Discover and read the best of Twitter Threads about #metagenomics
Most recents (10)
Wanna see something weird?! Ever thought about this? Every 2nd animal is a fish.
Despite this fact, much about the #microbiome in fish is unknown!
How is the #metagenome in Norwegian wild Atlantic #salmon as a case? In one word - surprising!
Here is a thread! (1/10)
Despite this fact, much about the #microbiome in fish is unknown!
How is the #metagenome in Norwegian wild Atlantic #salmon as a case? In one word - surprising!
Here is a thread! (1/10)
We have used genome-resolving metagenomics to discover some wild and surprising interactions
between 🐟 and 🦠 in Atlantic salmon featured in @ISME_microbes
Please have a read: rdcu.be/c5Pny (2/10)
between 🐟 and 🦠 in Atlantic salmon featured in @ISME_microbes
Please have a read: rdcu.be/c5Pny (2/10)
The first surprise we encountered was the simplicity of the microbiome of wild salmon! One 🦠 ruled over all the others no matter the sampling location - despite this being across 700 Km! (3/10)
Can you perform Bioinformatics analysis WITHOUT any knowledge in coding?
With Galaxy @galaxyproject yes you can!!
usegalaxy.org
(1/n) ... 🧵
#Bioinformatics #Biology #Genetics #molecularbiology #metagenomics #coding
With Galaxy @galaxyproject yes you can!!
usegalaxy.org
(1/n) ... 🧵
#Bioinformatics #Biology #Genetics #molecularbiology #metagenomics #coding
Galaxy is an open source, web-based platform (usegalaxy.org) for accessible, reproducible, and transparent computational biomedical research. (2/n)
It allows users WITHOUT programming experience to easily specify parameters and run individual tools as well as larger workflows (3/n)
GS: Lord Kelvin believed in meaningful measurement to see the whole picture. With nanopore sequencing you gain more comprehensive insights than ever before. #nanoporeconf
GS: In the 3 years since the last time we were at Old Billingsgate, @nanopore has released 200+ products, increased our single-molecule raw read accuracy from 95% to 99.6% & hugely improved our scalability & output. #nanoporeconf
Q: Which is better for taxonomic classification of #metagenomics samples - Kraken2 or MetaPhlAn 3?
A: It really depends!
Read the very short story in this thread, or the full story in my preprint w/ @BetaScience and André Comeau: bit.ly/3EWkYJf
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A: It really depends!
Read the very short story in this thread, or the full story in my preprint w/ @BetaScience and André Comeau: bit.ly/3EWkYJf
1/
Now, you may be thinking "but aren't there loads of studies that compare different metagenomic taxonomic classifiers already?" (& you would be right), but what they don't do is compare the impact of different parameters and reference databases on the classifications.
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What started about two years ago, as a quick test of which tool/parameters we should use to classify some samples, took on a whole life of its own and I'm really pleased it's finally out there. If you use Kraken or MetaPhlAn then I think some of this will be useful for you.
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Interested in #phages, #metagenomics and #microbiome? New method out to bin #phages from shotgun metagenomics data by @jojohansen from our group. (1/12)
nature.com/articles/s4146…
nature.com/articles/s4146…
Discover and analyse #phages in any #Metagenomics shotgun dataset by:
1. Bin and identify high quality phage bins
2. Automatically defines viral populations across samples
3. Analysis of viral-host interactions within samples
1. Bin and identify high quality phage bins
2. Automatically defines viral populations across samples
3. Analysis of viral-host interactions within samples
Using two paired #metagenomics and #metaviromics datasets:
17-36% of HQ viruses in metavirome was found from metagenomics samples using PHAMB
46-89% of HQ viruses found by PHAMB in metagenome data was not found in the metavirome
17-36% of HQ viruses in metavirome was found from metagenomics samples using PHAMB
46-89% of HQ viruses found by PHAMB in metagenome data was not found in the metavirome
"The live SARS-like coronavirus SL-CoV-WIV1 has been isolated for the first time from bat droppings; and such virus has been confirmed to invade the host cells through the ACE2 of human beings..."
Bat Severe Acute Respiratory Syndrome-Like Coronavirus WIV1
Encodes an Extra Accessory Protein, ORFX, Involved in Modulation of the Host Immune Response. (2016) #ZhengLiShi #PeterDaszak #EcoHealth
Funding: #NIAID 110964
Encodes an Extra Accessory Protein, ORFX, Involved in Modulation of the Host Immune Response. (2016) #ZhengLiShi #PeterDaszak #EcoHealth
Funding: #NIAID 110964
In this study, we have developed a fast and cost-effective method
for reverse genetics of coronaviruses by combining two approaches developed by others..As the genomes can be divided into multiple short fragments, mutations can be introduced into individual
fragments easily.
for reverse genetics of coronaviruses by combining two approaches developed by others..As the genomes can be divided into multiple short fragments, mutations can be introduced into individual
fragments easily.
It’s out! Our paper “Marine Sediments Illuminate Chlamydiae Diversity and Evolution” was published in @CurrentBiology today! Below a thread with major highlights 1/11
cell.com/current-biolog…
cell.com/current-biolog…
Big thanks to fantastic co-authors! Celebrating with @DanielTamarit, @eme_laura, @cstairs, @JoranMartijn, @hfixou, Steffen Jørgensen, @anjspa1, and @Ettema_lab. Work done @MolEvoUpp, @MIB_WUR, and @uibgeo.
For a visual summary, check out our graphical abstract 2/11
For a visual summary, check out our graphical abstract 2/11
In short: Phylogenetically diverse new lineages of #Chlamydiae (a bacterial phylum which includes the pathogen #Chlamydia) are abundant and active in deep #anoxic #marine #sediments taken from near Loki’s Castle #hydrothermal vent field 3/11
"Digital Orthodoxy," aka Deep Phenotyping or High-dimensional human data, is a great research tool w/ many proven advances, but has NO commercial/clinical validation and may be harmful
thelancet.com/journals/lance…
Our latest @TheLancet Digital Medicine essay
@EvanMuse @ScrippsRTI
thelancet.com/journals/lance…
Our latest @TheLancet Digital Medicine essay
@EvanMuse @ScrippsRTI
@TheLancet @EvanMuse @ScrippsRTI The multi-modal testing may someday be validated to benefit, but until that time we raise concerns about the practice, ethics and safety for companies to be charging individuals for such data accumulation.
@TheLancet @EvanMuse @ScrippsRTI In @TheLancet essay we briefly touched on advances that deep phenotyping of people has made in biomedical research. I'm going to briefly review 5
1. Pre-diabetes-> #diabetes
2. Individualized diet
3. Colon #cancer+ microbiome
4. Gut #metagenomics sequence Δ
5. Tumor microbiome
1. Pre-diabetes-> #diabetes
2. Individualized diet
3. Colon #cancer+ microbiome
4. Gut #metagenomics sequence Δ
5. Tumor microbiome
This team successfully identified key factors driving a complex multifactorial disease tied to persistent #infection! (necrotizing colitis)👉 They used a combo of genome-resolved #metagenomics + machine learning approaches to identify #microbial features predictive of the illness
Features considered included genes, #bacterial strain types, eukaryotes, bacteriophages, plasmids + growth rates 👉 ...which allowed the team to “uncover #biomarkers that could lead to early detection of necrotizing enterocolitis and targets for #microbiome-based therapeutics.”
Important consideration from study👉 “Bioinformatics techniques can also infer in situ bacterial replication rates directly from #metagenomic data, an important metric, as some #microbiome-related diseases have a signal related to bacterial replication but not relative abundance”
Our paper <Marine connectivity dynamics: clarifying cosmopolitan distributions of marine interstitial invertebrates and the meiofauna paradox> is out in @Mar_Biology 😁
1/n Here's a summary of what we found and discussed (and a personal significance at the end):
1/n Here's a summary of what we found and discussed (and a personal significance at the end):
* We did a literature survey and analyzed 700+ contributions
* Despite including keywords such as 'molecular OR cryptic OR ... dispersal OR phylo* OR biogeo* OR distribut*' only 7 contributions (>1%) focused on evolutionary biology!
2/n
* Despite including keywords such as 'molecular OR cryptic OR ... dispersal OR phylo* OR biogeo* OR distribut*' only 7 contributions (>1%) focused on evolutionary biology!
2/n
* Ecology and Taxonomy made up nearly 95% (488; 235 respectively) ... with a majority of contributions focusing on nematodes and arthropods (harpacticoid copepods).
* Paleontology, Development and Physiology added up to only 31 contributions!
3/n
* Paleontology, Development and Physiology added up to only 31 contributions!
3/n
