Weissenberger, S. | Search bioRxiv

bioRxiv2026

Probiotic formula intervention in infants leads to colonization and competitive strain displacement independent of IgA binding

Early-life microbiota assembly is affected by environmental exposure, diet, and immunity. We performed shotgun metagenomics sequencing of fecal samples (N=401) from a controlled infant intervention trial to evaluate how pre- and probiotic exposure affects bacterial strain dynamics, maternal-to-offspring strain transmissibility, strain persistence, and host immune responses. Species- and strain-level analyses revealed that the early-life intervention with Bifidobacterium longum subsp. infantis (BL subsp. infantis), Bifidobacterium breve, and galacto-oligosaccharides (GOS) replaced main resident strains of these species unlike breast-feeding and exclusive infant formula. BL subsp. infantis low-diversity clusters were representative of several populations and were enriched for genes linked to recombination, mobilization, and antimicrobial activity. lnterestingly, Bifidobacterium bifidum but not Bifidobacterium longum or B. breve was heavily targeted by mucosal lgA, regardless of feeding type. These findings suggest that early-life pro- and prebiotic interventions promote colonization of specific dominant strains, potentially by outcompeting and displacing existing strains, independently of host immune responses.

microbiology↗

bioRxiv2026

MetaGEAR Explorer: Rapid interactive searches and cross-cohort analyses of microbiome gene associations in disease

Background: Investigating functional gut microbiome signals remains challenging due to the large scale and sparsity of gene-level metagenomic profiles and reproducibility of microbial gene associations across microbiome studies is limited. Further, interactive tools for phenotype-aware cross-study meta-analysis are currently lacking. Results: We developed MetaGEAR Explorer, a web platform for interactive and programmatic gene-centric analyses that enables users to rapidly search genes of interest across 33 million gene families from 24 metagenomic cohorts spanning inflammatory bowel disease (IBD), colorectal cancer (CRC), and healthy individuals. To demonstrate our platform's capabilities, we first used narG, a well-characterized nitrate reductase gene in Enterobacteriaceae (including Escherichia coli and Klebsiella species), to evaluate the detection of remotely related, disease-relevant homologs. While sequence-based searches using the E. coli narG gene as a query failed to capture the known diversity of narG, MetaGEAR Explorer's domain-based search expansion identified 160 NarG-like gene families with consistent IBD enrichment across cohorts. This included narG homologs from Veillonella parvula and Veillonella atypica that have been recently implicated in intestinal inflammation. We further applied MetaGEAR Explorer to investigate the underexplored diversity of clbS, the self-protection gene against the bacterial genotoxin colibactin, which is implicated in CRC tumorigenesis. The canonical clbS is part of the E. coli clb operon, which produces colibactin. Our analysis showed that E. coli-associated clbS was rare in healthy individuals but increased in disease (1.85% in Healthy, 6.21% in IBD, and 7.62% in CRC). In contrast, domain-based expansion revealed widespread clbS-domain (DUF1706) homologs, present in 95.15% of healthy individuals, while disease-associated contributors shift from commensal Clostridia to Gammaproteobacteria. Notably, Proteus mirabilis was identified as a novel potential ClbS-like carrier enriched in IBD. Furthermore, much of this prevalence was driven by a single unclassified gene family, present in 63.40% of healthy individuals. Conclusions: MetaGEAR Explorer facilitates rapid cross-cohort functional meta-analyses and can identify reproducible, biologically interpretable microbial gene signatures in IBD and CRC, such as newly identified sequence-domain dynamics in nitrate respiration and colibactin self-protection.

bioinformatics↗