# Gut microbiome dysregulation is associated with segmental glomerulosclerosis in IgA nephropathy: insights from Oxford classification-based microbiome profiling

**Authors:** Bin Lu, Aiping Zhang, Mengqi Wu, Saiping Chen, Yuqing Wang, Jiarui Wang, Min Huang, Yanqin Zhu, Hong Liu, Fenggui Zhu, Xueyan Zeng, Shilei Chen, Xin Zhou, Riyang Lin

PMC · DOI: 10.3389/fcimb.2026.1644626 · Frontiers in Cellular and Infection Microbiology · 2026-02-20

## TL;DR

The gut microbiome in IgA nephropathy patients with segmental glomerulosclerosis shows distinct patterns linked to inflammation and disease progression.

## Contribution

This study identifies specific gut microbiota biomarkers and functional pathways associated with segmental glomerulosclerosis in IgA nephropathy.

## Key findings

- S1 patients showed enriched Firmicutes and Patescibacteria, with pro-inflammatory pathways like endoplasmic reticulum stress.
- S0 patients had higher Proteobacteria and protective pathways such as cytochrome P450 drug metabolism.
- Microbiome profiling reveals gut-kidney axis mechanisms and potential therapeutic targets for IgA nephropathy.

## Abstract

IgA nephropathy (IgAN) is a common immune-complex-mediated glomerulonephritis with segmental glomerulosclerosis (S lesion, S1 in Oxford classification) being an independent predictor of poor renal prognosis, where 20%–40% of IgAN-S1 patients progress to end-stage renal disease, but its pathogenesis is unclear.

This study enrolled 12 IgAN-S0 (without segmental sclerosis) and 19 IgAN-S1 (with segmental sclerosis) patients, performed 16S rRNA gene sequencing on fecal samples, and analyzed gut microbiota composition and functions.

S1 had enriched Firmicutes and Patescibacteria while S0 had more Proteobacteria, Campylobacterota, and Desulfobacterota; LEfSe analysis identified Subdoligranulum and unclassified_Erysipelotrichaceae_UCG-003 as S1-specific biomarkers and Phascolarctobacterium, Streptococcus_parasanguinis, and Proteobacteria as S0 biomarkers (P<0.05). Functional prediction showed S1 was enriched in pro-inflammatory pathways like endoplasmic reticulum stress and secondary bile acid biosynthesis, while S0 had activated protective pathways such as cytochrome P450 drug metabolism and ubiquitin system.

This study reveals gut microbiota dysregulation is closely associated with IgAN segmental sclerosis, with S1 showing pro-inflammatory microbial profiles and S0 retaining protective functions, providing new insights into gut-kidney axis mechanisms and potential microbiome-targeted therapies for IgAN.

## Linked entities

- **Diseases:** IgA nephropathy (MONDO:0005342), end-stage renal disease (MONDO:0004375)

## Full-text entities

- **Genes:** CD79A (CD79a molecule) [NCBI Gene 973] {aka IGA, IGAlpha, MB-1, MB1}, AHR (aryl hydrocarbon receptor) [NCBI Gene 196] {aka FVH3, RP85, bHLHe76}, NPHS2 (NPHS2 stomatin family member, podocin) [NCBI Gene 7827] {aka PDCN, SRN1}, FGB (fibrinogen beta chain) [NCBI Gene 2244] {aka HEL-S-78p}, CYP4F3 (cytochrome P450 family 4 subfamily F member 3) [NCBI Gene 4051] {aka CPF3, CYP4F, CYPIVF3, LTB4H}, C3 (complement C3) [NCBI Gene 718] {aka AHUS5, ARMD9, ASP, C3a, C3b, CPAMD1}, CDKN2A (cyclin dependent kinase inhibitor 2A) [NCBI Gene 1029] {aka ARF, CAI2, CDK4I, CDKN2, CMM2, INK4}, VEGFA (vascular endothelial growth factor A) [NCBI Gene 7422] {aka L-VEGF, MVCD1, VEGF, VPF}, FOXP3 (forkhead box P3) [NCBI Gene 50943] {aka AIID, DIETER, IPEX, JM2, PIDX, XPID}, NPHS1 (NPHS1 adhesion molecule, nephrin) [NCBI Gene 4868] {aka CNF, NPHN, nephrin}, TRPC6 (transient receptor potential cation channel subfamily C member 6) [NCBI Gene 7225] {aka FSGS2, TRP6}, GPBAR1 (G protein-coupled bile acid receptor 1) [NCBI Gene 151306] {aka BG37, GPCR19, GPR131, M-BAR, TGR5}, ALB (albumin) [NCBI Gene 213] {aka FDAHT, HSA, PRO0883, PRO0903, PRO1341}, TGFB1 (transforming growth factor beta 1) [NCBI Gene 7040] {aka CAEND1, CED, DPD1, IBDIMDE, LAP, TGF-beta1}, PRRT2 (proline rich transmembrane protein 2) [NCBI Gene 112476] {aka BFIC2, BFIS2, DSPB3, DYT10, EKD1, FICCA}, ACTN4 (actinin alpha 4) [NCBI Gene 81] {aka ACTININ-4, FSGS, FSGS1}, NR1H4 (nuclear receptor subfamily 1 group H member 4) [NCBI Gene 9971] {aka BAR, FXR, HRR-1, HRR1, PFIC5, RIP14}, C5AR1 (complement C5a receptor 1) [NCBI Gene 728] {aka C5A, C5AR, C5R1, CD88}, BTG2 (BTG anti-proliferation factor 2) [NCBI Gene 7832] {aka APRO1, PC3, TIS21}, SMAD3 (SMAD family member 3) [NCBI Gene 4088] {aka HSPC193, HsT17436, JV15-2, LDS1C, LDS3, MADH3}, APOL1 (apolipoprotein L1) [NCBI Gene 8542] {aka APO-L, APOL, APOL-I, FSGS4}, GDF10 (growth differentiation factor 10) [NCBI Gene 2662] {aka BIP, BMP-3b, BMP3B}, INF2 (inverted formin 2) [NCBI Gene 64423] {aka C14orf151, C14orf173, CMTDIE, FSGS5, pp9484}, EIF2A (eukaryotic translation initiation factor 2A) [NCBI Gene 83939] {aka CDA02, EIF-2A, MST089, MSTP004, MSTP089}, CYP2C9 (cytochrome P450 family 2 subfamily C member 9) [NCBI Gene 1559] {aka CPC9, CYP2C, CYP2C10, CYPIIC9, P450-2C9, P450IIC9}, UCHL1 (ubiquitin C-terminal hydrolase L1) [NCBI Gene 7345] {aka HEL-117, HEL-S-53, NDGOA, PARK5, PGP 9.5, PGP9.5}, PIK3CB (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta) [NCBI Gene 5291] {aka P110BETA, PI3K, PI3KBETA, PIK3C1}, CYP3A4 (cytochrome P450 family 3 subfamily A member 4) [NCBI Gene 1576] {aka CP33, CP34, CYP3A, CYP3A3, CYPIIIA3, CYPIIIA4}, F2 (coagulation factor II, thrombin) [NCBI Gene 2147] {aka PT, RPRGL2, THPH1}
- **Diseases:** renal function decline (MESH:D060825), lupus nephritis (MESH:D008181), chronic kidney disease (MESH:D051436), B (MESH:D006509), HL (MESH:C538324), mesangial IgA (MESH:D017098), inflammation (MESH:D007249), periodontitis (MESH:D010518), fibrosis (MESH:D005355), mitochondrial dysfunction (MESH:D028361), proteinuria (MESH:D011507), IgA nephropathy (MESH:D005922), non-segmental glomerulosclerosis (MESH:C538457), Henoch-Schonlein purpura nephritis (MESH:D011695), sclerosis (MESH:D012598), FSGS (MESH:D005923), obesity (MESH:D009765), scarring (MESH:D002921), ankylosing spondylitis (MESH:D013167), renal function deterioration (MESH:D058186), mesangial cell dysfunction (MESH:C537346), uremic (MESH:D006463), CKD (MESH:D012080), bile acid toxicity (MESH:C567652), Dilated cardiomyopathy (MESH:D002311), end - stage renal disease (MESH:D007676), hypertrophy (MESH:D006984), renal tubular atrophy (MESH:D000141), sclerotic lesions (MESH:C538213), glomerulonephritis (MESH:D005921), rheumatoid arthritis (MESH:D001172), alcoholic cirrhosis (MESH:D008104), segmental sclerosis (MESH:C537538), Immune dysregulation (OMIM:614878), glomerular injury (MESH:D007674), Arrhythmogenic right ventricular cardiomyopathy (MESH:D019571), African trypanosomiasis (MESH:D014353), S lesion (MESH:D000755), S (MESH:D018455)
- **Chemicals:** Lipoic acid (MESH:D008063), polysaccharides (MESH:D011134), p-cresyl sulfate (MESH:C408690), coenzyme Q10 (MESH:C024989), succinate (MESH:D019802), Linoleic acid (MESH:D019787), deoxycholic acid (MESH:D003840), Geraniol (MESH:C007836), Peptides (MESH:D010455), terpenoid (MESH:D013729), Retinol (MESH:D014801), butyrate (MESH:D002087), Caprolactam (MESH:D002209), amino acid (MESH:D000596), propionate (MESH:D011422), hydrogen peroxide (MESH:D006861), bile acid (MESH:D001647), tacrolimus (MESH:D016559), alpha-KG (MESH:D007656), IXS (MESH:D007200), tryptophan (MESH:D014364), alcohol (MESH:D000438), quinone (MESH:C004532), creatinine (MESH:D003404), indole (MESH:C030374), SCFA (MESH:D005232), ROS (MESH:D017382), calcium (MESH:D002118), steroid (MESH:D013256), lipid (MESH:D008055), p-cresol (MESH:C032538), Ubiquinone (MESH:D014451), agarose (MESH:D012685)
- **Species:** Eubacterium (genus) [taxon 1730], Mus musculus (house mouse, species) [taxon 10090], Acinetobacter (genus) [taxon 469], Streptococcus parasanguinis (species) [taxon 1318], Faecalibacterium (genus) [taxon 216851], Megamonas (genus) [taxon 158846], Escherichia coli (E. coli, species) [taxon 562], Anaerobutyricum hallii (species) [taxon 39488], Bacteroides thetaiotaomicron (species) [taxon 818], Actinomycetota (actinobacteria, phylum) [taxon 201174], Cyanobacteriota (blue-green algae, phylum) [taxon 1117], Pseudomonadota (proteobacteria, phylum) [taxon 1224], Phascolarctobacterium (genus) [taxon 33024], Lactobacillus johnsonii (species) [taxon 33959], Lactococcus (lactic streptococci, genus) [taxon 1357], Bifidobacterium (genus) [taxon 1678], Homo sapiens (human, species) [taxon 9606], Verrucomicrobiota (phylum) [taxon 74201], Bacteroidota (Bacteroides-Cytophaga-Flexibacter group, phylum) [taxon 976], Subdoligranulum (genus) [taxon 292632], Fusobacteriota (phylum) [taxon 32066], gut metagenome (species) [taxon 749906], Shigella (genus) [taxon 620], Bacillota (clostridial firmicutes, phylum) [taxon 1239]
- **Cell lines:** MG1655 — Homo sapiens (Human), Maple syrup urine disease, Transformed cell line (CVCL_D514)

## Full text

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## Figures

12 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12963279/full.md

## References

56 references — full list in the complete paper: https://tomesphere.com/paper/PMC12963279/full.md

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Source: https://tomesphere.com/paper/PMC12963279