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[Preprint]. 2025 Aug 1:2025.07.31.25332523.
doi: 10.1101/2025.07.31.25332523.

Fecal Short-Chain Fatty Acids Vary by Sex and Amyloid Status

Jessamine F Kuehn  1   2 , Qijun Zhang  1 , Margo B Heston  3 , Jea Woo Kang  3 , Sandra J Harding  3 , Nancy J Davenport-Sis  3 , Darby C Peter  3 , Robert L Kerby  1 , Vaibhav Vemuganti  1 , Emma C Schiffmann  1 , Michael M Tallon  1 , Joseph Harpt  1   3 , Arun Hajra  1 , J L Wheeler  3 , Sushma Shankar  3 , Alissa Mickol  3 , Justus Zemberi  3 , Hana Chow  3 , Eric Zhang  3 , Eleanor Clements  3 , Hanna Noughani  3 , Allison Forst  3 , Grace Everitt  3 , Gwendlyn Kollmorgen  4 , Clara Quijano-Rubio  5 , Bradley T Christian  3 , Cynthia M Carlsson  3 , Sterling C Johnson  3   6 , Sanjay Asthana  3   6 , Henrik Zetterberg  3   7   8   9   10   11   12 , Kaj Blennow  7   8   13   14 , Tyler K Ulland  3   15 , Federico E Rey  1   16 , Barbara B Bendlin  3   6
Affiliations

Fecal Short-Chain Fatty Acids Vary by Sex and Amyloid Status

Jessamine F Kuehn et al. medRxiv. .

Update in

  • Fecal short-chain fatty acids vary by sex and amyloid status.
    Kuehn JF, Zhang Q, Heston MB, Kang JW, Harding SJ, Davenport-Sis NJ, Peter DC, Kerby RL, Vemuganti V, Schiffmann EC, Tallon MM, Harpt J, Hajra A, Wheeler JL, Shankar S, Mickol A, Zemberi J, Chow H, Zhang E, Clements E, Noughani H, Forst A, Everitt G, Kollmorgen G, Quijano-Rubio C, Christian BT, Carlsson CM, Johnson SC, Asthana S, Zetterberg H, Blennow K, Ulland TK, Rey FE, Bendlin BB. Kuehn JF, et al. Alzheimers Dement. 2025 Nov;21(11):e70877. doi: 10.1002/alz.70877. Alzheimers Dement. 2025. PMID: 41273231 Free PMC article.

Abstract

Introduction: Short-chain fatty acids (SCFAs), produced by gut microbes, influence Alzheimer's disease (AD) pathology in animals. Less is known about SCFAs and AD in humans. We profiled feces of adults along the AD continuum to investigate gut microbiome and SCFA associations with AD pathology and cognition.

Methods: We measured SCFAs and bacterial abundances in fecal samples from 287 participants in the Wisconsin Alzheimer's Disease Research Center and Wisconsin Registry for Alzheimer's Prevention. We performed regressions examining associations between SCFAs or gut microbes and AD pathology and cognition.

Results: Fecal propionate, isovalerate, and propionate-producing bacteria are inversely associated with amyloid status. Mediation analysis found that propionate mediates sex-specific associations between SCFAs and CSF biomarkers. SCFA levels are associated with slower cognitive decline.

Discussion: These results link SCFAs and propionate-producing bacteria with AD. This may inform efforts to leverage diet and specific bacteria to boost SCFA production and potentially ameliorate AD progression.

Keywords: Alzheimer’s disease; Cerebrospinal fluid biomarkers; amyloid; bacteria; gut microbiome; metabolites; microbiota; short-chain fatty acids.

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Conflict of interest statement

HZ has served at scientific advisory boards and/or as a consultant for Abbvie, Acumen, Alector, Alzinova, ALZpath, Amylyx, Annexon, Apellis, Artery Therapeutics, AZTherapies, Cognito Therapeutics, CogRx, Denali, Eisai, Enigma, LabCorp, Merck Sharp & Dohme, Merry Life, Nervgen, Novo Nordisk, Optoceutics, Passage Bio, Pinteon Therapeutics, Prothena, Quanterix, Red Abbey Labs, reMYND, Roche, Samumed, ScandiBio Therapeutics AB, Siemens Healthineers, Triplet Therapeutics, and Wave, has given lectures sponsored by Alzecure, BioArctic, Biogen, Cellectricon, Fujirebio, LabCorp, Lilly, Novo Nordisk, Oy Medix Biochemica AB, Roche, and WebMD, is a co-founder of Brain Biomarker Solutions in Gothenburg AB (BBS), which is a part of the GU Ventures Incubator Program, and is a shareholder of MicThera (outside submitted work). BBB has received consulting fees from New Amsterdam, Cognito Therapeutics, and Merry Life Biomedical. BBB is the founder of Cognovance. Support includes funding from the Alzheimer’s Association. BBB has served on advisory boards, including the Weston Advisor Grant, the Rush ADRC External Advisory Board, and the Emory ADRC External Advisory Board. Amyloid and tau PET tracers and precursors were provided by AVID Radiopharmaceuticals under a materials transfer agreement for prior studies. GK is a full-time employee of Roche Diagnostics GmbH, Penzberg, Germany. CQR is a full-time employee of Roche Diagnostics International Ltd, Rotkreuz, Switzerland. The remaining authors have nothing to disclose.

Figures

Figure 1.
Figure 1.. Analysis dataset selection per study goal.
CONSORT flow diagram indicating selection criteria for inclusion in each analysis goal. Abbreviations: A+, amyloid status determined with 11C-PiB PET, CSF Aβ42/Aβ40, or plasma pTau217; APOE, apolipoprotein E; CSF, cerebrospinal fluid; PET, positron emission tomography; SCFA, short-chain fatty acids measured in fecal samples; T+, tau positive status measured with 18F-MK6240 PET neuroimaging.
Figure 2.
Figure 2.. Amyloid relationships with SCFA abundance.
(A) Fecal SCFA levels compared across A+ and A- participants and (B) forest plot with odds ratios depicting A+ risk as a function of SCFA level and modified by male sex. From left to right per panel, a scatter plot depicts individual participant values, a box plot shows median SCFA level per amyloid status, and a density plot shows the data distribution and highlights the mean SCFA level per amyloid status. SCFA levels in CU participants are depicted with circles, and in MCI or dementia participants with triangles. For each SCFA, abundances are normalized on the median abundance represented in the sample. Odds ratios for main SCFA effects and SCFA-by-sex interactions were derived from the logistic regression model Amyloid status ~ SCFA + sex + SCFA-by-sex + age + APOE ε4 carrier status + diagnosis + time between biomarker measurement and fecal collection. To allow for visual comparison of mean effects, the 95% confidence interval upper limits were annotated for coefficients with wide confidence intervals. Abbreviations: A+/−, amyloid positive or negative status determined with 11C-PiB PET, CSF Aβ42/Aβ40, or plasma pTau217; APOE, apolipoprotein E; CU, cognitively unimpaired; MCI, mild cognitive impairment; SCFA, short-chain fatty acids; UL, upper limit of the 95% confidence interval.
Figure 3.
Figure 3.. SCFAs significantly associated with CSF biomarkers of amyloid pathology and microglial activation in cognitively unimpaired participant subset.
(A) Forest plot with SCFA and SCFA-by-male sex effect coefficients on CSF biomarker outcomes. Effects were estimated with the regression model CSF biomarker ~ SCFA + sex + SCFA-by-sex + age + APOE ε4 carrier status + BSS + CSF biomarker batch. (B-D) CSF biomarker levels residualized on model covariates (age, sex, SCFA level, APOE ε4 carrier status, BSS, CSF biomarker batch) to demonstrate (B-C) Aβ42/Aβ40 relationships with isobutyrate and isovalerate and (D) sTREM2 relationships with butyrate. (E-H) Aβ42/Aβ40 residualized on model covariates (age, sex, APOE ε4 carrier status, BSS, CSF biomarker batch) to demonstrate amyloid relationships with (E) acetate, (F) butyrate, (G) isobutyrate, and (H) isovalerate main effects. Abbreviations: Aβ, amyloid-beta; APOE, apolipoprotein E; BSS, Bristol Stool Score; GFAP, glial fibrillary acidic protein; NfL, neurofilament light chain protein; pTau181, tau phosphorylated at amino acid 181; SCFA, short-chain fatty acids; sTREM2, soluble triggering factor expressed on myeloid cells 2; tTau, total tau; YKL-40, chitinase-3-like protein 1.
Figure 4.
Figure 4.. Effects of SCFAs on longitudinal trajectories of pTau217 and cognition in cognitively unimpaired subset.
(A) Effects of SCFAs on longitudinal trajectories of plasma pTau217 or (B) cognition (PACC3) by multiple linear regression: plasma pTau217 or cognition ~ SCFA + sex + SCFA-by-male sex + age2 + APOE ε4 carrier status + BSS. For visualization, SCFA levels (normally distributed) are grouped into even tertiles: high, medium, and low. Abbreviations: APOE, apolipoprotein E; BSS, Bristol Stool Score; PACC3, Preclinical Alzheimer Cognitive Composite score (three item version); SCFA, short-chain fatty acids.
Figure 5.
Figure 5.. Distributions of propionate- and butyrate-producing bacteria among cognitively unimpaired participants are shifted toward amyloid-negative status.
The distribution of log transformed odds ratios (μ) for metagenome-assembled genomes (MAGs) with genetic pathways for (A,C) propionate production and (B,D) butyrate production in A+ participants compared to A-, for producer MAGs vs. non-producer MAGs (labeled propionate or butyrate positive or negative by color), as assessed by a Wilcoxon rank-sum test for log transformed odds ratios, indicating the effect of each MAG on amyloid status (negative values = A-, positive values = A+). Effects of MAGs on amyloid status were assessed by logistic regression: Amyloid status ~ MAG + sex + age + APOE ε4 carrier status + BSS. (C,D): From top to bottom per panel, a density plot shows the data distribution, highlighting the mean MAG log transformed odds ratio per group, and a scatter plot depicts the log transformed odds ratio for each MAG. Propionate positive and Butyrate positive MAGs were classified based on gene content. Abbreviations: A+/−, amyloid positive or negative status determined with 11C-PiB PET, CSF Aβ42/Aβ40, or plasma pTau217; APOE, apolipoprotein E; BSS, Bristol Stool Score; MAG, metagenome-assembled genome.
Figure 6.
Figure 6.. MAGs significantly associated with CSF biomarkers of AD, neuroinflammation, and neurodegeneration in cognitively unimpaired participant subset.
Propionate- and butyrate-producing MAGs, as well as MAG-by-male sex interaction terms, have effects on CSF (A) Aβ42/Aβ40 and (B) sTREM2, as assessed by multiple linear regression: CSF biomarker ~ MAG + sex + MAG-by-male sex + age + APOE ε4 carrier status + BSS + CSF biomarker batch. P values shown are before FDR correction. Abbreviations: Aβ42/Aβ40, amyloid beta 42 to amyloid beta 40 ratio; APOE, apolipoprotein E; BSS, Bristol Stool Score; GFAP, glial fibrillary acidic protein; MAG, metagenome-assembled genome; NfL, neurofilament light chain protein; pTau181/Aβ42, phosphorylated tau 181 to amyloid beta 42 ratio; sTREM2, soluble triggering factor expressed on myeloid cells 2; tTau, total tau; YKL-40, chitinase-3-like protein 1; SCFA, short-chain fatty acid.
Figure 7.
Figure 7.. SCFA mediation of relationship between MAGs and AD biomarkers.
(A) Table of significant mediation relationships. Mediation assessed by (B) causal mediation analysis, accounting for the covariates sex, age, APOE ε4 carrier status, BSS, and CSF biomarker batch. (C) Propionate mediates relationship between Paraprevotella clara and A+ status. Propionate mediates relationship between propionate-producing MAGs and (D) CSF pTau181/Aβ42, and (E) CSF GFAP. Effects of SCFAs on CSF biomarkers were controlled for sex, age, APOE ε4 status, and BSS. Propionate producing and Butyrate producing MAGs were classified based on gene content. Yellow = propionate-producing MAG. Abbreviations: A+, amyloid positive status determined with 11C-PiB PET, CSF Aβ42/Aβ40, or plasma pTau217; Aβ42/Aβ40, amyloid beta 42 to amyloid beta 40 ratio; APOE, apolipoprotein E; B, butyrate producer; bm, biomarker; BSS, Bristol Stool Score; GFAP, glial fibrillary acidic protein; MAG, metagenome-assembled genome; P, propionate producer; pTau181/Aβ42, phosphorylated tau 181 to amyloid beta 42 ratio; SCFA, short-chain fatty acid; sTREM2, soluble triggering factor expressed on myeloid cells 2.
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