Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics

Nature Methods, Journal Year: 2023, Volume and Issue: 20(9), P. 1368 - 1378

Published: Aug. 3, 2023

Language: Английский

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Critical review of 16S rRNA gene sequencing workflow in microbiome studies: From primer selection to advanced data analysis

Molecular Oral Microbiology, Journal Year: 2023, Volume and Issue: 38(5), P. 347 - 399

Published: Oct. 1, 2023

Abstract The multi‐batch reanalysis approach of jointly reevaluating gene/genome sequences from different works has gained particular relevance in the literature recent years. large amount 16S ribosomal ribonucleic acid (rRNA) gene sequence data stored public repositories and information taxonomic databases same far exceeds that related to complete genomes. This review is intended guide researchers new studying microbiota, particularly oral using rRNA sequencing those who want expand update their knowledge optimise decision‐making improve research results. First, we describe advantages disadvantages as a phylogenetic marker latest findings on impact primer pair selection diversity assignment outcomes microbiome studies. Strategies for based these results are introduced. Second, identified key factors consider selecting technology platform. process particularities main steps processing gene‐derived described detail enable choose most appropriate bioinformatics pipeline analysis methods available evidence. We then produce an overview types advanced analyses, both widely used approaches. Several indices, metrics software microbial communities included, highlighting disadvantages. Considering principles clinical metagenomics, conclude future should focus rigorous analytical approaches, such developing predictive models identify microbiome‐based biomarkers classify health disease states. Finally, address batch effect concept microbiome‐specific accounting or correcting them.

Language: Английский

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Current concepts, advances, and challenges in deciphering the human microbiota with metatranscriptomics

Trends in Genetics, Journal Year: 2023, Volume and Issue: 39(9), P. 686 - 702

Published: June 25, 2023

Metatranscriptomics refers to the analysis of collective microbial transcriptome a sample. Its increased utilization for characterization human-associated communities has enabled discovery many disease-state related activities. Here, we review principles metatranscriptomics-based samples. We describe strengths and weaknesses popular sample preparation, sequencing, bioinformatics approaches summarize strategies their use. then discuss how have recently been examined may change. conclude that metatranscriptomics insights into human microbiotas under health disease not only expanded our knowledge on health, but also opened avenues rational antimicrobial drug use management.

Language: Английский

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Daily skin-to-skin contact alters microbiota development in healthy full-term infants

Gut Microbes, Journal Year: 2024, Volume and Issue: 16(1)

Published: Jan. 10, 2024

The gut microbiota is vital for human body development and function. Its in early life influenced by various environmental factors. In this randomized controlled trial, the was obtained as a secondary outcome measure study on effects of one hour daily skin-to-skin contact (SSC) five weeks healthy full-term infants. Specifically, we studied alpha/beta diversity, volatility, maturation, bacterial gut-brain-axis-related functional abundances assessed thrice first year. Pregnant Dutch women (n = 116) were randomly assigned to SSC or care-as-usual groups. group participants engaged from birth age. Stool samples collected at two, five, 52 V4 region sequenced. We observed significant differences composition, abundances, predicted pathways between exhibited lower volatility during infancy. Microbiota maturation slower year our results suggested that breastfeeding duration may have partially mediated relation. Our findings provide evidence postpartum influence development. Replication necessary validate generalize these results. Future studies should include direct stress measurements extend sampling beyond investigate mechanism research SSC's impact long-term trajectories.

Language: Английский

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Microbial fuel cells to monitor natural attenuation around groundwater plumes

Environmental Science and Pollution Research, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 4, 2025

Abstract This research presents a straightforward and economically efficient design for microbial fuel cell (MFC) that can be conveniently integrated into borehole to monitor natural attenuation in groundwater. The employs conventional, transparent, reusable PVC bailers with graphite tape granular activated carbon create high surface area electrodes. These electrodes are connected across redox environments nested boreholes through wire variable resistor setup. amended were installed pre-existing surrounding groundwater plume near former gasworks facility. Among all the MFC locations tested, at fringe exhibited highest electrical response displayed significant variations differential abundance of key bacterial archaeal taxa between anode cathode other configurations center uncontaminated showed little no response, suggesting minimal activity. approach enables informed decision-making regarding effectively monitoring, enhancing, or designing degradation strategies plumes. It offers valuable tool understanding managing contaminant such environments.

Language: Английский

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Computational Study Protocol: Leveraging Synthetic Data to Validate a Benchmark Study for Differential Abundance Tests for 16S Microbiome Sequencing Data

F1000Research, Journal Year: 2025, Volume and Issue: 13, P. 1180 - 1180

Published: Jan. 2, 2025

Background Synthetic data’s utility in benchmark studies depends on its ability to closely mimic real-world conditions and reproduce results obtained from experimental data. Building Nearing et al.’s study (1), who assessed 14 differential abundance tests using 38 16S rRNA datasets a case-control design, we are generating synthetic that the data verify their findings. We will employ statistical rigorously assess similarity between validate conclusions performance of these drawn by al. (1). This protocol adheres SPIRIT guidelines, demonstrating how established reporting frameworks can support robust, transparent, unbiased planning. Methods replicate (1) methodology, incorporating simulated two distinct tools, mirroring datasets. Equivalence be conducted non-redundant subset 46 characteristics comparing data, complemented principal component analysis for overall assessment. The applied datasets, evaluating consistency significant feature identification number features per tool. Correlation multiple regression explore differences may affect results. Conclusions enables validation findings through controlled experiments. well replicates try previous with most recent versions DA methods delineate strengths limitations studies. Moreover, our knowledge this is first computational systematically incorporate validating while strictly adhering pre-specified following contributing transparency, reproducibility, research.

Language: Английский

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Metagenomic analyses of gut microbiome composition and function with age in a wild bird; little change, except increased transposase gene abundance

ISME Communications, Journal Year: 2025, Volume and Issue: 5(1)

Published: Jan. 1, 2025

Abstract Studies on wild animals, mostly undertaken using 16S metabarcoding, have yielded ambiguous evidence regarding changes in the gut microbiome (GM) with age and senescence. Furthermore, variation GM function has rarely been studied such populations, despite metabolic characteristics potentially being associated host senescent declines. Here, we used 7 years of repeated sampling individuals shotgun metagenomic sequencing to investigate taxonomic functional Seychelles warblers (Acrocephalus sechellensis) age. Our results suggest that species richness declines terminal year, this decline occurring consistently across all ages. Taxonomic composition also shifted However, identified occurred linearly (or even mainly during early prior onset senescence species) little accelerated change later life or their year. Therefore, are not linked Interestingly, found a significant increase abundance group transposase genes age, which may accumulate passively due increased transposition induced as result stressors arise These findings reveal but senescence, vertebrate provide blueprint for future studies

Language: Английский

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Restoration plantations accelerate recovery of fungal communities from dead woody debris in southern Costa Rica

Global Ecology and Conservation, Journal Year: 2025, Volume and Issue: unknown, P. e03487 - e03487

Published: Feb. 1, 2025

Language: Английский

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CircoTax: a novel circular representation of differentially abundant microbial ranks

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

Published: Feb. 17, 2025

One of the most relevant and widely used applications NGS-based microbial abundance analysis is discovery taxa that appear as differentially represented between ecological niches. In last 10 years several methods have been proposed to accomplish this task. All such analyses invariantly report at appropriate taxonomic rank well a p-value (usually adjusted for multiple testing) fold change, representing confidence on differential call amount variation recorded, usually in log scale, respectively. This work describes CircoTax, an R function implementing specialized ggplot2 graph represent rank-aware collection abundant intuitive compact radial form. Specifically, CircoTax builds circular plot with sectors encoding taxonomy depth (from kingdom genus) and, departing from center, number bars reach sector whose color transparency are proportional change intensity direction. addition manageability providing custom tables plot, our implementation also integrates fast user-friendly ancillary functions which automate both display results while leaving user choice further customizations. The visualization graphically appealing, allowing accommodate tens ranks, biologically informative since variation, direction easily intelligible each glance.

Language: Английский

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Network based differential abundance analysis: bridging community interactions and host microbiome dynamics

Network Modeling Analysis in Health Informatics and Bioinformatics, Journal Year: 2025, Volume and Issue: 14(1)

Published: Feb. 24, 2025

Language: Английский

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