RFW captures species-level metagenomic functions by integrating genome annotation information DOI Creative Commons
Kai Mi, Rui Xu, Xingyin Liu

et al.

Cell Reports Methods, Journal Year: 2024, Volume and Issue: unknown, P. 100932 - 100932

Published: Dec. 1, 2024

MotivationMetagenomic functional profiling has emerged as an indispensable tool for elucidating microbiome activities. Through our investigations, we observed that the number of microbial functions reported by current metagenomic methods increases with sequencing depth at both taxon and community levels. This observation was further substantiated resampling ultra-deep data. These findings suggest analyzing makeup communities based on whole-metagenome shotgun (WMS) miss a significant amount information. To address this, developed framework called RFW (reference-based profile inference WMS) utilizes genome function annotation taxonomic data to infer more complete picture function.Highlights•Functional metagenome exhibits information loss•RFW improves profiles through integration•DFSCA-BC algorithm identifies absolute abundance changes in functions•RFW advances understanding microbe-host phenotype connectionsSummaryFunctional enables interactions. We demonstrate loss levels, particularly lower read depths. loss, develop framework, WMS), from annotations abundances WMS. Furthermore, provide change quantification between groups part framework. By applying several datasets related autism spectrum disorder colorectal cancer, show augments downstream analyses, such differential identification association analysis host phenotype. is open source freely available https://github.com/Xingyinliu-Lab/RFW.Graphical abstract

Language: Английский

Turicibacter and Catenibacterium as potential biomarkers in autism spectrum disorders DOI Creative Commons
Perla Gerges, Dhinoth Bangarusamy, Tania Bitar

et al.

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

Published: Oct. 5, 2024

Autism spectrum disorders (ASD) are neurodevelopmental characterized by social, behavioral, and cognitive impairments. Several comorbidities, including gastrointestinal (GI) dysregulations, frequently reported in ASD children. Although studies animals have shown the crucial role of microbiota key aspects neurodevelopment, there is currently no consensus on how alteration microbial composition affects pathogenesis ASD. Moreover, disruption gut–brain axis (GBA) has been although with limited conducted Mediterranean population. In our study, we aimed to investigate gut Lebanese subjects, their unaffected siblings, a control group from various regions Lebanon using 16 S-rRNA sequencing (NGS). Our study revealed lower abundance Turicibacter significant enrichment Proteobacteria siblings' groups compared controls, indicating that probably affected dietary habits, living conditions together host genetic factors. The also showed evidence changes microbiome children siblings unrelated control. Bacteroidetes controls conversely, Catenibacterium Tenericutes an increased group. Notably, identifies alterations suggesting possible link between these bacterial taxa contributing growing body linking

Language: Английский

Citations

4
The Role of Gut Microbiota in Modulating Brain Structure and Psychiatric Disorders: A Mendelian Randomization Study DOI Creative Commons
Ye Zheng, Yingying Gao, Jiaqi Yuan

et al.

NeuroImage, Journal Year: 2025, Volume and Issue: unknown, P. 121292 - 121292

Published: May 1, 2025

Language: Английский

Citations

0
Harnessing the Gut Microbiome: To What Extent Can Pre-/Probiotics Alleviate Immune Activation in Autism Spectrum Disorder? DOI Open Access
Yuqi Wu, Qi Su

Nutrients, Journal Year: 2024, Volume and Issue: 16(15), P. 2382 - 2382

Published: July 23, 2024

Children diagnosed with autism spectrum disorder (ASD) are at an increased risk of experiencing gastrointestinal (GI) discomfort, which has been linked to dysfunctions in the microbiome–gut–brain axis. The bidirectional communication between gut and brain plays a crucial role overall health individuals, alterations microbiome can contribute immune activation gut–brain dysfunction ASD. Despite limited controversial results pre-/probiotic applications ASD, this review comprehensively maps association ASD clinical symptoms specific bacterial taxa evaluates efficacy pre-/probiotics modulating microbiota composition, reducing inflammatory biomarkers, alleviating difficulties GI distress, sleep problems, core other ASD-associated symptoms, as well relieving parental concerns, separately, individuals Beyond simply targeting highlights potential supplementations strategy modulate homeostasis response, delineate mechanisms by its direct or mediating effects alleviate poor nutritional status management. Further well-designed randomized controlled trials needed strengthen existing evidence establish optimal protocols for use context

Language: Английский

Citations

3
Lacticaseibacillus rhamnosus GR-1 prevents autism-like behaviors by reshaping the maternal and offspring microbiome DOI Creative Commons
Ruili Yang,

Jinchun Xu,

Yi Xu

et al.

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 7, 2025

Abstract As a prevalent neurodevelopmental disease, whether ASD (autism spectrum disorder) can be ameliorated by the early use of single microbe remains unknown. Here we report that Lacticaseibacillus rhamnosus GR-1 (LGR-1) prevented occurrence autism-like behaviors when administered exclusively to pregnant mice, as evidenced improved and restored E/I balance in prefrontal cortex male pups. In parallel, offspring microbiome was reshaped LGR-1 treatment, mediated vertical transmission maternal microbiome, with its roles validated microbiota transplant cross-fostering. addition gut commensals, LGR-1-shaping vaginal also contributed establishment “beneficial” microbiome. Regarding key taxa offspring, Akkermansia muciniphila influenced exerted effect on ensuing behavior, through modulating immune pathways related IL-17-producing cell population. conclusion, applied in utero protects from via transmission, shedding light microbe-based avenue mitigate risk ASD.

Language: Английский

Citations

0
RFW captures species-level full profile of metagenomic functions via integrating genome annotation information DOI Creative Commons

Kai Mi,

Xingyin Liu

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 19, 2024

Abstract Functional profiling on whole-metagenome shotgun sequencing (WMS) has made great contribution to the development of our understanding in microbe-host interactions. In this work, we revealed that severe microbial functional information loss current methods existed at both taxon-level and community-level. To correct distortion brought by incompleteness, developed a new framework, RFW (Reference based profile inference WMS), infer abundance WMS through utilizing from genome function annotation taxonomic profile. Furthermore, built up algorithm for absolute change quantification between groups under framework. By applying several datasets related autism spectrum disorder colorectal cancer, greatly renewed knowledge downstream analysis, including differential identification, association analysis host phenotype, etc. are open-source freely available https://github.com/Xingyinliu-Lab/RFW .

Language: Английский

Citations

0
Maternal immune activation and neuropsychiatric disease in offspring: Pathogen's perspective DOI Creative Commons

Zhiyang Yin,

Catherine Gordon,

Zikai Zhou

et al.

Decoding Infection and Transmission, Journal Year: 2024, Volume and Issue: 2, P. 100029 - 100029

Published: Jan. 1, 2024

Language: Английский

Citations

0
RFW captures species-level metagenomic functions by integrating genome annotation information DOI Creative Commons
Kai Mi, Rui Xu, Xingyin Liu

et al.

Cell Reports Methods, Journal Year: 2024, Volume and Issue: unknown, P. 100932 - 100932

Published: Dec. 1, 2024

MotivationMetagenomic functional profiling has emerged as an indispensable tool for elucidating microbiome activities. Through our investigations, we observed that the number of microbial functions reported by current metagenomic methods increases with sequencing depth at both taxon and community levels. This observation was further substantiated resampling ultra-deep data. These findings suggest analyzing makeup communities based on whole-metagenome shotgun (WMS) miss a significant amount information. To address this, developed framework called RFW (reference-based profile inference WMS) utilizes genome function annotation taxonomic data to infer more complete picture function.Highlights•Functional metagenome exhibits information loss•RFW improves profiles through integration•DFSCA-BC algorithm identifies absolute abundance changes in functions•RFW advances understanding microbe-host phenotype connectionsSummaryFunctional enables interactions. We demonstrate loss levels, particularly lower read depths. loss, develop framework, WMS), from annotations abundances WMS. Furthermore, provide change quantification between groups part framework. By applying several datasets related autism spectrum disorder colorectal cancer, show augments downstream analyses, such differential identification association analysis host phenotype. is open source freely available https://github.com/Xingyinliu-Lab/RFW.Graphical abstract

Language: Английский

Citations

0