Location-Specific Gut Bacterial Biomarkers in Delta State, Nigeria: Lefse Identifies Beneficial Commensals Distinguishing Three Communities

Osinachi M. Nwachukwu; O. S. Egbule; BC Iweriebor; Nqobile Monate Mkolo; Donald Ibe Ofili; Kingsley Chukwuka Amaihunwa

doi:10.56201/rjpst.vol.9.no8.2026.pg37.42

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Location-Specific Gut Bacterial Biomarkers in Delta State, Nigeria: Lefse Identifies Beneficial Commensals Distinguishing Three Communities

Osinachi M. Nwachukwu, O. S. Egbule, BC Iweriebor, Nqobile Monate Mkolo, Donald Ibe Ofili, Kingsley Chukwuka Amaihunwa

Abstract

Introduction: The composition of the gut microbiota is shaped by diet, geography, and environment, and distinct populations can harbour distinguishable communities; yet African and Nigerian populations remain under-represented in microbiome research. This study set out to identify the gut bacterial taxa that are differentially abundant among residents of three communities in Delta State, Nigeria — Abraka, Asaba, and Patani. Methods: In a cross-sectional design, faecal samples were collected from 40 participants (22 adults aged 18–35 years and 18 children aged 2–5 years) across the three communities. The full-length 16S rRNA gene was sequenced on the PacBio SMRT platform; community profiling was performed in MicrobiomeAnalyst, and differentially abundant sequences were identified by Linear Discriminant Analysis Effect Size , with significance set at a raw p < 0.05 and an LDA score above 2.0, alongside false-discovery-rate correction. Results: LEfSe identified five sequences that discriminated among the communities. Three were exclusive to the Abraka residents; Faecalibacterium prausnitzii (LDA = 4.64), Romboutsia spp. (LDA = 4.44), and Bifidobacterium longum (LDA = 4.23) and two were associated with the Patani residents, Bifidobacterium spp. (LDA = 4.09) and Bifidobacterium pseudocatenulatum (LDA = 3.76); none was significantly enriched in the Asaba residents. All five sequences carried strong effect sizes at raw p < 0.05, although their FDR-corrected values (≈ 0.089–0.094) fell marginally above 0.05. Overall alpha diversity did not distinguish the communities. Notably, all five discriminating taxa are recognised beneficial commensals. Conclusion: Among these three Delta State communities, the differences in gut microbiota were carried by beneficial commensals, chiefly the butyrate producer F. prausnitzii and several bifidobacteria — rather than by potential pathogens, reflecting a shift in the identity of the dominant beneficial genera. These robust LEfSe-selected trends provide the first location- resolved microbial biomarkers for these communities and warrant confirmation in larger cohorts.

Keywords

gut microbiota; LEfSe; microbial biomarkers; Faecalibacterium prausnitzii; Bifidobacterium; Delta StateNigeria

References

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Location-Specific Gut Bacterial Biomarkers in Delta State, Nigeria: Lefse Identifies Beneficial Commensals Distinguishing Three Communities

Abstract

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