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# Assessing antimicrobial peptides, resistance genes, and functional gene clusters in microbial aDNA
<br>
12-09-2023
Jasmin Frangenberg / <img src="https://openmoji.org/data/color/svg/E045.svg" width=50> @jasmezz
_Leibniz-HKI, Jena, Germany_
---
Screening for functional components of nucleotide sequences from prokaryotic (meta-)genomes
---
## Funcscan screens for
| | |
|--|--|
|**AMP**s: antimicrobial peptides |  <!--part of the innate immune response, destabilize biological membranes, can form transmembrane channels, and may also have the ability to enhance immunity by functioning as immunomodulators, divided into subgroups on the basis of their amino acid composition and structure.[3] Antimicrobial peptides are generally between 12 and 50 amino acids. --> |
| **ARG**s: antibiotic resistance genes |  |
| **BGC**s: biosynthetic gene clusters |  |
<!--
---
## Research applications
- Natural product discovery
- Antibiotic research
- Environmental metagenomics
- Functional and genomic annotation
- Metabolic evolution
- ... -->
---
## Existing problems
<table>
<tr>
<th><p style="font-weight:bold;font-family: 'Roboto', sans-serif;">Efficiency</p></th>
<td><p style="font-family: 'Roboto', sans-serif;">➡️ Single-purpose tools <br>➡️ Non-standardized output</p></td>
</tr>
<tr>
<th><p style="color:#181a1b;font-weight:bold;font-family: 'Roboto', sans-serif;">Reproducibility</p></th>
<td><p style="color:#181a1b;font-family: 'Roboto', sans-serif;">-_- Versioning</p></td>
</tr>
<tr>
<th><p style="color:#181a1b;font-weight:bold;font-family: 'Roboto', sans-serif;">Data privacy</p></th>
<td><p style="color:#181a1b;font-family: 'Roboto', sans-serif;">-_- Webservices</p></td>
</tr>
<tr>
<th><p style="color:#181a1b;font-weight:bold;font-family: 'Roboto', sans-serif;">(Bio)informatics<br>skills needed</p></th>
<td><p style="color:#181a1b;font-family: 'Roboto', sans-serif;">-_- Custom bash scripts</p></td>
</tr>
</table>
---
## Existing problems
<table>
<tr>
<th><p style="font-weight:bold;font-family: 'Roboto', sans-serif;">Efficiency</p></th>
<td><p style="font-family: 'Roboto', sans-serif;">➡️ Single-purpose tools <br>➡️ Non-standardized output</p></td>
</tr>
<tr>
<th><p style="font-weight:bold;font-family: 'Roboto', sans-serif;">Reproducibility</p></th>
<td><p style="font-family: 'Roboto', sans-serif;">➡️ Versioning</p></td>
</tr>
<tr>
<th><p style="color:#181a1b;font-weight:bold;font-family: 'Roboto', sans-serif;">Data privacy</p></th>
<td><p style="color:#181a1b;font-family: 'Roboto', sans-serif;">-_- Webservices</p></td>
</tr>
<tr>
<th><p style="color:#181a1b;font-weight:bold;font-family: 'Roboto', sans-serif;">(Bio)informatics<br>skills needed</p></th>
<td><p style="color:#181a1b;font-family: 'Roboto', sans-serif;">-_- Custom bash scripts</p></td>
</tr>
</table>
---
## Existing problems
<table>
<tr>
<th><p style="font-weight:bold;font-family: 'Roboto', sans-serif;">Efficiency</p></th>
<td><p style="font-family: 'Roboto', sans-serif;">➡️ Single-purpose tools <br>➡️ Non-standardized output</p></td>
</tr>
<tr>
<th><p style="font-weight:bold;font-family: 'Roboto', sans-serif;">Reproducibility</p></th>
<td><p style="font-family: 'Roboto', sans-serif;">➡️ Versioning</p></td>
</tr>
<tr>
<th><p style="font-weight:bold;font-family: 'Roboto', sans-serif;">Data privacy</p></th>
<td><p style="font-family: 'Roboto', sans-serif;">➡️ Webservices</p></td>
</tr>
<tr>
<th><p style="color:#181a1b;font-weight:bold;font-family: 'Roboto', sans-serif;">(Bio)informatics<br>skills needed</p></th>
<td><p style="color:#181a1b;font-family: 'Roboto', sans-serif;">-_- Custom bash scripts</p></td>
</tr>
</table>
---
## Existing problems
<table>
<tr>
<th><p style="font-weight:bold;font-family: 'Roboto', sans-serif;">Efficiency</p></th>
<td><p style="font-family: 'Roboto', sans-serif;">➡️ Single-purpose tools <br>➡️ Non-standardized output</p></td>
</tr>
<tr>
<th><p style="font-weight:bold;font-family: 'Roboto', sans-serif;">Reproducibility</p></th>
<td><p style="font-family: 'Roboto', sans-serif;">➡️ Versioning</p></td>
</tr>
<tr>
<th><p style="font-weight:bold;font-family: 'Roboto', sans-serif;">Data privacy</p></th>
<td><p style="font-family: 'Roboto', sans-serif;">➡️ Webservices</p></td>
</tr>
<tr>
<th><p style="font-weight:bold;font-family: 'Roboto', sans-serif;">(Bio)informatics<br>skills needed</p></th>
<td><p style="font-family: 'Roboto', sans-serif;">➡️ Custom bash scripts</p></td>
</tr>
</table>
---
## Development
Assembling ideas in October 2021
---
## Development
Continues over 2022...
---
## Development
Continues over 2022...
---
## Overview
First release in 2023!
---
## Step 1: ORF annotation
<p style="color:#181a1b">.</p>
---
## Step 2: Functional identification
<p style="color:#181a1b">.</p>
---
## Step 3: Summary
<p style="color:#181a1b">.</p>
---
## How to run
➡️ runs all ARG tools and summarizes their output
---
## How to run
➡️ runs all ARG tools and summarizes their output
---
## Summary: h**AMR**onization
<div style="display: flex; justify-content: center; align-items:end;">
<p style="font-size: 0.5em;">
See:<br>https://github.com/<br>pha4ge/hAMRonization
</p>
</div>
---
## Paleofeces analyses
<div style="display: flex; justify-content: center; align-items:end;">
<p style="font-size: 0.5em;">
Borry et al. (2020) PeerJ. DOI: 10.7717/peerj.9001
</p>
</div>
---
## Paleofeces analyses
<div style="display: flex; justify-content: center; align-items:end;">
<p style="font-size: 0.5em;">
Borry et al. (2020) PeerJ. DOI: 10.7717/peerj.9001
</p>
</div>
---
## Paleofeces: ARGs
---
## Paleofeces: BGCs
---
## Paleofeces: AMPs
---
## The nf-core/funcscan crew
|||
|---|---|
|Jasmin Frangenberg||
|Louisa Perelo||
|Anan Ibrahim||
|Moritz E. Beber||
|James Fellows Yates||
|Christina Warinner||
|Pierre Stallforth||
---
## The Paleobiotechnology group at Leibniz-HKI
<div>
<!--  -->
<p style="font-size: 0.75em;">
ISBA10 poster: <b>METP-001</b> (Wednesday Session I)
</p>
</div>
<!--
Additional info:
- Assembly sizes:
- Z005: 222 contigs, 2.7 MB
- Z028: 199 contigs, 1.9 MB
- Origin: Cueva de los Muertos Chiquitos, Mexico, 1300 BP, human
-->
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