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

Nature Methods, Год журнала: 2023, Номер 20(9), С. 1368 - 1378

Опубликована: Авг. 3, 2023

Язык: 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, Год журнала: 2023, Номер 38(5), С. 347 - 399

Опубликована: Окт. 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.

Язык: Английский

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

Trends in Genetics, Год журнала: 2023, Номер 39(9), С. 686 - 702

Опубликована: Июнь 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.

Язык: Английский

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

Gut Microbes, Год журнала: 2024, Номер 16(1)

Опубликована: Янв. 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.

Язык: 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, Год журнала: 2025, Номер 13, С. 1180 - 1180

Опубликована: Янв. 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.

Язык: Английский

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Microbial fuel cells to monitor natural attenuation around groundwater plumes

Environmental Science and Pollution Research, Год журнала: 2025, Номер unknown

Опубликована: Янв. 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.

Язык: Английский

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Cefazolin shifts the kidney microbiota to promote a lithogenic environment

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Дек. 11, 2024

Clinical studies of the urinary tract microbiome, termed urobiome, suggest a direct, antibiotic-dependent, impact urobiome on kidney physiology. However, evidence for bacteria comes from indirect sources or infected tissue. Further, it is unclear how antibiotics bacteria. Here we show direct presence in kidneys, with microniches nephrons. In murine administration cefazolin, commonly used perioperative antibiotic, led to loss uroprotective Lactobacillus spp. and proliferation Enterobacteriaceae (which includes many known uropathogens). This effect was dependent treatment duration, recovery post treatment. Uroprotective L. crispatus strain stone-associated E. coli differentially influenced calcium oxalate (CaOx) crystallization through incorporation CaOx inhibitors promoters, respectively. humans, microbial signatures were identified kidney, unique niches between glomeruli tubules, established RNA sequencing analysis imaging two independent populations. Collectively, findings support hypothesis that kidneys harbor stable antibiotic-responsive microbiota can influence lithogenesis. The unique, age-dependent tubuli carry implications non-infectious diseases.

Язык: Английский

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Comprehensive evaluation of methods for differential expression analysis of metatranscriptomics data

Briefings in Bioinformatics, Год журнала: 2023, Номер 24(5)

Опубликована: Авг. 9, 2023

Abstract Understanding the function of human microbiome is important but development statistical methods specifically for microbial gene expression (i.e. metatranscriptomics) in its infancy. Many currently employed differential analysis have been designed different data types and not evaluated metatranscriptomics settings. To address this gap, we undertook a comprehensive evaluation benchmarking 10 data. We used combination real simulated to evaluate performance type I error, false discovery rate sensitivity) following methods: log-normal (LN), logistic-beta (LB), MAST, DESeq2, metagenomeSeq, ANCOM-BC, LEfSe, ALDEx2, Kruskal–Wallis two-part Kruskal–Wallis. The simulation was informed by supragingival biofilm from 300 preschool-age children enrolled study childhood dental disease (early caries, ECC), whereas validations were sought two additional datasets ECC an inflammatory bowel study. LB test showed highest sensitivity both small large samples reasonably controlled error. Contrarily, MAST hampered inflated Upon application LN tests study, found that genes C8PHV7 C8PEV7, harbored lactate-producing Campylobacter gracilis, had strongest association with disease. This model offers practical guidance selection appropriate rigorous analyses metatranscriptomics. Selection optimal method increases possibility detecting true signals while minimizing chance claiming ones.

Язык: 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, Год журнала: 2025, Номер 5(1)

Опубликована: Янв. 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

Язык: Английский

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

Global Ecology and Conservation, Год журнала: 2025, Номер unknown, С. e03487 - e03487

Опубликована: Фев. 1, 2025

Язык: Английский

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