Tag: ASVs

Simulated global warming affects endophytic bacterial and fungal communities of Antarctic pearlwort leaves and some bacterial isolates support plant growth at low temperatures

Sample collection Colobanthus quitensis samples were collected at King George Island near the Henryk Arctowski Polish Antarctic Station, Maritime Antarctica (62°14’ S, 58°48’ W) during the summer season (February 2018). Samples were collected inside the Antarctic Specially Protected Area (ASPA) 128 using permits provided by The Chilean Antarctic Institute (INACH)…

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Dietary selection of metabolically distinct microorganisms drives hydrogen metabolism in ruminants

Volatile fatty acid production and absorption is modulated by diet Animals were adapted to a starch-rich diet by gradually increasing dietary concentrate content from 50 to 90% over the three 100-d experimental periods (Fig. 1A). With both diets, rumen structure and epithelial morphology were robust and rumen pH remained above 6.0…

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Subsetting DESEQ2 VST Microbiome Data

Subsetting DESEQ2 VST Microbiome Data 1 @f8d5630d Last seen 16 hours ago Germany Hello there, the question is a bit off topic I am currently using DESEQ2 to normalize 16S microbiome data as advised several times in the recent literature. Currently I am facing the problem that I have 16S…

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Issues removing unwanted taxa from phyloseq object

Hi everyone, I am currently in the process of removing unwanted taxa (Kingdom=”Eukaryota”, Family=”Mitochondria”, and Order=”Chloroplast”) from a phyloseq object I created. This phyloseq object was created using my outputs from DADA2 (OTU table, taxonomy table, and metadata file). I have saved a taxonomy table in CSV format at every…

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The choice of OTUs vs. ASVs in 16S rRNA amplicon data analysis has stronger effects on diversity measures than rarefaction and OTU identity threshold

Advances in the analysis of amplicon sequence datasets have introduced a methodological shift in how research teams investigate microbial biodiversity, away from sequence identity-based clustering (producing Operational Taxonomic Units, OTUs) to denoising methods (producing amplicon sequence variants, ASVs). While denoising methods have several inherent properties that make them desirable compared…

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Phyloseq Objects for different time points

Phyloseq Objects for different time points 0 Hi I am very new to this microbiome analysis so this might be a very simple question… I have a question related to the microbiome analysis I’m doing. I have microbiome data from 3 different timepoints (T1, T7, and T13), for I made…

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How to get normalized count table from DESeq?

How to get normalized count table from DESeq? 1 Hi, I’m using Deseq compare differential abundance. Here is my code: ds.all <- phyloseq_to_deseq2(ps0.infant.pbs, ~ sample_type) geoMeans <- apply(counts(ds.all),1,gm_mean) ds.all <- estimateSizeFactors(ds.all,geoMeans = geoMeans) dds.all <- DESeq(ds.all,fitType = “local”) Then as the results I got 8 ASVs that showed significantly different….

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Relative abundance of differentially abundant ASVs after DESeq2

Relative abundance of differentially abundant ASVs after DESeq2 0 Hello, I used DESeq2 to see which ASVs were differentially abundant between different treatments on 16S metabarcoding data. I now want to plot the relative abundance (in %) of those ASVs. However, I am unsure which data would make to most…

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