To Impute or Not To Impute in Untargeted Metabolomics─That is the Compositional Question

Journal of the American Society for Mass Spectrometry, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 25, 2025

Untargeted metabolomics often produce large datasets with missing values. These values are derived from biological or technical factors and can undermine statistical analyses lead to biased interpretations. Imputation methods, such as k-Nearest Neighbors (kNN) Random Forest (RF) regression, commonly used, but their effects vary depending on the type of data, e.g., Missing Completely At (MCAR) Not (MNAR). Here, we determined impacts degree data accuracy kNN RF imputation using two datasets: a targeted metabolomic dataset spiked-in standards an untargeted dataset. We also assessed effect compositional approaches (CoDA), centered log-ratio (CLR) transform, interpretation since these methods increasingly being used in metabolomics. Overall, found that performed more accurately when proportion across samples for metabolic feature was low. However, imputations could not handle MNAR generated wildly inflated imputed where none should exist. Furthermore, show had strong impact imputation, which affected results. Our results suggest be extreme caution even modest levels especially missingness is unknown.

Language: Английский

---

Human Untargeted Metabolomics in High-Throughput Gut Microbiome Research: Ethanol vs Methanol

Analytical Chemistry, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 27, 2025

Untargeted metabolomics is frequently performed on human fecal samples in conjunction with sequencing to unravel the gut microbiome functionality. As sample collection efforts are rapidly expanding, individuals often collecting specimens at home, experiments should adapt accommodate safety and needs of bulk off-site collections improve high throughput. Here, we show that a 95% ethanol, safe be shipped handled, extraction part Matrix Method pipeline recovers comparable amounts metabolites as validated 50% methanol extraction, preserving metabolic profile differences between investigated subjects. Additionally, metabolome remains relatively stable when stored ethanol for up 1 week room temperature. Finally, suggest data analysis workflow based robust centered log ratio transformation, which removes variance introduced by possible different weights concentrations, allowing reliable integration-ready untargeted research.

Language: Английский

---

From Gut to Brain: The Role of Gut Dysbiosis, Bacterial Amyloids, and Metabolic Disease in Alzheimer’s Disease

Pharmacological Research, Journal Year: 2025, Volume and Issue: unknown, P. 107693 - 107693

Published: March 1, 2025

Gut microbial dysbiosis, or altered gut communities, in Alzheimer's Disease suggests a pathogenic role for inflammation and products shaping neuroinflammatory environment. Similarly, metabolic diseases, such as obesity diabetes, are also associated with an increased risk of Disease. As the landscape shifts during inflammation, turn impacts processes, we explore how these interconnected pathways may contribute to progression Additionally, discuss bacterial amyloids produced by microbes, which exacerbate amyloid aggregation brain neurodegenerative processes. Furthermore, highlight potential therapeutic strategies aimed at reducing improving health, decreasing content means mitigate progression. These approaches, targeting gut-brain-metabolic axis, could offer promising avenues delaying preventing cognitive decline affected individuals.

Language: Английский

---

The Impact of the Exposome on Alzheimer’s Disease: The Influence of Nutrition

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(7), P. 3015 - 3015

Published: March 26, 2025

Alzheimer's disease (AD) is a progressive neurodegenerative characterized by cognitive decline, memory loss, and behavioural changes. While genetic predispositions pathological processes have been the traditional focus, this review highlights fundamental role of environmental factors, particularly nutrition, within exposome framework in modulating risk progression AD. The exposome, which includes totality exposures an individual's lifetime, provides comprehensive approach to understanding complex aetiology In review, we explore impact dietary factors cyclic nucleotide pathways (cAMP/cGMP) on AD, emphasizing potential interventions as therapeutic strategies. We investigate key aspects how nutrition affects accumulation β-amyloid, aggregation tau proteins, neuroinflammation. also examine specific nutrients performance Additionally, discuss nutraceuticals with anti-phosphodiesterase activity various animal models AD (such 5xFAD, 3xTg-AD, Tg2576, APP/PS1 mice) demonstrating effects onset progression.

Language: Английский

---

Bibliometric analysis and description of research trends on nutritional management in Alzheimer’s disease patients (1988–2024)

Frontiers in Nutrition, Journal Year: 2025, Volume and Issue: 12

Published: March 28, 2025

Alzheimer's disease (AD) is a severe neurodegenerative disorder. Nutritional management has been recognized as potential therapeutic approach to mitigate AD progression. This study aimed analyze the bibliometric characteristics and research trends of publications on nutritional in AD. A systematic search was conducted Web Science Core Collection database identify related from 1988 2024. Bibliometric analysis performed using VOSviewers (V 1.6.20), CiteSpace 6.3.R1) R 4.3.3. total 554 311 countries led by USA were identified. The number increased annually. most cited article discussed role diet providing antioxidants combat oxidative stress diseases. University California system published articles, Rush had international collaborations. These came 3,298 authors, among which Mattson MP highest citations. Journal Disease articles received Keywords revealed evolving trends, with early emphasis "precursor protein" later shifts "dietary restriction," more recently, "insulin resistance" "synaptic plasticity." Emerging keywords include "obesity," "cognitive impairment" "association." represents first summary management. Future likely focus associations between nutrition, insulin resistance, synaptic plasticity, cognitive impairment patients. information provides valuable insights for scholars practitioners field.

Language: Английский

---