Questions tagged [microbiology]

The study of microbes, including bacteria, archaea and microscopic eukaryotes.

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Transcriptomics vs Proteomics for understanding molecular responses

I am planning some experiments to investigate how mono cultures of microbes respond to different nutrient concentrations. I want to use an -omics based approach to understand how, on a molecular level,...
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205 views

How to group rarefaction curves by metadata

I'm trying to generate a rarefaction curve plot from a phyloseq object. I'm using the function ggrare using rarecurve function from the vegan package: The function rarecurve allow the ploting of all ...
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1answer
83 views

How to create Beta Diversity distance boxplot

I'm trying to generate boxplot from Beta diversity boxplot between two conditions from a phyloseq object. I have a Morisita-horn distance generated by vegdist fonction : ...
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1answer
96 views

alpha diversity wilcox.test

I am trying to do Wilcox test to detect the significant difference in alpha diversity but it is showing an error? physeqN2 is a phyloseq object and Season is a metadata column. ...
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1answer
42 views

Sophisticated algorithms in biological systems [closed]

I am looking for examples of (known) algorithms/data structures in biological systems. My current understanding is that these don't exist - or haven't been found - beyond a relatively low level of ...
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1answer
52 views

MaCconkey Agar colour change in non-lactose fermentors [closed]

On Macconkey agar, lactose fermenting bacteria turn the agar bright red. Why does non-lactose fermenting bacteria turn the MaCconkey agar yellow?. Does it have to do with the alkalinity of waste ...
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1answer
232 views

What is a proper way for random subsampling of metagenomic data?

Let's say we have a metagenomic sample that is paired-end FASTQ files including 10,000,000 DNA reads collected using shotgun sequencing. How would one make a random subsample of the mentioned ...
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2answers
296 views

Microbial Classification with 16S Nanopore Data

I have recently been tasked with analyzing a heterogeneous microbial sample composed of 16S data generated on a MinION sequencer, with the goal of assigning taxonomies and calculating respective ...
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1answer
31 views

Is there a resource where I can donwload E. coli assemblies grouped by their pathotypes?

I will preface this by saying I'm not a microbiologist, so I apologise for any haziness and I'll be happy to expand. I would like to download the assemblies of different E. coli genomes and group ...
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2answers
692 views

What does it mean to over sample?

One of my studies (A) involve sequencing the microbiome. After selecting the variable region and the primers for the targeted region of the 16S sequence. The samples were sent to a platform. For ...
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1answer
258 views

How can I work out gram staining information from the species name?

I have a very long list of prokaryote organism names. I would like to know their gram staining (gram positive or gram negative) information. Please let me know if there is any database that keeps ...