The microbiome diversifies long- to short-chain fatty acid-derived N-acyl lipids

Helena Mannochio-Russo¹, Vincent Charron-Lamoureux¹, Martijn van Faassen², Santosh Lamichhane³, Wilhan D Gonçalves Nunes¹, Victoria Deleray¹, Adriana V Ayala⁴, Yuichiro Tanaka⁴, Abubaker Patan¹, Kyle Vittali¹, Prajit Rajkumar¹, Yasin El Abiead¹, Haoqi Nina Zhao¹, Paulo Wender Portal Gomes¹, Ipsita Mohanty¹, Carlynda Lee¹, Aidan Sund¹, Meera Sharma¹, Yuanhao Liu¹, David Pattynama¹, Gregory T Walker⁵, Grant J Norton⁵, Lora Khatib⁶, Mohammadsobhan S Andalibi⁷, Crystal X Wang⁸, Ronald J Ellis⁹, David J Moore⁸, Jennifer E Iudicello⁸, Donald Franklin Jr⁸, Scott Letendre¹⁰, Loryn Chin¹¹, Corinn Walker¹², Simone Renwick¹³, Jasmine Zemlin¹⁴, Michael J Meehan¹, Xinyang Song¹⁵, Dennis Kasper¹⁶, Zachary Burcham¹⁷, Jane J Kim¹⁸, Sejal Kadakia¹⁹, Manuela Raffatellu²⁰, Lars Bode¹³, Hiutung Chu²¹, Karsten Zengler¹¹, Mingxun Wang²², Dionicio Siegel¹, Rob Knight²³, Pieter C Dorrestein²⁴

Affiliations

¹ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
² Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, the Netherlands.
³ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Institute of Biomedicine, Faculty of Medicine, University of Turku & Turku Bioscience Center, University of Turku and Åbo Akademi University, 20520 Turku, Finland.
⁴ Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA.
⁵ Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
⁶ Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Neurosciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA.
⁷ Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Psychiatry, University of California, San Diego, La Jolla, CA 92093, USA; HIV Neurobehavioral Research Program, University of California, San Diego, La Jolla, CA 92093, USA.
⁸ Department of Psychiatry, University of California, San Diego, La Jolla, CA 92093, USA; HIV Neurobehavioral Research Program, University of California, San Diego, La Jolla, CA 92093, USA.
⁹ Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; HIV Neurobehavioral Research Program, University of California, San Diego, La Jolla, CA 92093, USA.
¹⁰ HIV Neurobehavioral Research Program, University of California, San Diego, La Jolla, CA 92093, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
¹¹ Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA.
¹² Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
¹³ Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MOMI CORE) and the Human Milk Institute (HMI), University of California, San Diego, La Jolla, CA 92093, USA.
¹⁴ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA.
¹⁵ Department of Immunology, Harvard Medical School, Boston, MA 02115, USA; Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China.
¹⁶ Department of Immunology, Harvard Medical School, Boston, MA 02115, USA.
¹⁷ Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA.
¹⁸ Department of Pediatrics, Division of Pediatric Endocrinology, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Hospital San Diego, San Diego, CA 92123, USA.
¹⁹ Division of Pediatric Endocrinology, Children's Hospital of Orange County, Orange, CA 92868, USA.
²⁰ Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA; Chiba University - UC San Diego Center for Mucosal Immunology, Allergy, and Vaccines, La Jolla, CA 92093, USA.
²¹ Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA; Chiba University - UC San Diego Center for Mucosal Immunology, Allergy, and Vaccines, La Jolla, CA 92093, USA.
²² Department of Computer Science and Engineering, University of California, Riverside, Riverside, CA 92521, USA.
²³ Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA; Halıcıoğlu Data Science Institute, University of California, San Diego, La Jolla, CA 92093, USA; Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
²⁴ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address: pdorrestein@health.ucsd.edu.

PMID: 40499541
PMCID: PMC12428309
DOI: 10.1016/j.cell.2025.05.015

The microbiome diversifies long- to short-chain fatty acid-derived N-acyl lipids

Helena Mannochio-Russo et al. Cell. 2025.

. 2025 Jul 24;188(15):4154-4169.e19.

doi: 10.1016/j.cell.2025.05.015. Epub 2025 Jun 10.

Authors

Affiliations

¹ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
² Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, the Netherlands.
³ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Institute of Biomedicine, Faculty of Medicine, University of Turku & Turku Bioscience Center, University of Turku and Åbo Akademi University, 20520 Turku, Finland.
⁴ Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA.
⁵ Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
⁶ Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Neurosciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA.
⁷ Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Psychiatry, University of California, San Diego, La Jolla, CA 92093, USA; HIV Neurobehavioral Research Program, University of California, San Diego, La Jolla, CA 92093, USA.
⁸ Department of Psychiatry, University of California, San Diego, La Jolla, CA 92093, USA; HIV Neurobehavioral Research Program, University of California, San Diego, La Jolla, CA 92093, USA.
⁹ Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; HIV Neurobehavioral Research Program, University of California, San Diego, La Jolla, CA 92093, USA.
¹⁰ HIV Neurobehavioral Research Program, University of California, San Diego, La Jolla, CA 92093, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
¹¹ Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA.
¹² Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
¹³ Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MOMI CORE) and the Human Milk Institute (HMI), University of California, San Diego, La Jolla, CA 92093, USA.
¹⁴ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA.
¹⁵ Department of Immunology, Harvard Medical School, Boston, MA 02115, USA; Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China.
¹⁶ Department of Immunology, Harvard Medical School, Boston, MA 02115, USA.
¹⁷ Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA.
¹⁸ Department of Pediatrics, Division of Pediatric Endocrinology, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Hospital San Diego, San Diego, CA 92123, USA.
¹⁹ Division of Pediatric Endocrinology, Children's Hospital of Orange County, Orange, CA 92868, USA.
²⁰ Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA; Chiba University - UC San Diego Center for Mucosal Immunology, Allergy, and Vaccines, La Jolla, CA 92093, USA.
²¹ Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA; Chiba University - UC San Diego Center for Mucosal Immunology, Allergy, and Vaccines, La Jolla, CA 92093, USA.
²² Department of Computer Science and Engineering, University of California, Riverside, Riverside, CA 92521, USA.
²³ Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA; Halıcıoğlu Data Science Institute, University of California, San Diego, La Jolla, CA 92093, USA; Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
²⁴ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address: pdorrestein@health.ucsd.edu.

PMID: 40499541
PMCID: PMC12428309
DOI: 10.1016/j.cell.2025.05.015

Abstract

N-Acyl lipids are important mediators of several biological processes including immune function and stress response. To enhance the detection of N-acyl lipids with untargeted mass spectrometry-based metabolomics, we created a reference spectral library retrieving N-acyl lipid patterns from 2,700 public datasets, identifying 851 N-acyl lipids that were detected 356,542 times. 777 are not documented in lipid structural databases, with 18% of these derived from short-chain fatty acids and found in the digestive tract and other organs. Their levels varied with diet and microbial colonization and in people living with diabetes. We used the library to link microbial N-acyl lipids, including histamine and polyamine conjugates, to HIV status and cognitive impairment. This resource will enhance the annotation of these compounds in future studies to further the understanding of their roles in health and disease and to highlight the value of large-scale untargeted metabolomics data for metabolite discovery.

Keywords: HIV; MASST; MassQL; N-acyl lipids; SCFA; metabolomics data mining; microbial; neurocognitive impairment; repository-scale analysis; short-chain fatty acids.

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Conflict of interest statement

Declaration of interests P.C.D. is an advisor and holds equity in Cybele, BileOmix, and Sirenas and is a scientific co-founder of, is an advisor to, and holds equity in Ometa, Enveda, and Arome with prior approval by the University of California, San Diego. P.C.D. also consulted for DSM animal health in 2023. M.W. is a co-founder of Ometa Labs LLC. R.K. is a scientific advisory board member of and consultant for BiomeSense, Inc., and has equity and receives income. He is a scientific advisory board member of and has equity in GenCirq. He is a consultant for DayTwo and receives income. He has equity in and acts as a consultant for Cybele. He is a co-founder of Biota, Inc., and has equity. He is a cofounder of Micronoma, has equity, and is a scientific advisory board member. The terms of these arrangements have been reviewed and approved by the University of California, San Diego, in accordance with its conflict-of-interest policies.

Figures

**Figure 1.. Repository-scale analysis of N-Acyl lipids in public mass spectrometry data and distribution among different tissues or biofluids.**
**(A)** N-acyl lipid definitions and isomers: this panel explains N-acyl lipids using a C5:1 tail example. A C5:1 lipid consists of a five-carbon fatty acid with one double bond. The image illustrates the possible isomers for this structure that can yield the same MS/MS spectrum. **(B)** Summary of the workflow followed to generate the N-acyl lipids spectral library and repository-scale searches. More detailed information on each step is available in Supplementary Figure 1C–E. **(C)** Heatmap of N-acyl lipids: the heatmap shows 851 N-acyl lipids identified from public MS data in the MassIVE/GNPS repository using MassQL queries. Compounds found in microbial cultures are marked with purple squares, those matched with synthetic standards are indicated by black stars, and those confirmed by retention time with biological samples are shown with red stars. **(D)** and **(E)** Heatmaps showing distribution in tissues and biofluids: number of matches of different fatty acid chain lengths in tissues and biofluids with metadata available in ReDU for **(D)** rodent and **(E)** human-related public datasets. All heatmaps are shown as log values of the matches obtained from the repository, regardless of the headgroup. Icons were obtained from Bioicons.com.

**Figure 2.. Evidence of microbial origins of N-acyl lipids.**
Heatmaps depict the distribution of different headgroups (A) and tails (B) across various microbial classes, with barplots showing the total counts for each class in microbeMASST. The Y-axis was taxonomically ordered according to the NCBI Taxonomy ID, while the X-axis was clustered using the Braycurtis metric for the headgroups, or in ascending order (in number of carbons and unsaturations) for the tails. C) UpSet plot of N-acyl lipid distribution: This plot highlights the distribution of N-acyl lipids across different datasets, including human-related, rodent-related, microbial monocultures, plant-, and food-associated data. D) Distribution of N-acyl lipid chain lengths: This summary shows the prevalence of short, medium, long, and very long chain N-acyl lipids in public data. Note that the exact location and cis/trans configurations of double bonds cannot be determined from the current queries, which are annotated at the molecular family level according to the Metabolomics Standards Initiative. E and F) Volcano plots of mouse fecal pellets from a dataset publicly available (GNPS/MassIVE: MSV000080918) showing N-acyl lipids up-regulated and down-regulated upon different diets (E) and antibiotic treatment (F). The significant thresholds are marked by dotted lines in the volcano plot (p < 0.05 and log2(FC) > 2 or <2). Differential compounds between the groups were evaluated using the non-parametric two-sided Mann-Whitney U test, and p-values were corrected for multiple comparisons using the Benjamini-Hochberg correction. Icons were obtained from Bioicons.com.

**Figure 3.. N-acyl lipids are correlated with HIV and neurocognitive impairment status and produced by microbes.**
(A) Forest plot illustrating the coefficient estimate of a linear mixed-effects model for individual N-acyl lipid species, with fixed covariates of HIV status (PWH, n = 226; PWoH, n = 87) and neurocognitive impairment status (impaired, n = 151; unimpaired, n = 162), accounting for random effects within individual samples/visit where stool samples were collected. Filled squares (HIV status) and circles (neurocognitive impairment status) with corresponding confidence intervals represent significant N-acyl lipid species. Faded circles and squares depict non-significant species. Each color represents a different headgroup. (B) Bar plot showing the correlation coefficients of association between CD4/CD8 ratio and various N-acyl lipids in a subset of the PWH (n = 171) with available metadata. Red bars represent positive correlations, while blue bars represent negative correlations, as determined by linear regression models. The p-values shown are nominal; adjusted p-values (corrected for multiple comparisons using the Benjamini-Hochberg method) are available in Supplementary Table S3. (C) Structures of all N-acyl lipids confirmed in this study with pure synthetic standards. (D) Network of the microbial taxonomic orders with co-occurrences > 6.0 and shared between histamine-C2:0 and histamine-C3:0. Nodes colored in pink are the orders selected for culturing experiments. (E) Concentrations of histamine-C2:0 and histamine-C3:0 in microbial extracts. Values in the y-axis represent the amount of these compounds in micromolar (μM) concentrations in the extracts. Cadaverine (C), putrescine (P) and histamine (H) were added to the medium.

**Figure 4.. N-acyl lipids have immunomodulatory activities.**
Flow cytometric quantification of Foxp3⁺ (left), Tbet⁺ (middle), RORγT⁺ (right) induction in naive CD4⁺ T cells. Cells were treated with 100 μM of N-acyl lipids on day 0 and CD4⁺ T cells were gated for analyses on day 3. Data is representative of two independent experiments. Bar plot shows mean and error bars represent SEM. One-way Dunnett’s multiple comparisons test provided significance.

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Update of

The microbiome diversifies N-acyl lipid pools - including short-chain fatty acid-derived compounds.
Mannochio-Russo H, Charron-Lamoureux V, van Faassen M, Lamichhane S, Nunes WDG, Deleray V, Patan A, Vittali K, Rajkumar P, El Abiead Y, Zhao HN, Gomes PWP, Mohanty I, Lee C, Sund A, Sharma M, Liu Y, Pattynama D, Walker GT, Norton GJ, Khatib L, Andalibi MS, Wang CX, Ellis RJ, Moore DJ, Iudicello JE, Franklin D Jr, Letendre S, Chin L, Walker C, Renwick S, Zemlin J, Meehan MJ, Song X, Kasper D, Burcham Z, Kim JJ, Kadakia S, Raffatellu M, Bode L, Zengler K, Wang M, Siegel D, Knight R, Dorrestein PC. Mannochio-Russo H, et al. bioRxiv [Preprint]. 2024 Nov 2:2024.10.31.621412. doi: 10.1101/2024.10.31.621412. bioRxiv. 2024. Update in: Cell. 2025 Jul 24;188(15):4154-4169.e19. doi: 10.1016/j.cell.2025.05.015. PMID: 39554097 Free PMC article. Updated. Preprint.

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The microbiome diversifies long- to short-chain fatty acid-derived N-acyl lipids

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The microbiome diversifies long- to short-chain fatty acid-derived N-acyl lipids

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Conflict of interest statement

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