Western dietary habits (WD) have been shown to promote chronic inflammation, which favors the development of many of today's non-communicable diseases. Recently, ketogenic diets (KD) have emerged as an immune-regulating countermeasure for WD-induced metaflammation. To date, beneficial effects of KD have been solely attributed to the production and metabolism of ketone bodies. Given the drastic change in nutrient composition during KD, it is reasonable to assume that there are widespread changes in the human metabolome also contributing to the impact of KD on human immunity. The current study was conducted to gain insight into the changes of the human metabolic fingerprint associated with KD. This could allow to identify metabolites that may contribute to the overall positive effects on human immunity, but also help to recognize potential health risks of KD. We conducted a prospective nutritional intervention study enrolling 40 healthy volunteers to perform a three-week ad-libitum KD. Prior to the start and at the end of the nutritional intervention serum metabolites were quantified, untargeted mass spectrometric metabolome analyses and urine analyses of the tryptophan pathway were performed. KD led to a marked reduction of insulin (-21.45% ± 6.44%, p = 0.0038) and c-peptide levels (-19.29% ± 5.45%, p = 0.0002) without compromising fasting blood glucose. Serum triglyceride concentration decreased accordingly (-13.67% ± 5.77%, p = 0.0247), whereas cholesterol parameters remained unchanged. LC-MS/MS-based untargeted metabolomic analyses revealed a profound shift of the human metabolism towards mitochondrial fatty acid oxidation, comprising highly elevated levels of free fatty acids and acylcarnitines. The serum amino acid (AA) composition was rearranged with lower abundance of glucogenic AA and an increase of BCAA. Furthermore, an increase of anti-inflammatory fatty acids eicosatetraenoic acid (p < 0.0001) and docosahexaenoic acid (p = 0.0002) was detected. Urine analyses confirmed higher utilization of carnitines, indicated by lower carnitine excretion (-62.61% ± 18.11%, p = 0.0047) and revealed changes to the tryptophan pathway depicting reduced quinolinic acid (-13.46% ± 6.12%, p = 0.0478) and elevated kynurenic acid concentrations (+10.70% ± 4.25%, p = 0.0269). A KD fundamentally changes the human metabolome even after a short period of only three weeks. Besides a rapid metabolic switch to ketone body production and utilization, improved insulin and triglyceride levels and an increase in metabolites that mediate anti-inflammation and mitochondrial protection occurred. Importantly, no metabolic risk factors were identified. Thus, a ketogenic diet could be considered as a safe preventive and therapeutic immunometabolic tool in modern medicine. German Clinical Trials Register; DRKS-ID: DRKS00027992 (www.drks.de).

This Data Descriptor presents an anonymized, shuffled dataset of creatinine-normalized urinary metabolite measurements from 73 Bulgarian children with autism spectrum disorder (ASD), released to support reuse in secondary analyses and cross-cohort comparisons. The public release represents a pathway-oriented 24-marker subset from a broader urinary diagnostic panel, assembled as a self-contained resource for investigators working in these metabolic domains. Spot urine results are provided as individual-level values after creatinine normalization; for trimethylamine, values below the limit of quantification (LOQ) were replaced with LOQ/2. The deposit contains measurements for 24 urinary markers grouped into three functional classes (neurotransmitters and aromatic amino acid precursors; one-carbon/methylation and vitamin-related metabolites; and energy metabolism/organic acids with microbiome-related amines). The underlying cohort comprised children aged 3–13 years, and no contemporaneous neurotypical control group was enrolled. Second-morning, midstream, acid-stabilized spot urine samples were collected within the provider’s workflow; metabolites were measured by LC–MS/MS, and spot urinary creatinine was measured enzymatically for normalization. The release includes the results table in both XLSX and CSV formats, a reference limits and units file for contextual interpretation, a data dictionary, a README, a changelog, and SHA-256 checksums for integrity verification. The public files contain de-identified analytical variables only and omit individual-level demographics, dates, standalone urinary creatinine, and richer clinical metadata to preserve anonymity.

This Data Descriptor presents an anonymized, shuffled dataset of creatinine-normalized urinary metabolite measurements from 73 Bulgarian children with autism spectrum disorder (ASD), released to support reuse in secondary analyses and cross-cohort comparisons. Spot urine results are provided as individual-level values after creatinine normalization; for trimethylamine, values below the limit of quantification (LOQ) were replaced with LOQ/2. The deposit contains measurements for 24 urinary markers grouped into three functional classes (neurotransmitters and aromatic amino acid precursors; one-carbon/methylation and vitamin-related metabolites; and energy metabolism/organic acids with microbiome-related amines). The release includes the results table in both XLSX and CSV formats, a reference limits and units file for contextual interpretation, a data dictionary, a README, a changelog, and SHA-256 checksums for integrity verification. Cohort-level demographics and additional sampling details are described in the companion publication cited in the main text. Dataset: https://doi.org/10.5281/zenodo.18614881 Dataset License: Creative Commons Attribution 4.0 International.