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Middle Author Bioinformatics @midauthorbio.bsky.social · 12d

Simply enter the genus, species, or strain name of a microbe and instantly explore its genomic pathways, from plastic degradation to metal metabolism and beyond.

Results will allow you to explore the distribution of genes across selected genomes.

Middle Author Bioinformatics @midauthorbio.bsky.social · 12d

Did you know that some bacteria can break down plastics? One such microbe is Ideonella sakaiensis.

Using our web platform MagicLamp, and its built-in module PlasticGenie, you can now identify plastic-degradation–related genes in any Ideonella genome that's on RefSeq.

www.magiclamp.midauthorbio.com

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Middle Author Bioinformatics @midauthorbio.bsky.social · Oct 4

Did you know that FeGenie has a simple-to-use GUI that requires no command-line experience?

omix.midauthorbio.com

Simply drop your (meta)genomes in and get results in minutes!

We dropped in several hundred Prochlorococcus genomes to investigate their potential for iron acquisition and storage.

Dot plot showing number if genes classified as belonging to one of four iron-gene categories shown (there are more categories not shown)

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The Daily Pub @thedailypub.bsky.social · Oct 1

Wastewater can tell a lot about antibiotic resistance trends. A study of sewage from a university and nearby town found that resistance genes were higher in the town's wastewater, but levels evened out when antibiotics usage spiked at the university. Reducing antibiotic use doesn't quickly lower...

Relating antimicrobial use to wastewater resistance gene patterns via metagenomic analysis of two neighboring treatment plants circa the COVID-19 pandemic.

Published in npj antimicrobials and resistance

doi.org

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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · Sep 21

MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n
📄 www.nature.com/articles/s41...
💿 mmseqs.com

GPU-accelerated homology search with MMseqs2 - Nature Methods

Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...

www.nature.com

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The Daily Pub @thedailypub.bsky.social · Sep 12

Bifidobacteria, the good microbes linked to health, have evolved alongside their animal hosts. Kujawska and the team found that these bacteria adapt based on the host's species, diet, and family line over generations. Their research gives insight into how these friendly microbes became such impor...

Microbial matchmakers: Bifidobacterium evolution across animal hosts.

Published in Cell host & microbe

doi.org

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Middle Author Bioinformatics @midauthorbio.bsky.social · Sep 12

And be sure to cite GToTree: academic.oup.com/bioinformati...

Middle Author Bioinformatics @midauthorbio.bsky.social · Sep 12

3. Open the .tre file with FigTree or similar software for viewing phylo trees/newick files

tree.bio.ed.ac.uk/software/fig...

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Middle Author Bioinformatics @midauthorbio.bsky.social · Sep 12

2. Check your email

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Middle Author Bioinformatics @midauthorbio.bsky.social · Sep 12

With our GToTree GUI, making a phylogenomic tree is easy:
1. Type the organism name and click "Run GToTree"

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Middle Author Bioinformatics @midauthorbio.bsky.social · Sep 12

Plasmodium falciparum is the protozoan parasite behind the most severe form of malaria, transmitted by Anopheles mosquitoes.

If you want to see where P. falciparum sits in the tree of life, you can now do so easily with our microbial omics web app: omix.midauthorbio.com in less than 1 min!

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The Daily Pub @thedailypub.bsky.social · Sep 8

Turns out hosts and their microbes have a complicated relationship. A cool model shows microbes can help hosts handle environmental changes smoothly. When parents pass their microbes to offspring, high transfer boosts microbe fitness, but low transfer helps the host. Balancing this can keep the m...

Within-host microbial selection and multiple microbial generations buffer the loss of host fitness under environmental change.

Published in FEMS microbiology ecology

doi.org

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The Daily Pub @thedailypub.bsky.social · Sep 8

Fighting the tough Mycobacterium abscessus is getting a bit easier! A new study suggests checking drug resistance in just a week could be as good as traditional tests. They found that a specific pattern in the bacteria's reaction to treatment predicted drug resistance pretty well. This method cou...

Optimizing macrolide resistance detection for Mycobacterium abscessus: a potential low-cost, time-saving alternative.

Published in Microbiology spectrum

doi.org

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Arkadiy Garber @ironark.bsky.social · Sep 1

Cool system. I was surprised to learn about circadian rhythms in bacteria. To aid in the identification of this system in genomes and metagenomes, @zombiephylotype.bsky.social and I included this pathway as part of our MagicLamp functional annotation suite: www.magiclamp.midauthorbio.com

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Vaughn Cooper @vscooper.micropopbio.org · Aug 31

Our efforts to govern research on mirror life covered by USA Today, featuring quotes by ⭐ @kateadamala.bsky.social and me. Good article, alarmist headline notwithstanding

www.usatoday.com/story/news/n...

Scientists fear microscopic 'mirror life' could wipe out humanity

Can a research ban save us?

www.usatoday.com

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The Daily Pub @thedailypub.bsky.social · Aug 27

A groundbreaking study has successfully cultivated 627 unique microbial strains from Central European lakes. These strains represent a significant portion of the world's most common freshwater bacteria, many of which were previously uncultured. This new collection not only expands the knowledge o...

Bringing the uncultivated microbial majority of freshwater ecosystems into culture.

Published in Nature communications

doi.org

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The Daily Pub @thedailypub.bsky.social · Aug 27

Using advanced long-read metagenomics, scientists uncovered crucial genetic variations, known as structural variants (SVs), in marine microbes and viruses. These SVs help microbes adapt to their environments by affecting nutrient uptake and metabolism. In nutrient-poor seas like the Mediterranean...

The hidden genetic reservoir: structural variants as drivers of marine microbial and viral microdiversity.

Published in Environmental microbiome

doi.org

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Paul Hoskisson 🧫 🦠🐸 @paulhoskisson.bsky.social · Aug 25

Adaptive radiation during long-term experimental evolution of the multicellular bacterium #Streptomyces www.biorxiv.org/content/10.1...

Adaptive radiation during long-term experimental evolution of the multicellular bacterium, Streptomyces

The rapid diversification of a single lineage into novel ecological niches underpins evolution of biodiversity, with adaptive radiations being important drivers of ecological diversity across the tree...

www.biorxiv.org

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Microbiome Virtual International Forum @microbiomevif.bsky.social · Aug 22

Program for #GloMiNe2025 "Preservation of microbial diversity” by @microbiotavault.bsky.social ‬and #MVIF is OUT:
cassyni.com/s/mvif-glomi...

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The Daily Pub @thedailypub.bsky.social · Aug 18

Lung cancer microbiomes might hold the secret to better treatments. A study analyzing lung tissue microbiome from tumors found remarkable consistency in microbial diversity across different tissues and patients, suggesting these microbes are resilient even in cancer. Although the diversity seems...

Assessing Diversity Scaling in Lung Cancer Microbiome Across Individuals and Tissue Types.

Published in MicrobiologyOpen

doi.org

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ᐯIᑕTOᖇ ᑎIᘔET, ᗰᗪ @nizet.bsky.social · Aug 18

We're having a significant leptospirosis outbreak among sea lions along the California coast with significant mortality from kidney failure in the mammals

Make sure your pet dogs who love the beach are vaccinated and don't get too close

Remember: leptospirosis is the most common zoonosis of humans

Disease outbreak among sea lions could spread to pets

As dozens of sea lions in California contract a bacterial infection, experts warn it could spread to humans and pets.

www.newsweek.com

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Middle Author Bioinformatics @midauthorbio.bsky.social · Aug 17

Ever wondered how many genomes of your favorite bug have been sequenced and from where?

We built a simple web app (GenBanker) that takes genus/species as name input and provides metadata sheet, including all relevant information from NCBI's GenBank database.

main.d2btq5ga9882fz.amplifyapp.com

Results from a sample run.

Genus: Shewanella
Species: oneidensis

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Emma R. Hasson @dodecalemma.bsky.social · Aug 14

Writing stories like this for @sciam.bsky.social, and getting to speak to all the people involved who are brilliant and so committed to making other people's lives better always gives me hope. I hope you all enjoy! 🧪🧠

This Brain Implant Can Read Out Your Inner Monologue

A new brain prosthesis can read out inner thoughts in real time, helping people with ALS and brain stem stroke communicate fast and comfortably

www.scientificamerican.com

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Middle Author Bioinformatics @midauthorbio.bsky.social · Aug 14

Of course. If you are going to go with a WGS approach, the alien-fungus should be diverged enough from your fungus-of-interest, so that there is no hogging of reads by either of the fungal genomes. Good luck!

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