Snaq: A Dynamic Snakemake Pipeline for Microbiome Data Analysis With QIIME2

Mohsen, Attayeb; Chen, Yi‐An; Osorio, Rodolfo S. Allendes; Higuchi, Chihiro; Mizuguchi, Kenji

doi:10.3389/fbinf.2022.893933

Cited by 3 publications

(2 citation statements)

References 27 publications

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“…The analysis was done using Snaq 82 , a snakemake pipeline for 16S data analysis with QIIME2. Briefly, quality trimming was done using bbduk (BBTools) with a quality threshold of 20.…”

Section: Methodsmentioning

confidence: 99%

Comparison of DNA extraction methods for 16S rRNA gene sequencing in the analysis of the human gut microbiome

Elie

Perret

Hage

et al. 2023

Sci Rep

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The gut microbiome is widely analyzed using high-throughput sequencing, such as 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing (SMS). DNA extraction is known to have a large impact on the metagenomic analyses. The aim of this study was to compare DNA extraction protocols for 16S sequencing. In that context, four commonly used DNA extraction methods were compared for the analysis of the gut microbiota. Commercial versions were evaluated against modified protocols using a stool preprocessing device (SPD, bioMérieux) upstream DNA extraction. Stool samples from nine healthy volunteers and nine patients with a Clostridium difficile infection were extracted with all protocols and 16S sequenced. Protocols were ranked using wet- and dry-lab criteria, including quality controls of the extracted genomic DNA, alpha-diversity, accuracy using a mock community of known composition and repeatability across technical replicates. SPD improved overall efficiency of three of the four tested protocols compared with their commercial version, in terms of DNA extraction yield, sample alpha-diversity, and recovery of Gram-positive bacteria. The best overall performance was obtained for the S-DQ protocol, SPD combined with the DNeasy PowerLyser PowerSoil protocol from QIAGEN. Based on this evaluation, we strongly believe that the use of such stool preprocessing device improves both the standardization and the quality of the DNA extraction in the human gut microbiome studies.

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“…The analysis was done using Snaq 82 , a snakemake pipeline for 16S data analysis with QIIME2. Briefly, quality trimming was done using bbduk (BBTools) with a quality threshold of 20.…”

Section: Methodsmentioning

confidence: 99%

Comparison of DNA extraction methods for 16S rRNA gene sequencing in the analysis of the human gut microbiome

Elie

Perret

Hage

et al. 2023

Sci Rep

View full text Add to dashboard Cite

show abstract

“…All bioinformatics analyses from quality trimming of reads to diversity analysis were automatically performed using Snaq (Mohsen et al, 2022), a snakemake pipeline for 16S microbiome data analysis with QIIME 2 (Bolyen et al, 2019). In this pipeline, the Frontiers in Physiology frontiersin.org DADA2 algorithm (Callahan et al, 2016) was used to infer amplicon sequence variants (ASVs), which were taxonomically classified using the SILVA 128 reference database (Quast et al, 2013) from the phylum to genus level.…”

Section: Bioinformatics Analysis Of Microbiomementioning

confidence: 99%

Voluntary exercise does not increase gastrointestinal motility but increases spatial memory, intestinal eNOS, Akt levels, and Bifidobacteria abundance in the microbiome

Bakonyi,

Kolonics,

Aczel

et al. 2023

Front. Physiol.

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The interaction between the gut and brain is a great puzzle since it is mediated by very complex mechanisms. Therefore, the possible interactions of the brain–exercise–intestine–microbiome axis were investigated in a control (C, N = 6) and voluntarily exercised (VE, N = 8) middle-aged rats. The endurance capacity was assessed by VO2max on the treadmill, spatial memory by the Morris maze test, gastrointestinal motility by EMG, the microbiome by 16S RNA gene amplicon sequencing, caveolae by electron microscopy, and biochemical assays were used to measure protein levels and production of reactive oxygen species (ROS). Eight weeks of voluntary running increased VO2max, and spatial memory was assessed by the Morris maze test but did not significantly change the motility of the gastrointestinal tract or production of ROS in the intestine. The protein kinase B (Akt) and endothelial nitric oxide synthase (eNOS) protein levels significantly increased in the intestine, while peroxisome proliferator–activated receptor gamma coactivator 1 alpha (PGC-1α), mitochondrial transcription factor A (TFAM), nuclear respiratory factor 1 (NFR1), SIRT1, SIRT3, nicotinamide phosphoribosyl transferase (NAMPT), and nuclear factor κB (NF-κB) did not change. On the other hand, voluntary exercise increased the number of caveolae in the smooth muscles of the intestine and relative abundance of Bifidobacteria in the microbiome, which correlated with the Akt levels in the intestine. Voluntary exercise has systemic effects and the relationship between intestinal Akt and the microbiome of the gastrointestinal tract could be an important adaptive response.

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Impact of weight variation on the microbiome of yak dams and calves

Wang,

Basang,

Pingcuo

et al. 2024

Front. Microbiol.

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IntroductionLimited information exists regarding the microbiome composition of yak calves of varying weights. Therefore, this study aimed to investigate the microbiomes of mother-calf pairs with different weight profiles.MethodsFecal and blood samples were collected from both lower-weight (CB) and higher-weight (HB) yak calves, along with their corresponding female yaks (CA, HA).ResultsThe results revealed significantly higher levels of T-AOC (total antioxidant capacity) and GSH-Px (glutathione peroxidase) in HB animals (p < 0.001). Sequencing yielded 652,181 and 643,369 filtered reads in female and calf yaks, respectively. Alpha diversity analysis indicated that Chao1, Faith_pd, and Observed species were significantly higher in CA compared to HA (p < 0.01). Furthermore, nine genera were notably different between HA and CA yaks, including Avispirillum, Fimenecus, CAG-1031, Odoribacter 865974, and Jeotgalicoccus A 310962. Compared to CB yaks, CA animals exhibited significant differences in one phylum and six genera, including CAG-485 (p < 0.05), CAG-83 (p < 0.01), Copromorpha (p < 0.01), Phocaeicola A 858004 (p < 0.05), and UBA2253 (p < 0.05).ConclusionIn summary, higher-weight yak calves demonstrated increased oxidative resistance, and weight profiles were linked to the microbiomes of both female yaks and their calves. These findings offer valuable insights for optimizing yak breeding practices in high-altitude regions.

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Snaq: A Dynamic Snakemake Pipeline for Microbiome Data Analysis With QIIME2

Cited by 3 publications

References 27 publications

Comparison of DNA extraction methods for 16S rRNA gene sequencing in the analysis of the human gut microbiome

Comparison of DNA extraction methods for 16S rRNA gene sequencing in the analysis of the human gut microbiome

Voluntary exercise does not increase gastrointestinal motility but increases spatial memory, intestinal eNOS, Akt levels, and Bifidobacteria abundance in the microbiome

Impact of weight variation on the microbiome of yak dams and calves

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