A robust microbiome signature for autism spectrum disorder across different studies using machine learning

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

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Exploring Cereal Metagenomics: Unravelling Microbial Communities for Improved Food Security

Microorganisms, Journal Year: 2024, Volume and Issue: 12(3), P. 510 - 510

Published: March 2, 2024

Food security is an urgent global challenge, with cereals playing a crucial role in meeting the nutritional requirements of populations worldwide. In recent years, field metagenomics has emerged as powerful tool for studying microbial communities associated cereal crops and their impact on plant health growth. This chapter aims to provide comprehensive overview its enhancing food through exploration beneficial pathogenic interactions. Furthermore, we will examine how integration other tools can effectively address adverse effects security. For this purpose, discuss metagenomic data machine learning providing novel insights into dynamic interactions shaping plant-microbe relationships. We also shed light potential applications leveraging diversity epigenetic modifications improving crop resilience yield sustainability. Ultimately, revolutionized by harnessing between microbiota, paving way sustainable agricultural practices.

Language: Английский

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Methodology for biomarker discovery with reproducibility in microbiome data using machine learning

BMC Bioinformatics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Jan. 15, 2024

Abstract Background In recent years, human microbiome studies have received increasing attention as this field is considered a potential source for clinical applications. With the advancements in omics technologies and AI, research focused on discovery biomarkers using machine learning tools has produced positive outcomes. Despite promising results, several issues can still be found these such datasets with small number of samples, inconsistent lack uniform processing methodologies, other additional factors lead to reproducibility biomedical research. work, we propose methodology that combines DADA2 pipeline 16s rRNA sequences Recursive Ensemble Feature Selection (REFS) multiple increase obtain robust reliable results Results Three experiments were performed analyzing data from patients/cases Inflammatory Bowel Disease (IBD), Autism Spectrum Disorder (ASD), Type 2 Diabetes (T2D). each experiment, biomarker signature one dataset applied further validation. The effectiveness proposed was compared feature selection methods K-Best F-score random base line. Area Under Curve (AUC) employed measure diagnostic accuracy used metric comparing methods. Additionally, use Matthews Correlation Coefficient (MCC) evaluate performance well comparison Conclusions We developed reproducible sequence analysis, addressing related dimensionality, validation across independent datasets. findings three experiments, 9 different datasets, show achieved higher This first approach reproducibility, provide results.

Language: Английский

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Protective effects of Abrus cantoniensis Hance against liver injury through modulation of intestinal microbiota and liver metabolites

Ecotoxicology and Environmental Safety, Journal Year: 2024, Volume and Issue: 279, P. 116495 - 116495

Published: May 30, 2024

Abrus cantoniensis Hance (ACH) is an ancient Chinese medicine herb known for its therapeutic effects. This study investigated the potential protective effect of ACH against carbon tetrachloride (CCl

Language: Английский

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Environmental DNA and RNA in aquatic community ecology: Toward methodological standardization

Environmental DNA, Journal Year: 2023, Volume and Issue: 5(6), P. 1133 - 1147

Published: Sept. 28, 2023

Abstract Molecular technologies have facilitated the expansion of biodiversity assessments across a broad range organisms and aquatic systems. Environmental DNA (eDNA) environmental RNA (eRNA), collectively referred to as nucleic acids (eNAs), revolutionized monitoring due their noninvasive nature high‐resolution capabilities when compared traditional survey methods. While eNA applications grown exponentially over past decade, methodological inconsistencies hinder reproducibility comparability. To assess current state methodologies in ecology, we conducted systematic review 300 peer‐reviewed studies that ecological communities diverse Of these papers, 291 examine eDNA, four eRNA, five consider both eDNA eRNA. The small number eRNA highlights field is its infancy. looked at, found clear geographic bias, with approximately 50% all occurring six high‐income countries, while less than 10% occur South America Africa. Further, report lack standardization studies, showing high variability water filtration volume, filter material, pore size, extraction method, marker choice, bioinformatic pipelines. We further highlight incomplete reference sequence databases for limit taxonomic assignment inferences. Finally, identify issue community ecology: missing details, which compromise reproducibility, especially newly emerging applications. facilitate systems permit integration monitoring, recommend improvement alongside guidelines encourage transparency.

Language: Английский

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Host genotype, soil composition, and geo-climatic factors shape the fonio seed microbiome

Microbiome, Journal Year: 2024, Volume and Issue: 12(1)

Published: Jan. 17, 2024

Fonio (Digitaria exilis), an orphan millet crop, is the oldest indigenous crop in West Africa. Although yield low due to pre-domestication characteristics, quick maturation time, drought tolerance, and ability thrive on poor soils make fonio a climate-smart crop. Being holobionts, plants evolve close interaction with microbial partners, which crucial for plant phenology fitness. As seeds are bottleneck of vertically transmitting microbiota, we proposed unravel seed microbiome under-domesticated resilient fonio. Our study investigated bacterial endophyte diversity across 126 sequenced accessions from distinct locations We conducted correlation structures functions seed-associated microbiomes native geo-climate soil structure data. also performed Genome-wide association studies (GWAS) identify genetic loci associated diversity.

Language: Английский

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Large scale exploration reveals rare taxa crucially shape microbial assembly in alkaline lake sediments

npj Biofilms and Microbiomes, Journal Year: 2024, Volume and Issue: 10(1)

Published: July 28, 2024

Abstract Alkaline lakes are extreme environments inhabited by diverse microbial extremophiles. However, large-scale distribution patterns, environmental adaptations, community assembly, and evolutionary dynamics of communities remain largely underexplored. This study investigated the characteristics on rare abundant taxa in alkaline lake sediments west northwest China. We observed that varied significantly with geographical distance, while remained unaffected regional differences. The assembly process was influenced dispersal limitation, whilst were predominantly driven heterogeneous selection. Network analysis indicated as core species for interactions stability. Rare exhibited higher speciation transition rate than taxa, serving a genetic reservoir potential candidates to become abundance highlighting their crucial role maintaining diversity. These insights underscore significant influence ecosystem biodiversity stability lakes.

Language: Английский

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ASV vs OTUs clustering: Effects on alpha, beta, and gamma diversities in microbiome metabarcoding studies

PLoS ONE, Journal Year: 2024, Volume and Issue: 19(10), P. e0309065 - e0309065

Published: Oct. 3, 2024

In microbial community sequencing, involving bacterial ribosomal 16S rDNA or fungal ITS, the targeted genes are basis for taxonomical assignment. The traditional bioinformatical procedure has decades made use of a clustering protocol by which sequences pooled into packages shared percent identity, typically at 97%, to yield Operational Technical Units (OTUs). Progress in data processing methods however led possibility minimizing technical sequencers errors, were main reason OTU choice, and analyze instead exact Amplicon Sequence Variants (ASV) is choice yielding much less agglomerated reads. We have tested two procedures on same metabarcoded amplicons dataset encompassing series samples from 17 adjacent habitats, taken across 700 meter-long transect different ecological conditions unfolding gradient spanning cropland, through meadows, forest all successional transitions up seashore, within coastal area. This design allowed scan high biodiversity basin measure alpha, beta gamma diversity area, verify effect bioinformatics as concerns values ten indexes other parameters. Two levels progressive OTUs clustering, (99% 97%) compared with ASV data. results showed that proportionally marked underestimation indicators species distorted behaviour dominance evenness respect direct Multivariate ordination analyses resulted also sensitive terms tree topology coherence. Overall, support view reference-based carries several misleading disadvantageous biases, including risk missing novel taxa yet unreferenced databases. Since its alternatives de novo hand drawbacks due heavier computational demand comparability, especially environmental studies contain uncharacterized species, based analysis, least prokaryotes, appears warrant significand advantages comparison every level identity cutoff.

Language: Английский

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A retrospective study on blood microbiota as a marker for cognitive decline: implications for detecting Alzheimer’s disease and amnestic mild cognitive impairment in Republic of Korea

Osong Public Health and Research Perspectives, Journal Year: 2025, Volume and Issue: unknown

Published: March 24, 2025

This study aimed to investigate the relationship between blood microbiota, specifically bacterial DNA, and cognitive decline in individuals with subjective (SCD) amnestic mild impairment (aMCI). The objective was identify potential microbial signatures that could serve as biomarkers for deterioration. Forty-seven participants were recruited, including 13 aMCI, 20 SCD, 14 normal cognition (NC). Blood samples collected, DNA analyzed using 16S rRNA sequencing on Illumina MiSeq platform. Bioinformatics analyses-including α- β-diversity measures differential abundance testing (using edgeR)-were employed assess diversity differences composition among groups. Logistic regression models used evaluate predictive impact of microbiota decline. Microbial differed significantly groups, NC exhibiting highest α-diversity. Both aMCI SCD groups showed reduced diversity. Taxa such Bacteroidia, Alphaproteobacteria, Clostridia decreased group compared (p<0.05). In contrast, Gammaproteobacteria increased both indicating progressive changes from aMCI. No significant found Distinct taxa-particularly increase along decreases Clostridia-are associated progression These findings suggest early detection However, small sample size lack control confounding factors diet medication limit findings. Larger studies are needed validate these results further explore role neurodegeneration.

Language: Английский

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Enriching electroactive microorganisms from ferruginous lake waters – Mind the sulfate reducers!

Bioelectrochemistry, Journal Year: 2024, Volume and Issue: 157, P. 108661 - 108661

Published: Feb. 1, 2024

Electroactive microorganisms are pivotal players in mineral transformation within redox interfaces characterized by pronounced oxygen and dissolved metal gradients. Yet, their systematic cultivation from such environments remains elusive. Here, we conducted an anodic enrichment using anoxic ferruginous waters a post-mining lake as inoculum. Weak electrogenicity (j = ∼5 µA cm−2) depended on electroactive planktonic cells rather than biofilms, with preference for formate electron donor. Addition of yeast extract decreased the lag phase but did not increase current densities. The enriched bacterial community varied depending substrate composition mainly comprised sulfate- nitrate-reducing bacteria (e.g., Desulfatomaculum spp. Stenotrophomonas spp.). A secondary strategy resulted different communities composed iron-reducing Klebsiella spp.) fermentative Paeniclostridium Secondary microscopy energy-dispersive X-ray spectroscopy results indicate precipitation sulfur- iron-rich organomineral aggregates at anode surface, presumably impeding production. Our findings that (i) containing geogenically derived metals can be used to enrich weak electricigens, (ii) it is necessary either specifically inhibit sulfate reducers. Otherwise, reducers tend dominate over EAM during cultivation, which lead passivation due biomineralization.

Language: Английский

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