Gut microbiota mediates intermittent-fasting alleviation of diabetes-induced cognitive impairment

[1]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[2]  Robert W Buzzeo,et al.  Melatonin treatment restores mitochondrial function in Alzheimer’s mice: a mitochondrial protective role of melatonin membrane receptor signaling , 2011, Journal of pineal research.

[3]  Daxesh P. Patel,et al.  Intermittent Fasting Promotes White Adipose Browning and Decreases Obesity by Shaping the Gut Microbiota. , 2017, Cell metabolism.

[4]  A. M. Habib,et al.  Short-Chain Fatty Acids Stimulate Glucagon-Like Peptide-1 Secretion via the G-Protein–Coupled Receptor FFAR2 , 2012, Diabetes.

[5]  Jingzhu Zhang,et al.  Intermittent Fasting Protects against Alzheimer’s Disease Possible through Restoring Aquaporin-4 Polarity , 2017, Front. Mol. Neurosci..

[6]  Alyssa C. Frazee,et al.  Ballgown bridges the gap between transcriptome assembly and expression analysis , 2015, Nature Biotechnology.

[7]  Kim-Anh Lê Cao,et al.  mixOmics: An R package for ‘omics feature selection and multiple data integration , 2017, bioRxiv.

[8]  R. Frye,et al.  Butyrate enhances mitochondrial function during oxidative stress in cell lines from boys with autism , 2018, Translational Psychiatry.

[9]  Steven L Salzberg,et al.  HISAT: a fast spliced aligner with low memory requirements , 2015, Nature Methods.

[10]  R. Castellani,et al.  Alzheimer disease. , 2010, Disease-a-month : DM.

[11]  K. Close,et al.  International Diabetes Federation 2017 , 2018, Journal of diabetes.

[12]  Ke Ma,et al.  Farnesoid X receptor is essential for normal glucose homeostasis. , 2006, The Journal of clinical investigation.

[13]  Satchidananda Panda,et al.  Time-restricted feeding without reducing caloric intake prevents metabolic diseases in mice fed a high-fat diet. , 2012, Cell metabolism.

[14]  R. Ratan,et al.  Butyrate, neuroepigenetics and the gut microbiome: Can a high fiber diet improve brain health? , 2016, Neuroscience Letters.

[15]  B. Yoon,et al.  Metronidazole-induced encephalopathy , 2004, Journal of the Neurological Sciences.

[16]  Ben Nichols,et al.  Distributed under Creative Commons Cc-by 4.0 Vsearch: a Versatile Open Source Tool for Metagenomics , 2022 .

[17]  Xinying Wang,et al.  Gut Microbiota as a Modulator of Paneth Cells During Parenteral Nutrition in Mice , 2018, JPEN. Journal of parenteral and enteral nutrition.

[18]  P. Filzmoser,et al.  Repeated double cross validation , 2009 .

[19]  B. Kemp,et al.  AMPK activation of muscle autophagy prevents fasting-induced hypoglycemia and myopathy during aging. , 2015, Cell metabolism.

[20]  Liping Zhao,et al.  Structural modulation of gut microbiota in life-long calorie-restricted mice , 2013, Nature Communications.

[21]  P. Dixon VEGAN, a package of R functions for community ecology , 2003 .

[22]  S. Ferreira,et al.  Inflammation, Defective Insulin Signaling, and Mitochondrial Dysfunction as Common Molecular Denominators Connecting Type 2 Diabetes to Alzheimer Disease , 2014, Diabetes.

[23]  T. Sakaguchi,et al.  Claudins regulate the intestinal barrier in response to immune mediators. , 2000, Gastroenterology.

[24]  Steve Horvath,et al.  WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.

[25]  Jesse R. Zaneveld,et al.  Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences , 2013, Nature Biotechnology.

[26]  G. Saretzki,et al.  Decreased mTOR signalling reduces mitochondrial ROS in brain via accumulation of the telomerase protein TERT within mitochondria , 2016, Aging.

[27]  Eoin L. Brodie,et al.  Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB , 2006, Applied and Environmental Microbiology.

[28]  T. Tsai,et al.  Pharmacokinetics of metronidazole in rat blood, brain and bile studied by microdialysis coupled to microbore liquid chromatography. , 2003, Journal of chromatography. A.

[29]  R. Morris Developments of a water-maze procedure for studying spatial learning in the rat , 1984, Journal of Neuroscience Methods.

[30]  Mark A. Smith,et al.  Faculty Opinions recommendation of Diabetes-accelerated memory dysfunction via cerebrovascular inflammation and Abeta deposition in an Alzheimer mouse model with diabetes. , 2010 .

[31]  C. Kahn,et al.  Gut microbiota modulate neurobehavior through changes in brain insulin sensitivity and metabolism , 2018, Molecular Psychiatry.

[32]  F. Bäckhed,et al.  Microbiota-Generated Metabolites Promote Metabolic Benefits via Gut-Brain Neural Circuits , 2014, Cell.

[33]  Lin Shi,et al.  Variable selection and validation in multivariate modelling , 2018, Bioinform..

[34]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..

[35]  Gavin M. Douglas,et al.  Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches , 2018, PeerJ.

[36]  Indigenous Bacteria from the Gut Microbiota Regulate Host Serotonin Biosynthesis , 2015, Cell.

[37]  Masahiro Tohkin,et al.  Targeted Disruption of the Nuclear Receptor FXR/BAR Impairs Bile Acid and Lipid Homeostasis , 2000, Cell.

[38]  A. Convit,et al.  Hippocampal damage and memory impairments as possible early brain complications of type 2 diabetes , 2007, Diabetologia.

[39]  E. Cadenas,et al.  Effects of Lipoic Acid on High-Fat Diet-Induced Alteration of Synaptic Plasticity and Brain Glucose Metabolism: A PET/CT and 13C-NMR Study , 2017, Scientific Reports.

[40]  Rumani Singh,et al.  Middle age onset short-term intermittent fasting dietary restriction prevents brain function impairments in male Wistar rats , 2015, Biogerontology.

[41]  M. Boulton,et al.  Restructuring of the Gut Microbiome by Intermittent Fasting Prevents Retinopathy and Prolongs Survival in db/db Mice , 2018, Diabetes.

[42]  William A. Walters,et al.  QIIME allows analysis of high-throughput community sequencing data , 2010, Nature Methods.

[43]  M. Mattson,et al.  Intermittent fasting attenuates lipopolysaccharide-induced neuroinflammation and memory impairment , 2014, Journal of Neuroinflammation.

[44]  Xuebo Liu,et al.  Extract of sesame cake and sesamol alleviate chronic unpredictable mild stress-induced depressive-like behaviors and memory deficits , 2018 .

[45]  R. Bibiloni,et al.  Changes in Gut Microbiota Control Metabolic Endotoxemia-Induced Inflammation in High-Fat Diet–Induced Obesity and Diabetes in Mice , 2008, Diabetes.

[46]  E. Nishida,et al.  Signalling through RHEB-1 mediates intermittent fasting-induced longevity in C. elegans , 2009, Nature.

[47]  Alyssa C. Frazee,et al.  Flexible isoform-level differential expression analysis with Ballgown , 2014 .

[48]  Á. Valverde,et al.  Modulation of microglia polarization dynamics during diabetic retinopathy in db/db mice. , 2016, Biochimica et biophysica acta.

[49]  E. Segal,et al.  Involvement of a gut–retina axis in protection against dietary glycemia-induced age-related macular degeneration , 2017, Proceedings of the National Academy of Sciences.

[50]  Lai Guan Ng,et al.  The gut microbiota influences blood-brain barrier permeability in mice , 2014, Science Translational Medicine.

[51]  E. Cadenas,et al.  Mitochondrial function in ageing: coordination with signalling and transcriptional pathways , 2016, The Journal of physiology.

[52]  Xuebo Liu,et al.  Sesamol ameliorates diet-induced obesity in C57BL/6J mice and suppresses adipogenesis in 3T3-L1 cells via regulating mitochondria-lipid metabolism. , 2017, Molecular nutrition & food research.

[53]  J. Rood,et al.  Effect of Alternate-Day Fasting on Weight Loss, Weight Maintenance, and Cardioprotection Among Metabolically Healthy Obese Adults: A Randomized Clinical Trial , 2017, JAMA internal medicine.

[54]  B. Poeggeler,et al.  Potent Neuroprotective Properties against the Alzheimer β-Amyloid by an Endogenous Melatonin-related Indole Structure, Indole-3-propionic Acid* , 1999, The Journal of Biological Chemistry.

[55]  Sandra Fischer,et al.  Distributed under Creative Commons Cc-by 4.0 Rhea: a Transparent and Modular R Pipeline for Microbial Profiling Based on 16s Rrna Gene Amplicons , 2022 .

[56]  J. Tuomilehto,et al.  Associations of serum indolepropionic acid, a gut microbiota metabolite, with type 2 diabetes and low-grade inflammation in high-risk individuals , 2018, Nutrition & Diabetes.

[57]  Daniel M. Rotroff,et al.  Altered bile acid profile associates with cognitive impairment in Alzheimer's disease—An emerging role for gut microbiome , 2018, Alzheimer's & Dementia.

[58]  Robert C. Edgar,et al.  UCHIME2: improved chimera prediction for amplicon sequencing , 2016, bioRxiv.

[59]  W. D. de Vos,et al.  Oral treatment with Eubacterium hallii improves insulin sensitivity in db/db mice , 2016, npj Biofilms and Microbiomes.

[60]  C. Vorhees,et al.  Morris water maze: procedures for assessing spatial and related forms of learning and memory , 2006, Nature Protocols.

[61]  Jun Yu,et al.  Gavage of Fecal Samples From Patients With Colorectal Cancer Promotes Intestinal Carcinogenesis in Germ-Free and Conventional Mice. , 2017, Gastroenterology.

[62]  M. Pop,et al.  Robust methods for differential abundance analysis in marker gene surveys , 2013, Nature Methods.

[63]  R. D'Hooge,et al.  TUDCA, a Bile Acid, Attenuates Amyloid Precursor Protein Processing and Amyloid-β Deposition in APP/PS1 Mice , 2012, Molecular Neurobiology.

[64]  Rumani Singh,et al.  Late-onset intermittent fasting dietary restriction as a potential intervention to retard age-associated brain function impairments in male rats , 2011, AGE.

[65]  Robert C. Edgar,et al.  UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing , 2016, bioRxiv.

[66]  Matej Oresic,et al.  A computational framework to integrate high-throughput ‘-omics’ datasets for the identification of potential mechanistic links , 2018, Nature Protocols.

[67]  P. Moreira,et al.  Alzheimer's disease and type 2 diabetes-related alterations in brain mitochondria, autophagy and synaptic markers. , 2015, Biochimica et biophysica acta.

[68]  Peter Filzmoser,et al.  Multivariate linear QSPR/QSAR models: Rigorous evaluation of variable selection for PLS , 2013, Computational and structural biotechnology journal.

[69]  H. Forssberg,et al.  Normal gut microbiota modulates brain development and behavior , 2011, Proceedings of the National Academy of Sciences.

[70]  Xianlin Han,et al.  Altered bile acid profile associates with cognitive impairment in Alzheimer's disease—An emerging role for gut microbiome , 2018, Alzheimer's & Dementia.

[71]  Hao Li,et al.  Normalization and integration of large-scale metabolomics data using support vector regression , 2016, Metabolomics.

[72]  Christopher C. Overall,et al.  Microbiota alteration is associated with the development of stress-induced despair behavior , 2017, Scientific Reports.

[73]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[74]  Xuebo Liu,et al.  Acrylamide aggravates cognitive deficits at night period via the gut–brain axis by reprogramming the brain circadian clock , 2018, Archives of Toxicology.

[75]  J. S. Kim,et al.  Metronidazole-induced encephalopathy in a patient with Crohn's disease , 2017, Intestinal research.

[76]  S. Salzberg,et al.  StringTie enables improved reconstruction of a transcriptome from RNA-seq reads , 2015, Nature Biotechnology.

[77]  J. Walsh,et al.  High-Fat Diet Induces Hepatic Insulin Resistance and Impairment of Synaptic Plasticity , 2015, PloS one.

[78]  P. Jena,et al.  Dysregulated bile acid synthesis and dysbiosis are implicated in Western diet–induced systemic inflammation, microglial activation, and reduced neuroplasticity , 2018, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[79]  Jeffrey T Leek,et al.  Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown , 2016, Nature Protocols.

[80]  Robert C. Edgar,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2001 .

[81]  Rob Knight,et al.  Analysis of composition of microbiomes: a novel method for studying microbial composition , 2015, Microbial ecology in health and disease.

[82]  E. Glaser The randomized clinical trial. , 1972, The New England journal of medicine.

[83]  A. Albanese,et al.  Tauroursodeoxycholic acid in the treatment of patients with amyotrophic lateral sclerosis , 2015, European journal of neurology.

[84]  L. Wen,et al.  The role of gut microbiota in the development of type 1, type 2 diabetes mellitus and obesity , 2015, Reviews in Endocrine and Metabolic Disorders.

[85]  Jing Shang,et al.  Selective inhibition of intestinal 5-HT improves neurobehavioral abnormalities caused by high-fat diet mice , 2019, Metabolic Brain Disease.

[86]  Max Nieuwdorp,et al.  Insights Into the Role of the Microbiome in Obesity and Type 2 Diabetes , 2014, Diabetes Care.

[87]  P. Sham,et al.  Alterations in Gastric Microbiota After H. Pylori Eradication and in Different Histological Stages of Gastric Carcinogenesis , 2017, Scientific Reports.

[88]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[89]  G. Weinstock,et al.  Intermittent Fasting Confers Protection in CNS Autoimmunity by Altering the Gut Microbiota. , 2018, Cell metabolism.

[90]  Lennart Eriksson,et al.  Model validation by permutation tests: Applications to variable selection , 1996 .

[91]  Mark P. Mattson,et al.  Intermittent fasting dissociates beneficial effects of dietary restriction on glucose metabolism and neuronal resistance to injury from calorie intake , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[92]  Ryuichi Morishita,et al.  Diabetes-accelerated memory dysfunction via cerebrovascular inflammation and Aβ deposition in an Alzheimer mouse model with diabetes , 2010, Proceedings of the National Academy of Sciences.

[93]  Susan Holmes,et al.  Faculty of 1000 evaluation for mixOmics: An R package for 'omics feature selection and multiple data integration. , 2018 .