Daniel Davila

Bioactive molecules unearthed by terabase-scale long-read sequencing of a soil metagenome - @rockefelleruniv.bsky.social go.nature.com/4606ozA

The X-Age Project to construct a Chinese aging clock Nature Aging - In this Perspective, members of the Aging Biomarker Consortium outline the X-Age Project, an Aging Biomarker Consortium plan for building standardized aging clocks in China. The...

Online now! In this Perspective members of the Aging Biomarker Consortium (ABC) outline the X-Age project, an ABC plan for building standardized aging clocks in China. (rdcu.be/eGFV0)
doi.org/10.1038/s435...

Bioactive molecules unearthed by terabase-scale long-read sequencing of a soil metagenome - Nature Biotechnology Optimized long-read sequencing constructs megabase-scale genome assemblies from complex soil samples.

Bioactive molecules unearthed by terabase-scale long-read sequencing of a soil metagenome www.nature.com/articles/s41... #jcampubs

Preprint out for myloasm, our new nanopore / HiFi metagenome assembler!

Nanopore's getting accurate, but

1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?

with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social

1 / N

GloMiNe2025

Atlantic session

Pacific session

Tomorrow begins #GloMiNe2025 organized by @microbiotavault.bsky.social & #MVIF

Atlantic session will be open by Gloria Dominguez-Bello & @cpavloud.bsky.social
Pacific session by Safarina Malik & Célio Dias Santos Júnior

Both sessions will be LIVE!

Check the details: cassyni.com/s/mvif-glomi...

Applied Computational Genomics Course at UU: Spring 2024
github.com/quinlan-lab... by the almighty Aaron Quinlan, author of bedtools and many other great tools for genomics analysis.

@hansenlab.bsky.social et al. study the evolution of bacterial symbionts of Pariaconus psyllids in Hawaii, demonstrating that island biogeography and host plant ecology shape symbiont losses and codiversification patterns.

🔗 doi.org/10.1093/gbe/evaf153

#genome #evolution #symbiont

Read the associated news and views:

Microbial chocolatiers of fine flavour 🍫

by Pablo Cruz-Morales

www.nature.com/articles/s41...

Applied HPC with R book-hpc.ggvy.cl/ #rstats

‘Sex reversal' is surprisingly common in birds, new study suggests Survey of five Australian avians finds numerous discordant individuals, including a genetically male bird that had laid an egg

Scientists have found instances of sex reversal—where an individual has the physical features of one sex but the genetic makeup of the other—in five different Australian bird species. https://scim.ag/41Dvamo

Breast milk IgG engages the mouse neonatal immune system to instruct responses to gut antigens Maternal antibodies fundamentally regulate gut immunity in the developing infant, yet the mechanisms underlying this process remain elusive. We found that maternal immunoglobulin G (IgG), ingested in ...

In mice, maternal antibodies ingested in breast milk in the first week after birth help to regulate immune responses in the newborn gut, according to a new study in Science.

Learn more: scim.ag/45yW4Nq

STEPS To It Announcing a new program, called STEPS, to simulate the dynamics of evolving microbial populations.

Excited to share new #program, STEPS, which can simulate #dynamics of the E. coli Long-Term Evolution Experiment (#LTEE) or other microbes in serial transfer regime.

telliamedrevisited.wordpress.com/2025/08/12/s...

STEPS developed by @devinmlake.bsky.social, Zachary Matson, Minako Izutsu, and me.

Emerging tools and best practices for studying gut microbial community metabolism - Nature Metabolism In this Perspective, Noecker and Turnbaugh provide a detailed guide for studying microbial community metabolism and discuss the best practices in the field.

#Throwback 🧪

PERSPECTIVE | Emerging tools and best practices for studying gut microbial community metabolism

‪@cecilianoecker.bsky.social‬ & P Turnbaugh

you can learn anything if you want:
Open Source Society University
github.com/ossu

A diverse and distinct microbiome inside living trees - Nature Microbiome analyses of living trees show that a single tree can host approximately one trillion bacteria, with microbial communities distinctly partitioned between heartwood and sapwood and with minim...

#NatMicroPicks

Hidden microbial world in trees🌳

Living wood hosts trillions of bacteria making trees a complex ecosystems with major roles in forest health and function.

#PlantMicro #MicroSky

www.nature.com/articles/s41...

The adoption of a westernized gut microbiome in Indian Immigrants and Indo-Canadians is associated with dietary acculturation - npj Biofilms and Microbiomes npj Biofilms and Microbiomes - The adoption of a westernized gut microbiome in Indian Immigrants and Indo-Canadians is associated with dietary acculturation

The successful integration of Indian immigrants in the Western culture is reflected in their gut microbiota! 😄

#MicrobiomeSky

www.nature.com/articles/s41...

An orthogonal T7 replisome for continuous hypermutation and accelerated evolution in E. coli Systems that perform continuous hypermutation of designated genes without compromising the integrity of the host genome can substantially accelerate the evolution of new or enhanced protein functions....

#NatMicroPicks

Synthetic evolution overdrive 🦠🔧🚅

A highly mutagenic DNA replication system speeds up evolution in Escherichia coli, without harming the host, opening a new way to accelerate protein engineering.

#SynBio #MicroSky

www.science.org/doi/10.1126/...

Counting soil microbial communities: the impact of qPCR platform and mastermix on accuracy and precision qPCR is used to measure soil microorganisms but can be affected by inhibitors, change in mastermix, and platform. This study measured precision and accurac

If you do #qPCR on soils you might be interested in this paper led by @aoifeduff.bsky.social @femsmicro.org which shows the effect of mastermix, sample type, platform and gene target on the inhibition, precision and accuracy of quantification academic.oup.com/femsec/artic...

You can not live without Rmarkdown if you use R for genomics data analysis. Cheatsheet from Posit:

rstudio.github.io/cheatsheets...

✨New issue!✨

🧪

Check out the latest in #metabolism research from across all disciplines.

Read about #Triglycerides in the #Brain, #CagriSema, #Exercise, #LipidMetabolism, the #Microbiome - and many more topics!

www.nature.com/natmetab/vol...

I am seeking a postdoc for my group at UCLA. We work at the intersection of population genetics x microbiome (garud.eeb.ucla.edu). If interested, please message me!

How Our Gut Microbiome Can Drive Sugar Cravings More Evidence for Our Gut Taking Center Stage for What We Eat

How our gut microbiome drives sugar cravings
erictopol.substack.com/p/how-our-gu...

AlphaFold - A practical guide AlphaFold - A practical guide

Recently I learnt that EMBL-EBI has a free online course about AlphaFold — how it works, strengths and limitations, how to use it — and it's very good!

There are also little quizzes and interactives.
www.ebi.ac.uk/training/onl...

A conversation about the human gut microbiome Still working on my next post, so I thought I’d share a recent conversation with Dr.

This week's #substack is a recent podcast conversation, where we chat about the human microbiome, health, and some new work from the lab that involves predicting diet from poop DNA. gibbological.substack.com/p/a-conversa...

Logo for the Sandpiper website

Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵

Do probiotics work? For a healthy microbiome, eating your greens is a surer bet

To keep the microbiome healthy, diet is key. Microbes thrive on foods rich in fibre and digestion-resistant starch, so munching on fresh fruit, vegetables, legumes and nuts is a good place to start

Nature Awards Global Grants for Gut Health Grants for researchers investigating the gut microbiota and its role in human health.

Attention microbiome researchers! 📣

The 2025 Global Grants for Gut Health application is now open: www.nature.com/immersive/gu...

This year's focus is on the role of nutrition in modulating the gut microbiota and gut barrier function.

@natureportfolio.nature.com #Yakult #GGGH

Do probiotics work? For a healthy microbiome, eating your greens is a surer bet

For a healthy microbiome, eating your greens is a surer bet

🎊Our August issue is live!

nature.com/nrmicro/volumes/23/issues/8

💊The preclinical and clinical antibacterial pipelines with global health perspectives

🦠Microbiota in IBD

⚖️Commensalism and pathogenesis of C. albicans

🌱Building climate-resilient agriculture through science and local action

This is a really good idea - helps to make functional sense out of microbial diversity.