Topic modeling for multi-omic integration in the human gut microbiome and implications for Autism DOI Creative Commons
Christine Tataru,

Marie Peras,

Erica Rutherford

et al.

Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)

Published: July 13, 2023

While healthy gut microbiomes are critical to human health, pertinent microbial processes remain largely undefined, partially due differential bias among profiling techniques. By simultaneously integrating multiple methods, multi-omic analysis can define generalizable processes, and is especially useful in understanding complex conditions such as Autism. Challenges with heterogeneous data produced by methods be overcome using Latent Dirichlet Allocation (LDA), a promising natural language processing technique that identifies topics documents. In this study, we apply LDA (16S rRNA amplicon, shotgun metagenomic, metatranscriptomic, untargeted metabolomic profiling) from the stool of 81 children without We identify topics, or summarize phenomena occurring within communities. then subset samples topic distribution, metabolites, specifically neurotransmitter precursors fatty acid derivatives, differ significantly between clusters deemed "cross-omic topics", which hypothesize representative observable regardless method. Interpreting find each represents particular diet, heuristically label cross-omic as: healthy/general function, age-associated transcriptional regulation, opportunistic pathogenesis.

Language: Английский

Neurodegenerative and Neurodevelopmental Diseases and the Gut-Brain Axis: The Potential of Therapeutic Targeting of the Microbiome DOI Open Access
Brian Bicknell, Ann Liebert, Thomas J. Borody

et al.

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(11), P. 9577 - 9577

Published: May 31, 2023

The human gut microbiome contains the largest number of bacteria in body and has potential to greatly influence metabolism, not only locally but also systemically. There is an established link between a healthy, balanced, diverse overall health. When becomes unbalanced (dysbiosis) through dietary changes, medication use, lifestyle choices, environmental factors, ageing, this profound effect on our health linked many diseases, including metabolic inflammatory neurological diseases. While humans largely association dysbiosis with disease, animal models, causative can be demonstrated. brain particularly important maintaining health, strong neurodegenerative neurodevelopmental This suggests that microbiota composition used make early diagnosis diseases modifying microbiome-gut-brain axis might present therapeutic target for have proved intractable, aim altering trajectory such as Alzheimer's Parkinson's multiple sclerosis, autism spectrum disorder, attention-deficit hyperactivity among others. other potentially reversible migraine, post-operative cognitive dysfunction, long COVID, which considered models therapy disease. role traditional methods microbiome, well newer, more novel treatments faecal transplants photobiomodulation, are discussed.

Language: Английский

Citations

68
Host-microbe multi-omics and succinotype profiling have prognostic value for future relapse in patients with inflammatory bowel disease DOI Creative Commons

Janet O’Sullivan,

Shriram Patel, Gabriel E. Leventhal

et al.

Gut Microbes, Journal Year: 2025, Volume and Issue: 17(1)

Published: Jan. 15, 2025

Crohn's disease (CD) and ulcerative colitis (UC) are chronic relapsing inflammatory bowel disorders (IBD), the pathogenesis of which is uncertain but includes genetic susceptibility factors, immune-mediated tissue injury environmental influences, most appear to act via gut microbiome. We hypothesized that host-microbe alterations could be used prognostically stratify patients experiencing relapses up four years after endoscopy. therefore examined multiple omics data, including published new datasets, generated from paired inflamed non-inflamed mucosal biopsies 142 with IBD (54 CD; 88 UC) 34 control (non-diseased) biopsies. The relapse-predictive potential 16S rRNA gene transcript amplicons (standing active microbiota) were investigated along host transcriptomics, epigenomics genetics. While standard single-omics analysis not distinguish between who relapsed those remained in remission within colonoscopy, we did find an association number flares a patient's succinotype. Our multi-omics machine learning approach was also able predict relapse when combining features microbiome human host. Therefore multi-omics, rather than single omics, better predicts 4 while succinotype associated higher frequency relapses.

Language: Английский

Citations

2
Microbiota in Autism Spectrum Disorder: A Systematic Review DOI Open Access
Zuzanna Lewandowska, Magdalena Figlerowicz, Katarzyna Mazur‐Melewska

et al.

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(23), P. 16660 - 16660

Published: Nov. 23, 2023

Autism spectrum disorder (ASD) is a complex neurodevelopmental condition characterized by several core symptoms: restricted interests, communication difficulties, and impaired social interactions. Many ASD children experience gastrointestinal functional disorders, impacting their well-being. Emerging evidence suggests that gut microbiota imbalance may exacerbate symptoms. Our review assesses the in with interventions targeting modulation. The analysis of forty-four studies (meta-analyses, reviews, original research) reveals insights into microbiota-ASD relationship. While specific alterations are mixed, some trends emerge. exhibit increased Firmicutes (36-81%) Pseudomonadota (78%) decreased Bacteroidetes (56%). to ratio tends be lower (56%) compared without ASD, which correlates behavioral abnormalities. Probiotics, particularly Lactobacillus, Bifidobacterium, Streptococcus strains, show promise alleviating symptoms (66%). Microbiota transfer therapy (MTT) seems have lasting benefits for one longitudinal study. Prebiotics can potentially help issues, needing further research conclusive efficacy due different being used. This highlights interplay, offering potential therapeutic avenues gut-brain axis. However, study heterogeneity, small sample sizes, methodological variations emphasize need comprehensive, standardized research. Future investigations unveil mechanisms linking ultimately enhancing quality life affected individuals.

Language: Английский

Citations

25
Sex shapes gut–microbiota–brain communication and disease DOI Open Access
Kenton C. Hokanson,

Caroline Hernández,

Grace E. Deitzler

et al.

Trends in Microbiology, Journal Year: 2023, Volume and Issue: 32(2), P. 151 - 161

Published: Oct. 7, 2023

Language: Английский

Citations

23
Protective effects of fecal microbiota transplantation against ischemic stroke and other neurological disorders: an update DOI Creative Commons

Tousif Ahmed Hediyal,

Chandrasekaran Vichitra,

Nikhilesh Anand

et al.

Frontiers in Immunology, Journal Year: 2024, Volume and Issue: 15

Published: Feb. 21, 2024

The bidirectional communication between the gut and brain or gut-brain axis is regulated by several microbes microbial derived metabolites, such as short-chain fatty acids, trimethylamine N-oxide, lipopolysaccharides. Gut microbiota (GM) produce neuroactives, specifically neurotransmitters that modulates local central neuronal functions. An imbalance intestinal commensals pathobionts leads to a disruption in dysbiosis, which affects barrier integrity gut-immune neuroimmune systems. Currently, fecal transplantation (FMT) recommended for treatment of recurrent

Language: Английский

Citations

17
A robust microbiome signature for autism spectrum disorder across different studies using machine learning DOI Creative Commons
Lucía N. Peralta Marzal, David Rojas-Velázquez,

Douwe Rigters

et al.

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Jan. 8, 2024

Abstract Autism spectrum disorder (ASD) is a highly complex neurodevelopmental characterized by deficits in sociability and repetitive behaviour, however there great heterogeneity within other comorbidities that accompany ASD. Recently, gut microbiome has been pointed out as plausible contributing factor for ASD development individuals diagnosed with often suffer from intestinal problems show differentiated microbial composition. Nevertheless, studies rarely agree on the specific bacterial taxa involved this disorder. Regarding potential role of pathophysiology, our aim to investigate whether set relevant classification using sibling-controlled dataset. Additionally, we validate these results across two independent cohorts several confounding factors, such lifestyle, influence both studies. A machine learning approach, recursive ensemble feature selection (REFS), was applied 16S rRNA gene sequencing data 117 subjects (60 cases 57 siblings) identifying 26 discriminate controls. The average area under curve (AUC) bacteria dataset 81.6%. Moreover, selected tenfold cross-validation scheme (a total 223 samples—125 98 controls). We obtained AUCs 74.8% 74%, respectively. Analysis REFS identified can be used predict status children three distinct AUC over 80% best-performing classifiers. Our indicate strong association should not disregarded target therapeutic interventions. Furthermore, work contribute use proposed approach signatures datasets.

Language: Английский

Citations

16
Multikingdom and functional gut microbiota markers for autism spectrum disorder DOI
Qi Su, Oscar W.H. Wong,

Wenqi Lu

et al.

Nature Microbiology, Journal Year: 2024, Volume and Issue: 9(9), P. 2344 - 2355

Published: July 8, 2024

Language: Английский

Citations

12
Impact of the gut microbiome composition on social decision-making DOI Creative Commons

Marie Falkenstein,

Marie‐Christine Simon, Aakash Mantri

et al.

PNAS Nexus, Journal Year: 2024, Volume and Issue: 3(5)

Published: April 30, 2024

Abstract There is increasing evidence for the role of gut microbiome in regulation socio-affective behavior animals and clinical conditions. However, whether how composition may influence social decision-making health remains unknown. Here, we tested causal effects a 7-week synbiotic (vs. placebo) dietary intervention on altruistic punishment an ultimatum game. Results showed that increased participants’ willingness to forgo monetary payoff when treated unfairly. This change was related changes fasting-state serum levels dopamine-precursor tyrosine proposing potential mechanistic link along gut–microbiota–brain-behavior axis. These results improve our understanding bidirectional body–brain interactions play why humans at times act “irrationally” according standard economic theory.

Language: Английский

Citations

10
Potential similarities in gut microbiota composition between autism spectrum disorder and neurotypical siblings: Insights from a comprehensive meta-analysis DOI

Hongli Xiao,

Han Zhu,

Tong-Ao Zeng

et al.

Neuroscience, Journal Year: 2025, Volume and Issue: 567, P. 172 - 181

Published: Jan. 8, 2025

Language: Английский

Citations

1
Autism spectrum disorders and the gastrointestinal tract: insights into mechanisms and clinical relevance DOI
Lin Y. Hung, Kara Gross Margolis

Nature Reviews Gastroenterology & Hepatology, Journal Year: 2023, Volume and Issue: 21(3), P. 142 - 163

Published: Dec. 19, 2023

Language: Английский

Citations

23