# Gut proteome and microbiome alterations: Analysis of transverse colon samples from pathologically confirmed Alzheimer's disease patients

**Authors:** Qiwen Cheng, Jennifer Nolz, Timothy Karr, Nicole Dorn, Benjamin Readhead, Rosa Krajmalnik‐Brown, Diego Mastroeni

PMC · DOI: 10.1002/alz.71021 · Alzheimer's & Dementia · 2026-01-13

## TL;DR

This study explores gut changes in Alzheimer's disease patients, finding altered proteins and microbes that may link gut health to brain pathology.

## Contribution

The first in-depth analysis of proteome and microbiome alterations in transverse colon tissues of Alzheimer's patients.

## Key findings

- Downregulation of immune and oxidative stress pathways in AD gut samples.
- Higher levels of amyloid beta 42 and altered microbial composition in AD patients.
- Gut microbial changes correlated with AD clinical features like plaque and tangle burden.

## Abstract

Alzheimer's disease (AD) has been regarded as a brain‐first disorder. Emerging evidence suggests that the gut may influence central nervous system pathology, but the mechanisms remain unclear.

We conducted a proteomic and microbial analysis of transverse colon samples from clinically and pathologically confirmed AD and control cases.

In the AD gut samples, antimicrobial humoral response and oxidative stress response were downregulated, while catabolic processes and insulin signaling were upregulated. Several complement (e.g., C5) and synaptic (e.g., synaptophysin) proteins were downregulated. Amyloid beta 42 was detected at higher levels. Christensenellaceae, Desulfovibrio, and Candida tropicalis amplicon sequence variants were higher in abundance, while Streptococcus, Lachnospiraceae, Blautia, and Nakaseomyces were lower. In general, bacterial composition correlated with AD clinical variables such as plaque and tangle burden.

These findings underscore the gut's possible involvement in AD pathogenesis and provide new insights into potential biomarkers and therapeutic targets.

This study provides the first in‐depth analysis of the proteome and microbiome in AD transverse colon tissues.Multiple immune and oxidative stress response pathways were downregulated in AD, while metabolic pathways were upregulated.Synaptic protein, complement protein, and Aβ42 levels were significantly different between AD and controls.Transverse colon microbial composition was associated with AD clinical variables.

This study provides the first in‐depth analysis of the proteome and microbiome in AD transverse colon tissues.

Multiple immune and oxidative stress response pathways were downregulated in AD, while metabolic pathways were upregulated.

Synaptic protein, complement protein, and Aβ42 levels were significantly different between AD and controls.

Transverse colon microbial composition was associated with AD clinical variables.

## Linked entities

- **Proteins:** C5 (complement C5)
- **Diseases:** Alzheimer's disease (MONDO:0004975)
- **Species:** Christensenellaceae (taxon 990719), Desulfovibrio (taxon 872), Candida tropicalis (taxon 5482), Streptococcus (taxon 1301), Lachnospiraceae (taxon 186803), Blautia (taxon 572511), Nakaseomyces (taxon 374468)

## Full-text entities

- **Genes:** C4A (complement C4A (Chido/Rodgers blood group)) [NCBI Gene 720] {aka C4, C4A2, C4A3, C4A4, C4A6, C4AD}, CFHR5 (complement factor H related 5) [NCBI Gene 81494] {aka CFHL5, CFHR5D, FHR-5, FHR5}, HTT (huntingtin) [NCBI Gene 3064] {aka HD, IT15, LOMARS}, C1QA (complement C1q A chain) [NCBI Gene 712] {aka C1QD1}, PRKCE (protein kinase C epsilon) [NCBI Gene 5581] {aka PKCE, nPKC-epsilon}, CD55 (CD55 molecule (Cromer blood group)) [NCBI Gene 1604] {aka CHAPLE, CR, CROM, DAF, TC}, INA (internexin neuronal intermediate filament protein alpha) [NCBI Gene 9118] {aka NEF5, NF-66, NF66, TXBP-1}, DOCK1 (dedicator of cytokinesis 1) [NCBI Gene 1793] {aka DOCK180, ced5}, TPD52 (tumor protein D52) [NCBI Gene 7163] {aka D52, N8L, PC-1, PrLZ, hD52}, SNCA (synuclein alpha) [NCBI Gene 6622] {aka NACP, PARK1, PARK4, PD1}, APOE (apolipoprotein E) [NCBI Gene 348] {aka AD2, APO-E, ApoE4, LDLCQ5, LPG}, C1QB (complement C1q B chain) [NCBI Gene 713] {aka C1QD2}, GLP1R (glucagon like peptide 1 receptor) [NCBI Gene 2740] {aka GLP-1, GLP-1-R, GLP-1R}, CFI (complement factor I) [NCBI Gene 3426] {aka AHUS3, ARMD13, C3BINA, C3b-INA, FI, IF}, APP (amyloid beta precursor protein) [NCBI Gene 351] {aka AAA, ABETA, ABPP, AD1, APPI, CTFgamma}, C1S (complement C1s) [NCBI Gene 716] {aka EDSPD2}, C4B (complement C4B (Chido/Rodgers blood group)) [NCBI Gene 721] {aka C4B1, C4B12, C4B3, C4B5, C4BD, C4F}, UNC13B (unc-13 homolog B) [NCBI Gene 10497] {aka MUNC13, UNC13, Unc13h2, munc13-2}, RAB27B (RAB27B, member RAS oncogene family) [NCBI Gene 5874] {aka C25KG}, GAPDH (glyceraldehyde-3-phosphate dehydrogenase) [NCBI Gene 2597] {aka G3PD, GAPD, HEL-S-162eP}, INS (insulin) [NCBI Gene 3630] {aka IDDM, IDDM1, IDDM2, ILPR, IRDN, MODY10}, CFHR2 (complement factor H related 2) [NCBI Gene 3080] {aka CFHL2, FHR2, HFL3}, INSR (insulin receptor) [NCBI Gene 3643] {aka CD220, HHF5}, C8B (complement C8 beta chain) [NCBI Gene 732] {aka C82}, C1RL (complement C1r subcomponent like) [NCBI Gene 51279] {aka C1RL1, C1RLP, C1r-LP, CLSPa}, SYP (synaptophysin) [NCBI Gene 6855] {aka MRX96, MRXSYP, XLID96}, CFHR1 (complement factor H related 1) [NCBI Gene 3078] {aka CFHL, CFHL1, CFHL1P, CFHR1P, FHL-1, FHR-1}, IRS1 (insulin receptor substrate 1) [NCBI Gene 3667] {aka HIRS-1}, GCG (glucagon) [NCBI Gene 2641] {aka GLP-1, GLP1, GLP2, GRPP}, FXYD6 (FXYD domain containing ion transport regulator 6) [NCBI Gene 53826], MAPT (microtubule associated protein tau) [NCBI Gene 4137] {aka DDPAC, FTD1, FTDP-17, MAPTL, MSTD, MTBT1}, CFH (complement factor H) [NCBI Gene 3075] {aka AHUS1, AMBP1, ARMD4, ARMS1, CFHL3, FH}, GPHN (gephyrin) [NCBI Gene 10243] {aka GEPH, GPH, GPHRYN, HKPX1, MOCODC}, CFB (complement factor B) [NCBI Gene 629] {aka AHUS4, ARMD14, BF, BFD, CFAB, CFBD}
- **Diseases:** cholinergic deficits (MESH:C535672), neuroinflammation (MESH:D000090862), neurodegeneration (MESH:D019636), infection (MESH:D007239), Dementia (MESH:D003704), neuronal loss (MESH:D009410), ENS dysfunction (MESH:D004751), RESEARCH (MESH:D014947), cognitive decline (MESH:D003072), death (MESH:D003643), Dysbiosis (MESH:D064806), constipation (MESH:D003248), gastrointestinal and autonomic disturbances (MESH:D005767), insulin resistance (MESH:D007333), amyloid (MESH:C000718787), AD (MESH:D000544), intestinal dysfunction (MESH:D007410), impaired motility (MESH:D015835), chronic inflammation (MESH:D007249), neurofibrillary tangles (MESH:D055956), brain-centric disorder (MESH:D001927), synaptic dysfunction (MESH:C536122), bile acid (MESH:C567652)
- **Chemicals:** sodium deoxycholate (MESH:D003840), propionate (MESH:D011422), amino acid (MESH:D000596), BCA (MESH:C047117), phosphoric acid (MESH:C030242), methanol (MESH:D000432), HCl (MESH:D006851), formic acid (MESH:C030544), leupeptin (MESH:C032854), SDS (MESH:D012967), lipid (MESH:D008055), butyrate (MESH:D002087), iodoacetamide (MESH:D007460), fatty acid (MESH:D005227), metal (MESH:D008670), Tricine (MESH:C100184), zinc (MESH:D015032), E64 (MESH:C024974), TEAB (MESH:D019789), carboxylic acid (MESH:D002264), SCFAs (MESH:D005232), S (MESH:D013455), TBS (MESH:D013725), acetonitrile (MESH:C032159), 6E10 (-), hydrogen sulfide (MESH:D006862), guanidine-HCl (MESH:D019791), polyvinylidene difluoride (MESH:C024865), carbohydrate (MESH:D002241), NP-40 (MESH:C010615), acetate (MESH:D000085), Tween 20 (MESH:D011136), NaCl (MESH:D012965), water (MESH:D014867), LPS (MESH:D008070), AEBSF (MESH:C002010), dithiothreitol (MESH:D004229), magnetite (MESH:D052203)
- **Species:** Christensenellaceae (family) [taxon 990719], Bifidobacterium (genus) [taxon 1678], Veillonella (genus) [taxon 29465], Nakaseomyces (genus) [taxon 374468], Streptococcus (genus) [taxon 1301], Pseudomonadota (proteobacteria, phylum) [taxon 1224], Desulfovibrio (genus) [taxon 872], Bacillota (clostridial firmicutes, phylum) [taxon 1239], Fungi (kingdom) [taxon 4751], Candida tropicalis (species) [taxon 5482], Lachnoclostridium (genus) [taxon 1506553], Homo sapiens (human, species) [taxon 9606]

## Full text

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## Figures

4 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12796839/full.md

## References

89 references — full list in the complete paper: https://tomesphere.com/paper/PMC12796839/full.md

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Source: https://tomesphere.com/paper/PMC12796839