the bacterial CAGs identified in our cohorts were conserved in 2 healthy cohorts and a Korean UC cohort.

Results: CAG3 and CAG8, dominated by bacteria from the family Lachnospiraceae, were associated with remission. Low abundance of CAG8 and elevated abundance of Candida genus were predictive of active UC. Constituents from CAG8 were influential hub species of the remission-associated microbial UC network, including Ruminococcus gnavus, Erysipelatoclostridium ramosum, Blautia, and Dorea species. These hub species interactions were preserved in 2 healthy cohorts and were partially recapitulated in a Korean UC cohort. CAG8 abundance correlated with the secondary bile acid production pathway. Bacterial CAGs did not correlate with Candida; however, Bifidobacterium adolescentis and Alistipes putredinis were negatively associated with Candida.

Conclusions: Lachnospiraceae-dominated bacterial CAGs were associated with remission in UC, with key bacterial interactions within the CAG also observed in 2 healthy cohorts and a Korean UC cohort. Bacterial CAG-based analyses may aid in designing candidate consortia for microbiome-based therapeutics.

Keywords: Microbiome; consortia; microbial modulation.

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Conflict of interest statement

SJ received consulting fees from Bristol Myers Squibb. NZ, KH, YSP, DSM, and HY declare no conflicts of interest.

Figures

Graphical Abstract
Graphical Abstract
Figure 1
Figure 1
Differential abundance of microbial taxa during remission vs activity utilizing DESeq2 with significant differences based on q values <0.05. Differential abundance of the family (A) Lachnospiraceae and (B) Desulfovibrionaceae, and (C) fungal genus Candida during remission (left bar) and activity (right bar).
Figure 2
Figure 2
CAG3 and CAG8 are significantly associated with remission in patients with UC. A, Correlations between bacteria within CAG3. B, Correlations between bacteria within CAG8. C, Relative abundance of CAG3 during remission (left bar) and activity (right bar). D, Relative abundance of CAG8 during remission (left bar) and activity (right bar). Abbreviation: CAG, co-abundance group.
Figure 3
Figure 3
Bacterial co-abundance network modeled using SparCC in (A) cohort of UC patients derived from the SPARC IBD Plexus data, with edges representing either positive (darker line) or negative (lighter line) interactions between microbes, with node size corresponding to eigenvector centrality measures and node color based on similar covariance and (B) cohort of UC patients derived from Korean cohort, with edges representing either positive (darker line) or negative (lighter line) interactions between microbes, with node size corresponding to eigenvector centrality measures and node color based on similar covariance. Abbreviations: CAG, co-abundance group; SPARC IBD, Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease.
Figure 4
Figure 4
Interaction network obtained from (A) Wellness Cohort, with node color representing family, with edges representing either positive correlations (red) or negative correlations (blue) and (B) Human Microbiome Project Cohort, with node color representing family, with edges representing either positive correlations (red) or negative correlations (blue). Abbreviation: CAG, co-abundance group.
Figure 4
Figure 4
Interaction network obtained from (A) Wellness Cohort, with node color representing family, with edges representing either positive correlations (red) or negative correlations (blue) and (B) Human Microbiome Project Cohort, with node color representing family, with edges representing either positive correlations (red) or negative correlations (blue). Abbreviation: CAG, co-abundance group.
Figure 5
Figure 5
Core gut microbiota from (A) the SPARC cohort (n = 212) and (B) the Korean cohort (n = 177). Bacterial families are given on the y-axis of the heat map and detection threshold (relative abundance, %) along the x-axis.
See this image and copyright information in PMC

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