Middle Author Bioinformatics

Abstracts due for the July Evolution and Medicine Conference in Kiel, Germany! Early discounted registration is also open

Dear friends and fans of evolutionary biology & medicine (#EvMed), deadlines for the 2026 meeting in Kiel Germany are coming up. Looks to be excellent!

March 1, 2026: Abstract submission deadline and travel award decisions

April 1, 2026: Abstract decisions

open.substack.com/pub/evmedrev...

The hologenome in brain health and disease.

Performance of cabin air filters used in waste collection trucks.

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.

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

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

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.

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...

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...

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

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...

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

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

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

2. Check your email

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

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!

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...

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...

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

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...

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...

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...

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...

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

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

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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...

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.

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

Results from a sample run. Genus: Shewanella Species: oneidensis

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

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

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! 🧪🧠

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!

If you just need a ballpark you may be able to go without spike-ins: e.g., estimate fungal genome equivalents from a metagenome, assuming a known genome size and reliable DNA quantification.

Hey #microbiome folks :) What’s the current best approach to quantify absolute abundance of fungi in a sample? qPCR of a certain gene (not ITS due to variable/high copy number)? Spike-in before extraction with a known alien-fungus cell count? Thank you!