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Human stool sample

ABSTRACT: 16S amplicon data for pediatric ASD patients receiving probiotic intervention with VISBIOME

PROVIDER: PRJNA941891 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR23871900_1.fastq.gz	Fastqsanger.gz
	SRR23871900_2.fastq.gz	Fastqsanger.gz
	SRR23871901_1.fastq.gz	Fastqsanger.gz
	SRR23871901_2.fastq.gz	Fastqsanger.gz
	SRR23871902_1.fastq.gz	Fastqsanger.gz

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16S rRNA sequencing analysis of bacteiral community composition in antibiotic-treated mouse fecal sample

Project description:Purpose: This study aims to compare and analyze the differences in bacterial community composition in fecal samples from mice treated with Control(DW), Vancomycin (VAN), Ampicillin (AMP), Neomycin (NEO), Metronidazole (MET), and a combination of all antibiotics (ALL, VANM) using 16S rRNA sequencing. Methods: Each antibiotics treated mice's fecal samples were collected and stored -80'c until analyzation. DNA was extracted using the NucleoSpin DNA Stool Kit (MACHEREY-NAGEL) following the manufacturer’s protocol. Metagenomic sequencing was performed on an Illumina MiSeq platform (Illumina), targeting the V3 and V4 regions of the 16S rRNA gene according to the manufacturer's instructions. PCR products were purified using AMPure XP beads, and sequencing adapters were added using the Nextera XT Index Kit (Illumina). The library was further purified with AMPure XP beads and quantified using automated electrophoresis with the TapeStation System (Agilent). Sequencing was performed using the MiSeq v3 reagent kit (Illumina), following the manufacturer’s protocol. Results: QIIME2 (v2023.02) was used to process and analyze 16S rRNA gene amplicon sequencing data, from sequence preprocessing to taxonomic classification. Paired-end sequences were merged and quality-filtered using Deblur. The resulting amplicon sequence variants (ASVs) were used for downstream analyses. Conclusions: Our study presents a comparative analysis of bacterial community composition in fecal samples from antibiotic-treated mice. We observed that microbiota composition varied distinctly depending on the type of antibiotic administered.

2026-01-28 | GSE291841 | GEO

Stool Sample

Project description:Gut Mycobiome from Healthy Individuals, and patients with bacterial keratitis, fungal keratitis and uveitis

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16S profile of stool from conventional unifected and C.rodentium infected mice

Project description:We aim to determine if mice in our mouse colony had similar of different microbiomes. To do this, we perfromed 16S sequencing of stool from unifected mice of the gentotypes listed below. We also looked at how infection causes dysbiosis of the mircobiome, measuring 16S sequencing over a C.rodentium infection timecourse.

2018-07-03 | GSE116491 | GEO

The anti-Shine-Dalgarno element of 16S rRNA is needed for translation of one gene, rpsU, in Flavobacterium johnsoniae

Project description:Bacteroidia ribosomes are “blind” to SD sequences, even though they contain the conserved anti-SD (ASD) element of 16S rRNA. A structure of the Flavobacterium johnsoniae ribosome shows that the 3’ tail of 16S rRNA is sequestered in a pocket formed by bS21, bS18, and bS6 on the 30S platform, explaining the basis of ASD inhibition. Interestingly, there is one gene of F. johnsoniae with a strong SD sequence—rpsU, which encodes bS21. F. johnsoniae ribosomes lacking bS21 exhibit a liberated ASD and translate rpsU at a higher rate, which sets up an autoregulatory cycle. Here, we targeted the ASD of each 16S rRNA gene in F. johnsoniae, ablating the core element (CCUCC to GAAGC). Consecutive replacement of each 16S gene with this quadruple-substituted (QS) allele had little effect on cell growth until the last gene was changed. The final strain, containing QS ribosomes only, grows very slowly. This growth defect can be largely rescued by replacing the native translation initiation region (TIR) with the SD-less TIR of tuf. Purified QS ribosomes are unable to translate native rpsU mRNA but are active on other mRNAs. We also selected suppressors of the ASD-ablated strain, many of which carried a single mutation in the SD of rpsU. Interestingly, wild-type ribosomes fail to initiate on these variant rpsU mRNAs, demonstrating that an extended SD-ASD duplex is normally needed for initiation on this message. These findings indicate that the main purpose of the ASD in F. johnsoniae is to facilitate translation of one gene, rpsU.

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Experimental tests strongly challenge the evidence of a healthy human blood microbiome

Project description:The study critically evaluate the results of 16S targeted amplicon sequencing performed on the total DNA collected from healthy donors’ blood samples in the light of specific negative controls.

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