# Not able to find E. coli in my taxonomy file
**URL:** https://forum.qiime2.org/t/not-able-to-find-e-coli-in-my-taxonomy-file/32050
**Category:** Silva
**Tags:** taxonomy, silva, feature-table
**Created:** [December 4, 2024, 7:50am UTC](https://forum.qiime2.org/t/not-able-to-find-e-coli-in-my-taxonomy-file/32050 "2024-12-04T07:50:44Z")
**Posts on this page:** 4
**Page:** 1
### Author:  [@NivedhithaU](https://forum.qiime2.org/u/NivedhithaU)
#### Post date: [December 4, 2024, 7:50am UTC](https://forum.qiime2.org/t/not-able-to-find-e-coli-in-my-taxonomy-file/32050/1 "2024-12-04T07:50:44Z")
Hello,
I am analyzing mouse fecal samples. We have sequenced the V3-V4 region of the 16s rRNA and the taxonomic classification has been done based on silva-138-99-tax.qza. The code I used is given below.
**1. Importing files into QIIME 2**
```auto
qiime tools import \
--type 'SampleData[PairedEndSequencesWithQuality]' \
--input-path manifest.tsv \
--output-path demux-paired-end.qza \
--input-format PairedEndFastqManifestPhred33V2.
```
**2. Trimming primer sequences using Cutadapt**
```auto
qiime cutadapt trim-paired \
--i-demultiplexed-sequences demux-paired-end.qza \
--p-front-f CCTACGGGNGGCWGCAG \
--p-front-r GACTACHVGGGTATCTAATCC \
--p-discard-untrimmed --o-trimmed-sequences demux-pe-trimmed.qza \
–verbose.
```
**3. Denoising using DADA2**
```auto
qiime dada2 denoise-paired \
--i-demultiplexed-seqs demux-pe-trimmed.qza \
--p-trunc-len-f 277 \
--p-trunc-len-r 202 \
--o-table table.qza \
--o-representative-sequences rep-seqs.qza \
--o-denoising-stats denoising-stats.qza \
--verbose --p-n-threads 2
```
**4. Assigning Taxonomy**
```auto
qiime feature-classifier extract-reads \
--i-sequences silva-138-99-seqs.qza \
--p-f-primer CCTACGGGNGGCWGCAG \
--p-r-primer GACTACHVGGGTATCTAATCC \
--o-reads ref-seqs.qza
```
```auto
qiime feature-classifier fit-classifier-naive-bayes \
--i-reference-reads ref-seqs.qza \
--i-reference-taxonomy silva-138-99-tax.qza \
--o-classifier classifier_naive_bayes.qza
```
```auto
qiime feature-classifier classify-sklearn \
--i-classifier classifier_naive_bayes.qza \
--i-reads rep-seqs.qza \
--o-classification taxonomy.qza
```
I am not sure if the taxonomy has been assigned properly. I am not able to find E. coli in the taxonomy file. [taxonomy.qzv](https://forum.qiime2.org/uploads/short-url/czK0oqUs3yxeqtp1c5owGAqU1gn.qzv) (1.5 MB)
---
### Author:  [@timanix](https://forum.qiime2.org/u/timanix)
#### Post date: [December 4, 2024, 8:49am UTC](https://forum.qiime2.org/t/not-able-to-find-e-coli-in-my-taxonomy-file/32050/2 "2024-12-04T08:49:15Z")
Hello and Welcome to the forum!
I am not surprised that you can't find it. E. coli is a species, and even full length 16S rRNA sequence is often not enough for species level annotations. The issue is that E. coli has 16S rRNA sequence that is very similar to a lot of 16S rRNA gene sequences from other species. So most of them are annotated as "g\_\_Escherichia-Shigella", because the classifier fails to differentiate species.
Best,
---
### Author:  [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [December 5, 2024, 4:11am UTC](https://forum.qiime2.org/t/not-able-to-find-e-coli-in-my-taxonomy-file/32050/3 "2024-12-05T04:11:42Z")
> [@timanix](#):
>
> very similar
The 16S rRNA sequence of some species of _Escherichia_ are more similar to species of _Shigella_ than other _Escherichia_! See [PMC5711669](https://pmc.ncbi.nlm.nih.gov/articles/PMC5711669/) Table 1
> **[Accurate differentiation of Escherichia coli and Shigella serogroups:...](https://pmc.ncbi.nlm.nih.gov/articles/PMC5711669/#tbl1)**
>
> Shigella spp. and Escherichia coli are closely related; both belong to the family Enterobacteriaceae. Phenotypically, Shigella spp. and E. coli share many common characteristics, yet they have separate entities in epidemiology and clinical...
---
### Author:  [@NivedhithaU](https://forum.qiime2.org/u/NivedhithaU)
#### Post date: [December 5, 2024, 9:27am UTC](https://forum.qiime2.org/t/not-able-to-find-e-coli-in-my-taxonomy-file/32050/4 "2024-12-05T09:27:49Z")
Thank you. This clarifies things !